Note : Les descriptions sont présentées dans la langue officielle dans laquelle elles ont été soumises.
CA 02273199 1999-06-O1 -
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CA 02273199 1999-06-O1
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NUCLEIC ACID AND AMINO ACID SEQUENCES RELATING TO
HELICOBACTER PYLORI AND VACCINE COMPOSITIONS THEREOF
Background of the Invention
Helicobacter pylori is a gram-negative, S-shaped, microaerophilic bacterium
that
was discovered and cultured from a human gastric biopsy specimen. (Warren,
J.R. and
B. Marshall, ( 1983 ) Lancet 1: 1273-1275; and Marshall et al., ( 1984)
Microbios Lett. _25
83-88). H. pylori has been strongly linked to chronic gastritis and duodenal
ulcer
disease- (Rathbone et. al., ( 1986) Gut 27: 635-641 ). Moreover, evidence is
accumulating for an etiologic role of H. pylori in nonulcer dyspepsia, gastric
ulcer
disease, and gastric adenocarcinoma. (Blaser M. J., (1993) Trends Microbiol.
_l : 255-
260). Transmission of the bacteria occurs via the oral route, and the risk of
infection
increases with age. (Taylor, D.N. and M. J. Blaser, ( 1991 ) Epidemiol. Rev
13: 42-50).
H. pylori colonizes the human gastric mucosa, establishing an infection that
usually
persists for decades. Infection by H. pylori is prevalent worldwide. Developed
countries have infection rates over 50% of the adult population, while
developing
countries have infection rates reaching 90% of the adults over the age of 20.
(Hopkins
R. J. and J. G. Morris ( 1994) Am. J. Med. 97: 265-277).
The bacterial factors necessary for colonization of the gastric environment,
and
for virulence of this pathogen, are poorly understood. Examples of the
putative
virulence factors include the following: urease, an enzyme that may play a
role in
neutralizing gastric acid pH (Eaton et al., ( 1991 ) Infect. Immunol. S 9:
2470-2475;
Ferrero, R.L. and A. Lee ( 1991 ) Microb. Ecol. Hlth. Dis. 4: 121-134; Labigne
et al.,
( 1991 ) J. Bacteriol. 173: 1920-1931 ); the bacterial flagellar proteins
responsible for
motility across the mucous layer. (Hazell et al., (1986) J. Inf. Dis. 153: 658-
663; Leying
et al., ( 1992) Mol. Microbiol. 6: 2863-2874; and Haas et al., ( 1993 ) Mol.
Microbiol. _8
753-760); Vac A, a bacterial toxin that induces the formation of intracellular
vacuoles in
epithelial cells {Schmitt, W. and R. Haas, (1994) Molecular Microbiol. 12(2):
307-319);
and several gastric tissue-specific adhesins. (Boren et al., (1993) Science
262: 1892-
1895; Evans et al., (1993) J. Bacteriol. 175: 674-683; and Falk et al., (1993)
Proc. Natl.
Acad. Sci. USA 90: 2035-203).
Numerous therapeutic agents are currently available that eradicate H. pylori
infections in vitro. (Huesca et. al., (1993) Zbl. Bakt. 280: 244-252; Hopkins,
R. J. and J.
G. Morris, supra). However, many of these treatments are suboptimally
effective in vivo
because of bacterial resistance, altered drug distribution, patient non-
compliance or poor
drug availabilty. (Hopkins, R. J. and J. G. Morris, supra). Treatment with
antibiotics
combined with bismuth are part of the standard regime used to treat H. pylori
infection.
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(Malfertheiner, P. and J. E. Dominguez-Munoz (1993) Clinical Therapeutics 15
Supp.
B: 37-48). Recently, combinations of a proton pump inhibitors and a single
antibiotic
have been shown to ameliorate duodenal ulcer disease. (Malfertheiner, P. and
J. E.
Dominguez-Munoz supra). However, methods employing antibiotic agents can have
the
problem of the emergence of bacterial strains which are resistant to these
agents.
(Hopkins, R. J. and J. G. Morris, supra). These limitations demonstrate that
new more
effective methods are needed to combat H. pylori infections in vivo. In
particular, the
design of new vaccines that may prevent infection by this bacterium is highly
desirable.
Summary of the Invention
This invention relates to novel genes, e.g., genes encoding polypeptides such
as
bacterial surface proteins, from the organism Helicobacter pylori (H. pylori),
and other
related genes, their products, and uses thereof. The nucleic acids and
peptides of the
present invention have utility for diagnostic and therapeutics for H. pylori
and other
Helicobacter species. They can also be used to detect the presence of H.
pylori and
other Helicobacter species in a sample; and for use in screening compounds for
the
ability to interfere with the H. pylori life cycle or to inhibit H. pylori
infection. More
specifically, this invention features compositions of nucleic acids
corresponding to
entire coding sequences of H. pylori proteins, including surface or secreted
proteins or
parts thereof, nucleic acids capable of binding mRNA from H. pylori proteins
to block
protein translation, and methods for producing H. pylori proteins or parts
thereof using
peptide synthesis and recombinant DNA techniques. This invention also features
antibodies and nucleic acids useful as probes to detect H. pylori infection.
In addition,
vaccine compositions and methods for the protection or treatment of infection
by H.
pylori are within the scope of this invention.
Detailed Description of the Drawings
Figure 1 depicts an amino acid sequence alignment of five H. pylori proteins
(depicted in the single letter amino acid code and designated by their amino
acid
Sequence ID Numbers; shown N-terminal to C-terminal, left to right).
Figure 2 depicts the N-terminal portion of three H. pylori proteins (depicted
in
the single letter amino acid code and designated by their amino acid Sequence
ID
Numbers; shown N-terminal to C-terminal, left to right).
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Detailed Description of the Invention -
In one aspect, the invention features a recombinant or substantially pure
preparation of H. pylori polypeptide of SEQ ID NO: 98. The invention also
includes
substantially pure nucleic acid encoding an H. pylori polypeptide of SEQ ID
NO: 98,
such nucleic acid is contained in SEQ ID NO: 1. The H. pylori polypeptide
sequences
of the invention described herein are contained in the Sequence Listing, and
the nucleic
acids encoding H. pylori polypeptides of the invention are contained in the
Sequence
Listing.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
99,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 2.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pvlori polypeptide having an amino acid sequence of SEQ ID NO:
100,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
101,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 4:
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
102,
such as a nucleic acid comprising a nucleotide sequence of SEQ TD NO: 5.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
103,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 6.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
104,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 7.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
105,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 8.
In another aspect, the invention features a substantially pure nucleic acid
-- encoding an H. pylori polypeptide havin? a~ i amino acid sequence of SEQ ID
NO: 106,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 9.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
107,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 10.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
108,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 11.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
109,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 12.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
110,
such asp nucleic acid comprising a nucleotide sequence of SEQ ID NO: 13.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
111,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 14.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
112,
1 S such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 15.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
113,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 16.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
114,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 17.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
11 S,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 18.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
116,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 19.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
117,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 20.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
118,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 21.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
119,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 22.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
120,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 23.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
121,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 24.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
122,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 25.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
123,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 26.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
124,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 27.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
125,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 28.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
i 26,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 29.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid-sequence of SEQ ID NO:
127,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 30.
In another aspect, the invention features a substantiaily pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
128,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 31.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
I29,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 32.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
130,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 33.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori poiypeptide having an amino acid sequence of SEQ ID NO:
131,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 34.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
132,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 35.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
133,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 36.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
134,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 37. -
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
135,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 38.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
136,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 39.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
137,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 40.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
138,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 41.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
139,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 42.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
140,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID N0:43.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
141,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 44.
In another aspect, the invention features a substantially pyre nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
142,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 45.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
143,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 46.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
144,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 47.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
145,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 48.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
146,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 49.
l 0 In another aspect, the invention features a substantially pure nucleic
acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
147,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 50.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
148,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 51.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
149,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 52.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
150,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 53.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
151,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 54.
In another aspect, the invention features a substantially pure nucleic acid
encoding an X. pylori polypeptide having an amino acid sequence of SEQ ID NO:
152,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 55.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
153,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 56.
In another aspect, the irve~ ction features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
154,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 57.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
155,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 58.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
156,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 59.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
157,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 60.
In another aspect, the invention features a substantially pure nucleic acid
encoding an N. pylori polypeptide having an amino acid sequence of SEQ ID NO:
158,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 61.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
159,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 62.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
160,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 63.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
161,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 64.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
162,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 65.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
163,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 66.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
164,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 67.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
165,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 68.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
166,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 69.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
167,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 70.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
168,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 71.
In another aspect, the invention features a substantially pure nucleic acid
S encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID
NO: 169,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 72.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
170,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 73.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
17I,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 74.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
172;
1 S such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 75.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
173,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 76.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
174,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 77.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
175,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 78.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
176,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 79.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
177,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 80.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
I78,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 81.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori palypeptide having an amino acid sequence of SEQ ID NO:
179,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 82.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
180,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 83.
In another aspect, the invention features a substantially pure nucleic acid
S encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID
NO: 181,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 84.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
182,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 85.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori poIypeptide having an amino acid sequence of SEQ ID NO:
183,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 86.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
184,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 87.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
185,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 88.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
186,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 89.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
187,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 90.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
188,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 91.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
189,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 92.
In another aspect, the invention features a substa itially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
190,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 93.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
191,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 94.
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In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
192,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 95.
In another aspect, the invention features a substantially pure nucleic acid
S encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID
NO: 193,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 96.
In another aspect, the invention features a substantially pure nucleic acid
encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO:
194,
such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 97.
In another aspect, the invention features an isolated nucleic acid having a
nucleotide sequence encoding an H. pylori polypeptide at least about 60%
homologous
to an amino acid sequence selected from the group consisting of SEQ ID NO: 98-
SEQ
ID NO: 194. In a preferred embodiment, the isolated nucleic acid includes a
nucleotide
sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or
a
complement thereof.
In another aspect, the invention features an isolated nucleic acid having a
nucleotide sequence encoding an H. pylori polypeptide selected from the group
consisting of SEQ ID NO: 98-SEQ ID NO: 194.
In another aspect, the invention features an isolated nucleic acid which
encodes
an H. pylori polypeptide, having a nucleotide sequence at least about 60%
homologous
to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-
SEQ ID
NO: 97, or a complement thereof.
In another aspect, the invention features an isolated nucleic acid molecule
encoding an H. pylori polypeptide, having a nucleotide sequence which
hybridizes under
stringent hybridization conditions to a nucleic acid molecule having the
nucleotide
sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or
a
complement thereof.
In another aspect, the invention features an isolated nucleic acid having a
nucleotide sequence of at least 8 nucleotides in length, wherein the sequence
hybridizes
under stringent hybridization conditions to a nucleic acid having a nucleotide
sequence
selected from the group c insisting of SEQ ID NO: 1-SEQ ID NO: 97, or a
complement
thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori cell envelope polypeptide or a fragment thereof, the
nucleic acid
selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO:
8,
SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24,
SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61,
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SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91,
SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36,
SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30,
SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17,
SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38,
SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ
ID NO: 35, SEQ ID NO: 60, SEQ ID NO: 69, and SEQ ID NO: 83, or a complement
thereof.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof
is an H. pylori flagella-associated polypeptide or a fragment thereof encoded
by a
nucleic acid having a nucleotide sequence of SEQ ID NO: 63, or a complement
thereof.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori inner membrane polypeptide or a fragment thereof
encoded by a
nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO:
49,
SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44,
SEQ ID NO: 38, and SEQ ID NO: 39, or a complement thereof.
In another embodiment, the H. pylori inner membrane polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in
transport encoded
by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID
NO:
49. SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID
NO: 44, or a complement thereof.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori outer membrane polypeptide or a fragment thereof
encoded by a
nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8,
SEQ
ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID
NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID
NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID
NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID
NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID
NO: 65, and SEQ ID NO: 66, or a complement thereof.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue or
a
fragment thereof encoded by a nucleic acid selected from the group consisting
of SEQ
ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID
NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID
NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID
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NO: 52, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID
NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94, or a complement thereof.
In another embodiment, H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue
and a C-
terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid
selected from
the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID
NO:
42, and SEQ ID NO: 52, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori cell envelope polypeptide or a fragment thereof selected
from the
group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO:
106, SEQ ID NO: 110, SEQ ID NO: 1 I 1, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID
NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ
ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188,
SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO:
133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID
NO: 127, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ
ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141,
SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO:
103, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ
1D NO: 180.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an N. pylori flagella-associated polypeptide or a fragment thereof
having an
amino acid sequence of SEQ ID NO: 160.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori inner membrane polypeptide or a fragment thereof
selected from
the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID
NO: 11 S, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and
SEQ ID NO: 136.
In another embodiment, the H. pylori inner membrane polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in
transport selected
from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NC: 114,
SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, and SEQ ID NO: 141.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori outer membrane polypeptide or a fragment thereof
selected from
the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID
NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ
ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176,
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SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: I88, SEQ ID NO:
191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID
NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: I27, SEQ
ID NO: 162, and SEQ ID NO: 163.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue or
a
fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID
NO:
105, SEQ ID NO: 106, SEQ ID_NO: I08, SEQ ID NO: 110, SEQ ID NO: 11 I, SEQ ID
NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ
ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: I49,
SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO:
182, SEQ ID NO: 188, and SEQ TD NO: 191.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue
and a C-
terminal tyrosine cluster or a fragment thereof selected from the group
consisting of
SEQ ID NO: 108, SEQ ID NO: I23, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID
NO: I49.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori cytoplasmic polypeptide or a fragment thereof, wherein
the
nucleic acid is selected from the group consisting of SEQ ID NO: 57, SEQ ID
NO: 58,
SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92,
and SEQ ID NO: 93, or a complement thereof.
In one embodiment, the H. pvlori cytoplasmic polypeptide or a fragment thereof
is an H. pylori polypeptide or a fragment thereof involved in mRNA
translation, wherein
the nucleic acid is selected from the group consisting of SEQ ID NO: 57 and
SEQ ID
NO: 58, or a complement thereof.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in genome
replication,
transcription, recombination and repair, wherein the nucleic acid is selected
from the
group consisting of SEQ ID NO: 86, SEQ ID NO: 87, or a complement thereof.
Particularly preferred is an isolated ruc'.eic acid having a nucleotide
sequence
encoding an H. pylori cytoplasmic polypeptide or a fragment thereof selected
from the
group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO:
184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190.
In one embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof
is an H. pylori polypeptide or a fragment thereof involved in mRNA translation
selected
from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
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In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in genome
replication,
transcription, recombination and repair selected from the group consisting of
SEQ ID
NO: 183 and SEQ ID NO: 184.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori secreted polypeptide or a fragment thereof, the nucleic
acid
selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO:
10,
SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 32,
SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67,
SEQ ID NO: 70, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 81, SEQ ID NO: 82,
SEQ ID NO: 90, SEQ ID NO: 95, and SEQ ID NO: 97, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori secreted polypeptide or a fragment thereof selected from
the group
consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109,
SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO:
142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID
NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ
ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori cellular polypeptide or a fragment thereof, the nucleic
acid
selected from the group consisting of SEQ ID NO: i 5, SEQ ID NO: 16, SEQ ID
NO: 21,
SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47,
SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62,
SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74,
SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide
sequence
encoding an H. pylori cellular polypeptide or a fragment thereof selected from
the group
consisting of SEQ ID NO: I 12, SEQ ID NO: 113, SEQ ID NO: I 18; SEQ ID NO:
130,
SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO:
151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID
- NO: 165, SEn Io NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ
ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
In another aspect, the invention features a probe having a nucleotide sequence
consisting of at least 8 nucleotides of a nucleotide sequence selected from
the group
. 35 consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
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In another aspect, the invention features an isolated H. pylori polypeptide
having
an amino acid sequence at least about 60% homologous to an H. pylori
polypeptide
selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
In another aspect, the invention features an isolated H. pylori polypeptide
which
is encoded by a nucleic acid having a nucleotide sequence at least about 60%
homologous to a nucleotide sequence selected from the group consisting of SEQ
ID NO:
1-SEQ ID NO: 97. In one embodiment, the isolated H. pylori polypeptide is
encoded by
a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ
ID NO:
97. _
In another aspect, the invention features an isolated H. pylori polypeptide
which
is encoded by a nucleic acid which hybridizes under stringent hybridization
conditions
to a nucleic acid selected from the group consisting of SEQ ID NO: 1-SEQ ID
NO: 97,
or a complement thereof.
In another aspect, the invention features an isolated H. pylori polypeptide
having
an amino acid sequence selected from the group consisting of SEQ ID NO: 97-SEQ
ID
NO: I 94.
Particularly preferred is an isolated H pylori cell envelope polypeptide or a
fragment thereof, wherein the polypeptide is selected from the group
consisting of SEQ
ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110,
SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO:
125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID
NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ
ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139,
SEQ ID NO: 149, SEQ ID NO: I 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO:
162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID
NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ
ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 103, SEQ ID NO: 131,
SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ ID NO: I 80.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof
is an H. pylori flagella-associated polypeptide or a fragment thereof having
an amino
-- acid sequence of SEQ ID NO: 160.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori inner membrane polypeptide or a fragment thereof
selected from
- the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ
ID
NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and
SEQ ID NO: 136.
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In another embodiment, the H. pylori inner membrane polypeptide or a fragment
thereof is an H. pylori polypeptitle or a fragment thereof involved in
transport selected
from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114,
SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO:
i 35, and SEQ ID NO: 136.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori outer membrane polypeptide or a fragment thereof
selected from
the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID
NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ
ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176,
SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO:
191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: I33, SEQ ID
NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ
ID NO: 162, and SEQ ID NO: 163.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue or
a
fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID
NO:
105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID
NO: I 20, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ
ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149,
SEQ ID NO: 158, SEQ ID NO: I76, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO:
182, SEQ ID NO: 188, and SEQ ID NO: 191.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue
and a C-
terminal tyrosine cluster or a fragment thereof selected from the group
consisting of
SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID
NO: 149.
Particularly preferred is an isolated H. pylori cell envelope golypeptide or a
fragment thereof, wherein the polypeptide is encoded by a nucleic acid
selected from the
group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9,
SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: ?4. SEQ ID NO: 27,
SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79,
SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94,
SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42,
SEQ ID NO: 52, SEQ ID NO: 22, SEQ iD NO: 29, SEQ ID NO: 30, SEQ ID NO: 65,
SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18,
SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39,
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SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ
ID NO: 60, and SEQ ID NO: 69, SEQ ID NO: 83.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof
is an H. pylori flagella-associated polypeptide or a fragment thereof encoded
by a
nucleic acid having a nucleotide sequence of SEQ ID NO: 63.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori inner membrane polypeptide or a fragment thereof
encoded by a
nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO:
49,
SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44,
SEQ ID NO: 38, and SEQ ID NO: 39.
In another embodiment, the H. pylori inner membrane po~lypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in
transport encoded
by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID
NO:
49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID
1 S NO: 44.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment
thereof is an H. pylori outer membrane polypeptide or a fragment thereof
encoded by a
nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8,
SEQ
ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID
NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID
NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID
NO: 94, SEQ ID NO: S, SEQ ID NO: 1 l, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID
NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID
NO: 65, and SEQ ID NO: 66.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue or
a
fragment thereof encoded by a nucleic acid selected from the group consisting
of SEQ
ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID
NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID
NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID
NO: 52, SEQ ID NO: 61, SEQ ID NO. 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID
NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment
thereof is an H. pylori polypeptide having a terminal phenylalanine residue
and a C-
terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid
selected from
the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID
NO:
42, and SEQ ID NO: 52.
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Particularly preferred is an isolated H. pylori cytoplasmic polypeptide or a
fragment thereof, wherein the polypeptide is selected from the group
consisting of SEQ
ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185,
SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA
translation
selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in genome
replication, transcription, recombination and repair selected from the group
consisting of
SEQ ID NO: 183 and SEQ ID NO: 184.
Particularly preferred is an isolated H. pylori cytoplasmic polypeptide or a
fragment thereof, wherein the polypeptide is encoded by a nucleic acid
selected from the
group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO:
87,
SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93.
In one embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof
is an H. pylori polypeptide or a fragment thereof involved in mRNA
translation, wherein
the polypeptide is encoded by a nucleic acid selected from the group
consisting of SEQ
ID NO: 57, and SEQ ID NO: 58.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment
thereof is an H. pylori polypeptide or a fragment thereof involved in genome
replication,
transcription, recombination and repair, wherein the polypeptide is encoded by
a nucleic
acid selected from the group consisting of SEQ ID NO: 86 and SEQ ID NO: 87.
Particularly preferred is an isolated H. pylori cellular polypeptide or a
fragment
thereof, wherein the polypeptide is selected from the group consisting of SEQ
ID NO:
112, SEQ ID NO: 113, SEQ ID NO: 118, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID
NO: 137, SEQ ID N0: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ
ID NO: 153, SEQ ID NO: I56, SEQ ID NO: 159, SEQ ID NO: I65, SEQ ID NO: 168,
SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO:
173, and SEQ ID NO: 193.
F articularly preferred is an isolated H. pylori cellular polypeptide or a
fragment
thereof, wherein the poiypeptide is encoded by a nucleic acid selected from
the group
consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21, SEQ ID NO: 33, SEQ
ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ
ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID
NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID
NO: 76, and SEQ ID NO: 96.
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Particularly preferred is an isolated H pylori secreted polypeptide or a
fragment
thereof, wherein the polypeptide is selected from the group consisting of SEQ
ID NO:
100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109,_SEQ ID NO: 117, SEQ ID
NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ
ID NO: 150 SEQ ID N~: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174,
SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO:
192, and SEQ ID NO: I 94.
Particularly preferred is an isolated H. pylori secreted polypeptide or a
fragment
thereof, wherein the polypeptide is encoded by a nucleic acid selected from
the group
consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID
NO: 20, SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID
NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID
NO: 77, SEQ ID NO: 78, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID
NO: 95, and SEQ ID NO: 97.
In another aspect, the invention features a chimeric H. pylori polyneptide
comprising at least two H. pylori polypeptides or fragments thereof, wherein
the
polypeptides are encoded by nucleic acid sequences selected from the group
consisting
of SEQ ID NO:1-SEQ ID N0:97.
In another aspect, the invention features a chimeric H. pylori polypeptide
comprising at least two H. pylori polypeptides or fragments thereof, wherein
the
polypeptides are selected from the group consisting of SEQ ID N0:98-SEQ ID
N0:194.
In another aspect, the invention features a fusion protein comprising an H.
pylori
polypeptide which comprises an amino acid sequence selected from the group
consisting
of SEQ ID NO: 98-SEQ ID NO: 194 operatively linked to a non-H. pylori
polypeptide.
In another aspect, the invention features a vaccine formulation
for,prophylactic
or therapeutic treatment of an H. pylori infection comprising an effective
amount of at
least one isolated nucleic acid of the invention.
In another aspect, the invention features a vaccine formulation for
prophylactic
or therapeutic treatment of an H. pylori infection comprising an effective
amount of at
least one H. pylori polypeptide of the invention.
Preferably, the vaccine formulation of the invention further includes a
pharmaceutically acceptable carrier. In one embodiment, the pharmaceutically
acceptable carrier includes an adjuvant. In another embodiment, the
pharmaceutically
acceptable carrier includes a delivery system, e.g., a live vector, e.g., a
bacteria or a
virus. In another embodiment, the pharmaceutically acceptable carrier includes
both an
adjuvant and a delivery system.
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In another aspect, the invention features a method of treating or reducing a
risk
of H. pylori infection in a subject. The method includes administering to a
subject a
vaccine formulation of the invention, such that treatment or reduction of risk
of H. pylori
infection occurs.
In another aspect, the invention features a method of producing a vaccine
formulation of the invention. The method includes combining at least one
isolated H.
pylori polypeptide or a fragment thereof selected from the group consisting of
SEQ ID
NO: 98-SEQ ID NO: 194 with a pharmaceutically acceptable carrier to thereby
form a
vaccine formulation.
In another aspect, the invention features a method of producing a vaccine
formulation of the invention. The method includes culturing a cell undez
condition that
permit expression of an H. pylori polypeptide or a fragment thereof selected
from the
group consisting of SEQ ID NO: 98-SEQ ID NO: 194; isolating the H. pylori
polypeptide from the cell; and combining at least one isolated H. pylori
polypeptide or a
1 S fragment thereof with a pharmaceutically acceptable carrier to thereby
form a vaccine
formulation.
In another aspect, the invention pertains to any individual H. pylori
polypeptide
member or nucleic acid encoding such a member from the above-identified groups
of H.
pylori polypeptides.
In another aspect, the invention features nucleic acids capable of binding
mRNA
of H. pylori. Such nucleic acid is capable of acting as antisense nucleic acid
to control
the translation of mRNA of H. pylori. A further aspect features a nucleic acid
which is
capable of binding specifically to an H. pylori nucleic acid. These nucleic
acids are also
referred to herein as complements and have utility as probes and as capture
reagents.
In another aspect, the invention features an expression system comprising an
open reading frame corresponding to H. pylori nucleic acid. The nucleic acid
further
comprises a control sequence compatible with an intended host. The expression
system
is useful for making polypeptides corresponding to H. pylori nucleic acid.
In another aspect, the invention features a cell transformed with the
expression
system to produce H. pylori polypeptides.
In another aspect, the invention features a method of generating antibodies
against H. pylori polypeptides which are capable of binding specifically to H.
pylori
polypeptides. Such antibodies have utility as reagents for immunoassays to
evaluate the
abundance and distribution of H. pylori-specific antigens.
In another aspect, the invention features a method of generating vaccines for
immunizing an individual against H. pylori. The vaccination method includes:
immunizing a subject with at least one H. pylori polypeptide according to the
present
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invention, e.g., a surface or secreted polypeptide, or active portion thereof,
and a
pharmaceutically acceptable carrier. Such vaccines have therapeutic and/or
prophylactic
utilities.
In another aspect, the invention provides a method for generating a vaccine
comprising a modified immunogenic H. pylori polypeptide, e.g., a surface or
secreted
polypeptide, or active portion thereof, and a pharmacologically acceptable
carrier.
In another aspect, the invention features a method of evaluating a compound,
e.g.
a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to
bind an H.
pylori polypeptide. The method includes: contacting the candidate compound
with an
H. pylori polypeptide and determining if the compound binds or otherwise
interacts with
an H. pylori polypeptide. Compounds which bind H. pylori are candidates as
activators
or inhibitors of the bacterial life cycle. These assays can be performed in
vitro or in
VIVO.
In another aspect, the invention features a method of evaluating a compound,
e.g.
I 5 a polypeptide, e.g., a fragment of a host cell polypeptide, for the
ability to bind an H.
pylori nucleic acid, e.g., DNA or RNA. The method includes: contacting the
candidate
compound with an H. pylori nucleic acid and determining if the compound binds
or
otherwise interacts with an H. pylori polypeptide. Compounds which bind H.
pylori are
candidates as activators or inhibitors of the bacterial life cycle. These
assays can be
performed in vitro or in vivo.
The invention features H. pylori polypeptides, preferably a substantially pure
preparation of an H. pylori polypeptide, or a recombinant H. pylori
polypeptide. In
preferred embodiments: the polypeptide has biological activity; the
polypeptide has an
amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% identical or
homologous to an amino acid sequence of the invention contained in the
Sequence
Listing, preferably it has about 65% sequence identity with an amino acid
sequence of
the invention contained in the Sequence Listing, and most preferably it has
about 92% to
about 99% sequence identity with an amino acid sequence of the invention
contained in
the Sequence Listing; the polypeptide has an amino acid sequence essentially
the same
as an amino acid sequence of the invention contained in the Sequence Listing;
the
polypeptide is at least 5, 1 ~, 2 J, 50, 100, or I 50 amino acid residues in
length; the
polypeptide includes at least 5, preferably at least 10, more preferably at
least 20, more
preferably at least 50, 100, or I SO contiguous amino acid residues of the
invention
contained in the Sequence Listing. In yet another preferred embodiment, the
amino acid
sequence which differs in sequence identity by about 7% to about 8% from the
H. pylori
amino acid sequences of the invention contained in the Sequence Listing is
also
encompassed by the invention.
___...._____ ..... r._~_..
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In preferred embodiments: the H. pylori polypeptide is encoded by a nucleic
acid of the invention contained in the Sequence Listing, or by a nucleic acid
having at
least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleic acid of the
invention contained in the Sequence Listing.
S In a preferred embodiment, the subject H. pylori polypeptide differs in
amino
acid sequence at 1, 2, 3, 5, 10 or more residues from a sequence of the
invention
contained in the Sequence Listing. The differences, however, are such that the
H. pylori
polypeptide exhibits an H. pylori biological activity, e.g., the H. pylori
polypeptide
retains a biological activity of a naturally occurring H. pylori polypeptide.
In preferred embodiments, the polypeptide includes all or a fragment of an
amino
acid sequence of the invention contained in the Sequence Listing; fused, in
reading
frame, to additional amino acid residues, preferably to residues encoded by
genomic
DNA 5' or 3' to the genomic DNA which encodes a sequence of the invention
contained
in the Sequence Listing.
In yet other preferred embodiments, the H. pylori polypeptide is a recombinant
fusion protein having a first H. pylori polypeptide portion and a second
polypeptide
portion, e.g., a second polypeptide portion having an amino acid sequence
unrelated to
H. pylori. The second polypeptide portion can be, e.g., any of glutathione-S-
transferase,
a DNA binding domain, or a polymerase activating domain. In preferred
embodiment
the fusion protein can be used in a two-hybrid assay.
Polypeptides of the invention include those which arise as a result of
alternative
transcription events, alternative RNA splicing events, and alternative
translational and
postranslational events.
The invention also encompasses an immunogenic component which includes at
least one H. pylori polypeptide in an immunogenic preparation; the immunogenic
component being capable of eliciting an immune response specific for the H.
pylori
polypeptide, e.g., a humoral response, an antibody response, or a cellular
response. In
preferred embodiments, the immunogenic component comprises at least one
antigenic
determinant from a polypeptide of the invention contained in the Sequence
Listing.
In another aspect, the invention provides a substantially pure nucleic acid
having
a nucleotide sequence which encodes an H. pylori polypeptide. In preferred
embodiments: the encoded polypeptide has biological activity; the encoded
polypeptide
has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99%
homologous to an amino acid sequence of the invention contained in the
Sequence
Listing; the encoded polypeptide has an amino acid sequence essentially the
same as an
amino acid sequence of the invention contained in the Sequence Listing; the
encoded
polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length; the
encoded
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polypeptide comprises at least 5, preferably at least 10, more preferably at
least 20, more
preferably at least 50, 100, or 150 contiguous amino acids of the invention
contained in
the Sequence Listing.
In preferred embodiments: the nucleic acid of the invention is that contained
in
the Sequence Listing; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%,
98%, or
99% homologous with a nucleic acid sequence of the invention contained in the
Sequence Listing.
In a preferred embodiment, the encoded H. pylori polypeptide differs (e.g., by
amino acid substitution, addition or deletion of at least one amino acid
residue) in amino
acid sequence at 1, 2, 3, 5, 10 or more residues, from a sequence of the
invention
contained in the Sequence Listing. The differences, however, are such that:
the H.
pylori encoded polypeptide exhibits a H. pylori biological activity, e.g., the
encoded H.
pylori enzyme retains a biological activity of a naturally occurring H.
pylori.
In preferred embodiments, the encoded polypeptide includes all or a fragment
of
an amino acid sequence of the invention contained in the Sequence Listing;
fused, in
reading frame, to additional amino acid residues, preferably to residues
encoded by
genomic DNA 5' or 3' to the genomic DNA which encodes a sequence of the
invention
contained in the Sequence Listing.
In preferred embodiments, the subject H. pylori nucleic acid will include a
transcriptional regulatory sequence, e.g. at least one of a transcriptional
promoter or
transcriptional enhancer sequence, operably linked to the H. pylori gene
sequence, e.g.,
to render the H. pylori gene sequence suitable for expression in a recombinant
host cell.
In yet a further preferred embodiment, the nucleic acid which encodes an H.
pylori polypeptide of the invention, hybridizes under stringent conditions to
a nucleic
acid probe corresponding to at least 8 consecutive nucleotides of the
invention contained
in the Sequence Listing; more preferably to at least 12 consecutive
nucleotides of the
invention contained in the Sequence Listing; more preferably to at least 20
consecutive
nucleotides of the invention contained in the Sequence Listing; more
preferably to at
least 40 consecutive nucleotides of the invention contained in the Sequence
Listing.
In a preferred embodiment, the nucleic acid encodes a peptide which differs by
at
least one amino acid residue from the sequences of the invention contained in
the
Sequence Listing.
In a preferred embodiment, the nucleic acid differs by at least one nucleotide
from a nucleotide sequence of the invention contained in the Sequence Listing
which
encodes amino acids of the invention contained in the Sequence Listing.
In another aspect, the invention encompasses: a vector including a nucleic
acid
which encodes an H. pylori polypeptide or an H. pylori polypeptide variant as
described
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herein; a host cell transfected with the vector; and a method of producing a
recombinant
H. pylori poiypeptide or H. pylori polypeptide variant; including culturing
the cell, e.g.,
in a cell culture medium, and isolating the H. pylori or H. pylori polypeptide
variant,
e.g., from the cell or from the cell culture medium.
In another aspect, the invention features, a purified recombinant nucleic acid
having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a
sequence of the invention contained in the Sequence Listing.
The invention also provides a probe or primer which includes a substantially
purified oligonucleotide. The oligonucleotide includes a region of nucleotide
sequence
which hybridizes under stringent conditions to at least 8 consecutive
nucleotides of
sense or antisense sequence of the invention contained in the Sequence
Listing, or
naturally occurring mutants thereof. In preferred embodiments, the probe or
primer
further includes a label group attached thereto. The label group can be, e.g.,
a
radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor.
Preferably the oligonucleotide is at least 8 and less than 10, 20, 30, 50,
100, or 150
nucleotides in length.
The invention also provides an isolated H. pylori polypeptide which is encoded
by a nucleic acid which hybridizes under stringent hybridization conditions to
a nucleic
acid contained in the Sequence Listing.
The invention further provides nucleic acids, e.g., RNA or DNA, encoding a
polypeptide of the invention. This includes double stranded nucleic acids as
well as
coding and antisense single strands.
The H. pylori strain, from which genomic sequences have been sequenced, has
been deposited in the American Type Culture Collection (ATCC # 55679;
deposited by
Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) as
strain
HP-J99.
Included in the invention are: allelic variations; natural mutants; induced
mutants; proteins encoded by DNA that hybridizes under high or low stringency
conditions to a nucleic acid which encodes a polypeptide of the invention
contained in
the Sequence Listing (for definitions of high and low stringency see Current
Protocols in
Molecular Biology, John Wiley & Sons, New Ynrk. 1989, 6.3.1 - 6.3.6 and 6.4.1-
6.4.10,
hereby incorporated by reference); and, polypeptides specifically bound by
antisera to H.
pylori polypeptides, especially by antisera to an active site or binding
domain of H.
- pylori polypeptide. The invention also includes fragments, preferably
biologically
active fragments. These and other polypeptides are also referred to herein as
H. pylori
polypeptide analogs or variants.
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Putative functions have been determined for several of the H. pylori
polypeptides
of the invention, as shown in Table 1.
Accordingly, uses of the claimed H. pylori polypeptides based on these
identified
functions, as well as other functions as described herein, are also within the
scope of the
S invention.
In addition, the present invention encompasses H. pylori polypeptides
characterized as shown in Table 1 below, including: H. pylori cell envelope
proteins, H.
pylori secreted proteins, H. pylori cytoplasmic proteins and H. pylori
cellular proteins.
Members of these groups were identified by BLAST homology searches and by
searches
for secretion signal or transmembrane protein motifs. Polypeptides related by
significant homology to the polypeptides of Table 1 are also considered to be
classified
in the manner of the homologs shown in Table 1.
TABLE 1
ntSeqID[PCT]aaSeqID[PCT]
A. CELL ENVELOPE
A.1 Flagella-associated
hp1p13939_24322162_f3_17 63 160
A.2 Outer membrane
A.2.1 Terminal phe residue
02ge10116 23462 f2_43 7 104
02ge10116 804550 f2_44 8 105
02ge41622 14875000 c2 9 106
65
01cp20708 214843 c2 49 13 110
01cp20708 4960952 c1 43 14 111
06ae11016 4729625 c3 68 23 120
06ep10615 49068 c2 87 24 121
06gp71906 35158328 f3 27 124
85
06gp71906 3941642 f2 70 28 125
13ae10610 156411 c3 33 50 147
13ae10610 6522827 c3 -37 51 148
hp4e53394_11798952_c2_10161 158
06ge20501 4298568 c3 53 79 176
11ae12004 3367666 c2 41 80 177
hp7e10433_5345837 c3_13 84 181
14ce61516_2460~ g 1' i_f2_985 182
11ap20714 2077 c3 103 91 188
02cp10615 21908138 f1 94 191
4
A.2.2 No terminal phe
residue
07gp11909_26460892 f2 5 102
6
A.2.3 Phe and Tyr cluster
at C-
terminus
02ge41622 34176513 c1 11 108
50
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06gp71906 20486556_f2 26 123
65
hp7e10520_14728137_f1_1 36 133
02ae31010 417818 f3 29 2 139
4
13ae10610 26855313 f3 52 149
15
A.2.4 Via homology
hp5p15212_13729635_c3_35 22 119
07ee11402 1046877 c3 100 29 126
14ee41924 1046877 c3 104 30 127
hp1p13939 21641016 f1 65 162
1
~
hp4p62853_ 66 163
4766691_f3 23
A.3 Inner membrane
A.3.1 Proteins involved
in transport
06cp30603 664083 c1 94 48 145
09cp10713 36359687 c1_11949 146
04ep4i903 16667055 c1_37 17 114
04ep41903 19689182 c1 18 115
43
14ce31519 24650009 c1 19 116
17
09ce10413 26734687 f3 43 140
23
hp6p10904_6726062_f3_13 44 141
A.3.2 Other inner membrane
proteins
02ae31010 16679640 f2 38 135
21
07ee50709 16679640 f3 39 136
60
A.4 Other cell envelope
proteins
01ce61016 1056562 c3 123 1 gg
09cp61003 16619192 c2 2 gg
83
02ge10116 15632000 c2 6 103
114
04ae61517 12345837 f2 34 131
4
04ae61517 21744091 f3 35 132
5
hp4e13394_26750068_c3_11360 157
hp5p15575_1053590_c1_35 69 166
hp7e10433_5345837_c2_8 83 180
B. CYTOPLASMIC PROTEINS
B.1. Proteins involved
in mRNA
translation
hp3e10946_32609412 f3 57 154
4
hp3e10946_34175837_f3_3 58 155
B.2 Proteins involved
in genome
replication, transcription,
recombination and repair
_ 14ce61516 12600937 f2 86 183
11
14cp11908 25402267 c3 87 184
104
B.3 Other cytoplasmic
proteins
05ce10910 23712780 ci 88 1 85
4
_ hp7e10192_237i2780_f2_5 89 186
11ap20714 34663910 f3 92 189
29
hp8e10065 4962812 f2 18 93 190
C. SECRETED PROTEINS
01ce61016 23593955 c3 3 100
140
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09cp61003 23593955 c1 4 101
79
02ge41622 20730462 f1_19 10 107
01cp20708 10628177 c2 12 109
50
05ae30220 24415693 c3 20 117
175
06gp10409 4015687 f2 11 25 122
hp2e10911_10213593 c1_73 31 128
hp2e10911_35567005_c2_88 32 129
09ze10333 1457137 f3 11 45 142
06cp30603 10744075 c3 46 143
136
12ae10622 30273255 f1 53 150
13
05ce10208 4707035 c2 17 64 161
-
06ep30223 176437 c2 134 67 164
hp5p15575_26016387_f2_16 70 167
hp6p12244_4881375_c3_97 77 174
06ce20610 34647187 c2 78 175
33
hp7e10433_36339535 f3_3 81 17$
hp7e10433_36339535_f3_3 82 179
hp7e10420_24391078_f1_3 90 187
02ce71018 35720091 c3 95 192
4
hpE~10363_30517031_f3_3 97 194
D. OTHER CELLULAR PROTEINS
01ae11010 26437877 c2 15 112
52
hp4p33322_5891077_c2 45 16 113
hp3p21118_54628_c3_3 21 118
02ae31010 1064125 f1 11 33 130
hp2e10911_15680337_c3_10537 134
hp2e10911_24804577_c3_10440 137
hp2e10911_32234750_c1_68 41 138
06cp30603 26070252 c3 47 144
140
03ae10804 235286 f3 19 54 151
09ge11604 4804692 c1 8 55 152
hp2p10610_21987687 c2 56 153
hp4e13394_26182793 f2 59 156
45
hp4e53394 2082126 c2 102 62 159
06ep30223 25402187 c1 68 165
112
hp6e10491_12712706_f3_12 71 168
hp6p12129_12542880_c3 72 169
29
hp6p12129 17067265 c3_29 73 170
hp6p12129_214055 f1 2 74 171
hp6p12129_214055_f3_17 75 172
hp6p12244_33492712_c3_88 76 173
hp1e13054 22360653_f2 96 193
4
[In Table l, "nt" represents nucleotide Seq. ID number and "aa" represents
amino acid
Seq. ID number]
_ .___ _ . __. _.~~.___..
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Definitions
The terms "purified polypeptide" and "isolated polypeptide" and "a
substantially
pure preparation of a polypeptide" are used interchangeably herein and, as
used herein,
mean a poIypeptide that has been substantially, and preferably completely,
separated
from other proteins, lipids, and nucleic acids with which it naturally occurs.
Preferably,
the polypeptide is also separated from substances, e.g., antibodies or gel
matrix, e.g.,
polyacrylamide, which are used to purify it. Preferably, the polypeptide
constitutes at
least 10, 20, SO 70, 80 or 95% dry weight of the purified preparation.
Preferably, the
preparation contains: sufficient polypeptide to allow protein sequencing; at
least 1, 10,
or 100 pg of the polypeptide; at least 1, 10, or 100 mg of the polypeptide.
Furthermore,
the terms "purified polypeptide" and "isolated polypeptide" and "a
substantially pure
preparation of a polypeptide," as used herein, refer to both a polypeptide
obtained from
nature or produced by recombinant DNA techniques as described herein.
For example, an "isolated" or "purified" protein or biologically active
portion
thereof is substantially free of cellular material or other contaminating
proteins from the
cell or tissue source from which the H. pylori protein is derived, or
substantially free
from chemical precursors or other chemicals when chemically synthesized. The
language "substantially free of cellular material" includes preparations of H.
pylori
protein in which the protein is separated from cellular components of the
cells from
which it is isolated or recombinantly produced. In one embodiment, the
language
"substantially free of cellular material" includes preparations of H. pylori
protein having
less than about 30% (by dry weight) of non-H. pylori protein (also referred to
herein as a
"contaminating protein"), more preferably less than about 20% of non-H. pylori
protein,
still more preferably Less than about 10% of non-H. pylori protein, and most
preferably
less than about 5% non-H. pylori protein. When the H. pylori protein or
biologically
active portion thereof is recombinantly produced, it is also preferably
substantially free
of culture medium, i.e., culture medium represents less than about 20%, more
preferably
less than about 10%, and most preferably less than about 5% of the volume of
the
protein preparation.
The language "subst ntially free of chemical precursors or other chemicals"
includes preparations of H. pylori protein ial which the protein is separated
from
chemical precusors or other chemicals which are involved in the synthesis of
the protein.
In one embodiment, the language "substantially free of chemical precursors or
other
chemicals" includes preparations of H. pylori protein having less than about
30% (by dry
weight) of chemical precursors or non-H. pylori chemicals, more preferably
less than
about 20% chemical precursors or non-H. pylori chemicals, still more
preferably less
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than about 10% chemical precursors or non-H. pylori chemicals, and most
preferably
less than about 5% chemical precursors or non-H. pylori chemicals.
A purified preparation of cells refers to, in the case of plant or animal
cells, an in
vitro preparation of cells and not an entire intact plant or animal. In the
case of cultured
cells or microbial cells, it consists of a preparation of at least 10% and
more preferably
50% of the subject cells.
A purified or isolated or a substantially pure nucleic acid, e.g., a
substantially
pure DNA, (are terms used interchangeably herein) is a nucleic acid which is
one or both
of the following: not immediately contiguous with both of the coding sequences
with
which it is immediately contiguous (i.e., one at the 5' end and one at the 3'
end) in the
naturally-occurring genome of the organism from which the nucleic acid is
derived; or
which is substantially free of a nucleic acid with which it occurs in the
organism from
which the nucleic acid is derived. The term includes, for example, a
recombinant DNA
which is incorporated into a vector, e.g., into an autonomously replicating
plasmid or
virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists
as a
separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or
restriction endonuclease treatment) independent of other DNA sequences. -
Substantially
pure DNA also includes a recombinant DNA which is part of a hybrid gene
encoding
additional H. pylori DNA sequence.
A "contig" as used herein is a nucleic acid representing a continuous stretch
of
genomic sequence of an organism.
An "open reading frame", also referred to herein as ORF, is a region of
nucleic
acid which encodes a polypeptide. This region may represent a portion of a
coding
sequence or a total sequence and can be determined from a stop to stop codon
or from a
start to stop codon.
As used herein, a "coding sequence" is a nucleic acid which is transcribed
into
messenger RNA and/or translated into a polypeptide when placed under the
control of
appropriate regulatory sequences. The boundaries of the coding sequence are
determined by a translation start codon at the five prime terminus and a
translation stop
code at the three prime terminus. A coding sequence can include but is not
limited to
messenger R:~1A, synthetic DNA, and recombinant nucleic acid sequences.
A "complement" of a nucleic acid as used herein referes to an anti-parallel or
antisense sequence that participates in Watson-Crick base-pairing with the
original
sequence.
A "gene product" is a protein or structural RNA which is specifically encoded
by
a gene.
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As used herein, the term "probe" refers to a nucleic acid, peptide or other
chemical entity which specifically binds to a molecule of interest. Probes are
often
associated with or capable of associating with a label. A label is a chemical
moiety
capable of detection. Typical labels comprise .dyes, radioisotopes,
luminescent and
chemiluminescent moieties, fluorophores, enzymes, precipitating agents,
amplification
sequences, and the like. Similarly, a nucleic acid, peptide or other chemical
entity which
specifically binds to a molecule of interest and immobilizes such molecule is
referred
herein as a "capture ligand". Capture ligands are typically associated with or
capable of
associating with a support such as nitro-cellulose, glass, nylon membranes,
beads,
particles and the like. The specificity of hybridization is dependent on
conditions such
as the base pair composition of the nucleotides, and the temperature and salt
concentration of the reaction. These conditions are readily discernable to one
of
ordinary skill in the art using routine experimentation.
Homologous refers to the sequence similarity or sequence identity between two
1 S polypeptides or between two nucleic acid molecules. When a position in
both of the two
compared sequences is occupied by the same base or amino acid monomer subunit,
e.g.,
if a position in each of two DNA molecules is occupied by adenine, then the
molecules
are homologous at that position. The percent of homology between two sequences
is a
function of the number of matching or homologous positions shared by the two
sequences divided by the number of positions compared x 100. For example, if 6
of 10
of the positions in two sequences are matched or homologous then the two
sequences are
60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC
share 50% homology. Generally, a comparison is made when two sequences are
aligned
to give maximum homology.
Nucleic acids are hybridizable to each other when at least one strand of a
nucleic
acid can anneal to the other nucleic acid under defined stringency conditions.
Stringency of hybridization is determined by: (a) the temperature at which
hybridization
andlor washing is performed; and. (b) the ionic strength and polarity of the
hybridization
and washing solutions. Hybridization requires that the two nucleic acids
contain
complementary sequences; depending on the stringency of hybridization,
however,
mismatches may be tolerated. Typically, hybridization of two sequences at high
stingency (such as, for example, in a solution of 0.5X SSC, at 65° C)
requires that the
sequences be essentially completely homologous. - Conditions of intermediate
stringency
(such as, for example, 2X SSC at 65 ° C) and low stringency (such as,
for example 2X
SSC at 55° C), require correspondingly less overall complementarity
between the
hybridizing sequences. ( 1 X SSC is 0.15 M NaCI, 0.015 M Na citrate). A
preferred,
non-limiting example of stringent hybridization conditions are hybridization
in 6X
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sodium chIoride/sodium citrate (SSC) at about 45~C, followed by one or more
washes in
0.2 X SSC, 0.1% SDS at 50-65pC.
The terms peptides, proteins, and polypeptides are used interchangeably
herein.
As used herein, the term "surface protein" refers to all surface accessible
proteins, e.g. inner and outer membrane proteins, proteins adhering to the
cell wall, and
secreted proteins.
A polypeptide has H. pylori biological activity if it has one, two and
preferably
more of the following properties: (1) if when expressed in the course of an H.
pylori
infection, it can promote, or mediate the attachment of H. pylori to a cell;
(2) it has an
enzymatic activity, structural or regulatory function characteristic of an N.
pylori
protein; (3) the gene which encodes it can rescue a lethal mutation in an H.
pylori gene;
(4) or it is immunogenic in a subject. A polypeptide has biological activity
if it is an
antagonist, agonist, or super-agonist of a polypeptide having one of the above-
listed
properties.
A biologically active fragment or analog is one having an in vivo or in vitro
activity which is characteristic of the H. pylori polypeptides of the
invention contained
in the Sequence Listing, or of other naturally occurring H. pylori
polypeptides, e.g., one
or more of the biological activities described herein. Especially preferred
are fragments
which exist in vivo, e.g., fragments which arise from post transcriptional
processing or
which arise from translation of alternatively spliced RNA's. Fragments include
those
expressed in native or endogenous cells as well as those made in expression
systems,
e.g., in CHO cells. Because peptides such as H. pylori polypeptides often
exhibit a
range of physiological properties and because such properties may be
attributable to
different portions of the molecule, a useful H. pylori fragment or H. pylori
analog is one
which exhibits a biological activity in any biological assay for H. pylori
activity. Most
preferably the fragment or analog possesses 10%, preferably 40%, more
preferably 60%,
70%, 80% or 90% or greater of the activity of H. pylori, in any in vivo or in
vitro assay.
Analogs can differ from naturally occurring H. pylori polypeptides in amino
acid
sequence or in ways that do not involve sequence, or both. Non-sequence
modifications
include changes in acetylation, methylation, phosphorylation, carboxylation,
or
glycosylation. Preferred analogs include H. pylori polypeptides (or
biologically act'.ve
fragments thereof) whose sequences differ from the wild-type sequence by one
or more
conservative amino acid substitutions or by one or more non-conservative amino
acid
substitutions, deletions, or insertions which do not substantially diminish
the biological
activity of the H. pylori polypeptide. Conservative substitutions typically
include the
substitution of one amino acid for another with similar characteristics, e.g.,
substitutions
within the following groups: valine, gIycine; glycine, alanine; valine,
isoleucine,
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leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine,
threonine; lysine,
arginine; and phenylalanine, tyrosine. Other conservative substitutions can be
made in
view of the table below.
TABLE 2
CONSERVATIVE AMINO ACID REPLACEMENTS
For Amino Acid Code Replace with any of
Alanine A D-Ala, Gly, beta-Ala, L-Cys, D-Cys
Arginine R - D-Arg, Lys, D-Lys, homo-Arg, D-homo-Arg,
Met, Ile,
D-Met, D-Ile, Orn, D-Orn
Asparagine N D-Asn, Asp, D-Asp, Glu, D-Glu, Gln,
D-Gln
Aspartic Acid D D-Asp, D-Asn, Asn, Glu, D-Glu, Gln,
D-Gln
Cysteine C D-Cys, S-Me-Cys, Met, D-Met, Thr, D-Thr
Glutamine Q D-Gln, Asn, D-Asn, Glu, D-Giu, Asp,
D-Asp
Glutamic Acid E D-Glu, D-Asp, Asp, Asn, D-Asn, Gln,
D-Gln
Glycine G Ala, D-Ala, Pro, D-Pro, J3-Ala, Acp
Isoleucine I D~~IIe, Val, D-Val, Leu, D-Leu, Met,
D-Met
Leucine L D-Leu, Val, D-Val, Leu, D-Leu, Met,
D-Met
Lysine K D-Lys, Arg, D-Arg, homo-Arg, D-homo-Arg,
Met, D-
Met, Ile, D-Ile, Orn, D-Orn
Methionine M D-Met, S-Me-Cys, Ile, D-Ile, Leu, D-Leu,
Val, D-Val
Phenylalanine F D-Phe, Tyr, D-Thr, L-Dopa, His, D-His,
Trp, D-Trp,
Trans-3,4, or 5-phenylproline, cis-3,4,
or 5-
phenylproline
Proline P D-Pro, L-I-thioazolidine-4-carboxylic
acid, D-or L-1-
oxazolidine-4-carboxylic acid
Serine S D-Ser, Thr, D-Thr, alto-Thr, Met, D-Met,
Met(O),
D-Met(O), L-Cys, D-Cys
Threonine T D-Thr, Ser, D-Ser, allo-Thr, Met, D-Met,
Met(O),
D-Met(O), Val, D-Val
Tyrosine Y D-Tyr, Phe, D-Phe, L-Dopa, His, D-His
Valine V D-Val, Leu, D-Leu, Ile, D-Ile, Met,
D-Met
Other analogs within the invention are those with modifications which increase
peptide stability; such analogs may contain, for example, one or more non-
peptide bonds
(which replace the peptide bonds) in the peptide sequence. Also included are:
analogs
that include residues other than naturally occurring L-amino acids, e.g., D-
amino acids
or non-naturally occurring or synthetic amino acids, e.g., ~i or y amino
acids; and cyclic
analogs.
As used herein, the term "fragment", as applied to an X. pylori analog, will
ordinarily be at least about 20 residues, more typically at least about 40
residues,
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preferably at least about 60 residues in length. Fragments of H pylori
polypeptides can
be generated by methods known to those skilled in the art. The ability of a
candidate
fragment to exhibit a biological activity of H. pylori polypeptide can be
assessed by
methods known to those skilled in the art as described herein. Also included
are H.
pylori polypeptides containing residues that are not required for biological
activity of the
peptide or that result from alternative mRNA splicing or alternative protein
processing
events.
An "immunogenic component" as used herein is a moiety, such as an H. pylori
polypeptide, analog or fragment thereof, that is capable of eliciting a
humoral and/or
cellular immune response in a host animal alone or in combination with an
adjuvant.
An "antigenic component" as used herein is a moiety, such as an H. pylori
polypeptide, analog or fragment thereof, that is capable of binding to a
specific antibody
with sufficiently high affinity to form a detectable antigen-antibody complex.
As used herein, the term "transgene" means a nucleic acid (encoding, e.g., one
or
more polypeptides), which is partly or entirely heterologous, i.e., foreign,
to the
transgenic animal or cell into which it is introduced, or, is homologous to an
endogenous
gene of the transgenic animal or cell into which it is introduced, but which
is designed to
be inserted, or is inserted, into the cell's genome in such a way as to alter
the genome of
the cell into which it is inserted (e.g., it is inserted at a location which
differs from that
of the natural gene or its insertion results in a knockout). A transgene can
include one or
more transcriptional regulatory sequences and any other nucleic acid, such as
introns,
that may be necessary for optimal expression of the selected nucleic acid, all
operably
linked to the selected nucleic acid, and may include an enhancer sequence.
As used-herein, the term "transgenic cell" refers to a cell containing a
transgene.
As used herein, a "transgenic animal" is any animal in which one or more, and
preferably essentially all, of the cells of the animal includes a transgene.
The transgene
can be introduced into the cell, directly or indirectly by introduction into a
precursor of
the cell, by way of deliberate genetic manipulation, such as by a process of
transformation of competent cells or by microinjection or by infection with a
recombinant virus. This molecule may be integrated within a chromosome, or it
may be
extrachromosomallv r~:plicating DNA.
The term "antibody" as used herein is intended to include fragments thereof
which are specifically reactive with H. pylori polypeptides.
As used herein, the term "cell-specific promoter" means a DNA sequence that
serves as a promoter, i.e., regulates expression of a selected DNA sequence
operably
linked to the promoter, and which effects expression of the selected DNA
sequence in
specifc cells of a tissue. The term also covers so-called "leaky" promoters,
which
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regulate expression of a selected DNA primarily in one tissue, but cause
expression in
other tissues as well.
Misexpression, as used herein, refers to a non-wild type pattern of gene
expression. It includes: expression at non-wild type levels, i.e., over or
under
S expression; a pattern of expression that differs from wild type in terms of
the time or
stage at which the gene is expressed, e.g., increased or decreased expression
(as
compared with wild type) at a predetermined developmental period or stage; a
pattern of
expression that differs from wild type in terms of decreased expression (as
compared
with wild type) in a predetermined cell type or tissue type; a pattern of
expression that
differs from wild type in terms of the splicing size, amino acid sequence,
post-
transitional modification, or biological activity of the expressed
polypeptide; a pattern of
expression that differs from wild type in terms of the effect of an
environmental stimulus
or extracellular stimulus on expression of the gene, e.g., a pattern of
increased or
decreased expression (as compared with wild type) in the presence of an
increase or
decrease in the strength of the stimulus.
As used herein, "host cells" and other such terms denoting microorganisms or
higher eukaryotic cell lines cultured as unicellular entities refers to cells
which can
become or have been used as recipients for a recombinant vector or other
transfer DNA,
and include the progeny of the original cell which has been transfected. It is
understood
by individuals skilled in the art that the progeny of a single parental cell
may not
necessarily be completely identical in genomic or total DNA compliment to the
original
parent, due to accident or deliberate mutation.
As used herein, the term "control sequence" refers to a nucleic acid having a
base
sequence which is recognized by the host organism to effect the expression of
encoded
sequences to which they are ligated. The nature of such control sequences
differs
depending upon the host organism; in prokaryotes, such control sequences
generally
include a promoter, ribosomal binding site, terminators, and in some cases
operators; in
eukaryotes, generally such control sequences include promoters, terminators
and in
some instances, enhancers. The term control sequence is intended to include at
a
- 30 minimum, all components whose presence is necessary for expression, and
may also
include additional components whose presence is advantageous, for example,
leader
sequences.
As used herein, the term "operably linked" refers to sequences joined or
ligated
to function in their intended manner. For example, a control sequence is
operably linked
to coding sequence by ligation in such a way that expression of the coding
sequence is
achieved under conditions compatible with the control sequence and host cell.
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The metabolism of a substance, as used herein, means any aspect of the,
expression, function, action, or regulation of the substance. The metabolism
of a
substance includes modifications, e.g., covalent or non-covalent modifications
of the
substance. The metabolism of a substance includes modifications, e.g.,
covalent or non-
covalent modification, the substance induces in other substances. The
metabolism of a
substance also includes changes in the distribution of the substance. The
metabolism of
a substance includes changes the substance induces in the distribution of
other
substances.
A "sample" as used herein refers to a biological sample, such as, for example,
tissue or fluid isloated from an individual (including without limitation
plasma, serum,
cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in
vitro cell culture
constituents, as well as samples from the environment.
The practice of the invention will employ, unless otherwise indicated,
conventional techniques of chemistry, molecular biology, microbiology,
recombinant
DNA, and immunology, which are within the skill of the art. Such techniques
are
explained fully in the literature. See e.g., Sambrook, Fritsch, and Maniatis,
Molecular
Cloning; Laboratory Manual 2nd ed. (1989); DNA Cloning, Volumes I and II (D.N
Glover ed. 1985); Oligonucleotide Synthesis (M.J. Gait ed, 1984); Nucleic Acid
Hybridization (B.D. Hames & S.J. Higgins eds. 1984); the series, Methods in
Enzymoloqy (Academic Press, Inc.), particularly Vol. 154 and Vol. 155 (Wu and
Grossman, eds.) and PCR-A Practical Approach (McPherson, Quirke, and Taylor,
eds.,
1991 ).
I. Isolation of Nucleic Acids of H.~vlori and Uses Therefor
H. pylori Genomic Sequence
This invention provides nucleotide sequences of the genome of H. pylori which
thus comprises a DNA sequence library of H. pylori genomic DNA.The detailed
description that follows provides nucleotide sequences of H. pylori, and also
describes
how the sequences were obtained and how ORFs and protein-coding sequences were
identified. Also described are methods of using the disclosed H. pylori sec
uences in
methods including diagnostic and therapeutic applications. Furthermore, the
library can
be used as a database for identification and comparison of medically important
sequences in this and other strains of H. pylori.
To determine the genomic sequence of H. pylori, DNA was isolated from a strain
of H. pylori (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100
Beaver Street, Waltham, MA 02154) and mechanically sheared by nebulization to
a
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median size of 2 kb. Following size fractionation by gel electrophoresis, the
fragments
were blunt-ended, ligated to adapter oligonucleotides, and cloned into each of
20
different pMPX vectors (Rice et al., abstracts of Meeting of Genome Mapping
and
Sequencing, Cold Spring Harbor, NY, 5/I 1-5/15, 1994, p. 225) to construct a
series of
S "shotgun" subclone libraries.
DNA sequencing was achieved using multiplex sequencing procedures
essentially as disclosed in Church et al., 1988, Science 240:185; U.S. Patents
No.
4,942,124 and 5,149,625). DNA was extracted from pooled cultures and subjected
to
chemical or enzymatic sequencing. Sequencing reactions were resolved by
electrophoresis, and the products were transferred and covalently bound to
nylon
membranes. Finally, the membranes were sequentially hybridized with a series
of
labelled oligonucleotides complimentary to "tag" sequences present in the
different
shotgun cloning vectors. In this manner, a large number of sequences could be
obtained
from a single set of sequencing reactions. The cloning and sequencing
procedures are
described in more detail in the Exemplification.
Individual sequence reads obtained in this manner were assembled using the
FALCONTM program (Church et al., 1994, Automated DNA Sequencing and Analysis,
J.C. Venter, ed., Academic Press) and PHRAP (P. Green, Abstracts of DOE Human
Genome Program Contractor-Grantee Workshop V, Jan. 1996, p.157). The average
contig length was about 3-4 kb.
A variety of approaches are used to order the contigs so as to obtain a
continuous
sequence representing the entire H. pylori genome. Synthetic oligonucleotides
are
designed that are complementary to sequences at the end of each contig. These
oligonucleotides may be hybridized to libaries of H. pylori genomic DNA in,
for
example, lambda phage vectors or plasmid vectors to identify clones that
contain
sequences corresponding to the functional regions between individual contigs.
Such
clones are then used to isolate template DNA and the same oligonucleotides are
used as
primers in polymerase chain reaction (PCR) to amplify functional fragments,
the
nucleotide sequence of which is then determined.
The H. pylori sequences were analyzed for the presence of open reading frames
(ORFs) comprising at least 180 nucleotides As a result of the analysis of ORFs
based
on stop-to-stop codon reads, it should be understood that these ORFs may not
correspond to the ORF of a naturally-occurring H. pylori polypeptide. These
ORFs may
contain start codons which indicate the initiation of protein synthesis of a
naturally-
occurnng H. pylori polypeptide. Such start codons within the ORFs provided
herein can
be identified by those of ordinary skill in the relevant art, and the
resulting ORF and the
encoded H. pylori polypeptide is within the scope of this invention. For
example, within
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the ORFs a codon such as AUG or GUG (encoding methionine or valine) which is
part
of the initiation signal for protein synthesis can be identified and the ORF
modified to
correspond to a naturally-occurring H. pylori polypeptide. The predicted
coding regions
were defined by evaluating the coding potential of such sequences with the
program
GENEMARKT"' (Borodovsky and McIninch, 1993, Comp. Chem. 17:123).
Other H. pylori Nucleic Acids
The nucleic acids of this invention may be obtained directly from the DNA of
the
above referenced H. pylori strain by using the polymerase chain reaction
(PCR). See
"PCR, A Practical Approach" (McPherson, Quirke, and Taylor, eds., IRL Press,
Oxford,
UK, 1991 ) for details aboutthe PCR. High fidelity PCR can be used to ensure a
faithful
DNA copy prior to expression. In addition, the authenticity of amplified
products can be
checked by conventional sequencing methods. Clones carrying the desired
sequences
described in this invention may also be obtained by screening the libraries by
means of
the PCR or by hybridization of synthetic oligonucleotide probes to filter
lifts of the
library colonies or plaques as known in the art (see, e.g., Sambrook et al.,
Molecular
Cloning, A Laboratory Manual 2nd edition, 1989, Cold Spring Harbor Press, NY).
It is also possible to obtain nucleic acids encoding H. pylori polypeptides
from a
cDNA library in accordance with protocols herein described. A cDNA encoding an
H.
pylori polypeptide can be obtained by isolating total mRNA from an appropriate
strain.
Double stranded cDNAs can then be prepared from the total mRNA. Subsequently,
the
cDNAs can be inserted into a suitable plasmid or viral (e.g., bacteriophage)
vector using
any one of a number of known techniques. Genes encoding H. pylori polypeptides
can
also be cloned using established polymerase chain reaction techniques in
accordance
with the nucleotide sequence information provided by the invention. The
nucleic acids
of the invention can be DNA or RNA. Preferred nucleic acids of the invention
are
contained in the Sequence Listing.
The nucleic acids of the invention can also be chemically synthesized using
standard techniques. Various methods of chemically synthesizing
polydeoxynucleotides
-- 30 are known, including solid-phase synthesis which, like peptide
synthesis, has been fully
automated in commercially available DNA synthesizers (See e.g., Itakura et al.
U.S.
Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura
U.S.
Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
Nucleic acids isolated or synthesized in accordance with features of the
present
invention are useful, by way of example, without limitation, as probes,
primers, capture
ligands, antisense genes and for developing expression systems for the
synthesis of
proteins and peptides corresponding to such sequences. As probes, primers,
capture
_~.._____
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ligands and antisense agents, the nucleic acid normally consists of all or
part
(approximately twenty or more nucleotides for specificity as well as the
ability to form
stable hybridization products) of the nucleic acids of the invention contained
in the
Sequence Listing. These uses are described in further detail below.
Probes
A nucleic acid isolated or synthesized in accordance with the sequence of the
invention contained in the Sequence Listing can be used as a probe to
specifically detect
H pylori. With the sequence information set forth in the present application,
sequences
of twenty ar more nucleotides are identified which provide the desired
inclusivity and
exclusivity with respect to H. pylori, and extraneous nucleic acids likely to
be
encountered during hybridization conditions. More preferably, the sequence
will
comprise at least twenty to thirty nucleotides to convey stability to the
hybridization
product formed between the probe and the intended target molecules.
Sequences larger than 1000 nucleotides in length are difficult to synthesize
but
1 S can be generated by recombinant DNA techniques. Individuals skilled in the
art will
readily recognize that the nucleic acids, for use as probes, can be provided
with a label to
facilitate detection of a hybridization product.
Nucleic acid isolated and synthesized in accordance with the sequence of the
invention contained in the Sequence Listing can also be useful as probes to
detect
homologous regions (especially homologous genes) of other Helicobacter species
using
appropriate stringency hybridization conditions as described herein.
Capture Ligand
For use as a capture ligand, the nucleic acid selected in the manner described
above with respect to probes, can be readily associated with a support. The
manner in
which nucleic acid is associated with supports is well known. Nucleic acid
having
twenty or more nucleotides in a sequence of the invention contained in the
Sequence
Listing have utility to separate H. pylori nucleic acid from the nucleic acid
of each other
and other organisms. Nucleic acid having twenty or more nucleotides in a
sequence of
the invention contained in the Sequence Listing can also have utility to
separate other
Helicobacter species from each other and from other organisms. Preferably, the
- sequence will comprise at least twenty nucleotides to convey stability to
the
hybridization product formed between the probe and the intended target
molecules.
Sequences larger than 1000 nucleotides in length are difficult to synthesize
but can be
- generated by recombinant DNA techniques.
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Primers
Nucleic acid isolated or synthesized in accordance with the sequences
described
herein have utility as primers for the amplification of H. pylori nucleic
acid. These
nucleic acids may also have utility as primers for the amplification of
nucleic acids in
other Helicobacter species. With respect to polymerise chain reaction (PCR)
techniques, nucleic acid sequences of > 10-15 nucleotides of the invention
contained in
the Sequence Listing have utility in conjunction with suitable enzymes and
reagents to
create copies of H. pylori nucleic acid. More preferably, the sequence will
comprise
twenty or more nucleotides to convey stability to the hybridization product
formed
between the primer and the intended target molecules. Binding conditions of
primers
greater than 100 nucleotides are more difficult to control to obtain
specificity. High
fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In
addition,
amplified products can be checked by conventional sequencing methods.
The copies can be used in diagnostic assays to detect specific sequences,
including genes from H. pylori and/or other Helicobacter species. The copies
can also
be incorporated into cloning and expression vectors to generate polypeptides
corresponding to the nucleic acid synthesized by PCR, as is described in
greater detail
herein.
Antisense
Nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized
in
accordance with the sequences described herein have utility as antisense
agents to
prevent the expression of H. pylori genes. These sequences also have utility
as antisense
agents to prevent expression of genes of other Helicobacter species.
In one embodiment, nucleic acid or derivatives corresponding to H. pylori
nucleic acids is loaded into a suitable carrier such as a liposome or
bacteriophage for
introduction into bacterial cells. For example, a nucleic acid having twenty
or more
nucleotides is capable of binding to bacteria nucleic acid or bacteria
messenger RNA.
Preferably, the antisense nucleic acid is comprised of 20 or more nucleotides
to provide
necessary stability of a hybridization product of non-naturally occurring
nucleic acid and
bacterial nucleic acid and/or bacterial messenger RNA. Nucle~c ~ aid having a
sequence
greater than 1000 nucleotides in length is difficult to synthesize but can be
generated by
recombinant DNA techniques. Methods for loading antisense nucleic acid in
liposomes
is known in the art as exemplified by U.S. Patent 4,241,046 issued December
23, 1980
to Papahadjopoulos et al.
_~._ _ _ r _ . _
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II. Exyression of H. pylori Nucleic Acids
Nucleic acid isolated or synthesized in accordance with the sequences
described
herein have utility to generate polypeptides. The nucleic acid of the
invention
exemplified in the Sequence Listing or fragments of the nucleic acid encoding
active
portions of H. pylori polypeptides can be cloned into suitable vectors or used
to isolate
nucleic acid. The isolated nucleic acid is combined with suitable DNA linkers
and
cloned into a suitable vector.
The function of a specific gene or operon can be ascertained by expression in
a
bacterial strain under conditions where the activity of the gene products)
specified by
the gene or operon in question can be specifically measured. Alternatively, a
gene
product may be produced in large quantities in an expressing strain fir use as
an antigen,
an industrial reagent, for structural studies, etc. This expression can be
accomplished in
a mutant strain which lacks the activity of the gene to be tested, or in a
strain that does
not produce the same gene products}. This includes, but is not limited to
other
1 S Helicobacter strains, or other bacterial strains such as E. toll,
Norcardia,
Corynebacterium, Campylobacter, and Streptomyces species. In some cases the
expression host will utilize the natural Helicobacter promoter whereas in
others, it will
be necessary to drive the gene with a promoter sequence derived from the
expressing
organism (e.g., an E. toll beta-galactosidase promoter for expression in E.
toll).
To express a gene product using the natural H. pylori promoter, a procedure
such
as the following can be used. A restriction fragment containing the gene of
interest,
together with its associated natural promoter element and regulatory sequences
(identified using the DNA sequence data) is cloned into an appropriate
recombinant
plasmid containing an origin of replication that functions in the host
organism and an
appropriate selectable marker. This can be accomplished by a number of
procedures
known to those skilled in the art. It is most preferably done by cutting the
plasmid and
the fragment to be cloned with the same restriction enzyme to produce
compatible ends
that can be ligated to join the two pieces together. The recombinant plasmid
is
introduced into the~host organism by, for example, electroporation and cells
containing
the recombinant plasmid are identified by selection for the marker on the
plasmid.
Expression of the desired gene rro~~uct is detected using an assay specific
for that gene
product.
In the case of a gene that requires a different promoter, the body of the gene
(coding sequence) is specifically excised and cloned into an appropriate
expression
plasmid. This subcloning can be done by several methods, but is most easily
accomplished by PCR amplification of a specific fragment and Iigation into an
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expression plasmid after treating the PCR product with a restriction enzyme or
exonuclease to create suitable ends for cloning.
A suitable host cell for expression of a gene can be any procaryotic or
eucaryotic
cell. For example, an H. pylori polypeptide can be expressed in bacterial
cells such as E.
coli, insect cells (baculovirus), yeast, or mammalian cells such as Chinese
hamster ovary
cell (CHO). Other suitable host cells are known to those skilled in the art.
Expression in eucaryotic cells such as mammalian, yeast, or insect cells can
lead
to partial or complete glycosylation and/or formation of relevant inter- or
intra-chain
disulfide bonds of a recombinant peptide product. Examples of vectors for
expression in
yeast S. cerivisae include pYepSec 1 (Baldari. et al., ( 1987) Embo J. 6:229-
234), pMFa
(Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al.,
(1987) Gene
54:I 13-123), and pYES2 (Invitrogen Corporation, San Diego, CA). Baculovirus
vectors
available for expression of proteins in cultured insect cells (SF 9 cells)
include the pAc
series (Smith et al., ( 1983) Mol. Cell Biol. 3:2156-2165) and the pVL series
(Lucklow,
V.A., and Summers, M.D., (1989) Virology 170:31-39). Generally, COS cells
(Gluzman, Y., ( 1981 ) Cell 23:175-I 82) are used in conjunction with such
vectors as
pCDM 8 (Aruffo, A. and Seed, B., (1987) Proc. Natl. Acad. Sci. USA 84:8573-
8577) for
transient amplification/expression in mammalian cells, while CHO (dhfr-
Chinese
Hamster Ovary) cells are used with vectors such as pMT2PC (Kaufman et al. (
1987},
EMBO J. 6: I 87-195) for stable amplification/expression in mammalian cells.
Vector
DNA can be introduced into mammalian cells via conventional techniques such as
calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated
transfection, or electroporation. Suitable methods for transforming host cells
can be
found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition,
Cold
Spring Harbor Laboratory press ( 1989)), and other laboratory textbooks.
Expression in procaryotes is most often carried out in E. coli with either
fusion
or non-fusion inducible expression vectors. Fusion vectors usually add a
number of
NH2 terminal amino acids to the expressed target gene. These NH2 terminal
amino
acids often are referred to as a reporter group. Such reporter groups usually
serve two
purposes: 1 ) to increase the solubility of the target recombinant protein;
and 2) to aid in
- the parification of the target recombinant protein by acting as a ligand in
affinity
purification. Often, in fusion expression vectors, a proteolytic cleavage site
is
introduced at the junction of the reporter group and the target recombinant
protein to
- enable separation of the target recombinant protein from the reporter group
subsequent
to purification of the fusion protein. Such enzymes, and their cognate
recognition
sequences, include Factor Xa, thrombin and enterokinase. Typical fusion
expression
vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England
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Biolabs, Beverly, MA) and pRITS (Pharmacia, Piscataway, NJ) which fuse
glutathione
S-transferase, maltose E binding piotein, or protein A, respectively, to the
target
recombinant protein. A preferred reporter group is poly(His), which may be
fused to the
amino or carboxy terminus of the protein and which renders the recombinant
fusion
protein easily purifiable by metal chelate chromatography.
Inducible non-fusion expression vectors include pTrc (Amann et al., (1988)
Gene
69:301-31 S) arid pET 1 I d (Studier et al., Gene Expression Technolo~w
Methods in
Enzymology 185, Academic Press, San Diego, California (1990) 60-89). While
target
gene expression relies on host RNA polymerase transcription from the hybrid
trp-lac
fusion promoter in pTrc, expression of target genes inserted into pETl 1 d
relies on
transcription from the T7 gn 10-lac 0 fusion promoter mediated by coexpressed
viral
RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains
BL21 (DE3) or HMS 174(DE3) from a resident ~, prophage harboring a T7 gn 1
under the
transcriptional control of the IacUV 5 promoter.
1 S For example, a host cell transfected with a nucleic acid vector directing
expression of a nucleotide sequence encoding an H. pylori polypeptide can be
cultured
under appropriate conditions to allow expression of the polypeptide to occur.
The
polypeptide may be secreted and isolated from a mixture of cells and medium
containing
the peptide. Alternatively, the polypeptide may be retained cytoplasmically
and the cells
harvested, lysed and the protein isolated. A cell culture includes host cells,
media and
other byproducts. Suitable media for cell culture are well known in the art.
Polypeptides of the invention can be isolated from cell culture medium, host
cells, or
both using techniques known in the art for purifying proteins including ion-
exchange
chromatography, gel filtration chromatography, ultrafiltration,
electrophoresis, and
immunoaffinity purification with antibodies specific for such polypeptides.
Additionally, in many situations, polypeptides can be produced by chemical
cleavage of
a native protein (e.g., tryptic digestion) and the cleavage products can then
be purified
by standard techniques. _
In the case of membrane bound proteins, these can be isolated from a host cell
by
contacting a membrane-associated protein fraction with a detergent forming a
solubilized complex, where the membrane-associated protein is no longer
entirely
embedded in the membrane fraction and is solubilized at least to an extent
which allows
it to be chromatographically isolated from the membrane fraction. Several
different
criteria are used for choosing a detergent suitable for solubilizing these
complexes. For
example, one property considered is the ability of the detergent to solubilize
the H.
pylori protein within the membrane fraction at minimal denaturation of the
membrane-
associated protein allowing for the activity or functionality of the membrane-
associated
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protein to return upon reconstitution of the protein. Another property
considered when
selecting the detergent is the critical micelle concentration (CMC) of the
detergent in
that the detergent of choice preferably has a high CMC value allowing for ease
of
removal after reconstitution. A third property considered when selecting a
detergent is
the hydrophobicity of the detergent. Typically, membrane-associated proteins
are very
hydrophobic and therefore detergents which are also hydrophobic, e.g., the
triton series,
would be useful for solubilizing the hydrophobic proteins. Another property
important
to a detergent can be the capability of the detergent to remove the H. pylori
protein with
minimal protein-protein interaction facilitating further purification. A fifth
property of
the detergent which should be considered is the charge of the detergent. For
example, if
it is desired to use ion exchange resins in the purification process then
preferably
detergent should be an uncharged detergent. Chromatographic techniques which
can be
used in the final purification step are known in the art and include
hydrophobic
interaction, lectin affinity, ion exchange, dye affinity and immunoaffinity.
1 S One strategy to maximize recombinant H. pylori peptide expression in E.
coli is
to express the protein in a host bacteria with an impaired capacity to
proteolytically
cleave the recombinant protein (Gottesman, S., Gene Expression Technolow
Methods
in Enz~ogy_ I 85, Academic Press, San Diego, California (1990) 119-128).
Another
strategy would be to alter the nucleic acid encoding an H. pylori peptide to
be inserted
into an expression vector so that the individual codons for each amino acid
would be
those preferentially utilized in highly expressed E. coli proteins (Wada et
al., ( 1992)
Nuc. Acids Res. 20:2111-2118). Such alteration of nucleic acids of the
invention can be
carried out by standard DNA synthesis techniques.
The nucleic acids of the invention can also be chemically synthesized using
standard techniques. Various methods of chemically synthesizing
polydeoxynucleotides
are known, including solid-phase synthesis which, like peptide synthesis, has
been fully
automated in commercially available DNA synthesizers (See, e.g., Itakura et
al. U.S.
Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura
U.S.
Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
III. H. pylori Polypeptides
This invention encompasses isolated H. pylori polypeptides encoded by the
disclosed H. pylori genomic sequences, including the polypeptides of the
invention
contained in the Sequence Listing. Polypeptides of the invention are
preferably at least
5 amino acid residues in length. Using the DNA sequence information provided
herein,
the amino acid sequences of the polypeptides encompassed by the invention can
be
deduced using methods well-known in the art. It will be understood that the
sequence of
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an entire nucleic acid encoding an H. pylori polypeptide can be isolated and
identified
based on an ORF that encodes only a fragment of the cognate protein-coding
region.
This can be acheived, for example, by using the isolated nucleic acid encoding
the ORF,
or fragments thereof, to prime a polymerise chain reaction with genomic H.
pylori DNA
as template; this is followed by sequencing the amplified product.
The polypeptides of the invention can be isolated from wild-type or mutant H.
pylori cells or from heterologous organisms or cells (including, but not
limited to,
bacteria, yeast, insect, plant and mammalian cells) into which an H. pylori
nucleic acid
has been introduced and expressed. In addition, the polypeptides can be part
of
recombinant fusion proteins.
H. pylori polypeptides of the invention can be chemically synthesized using
commercially automated procedures such as those referenced herein.
H. pylori polypeptides of the invention are also intended to include chimeric
proteins and truncated proteins as decribed herein.
Chimeric H. pylori proteins
H. pylori chimeric polypeptides comprise one or more H. pylori polypeptides
fused together. These combined sequences can be made by combining two or more
genes, or two or more polypeptide encoding sequences, or at least one gene and
at least
one polypeptide encoding sequence in tandem, and the subsequent expression of
the
encoded proteins by conventional molecular biological techniques. The combined
nucleotide sequences may be composed of a combination of either full length H.
pylori
nucleotide sequences or fragments of such sequences, e.g., fragments which
contain
immunoIogically relevant portions of the encoded H. pylori protein. These
chimeric H.
pylori proteins then contain the combined or synergistic vaccine potential of
each
individual H. pylori protein sequence and can be used in vaccine formulations
of the
invention.
Truncated~ene expression and,proteinproduction
H. pylori proteins encoded by a given nucleotide sequence can also be used in
a
biologically active truncat ~d form. Such truncation can be produced, for
example, by
the elimination of either 5' and/or 3' regions of the encoding nucleotide
sequence.
These truncations can affect recombinant expression of the encoded protein
and/or
subsequent purification of the protein. For example, truncation of a
nucleotide sequence
encoding a predicted export sequence of a specific protein may alter
expression of the
protein. Alternatively, C-terminal truncation of an H. pylori polypeptide by
elimination
of the 3' end of the nucleic acid coding region may also improve protein
expression and
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subsequent purification and use, as is outlined in Example VIII below.
Deletion of
nucleic acid regions encoding internal H. pylori protein regions can also
result in
improved protein expression, purification and/or efficacy as a vaccine
candidate.
IV. Identification of Nucleic Acids Encoding Vaccine Components and Tar etg s
for
Agents Effective Against H. pylori
The disclosed H. pylori genome sequence includes segments that direct the
synthesis of ribonucleic acids and polypeptides, as well as origins of
replication,
promoters, other types of regulatory sequences, and intergenic nucleic acids.
The
invention encompasses nucleic acids encoding immunogenic components of
vaccines
and targets for agents effective against H. pylori. Identification of said
immunogenic
components involved in the determination of the function of the disclosed
sequences can
be achieved using a variety of approaches. Non-limiting examples of these
approaches
are described briefly below.
Homologyy to known sequences: Computer-assisted comparison of the disclosed
H. pylori sequences with previously reported sequences present in publicly
available
databases is useful for identifying functional H. pylori nucleic acid and
polypeptide
sequences. It will be understood that protein-coding sequences, for example,
may be
compared as a whole, and that a high degree of sequence homology between two
proteins (such as, for example, >80-90%) at the amino acid level indicates
that the two
proteins also possess some degree of functional homology, such as, for
example, among
enzymes involved in metabolism, DNA synthesis, or cell wall synthesis, and
proteins
involved in transport, cell division, etc. In addition, many structural
features of
particular protein classes have been identified and correlate with specific
consensus
sequences, such as, for example, binding domains for nucleotides, DNA, metal
ions, and
other small molecules; sites for covalent modifications such as
phosphorylation,
acylation, and the like; sites of protein:protein interactions, etc. These
consensus
sequences may be quite short and thus may represent only a fraction of the
entire
protein-coding sequence. Identification of such a feature in an H. pylori
sequence is
therefore useful in determining the function of the encoded protein and
identifying
useful targets of antibacterial drugs.
Of particular relevance to the present invention are structural features that
are
common to secretory, transmembrane, and surface proteins, including secretion
signal
peptides and hydrophobic transmembrane domains. H. pylori proteins identified
as
containing putative signal sequences and/or transmembrane domains are useful
as
immunogenic components of vaccines.
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Identification of essential eg nes: Nucleic acids that encode proteins
essential for
growth or viability of H. pylori are preferred drug targets. H. pylori genes
can be tested
for their biological relevance to the organism by examining the effect of
deleting and/or
disrupting the genes, i.e., by so-called gene "knockout", using techniques
known to
those skilled in the relevant art. In this manner, essential genes may be
identified.
Strain-specific sequences: Because of the evolutionary relationship between
different H. pylori strains, it is believed that the presently disclosed H.
pylori sequences
are useful for identifying, and/or discriminating between, previously known
and new H.
pylori strains. It is believed that other H. pylori strains will exhibit at
least 70%
sequence homology with the presently disclosed sequence. Systematic and
routine
analyses of DNA sequences derived from samples containing H. pylori strains,
and
comparison with the present sequence allows for the identification of
sequences that can
be used to discriminate between strains, as well as those that are common to
all H. pylori
strains. In one embodiment, the invention provides nucleic acids, including
probes, and
peptide and polypeptide sequences that discriminate between different strains
of H.
pylori. Strain-specific components can also be identified functionally by
their ability to
elicit or react with antibodies that selectively recognize one or more H.
pylori strains.
In another embodiment, the invention provides nucleic acids, including probes,
and peptide and polypeptide sequences that are common to all H. pylori strains
but are
not found in other bacterial species.
Specific Example: Determination Of Candidate Protein Antigens For Antibod~nd
Vaccine Development
The selection of candidate protein antigens for vaccine development can be
derived from the nucleic acids encoding H. pylori polypeptides. First, the
ORF's can be
analyzed for homology to other known exported or membrane proteins and
analyzed
using the discriminant analysis described by Klein, et al. (Klein, P.,
Kanehsia, M., and
DeLisi, C. ( 1985) Biochimica et Biophysica Acta 815, 468-476) for predicting
exported
and membrane proteins.
- 30 Homology searches can be performed using the BLAST algorithm contained in
the Wisconsin Sequence Analysis Package (Genetics Computer Group, Unweaity
Research Park, 575 Science Drive, Madison, WI 53711 ) to compare each
predicted ORF
amino acid sequence with all sequences found in the current GenBank, SWISS-
PROT
and PIR databases. BLAST searches for local alignments between the ORF and the
databank sequences and reports a probability score which indicates the
probability of
finding this sequence by chance in the database. ORF's with significant
homology (e.g.
probabilities lower than 1 x 10-6 that the homology is only due to random
chance) to
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membrane or exported proteins represent protein antigens for vaccine
development.
Possible functions can be provided to H. pylori genes based on sequence
homology to
genes cloned in other organisms.
Discriminant analysis (Klein, et al. supra) can be used to examine the ORF
amino acid sequences. This algorithm uses the intrinsic information contained
in the
ORF amino acid sequence and compares it to information derived from the
properties of
known membrane and exported proteins. This comparison predicts which proteins
will
be exported, membrane associated or cytoplasmic. ORF amino acid sequences
identified as exported or membrane associated by this algorithm are likely
protein
antigens for vaccine development.
Surface exposed outer membrane proteins are likely to represent the best
antigens to provide a protective immune response against H. pylori. Among the
algorithms that can be used to aid in prediction of these outer membrane
proteins include
the presence of an amphipathic beta-sheet region at their C-terminus. This
region which
has been detected in a large number of outer membrane proteins in Gram
negative
bacteria is often characterized by hydrophobic residues (Phe or Tyr)
approximately at
positions 1, 3, 5, 7 and 9 from the C-terminus (e.g., see Figure 1, block F).
Importantly,
these sequences have not been detected at the C-termini of periplasmic
proteins, thus
allowing preliminary distinction between these classes of proteins based on
primary
sequence data. This phenomenon has been reported previously by Struyve et al.
(J. Mol.
Biol. 218:141-148, 1991 ).
Also illustrated in Figure 1 are additional amino acid sequence motifs found
in
many outer membrane proteins of H. pylori. The amino acid sequence alignment
in
Figure 1 depicts portions of the sequence of five H. pylori proteins (depicted
in the
single letter amino acid code) labeled with their amino acid Sequence ID
Numbers and
shown N-terminal to C-terminal, left to right. Six distinct blocks (labeled A
through F)
of similar amino acid residues are found including the distinctive hydrophobic
residues
(Phe or Tyr; F or Y according to the single letter code for amino acid
residues)
frequently found at positions near the C-terminus of outer membrane proteins.
The
presence of several shared motifs clearly establishes the similarity between
members of
this group of proteins.
In addition, outer membrane proteins isolated from H. pylori frequently share
a
motif near the mature N-terminus (i.e., after processing to remove the
secretion signal)
as illustrated in the blocked amino acid residues in Figure 2. Figure 2
depicts the N-
terminal portion of three H. pylori proteins (designated by their amino acid
Sequence ID
Numbers and shown N-terminal to C-terminal, left to right).
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One skilled in the art would know that these shared sequence motifs are highly
significant and establish a similarity among this group of proteins.
Infrequently it is not possible to distinguish between multiple possible
nucleotides at a given position in the nucleic acid sequence. In those cases
the
ambiguities are denoted by an extended alphabet as follows:
These are the official IUPAC-IUB single-letter base codes
Code Base Description
G Guanine
A Adenine
T Thymine
C Cytosine
R Purine (A or G)
Y Pyrimidine (C or T or
U)
M Amino (A or C)
K Ketone (G or T)
S Strong interaction (C or G)
W Weak interaction (A or T)
H Not-G (A or C or
T)
B Not-A (C or G or
T)
V Not-T (not-U) (A or C or
G)
D Not-C (A or G or
T)
N Any (A or C or
G or T)
The amino acid translations of this invention account for the ambiguity in the
nucleic acid sequence by translating the ambiguous codon as the letter "X". In
all cases,
the permissible amino acid residues at a position are clear from an
examination of the
nucleic acid sequence based on the standard genetic code.
V. Production of Fragments and Analo, s~pylori Nucleic Acids and Polypeptides
1 S Based or the discovery of the H. pylori gene products of the invention
provided
in the Sequence Lsiting, one skilled in the art can alter the disclosed
structure (of H.
pylori genes), e.g., by producing fragments or analogs, and test the newly
produced
structures for activity. Examples of techniques known to those skilled in the
relevant art
which allow the production and testing of fragments and analogs are discussed
below.
These, or analogous methods can be used to make and screen libraries of
polypeptides,
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e.g., libraries of random peptides or libraries of fragments or analogs of
cellular proteins
for the ability to bind H. pylori polypeptides. Such screens are useful for
the
identification of inhibitors of H. pylori.
Generation of Fragments
Fragments of a protein can be produced in several ways, e.g., recombinantly,
by
proteolytic digestion, or by chemical synthesis. Internal or terminal
fragments of a
polypeptide can be generated by removing one or more nucleotides from one end
(for a
terminal fragment) or both ends (for an internal fragment) of a nucleic acid
which
encodes the polypeptide. Expression of the mutagenized DNA produces
polypeptide
fragments. Digestion with"end-nibbling" endonucleases can thus generate DNA's
which encode an array of fragments. DNA's which encode fragments of a protein
can
also be generated by random shearing, restriction digestion or a combination
of the
above-discussed methods.
Fragments can also be chemically synthesized using techniques known in the art
such as conventional Merrifield solid phase f Moc or t-Boc chemistry. For
example,
peptides of the present invention may be arbitrarily divided into fragments of
desired
length with no overlap of the fragments, or divided into overlapping fragments
of a
desired length.
Alteration of Nucleic Acids and Polvpeptides: Random Methods
Amino acid sequence variants of a protein can be prepared by random
mutagenesis of DNA which encodes a protein or a particular domain or region of
a
protein. Useful methods include PCR mutagenesis and saturation mutagenesis. A
library of random amino acid sequence variants can also be generated by the
synthesis of
a set of degenerate oligonucleotide sequences. (Methods for screening proteins
in a
library of variants are elsewhere herein).
(Al PCR Muta~enesis
-- 30 In PCR mutagenesis, reduced Taq polymerase fidelity is used to introduce
random mutations into a cloned fragment of DNA (Leung et aL, 1989, Technique I
: I 1-
1 S). The DNA region to be mutagenized is amplified using the polymerase chain
reaction (PCR) under conditions that reduce the fidelity of DNA synthesis by
Taq DNA
polymerase, e.g., by using a dGTP/dATP ratio of five and adding Mn2+ to the
PCR
reaction. The pool of amplified DNA fragments are inserted into appropriate
cloning
vectors to provide random mutant libraries.
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~B) Saturation Mutaeenesis
Saturation mutagenesis allows for the rapid introduction of a large number of
single base substitutions into cloned DNA fragments (Mayers et al., 1985,
Science
229:242). This technique includes generation of mutations, e.g., by chemical
treatment
or irradiation of single-stranded DNA in vitro, and synthesis of a
complimentary DNA
strand. The mutation frequency can be modulated by modulating the severity of
the
treatment, and essentially all possible base substitutions can be obtained.
Because this
procedure does not involve a genetic selection for mutant fragments both
neutral
substitutions, as well as those that alter function, are obtained. The
distribution of point
mutations is not biased toward conserved sequence elements.
~C) De;generate Oli~onucleotides
A library of homologs can also be generated from a set of degenerate
oligonucleotide sequences. Chemical synthesis of a degenerate sequences can be
carried
out in an automatic DNA synthesizer, and the synthetic genes then ligated into
an
appropriate expression vector. The synthesis of degenerate oligonucleotides is
known in
the art (see for example, Narang, SA ( I 983) Tetrahedron 39:3; Itakura et al.
( I 981 )
Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. AG Walton,
Amsterdam: Elsevier pp273-289; Itakura et al. (1984) Anhu. Rev. Biochem.
53:323;
Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. I
1:477. Such
techniques have been employed in the directed evolution of other proteins
(see, for
example. Scott et al. ( 1990) Science 249:386-390; Roberts et al. ( 1992) PNAS
89:2429-
2433; Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87:
6378-
6382; as well as U.S. Patents Nos. 5,223,409, 5,198,346, and 5,096,815).
Alteration of Nucleic Acids and Polvpeptides~ Methods for Directed Muta enesis
Non-random or directed, mutagenesis techniques can be used to provide specific
sequences or mutations in specific regions. These techniques can be used to
create
variants which include, e.g., deletions, insertions, or substitutions, of
residues of the
known amino acid sequence of a protein. The sites for mutation can be modified
w individually or in series, e.g., by ( 1 ) substituting first with conserved
amino acids and
then with more radical choices depending upon results achieved, (2) deleting
the target
residue, or (3) inserting residues of the same or a different class adjacent
to the located
- site, or combinations of options 1-3.
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(Al Alanine Scanning Muta~ enesis
Alanine scanning mutagenesis is a useful method for identification of certain
residues or regions of the desired protein that are preferred locations or
domains for
mutagenesis, Cunningham and Wells (Science 244:1081-1085, 1989). In alanine
S scanning, a residue or group of target residues are identified (e.g.,
charged residues such
as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively
charged amino
acid (most preferably alanine or polyalanine). Replacement of an amino acid
can affect
the interaction of the amino acids yvith the surrounding aqueous environment
in or
outside the cell. Those domains demonstrating functional sensitivity to the
substitutions
are then refined by introducing further or other variants at or for the sites
of substitution.
Thus, while the site for introducing an amino acid sequence variation is
predetermined,
the nature of the mutation per se need not be predetermined. For example, to
optimize
the performance of a mutation at a given site, alanine scanning or random
mutagenesis
may be conducted at the target codon or region and the expressed desired
protein subunit
variants are screened for the optimal combination of desired activity.
(B) Oligonucleotide-Mediated Muta enesis
Oligonucleotide-mediated mutagenesis is a useful method for preparing
substitution, deletion, and insertion variants of-DNA, see, e.g., Adelman et
al., (DNA
2:183, 1983). Briefly, the desired DNA is altered by hybridizing an
oligonucleotide
encoding a mutation to a DNA template, where the template is the single-
stranded form
of a plasmid or bacteriophage containing the unaltered or native DNA sequence
of the
desired protein. After hybridization, a DNA polymerase is used to synthesize
an entire
second complementary strand of the template that will thus incorporate the
oligonucleotide primer, and will code for the selected alteration in the
desired protein
DNA. Generally, oligonucleotides of at least 25 nucleotides in length are
used. An
optimal oligonucleotide will have 12 to 15 nucleotides that are completely
complementary to the template on either side of the nucleotides) coding for
the
mutation. This ensures that the oligonucleotide will hybridize properly to the
single-
stranded DNA template molecule. The oligonucleotides are readily synthesized
using
techniques known in the art such a~ th at described by Crea et al. (Proc.
Natl. Acad Sci.
USA, 75: 5765 [ 1978]).
(C) Cassette Mut~enesis
Another method for preparing variants, cassette mutagenesis, is based on the
technique described by Wells et al. (Gene, 34:315[1985)). The starting
material is a
plasmid (or other vector) which includes the protein subunit DNA to be
mutated. The
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codon(s) in the protein subunit DNA to be mutated are identified. There must
be a
unique restriction endonuclease site on each side of the identified mutation
site(s). If no
such restriction sites exist, they may be generated using the above-described
oligonucleotide-mediated mutagenesis method to introduce them at appropriate
locations
in the desired protein subunit DNA. After the restriction sites have been
introduced into
the plasmid, the plasmid is cut at these sites to linearize it. A double-
stranded
oligonucleotide encoding the sequence of the DNA between the restriction sites
but
containing the desired mutations) is synthesized using standard procedures.
The two
strands are synthesized separately and then hybridized together using standard
techniques. This double-stranded oligonucleotide is referred to as the
cassette. This
cassette is designed to have 3' and S' ends that are comparable with the ends
of the
linearized plasmid, such that it can be directly ligated to the plasmid. This
plasmid now
contains the mutated desired protein subunit DNA sequence.
~D) Combinatorial Muta eg nesis
Combinatorial mutagenesis can also be used to generate mutants (Ladner et al.,
WO 88/06630). In this method, the amino acid sequences for a group of homologs
or
other related proteins are aligned, preferably to promote the highest homology
possible.
All of the amino acids which appear at a given position of the aligned
sequences can be
selected to create a degenerate set of combinatorial sequences. The variegated
library of
variants is generated by combinatorial mutagenesis at the nucleic acid level,
and is
encoded by a variegated gene library. For example, a mixture of synthetic
oligonucleotides can be enzymatically ligated into gene sequences such that
the
degenerate set of potential sequences are expressible as individual peptides,
or
alternatively, as a set of larger fusion proteins containing the set of
degenerate
sequences.
Other Modifications of Hwlori Nucleic Acids and Polypeptides
It is possible to modify the structure of an H. pylori polypeptide for such
purposes as increasing solubility, enhancing stability (e.g., shelf life ex
vivo and
resi~tar ce to proteolytic degradation in vivo). A modified H. pylori protein
or peptide
can be produced in which the amino acid sequence has been altered, such as by
amino
acid substitution, deletion, or addition as described herein.
An H. pylori peptide can also be modified by substitution of cysteine residues
preferably with alanine, serine, threonine, leucine or glutarnic acid residues
to minimize
dimerization via disulfide linkages. In addition, amino acid side chains of
fragments of
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the protein of the invention can be chemically modified. Another modification
is
cyclization of the peptide.
In order to enhance stability and/or reactivity, an N. pylori polypeptide can
be
modified to incorporate one or more polymorphisms in the amino acid sequence
of the
protein resulting from any natural allelic variation. Additionally, D-amino
acids, non-
natural amino acids, or non-amino acid analogs can be substituted or added to
produce a
modified protein within the scope of this invention. Furthermore, an H. pylori
polypeptide can be modified using polyethylene glycol (PEG) according to the
method
of A. Sehon and co-workers (Wie et al., supra) to produce a protein conjugated
with
PEG. In addition, PEG can be added during chemical synthesis of the protein.
Other
modifications of H. pylori proteins include reduction/alkyIation (Tarr,
Methods of
Protein Microcharacterization, J. E. Silver ed., Humana Press, Clifton NJ 155-
194
( 1986)); acylation (Tarr, supra); chemical coupling to an appropriate carrier
(Mishell and
Shiigi, eds, Selected Methods in Cellular Immunology, WH Freeman, San
Francisco, CA
1 S ( 1980), U.S. Patent 4,939,239; or mild formalin treatment (Marsh, ( 1971
) Int. Arch. of
Allergy and Appl. Immunol., 41: 199 - 215).
To facilitate purification and potentially increase solubility of an H. pylori
protein or peptide, it is possible to add an amino acid fusion moiety to the
peptide
backbone. For example, hexa-histidine can be added to the protein for
purification by
immobilized metal ion affinity chromatography (Hochuli, E. et al., ( 1988)
BiolTechnology, 6: 1321 - 1325). In addition, to facilitate isolation of
peptides free of
irrelevant sequences, specific endoprotease cleavage sites can be introduced
between the
sequences of the fusion moiety and the peptide.
To potentially aid proper antigen processing of epitopes within an H. pylori
polypeptide, canonical protease sensitive sites can be engineered between
regions, each
comprising at least one epitope via recombinant or synthetic methods. For
example,
charged amino acid pairs, such as KK or RR, can be introduced between regions
within
a protein or fragment during recombinant construction thereof. The resulting
peptide
can be rendered sensitive to cleavage by cathepsin andlor other trypsin-like
enzymes
which would generate portions of the protein containing one or more epitopes.
In
addition, such charged amino acid residues can result in an increase in the
solubility of
the peptide.
- Primary Methods for Screenin~L Polyneptides and Analogs
Various techniques are known in the art for screening generated mutant gene
products. Techniques for screening large gene libraries often include cloning
the gene
library into replicable expression vectors, transforming appropriate cells
with the
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resulting library of vectors, and expressing the genes under conditions in
which
detection of a desired activity, e.g:; in this case, binding to H. pylori
polypeptide or an
interacting protein, facilitates relatively easy isolation of the vector
encoding the gene
whose product was detected. Each of the techniques described below is amenable
to
high through-put analysis for screening large numbers of sequences created,
e.g., by
random mutagenesis techniques.
(A) Two Hybrid Systems
Two hybrid assays such as the system described above (as with the other
screening methods described herein), can be used to identify polypeptides,
e.g.,
fragments or analogs of a naturally-occurring H. pylori polypeptide, e.g., of
cellular
proteins, or of randomly generated polypeptides which bind to an H. pylori
protein.
(The H. pylori domain is used as the bait protein and the library of variants
are expressed
as fish fusion proteins.) In an analogous fashion, a two hybrid assay (as with
the other
screening methods described herein), can be used to find polypeptides which
bind a H.
pylori polypeptide.
(B) Display Libraries
In one approach to screening assays, the candidate peptides are displayed on
the
surface of a cell or viral particle, and the ability of particular cells or
viral particles to
bind an appropriate receptor protein via the displayed product is detected in
a "panning
assay". For example, the gene library can be cloned into the gene for a
surface
membrane protein of a bacterial cell, and the resulting fusion protein
detected by
panning (Ladner et al., WO 88/06630; Fuchs et al. ( 1991 ) BiolTechnology
9:1370-1371;
and Goward et al. (1992) ?'IBS 18:136-140). In a similar fashion, a detectably
labeled
ligand can be used to score for potentially functional peptide homologs.
Fluorescently
labeled ligands, e.g., receptors, can be used to detect homologs which retain
ligand-
binding activity. The use of fluorescently labeled ligands, allows cells to be
visually
inspected and separated under a fluorescence microscope, or, where the
morphology of
the cell permits, to be separated by a fluorescence-activated cell sorter. .
A gene library can be expressed as a fusion prote~n r n the surface of a viral
particle. For instance, in the filamentous phage system, foreign peptide
sequences can
be expressed on the surface of infectious phage, thereby conferring two
significant
benefits. First, since these phage can be applied to affinity matrices at
concentrations
3 S well over 1 O 13 phage per milliliter, a large number of phage can be
screened at one time.
Second, since each infectious phage displays a gene product on its surface, if
a particular
phage is recovered from an affinity matrix in low yield, the phage can be
amplified by
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another round of infection. The group of almost identical E. toll filamentous
phages
M 13, fd., and fl are most often used in phage display libraries. Either of
the phage gIII
or gVIII coat proteins can be used to generate fusion proteins without
disrupting the
ultimate packaging of the viral particle. Foreign epitopes can be expressed at
the NH2-
terminal end of pIII and phage bearing such epitopes recovered from a large
excess of
phage lacking this epitope (Ladner et al. PCT publication WO 90/02909; Garrard
et al.,
PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267:16007-
16010;
Griffiths et al. ( 1993) EMBO J 12:725-734; Clackson et al. ( I99I ) Nature
352:624-628;
and Barbas et al. (1992) PNAS 89:4457-4461). -
IO A common approach uses the maltose receptor of E. toll (the outer membrane
protein, Lama) as a peptide fusion partner (Charbit et al. (1986) EMBO 5, 3029-
3037).
Oligonucleotides have been inserted into plasmids encoding the Lama gene to
produce
peptides fused into one of the extracellular loops of the protein. These
peptides are
available for binding to ligands, e.g., to antibodies, and can elicit an
immune response
when the cells are administered to animals. Other cell surface proteins, e.g.,
OmpA
(Schorr et al. (1991) Vaccines 91, pp. 387-392), PhoE (Agterberg, et aI.
(1990) Gene 88,
37-45), and PAL (Fuchs et al. (1991) BiolTech 9, 1369-1372), as well as large
bacterial
surface structures have served as vehicles for peptide display. Peptides can
be fused to
pilin, a protein which polymerizes to form the pilus-a conduit for
interbacterial exchange
of genetic information (Thiry et al. (1989) Appl. Environ. Microbiol. 55, 984-
993).
Because of its role in interacting with other cells, the pilus provides a
useful support for
the presentation of peptides to the extracellular environment. Another large
surface
structure used for peptide display is the bacterial motive organ, the
flagellum. Fusion of
peptides to the subunit protein flagellin offers a dense array of many peptide
copies on
the host cells (Kuwajima et al. (1988) BiolTech. 6, 1080-1083). Surface
proteins of
other bacterial species have also served as peptide fusion partners. Examples
include the
Staphylococcus protein A and the outer membrane IgA protease of Neisseria
(Hansson
et al. ( 1992) J. Bacteriol. 174, 423 9-4245 and Klauser et al. ( 1990) EMBD
J. 9, 1991-
1999).
-- 30 In the filamentous phage systems and the Lama system described above,
the
physical link between the per fide and its encoding DNA occurs by the
containment of
the DNA within a particle (cell or phage) that carries the peptide on its
surface.
Capturing the peptide captures the particle and the DNA within. An alternative
scheme
uses the DNA-binding protein LacI to form a link between peptide and DNA (Cull
et al.
3 S ( 1992) PNAS USA 89:1865-1869). This system uses a plasmid containing the
LacI gene
with an oligonucleotide cloning site at its 3'-end. Under the controlled
induction by
arabinose, a LacI-peptide fusion protein is produced. This fusion retains the
natural
_ -.~..r.._.~__.~_
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ability of LacI to bind to a short DNA sequence known as LacO operator (LacO).
By
installing two copies of LacO on the expression plasmid, the LacI-peptide
fusion binds
tightly to the plasmid that encoded it. Because the plasmids in each cell
contain only a
single oligonucleotide sequence and each cell expresses only a single peptide
sequence,
the peptides become specifically and stably associated with the DNA sequence
that
directed its synthesis. The cells of the library are gently lysed and the
peptide-DNA
complexes are exposed to a matrix of immobilized receptor to recover the
complexes
containing active peptides. The associated plasmid DNA is then reintroduced
into cells
for amplification and DNA sequencing to determine the identity of the peptide
ligands.
As a demonstration of the practical utility of the method, a large random
library of
dodecapeptides was made and selected on a monoclonal antibody raised against
the
opioid peptide dynorphin B. A cohort of peptides was recovered, all related by
a
consensus sequence corresponding to a six-residue portion of dynorphin B.
(Cull et al.
(1992) Proc. Natl. Acad. Sci. U.S.A. 89-1869)
This scheme, sometimes referred to as peptides-on-plasmids, differs in two
important ways from the phage display methods. First, the peptides are
attached to the
C-terminus of the fusion protein, resulting in the display of the library
members as
peptides having free carboxy termini. Both of the filamentous phage coat
proteins, pIII
and pVIII, are anchored to the phage through their C-termini, and the guest
peptides are
placed into the outward-extending N-terminal domains. In some designs, the
phage-
displayed peptides are presented right at the amino terminus of the fusion
protein.
(Cwirla, et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6378-6382) A second
difference
is the set of biological biases affecting the population of peptides actually
present in the
libraries. The LacI fusion molecules are confined to the cytoplasm of the host
cells.
The phage coat fusions are exposed briefly to the cytoplasm during translation
but are
rapidly secreted through the inner membrane into the periplasmic compartment,
remaining anchored in the membrane by their C-terminal hydrophobic domains,
with the
N-termini, containing the peptides, protruding into the periplasm while
awaiting
assembly into phage particles. The peptides in the LacI and phage libraries
may differ
significantly as a result of their exposure to different proteolytic
activities. The phage
coat proteins require transport across the inner membrane and signal peptidase
processing as a prelude to incorporation into phage. Certain peptides exert a
deleterious
effect on these processes and are underrepresented in the libraries (Gallop et
al. ( 1994) J.
Med. Chem. 37(9):1233-1251). These particular biases are not a factor in the
LacI
display system.
The number of small peptides available in recombinant random libraries is
enormous. Libraries of 107-109 independent clones are routinely prepared.
Libraries as
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large as 1011 recombinants have been created, but this size approaches the
practical
limit for clone libraries. This limitation in library size occurs at the step
of transforming
the DNA containing randomized segments into the host bacterial cells. To
circumvent
this limitation, an in vitro system based on the display of nascent peptides
in polysome
complexes has recently been developed. This display library method has the
potential of
producing libraries 3-6 orders of magnitude larger than the currently
available
phage/phagemid or plasmid libraries. Furthermore, the construction of the
libraries,
expression of the peptides, and screening, is done in an entirely cell-free
format.
In one application of this method (Gallop et al. ( 1994) J. Med. Chem.
37(9):1233-1251 ), a molecular DNA library encoding 1012 decapeptides was
constructed and the library expressed in an E. coli S30 in vitro coupled
transcription/translation system. Conditions were chosen to stall the
ribosomes on the
mRNA, causing the accumulation of a substantial proportion of the RNA in
polysomes
and yielding complexes containing nascent peptides still linked to their
encoding RNA.
The polysomes are sufficiently robust to be affinity purified on immobilized
receptors in
much the same way as the more conventional recombinant peptide display
libraries are
screened. RNA from the bound complexes is recovered, converted to cDNA, and
amplified by PCR to produce a template for the next round of synthesis and
screening.
The polysome display method can be coupled to the phage display system.
Following
several rounds of screening, cDNA from the enriched pool of polysomes was
cloned into
a phagemid vector. This vector serves as both a peptide expression vector,
displaying
peptides fused to the coat proteins, and as a DNA sequencing vector for
peptide
identification. By expressing the polysome-derived peptides on phage, one can
either
continue the affinity selection procedure in this format or assay the peptides
on
individual clones for binding activity in a phage ELISA, or for binding specif
city in a
completion phage ELISA (Barret, et al. (1992) Anal. Biochem 204,357-364). To
identify the sequences of the active peptides one sequences the DNA produced
by the
phagemid host.
Secondary Screenin of Polype~tides and Analogs
The high through-put assays described above can be followed by secondar r
screens in order to identify further biological activities which will, e.g.,
allow one skilled
in the art to differentiate agonists from antagonists. The type of a secondary
screen used
will depend on the desired activity that needs to be tested. For example, an
assay can be
developed in which the ability to inhibit an interaction between a protein of
interest and
its respective ligand can be used to identify antagonists from a group of
peptide
fragments isolated though one of the primary screens described above.
.T. .__. ... . ...
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Therefore, methods for generating fragments and analogs and testing them for
activity are known in the art. Once the core sequence of interest is
identified, it is
routine for one skilled in the art to obtain analogs and fragments.
Peptide Mimetics of H. pylori Polypeptides
The invention also provides for reduction of the protein binding domains of
the
subject H. pylori polypeptides to generate mimetics, e.g. peptide or non-
peptide agents.
The peptide mimetics are able to disrupt binding of a polypeptide to its
counter ligand,
e.g., in the case of an H. pylori polypeptide binding to a naturally occurring
ligand. The
critical residues of a subject H. pylori polypeptide which are involved in
molecular
recognition of a polypeptide can be determined and used to generate H. pylori-
derived
peptidomimetics which competitively or noncompetitively inhibit binding of the
H.
pylori polypeptide with an interacting polypeptide (see, for example, European
patent
applications EP-412,762A and EP-B31,080A).
For example, scanning mutagenesis can be used to map the amino acid residues
of a particular H. pylori polypeptide involved in binding an interacting
polypeptide,
peptidomimetic compounds (e.g. diazepine or isoquinoline derivatives) can be
generated
which mimic those residues in binding to an interacting polypeptide, and which
therefore can inhibit binding of an H. pylori polypeptide to an interacting
polypeptide
and thereby interfere with the function of H. pylori polypeptide. For
instance, non-
hydrolyzable peptide analogs of such residues can be generated using
benzodiazepine
(e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G.R. Marshall
ed.,
ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al.
in
Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden,
Netherlands, 1988), substituted gama lactam rings (Garvey et al. in Peptides:
Chemistry
and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988),
keto-
methylene pseudopeptides (Ewenson et al. ( 1986) J Med Chem 29:295; and
Ewenson et
al. in Peptides: Structure and Function (Proceedings of the 9th American
Peptide
Symposium) Pierce Chemical Co. Rockland, IL, 1985), ~i-turn dipeptide cores
(Nagai et
al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) JChem Soc Perkin
Trans
1:1231 ), and ~i-aminoalcohols (cordon et al. ( 1085 ~ Biochem Biophys Res
Commun 126:419; and Dann et al. ( 1986) Biochem Biophys Res Commun 134:71 ).
VI. Vaccine Formulations for H. pvlori Nucleic Acids and Polyp~tides
This invention also features vaccine compositions or formulations (used
interchangeably herein) for protection against infection by H. pylori or for
treatment of
H. pylori infection. As used herein, the term "treatment of H. pylori
infection" refers to
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therapeutic treatment of an existing or established X. pylori infection. The
terms
"protection against H. pylori infection" or "prophylactic treatment" refer to
the use of H.
pylori vaccine formulation for reducing the risk of or preventing an infection
in a subject
at risk for H pylori infection. In one embodiment, the vaccine compositions
contain one
or more immunogenic components, such as a surface protein, from H. pylori, or
portion
thereof, and a pharmaceutically acceptable carrier. For example, in one
embodiment, the
vaccine formulations of the invention contain at least one or combination of
H. pylori
polypeptides or fragments thereof, from same or different H. pylori antigens.
Nucleic
acids and H. pylori poIypeptides for use in the vaccine formulations of the
invention
include the nucleic acids and polypeptides set forth in the Sequence Listing,
preferably
those H. pylori nucleic acids that encode surface proteins and surface
proteins or
fragments thereof. For example, a preferred nucleic acid and H. pylori
polypeptide for
use in a vaccine composition of the invention is selected from the group of
nucleic acids
which encode cell envelope proteins and H. pylori cell envelope proteins as
set forth in
Table 1.- However, any nucleic acid encoding an immunogenic H. pylori protein
and H.
pylori polypetide, or portion thereof, can be used in the present invention.
These
vaccines have therapeutic and/or prophylactic utilities.
One aspect of the invention provides a vaccine composition for protection
against infection by H. pylori which contains at least one immunogenic
fragment of an
H. pylori protein and a pharmaceutically acceptable carrier. Preferred
fragments include
peptides of at least about 10 amino acid residues in length, preferably about
10-20 amino
acid residues in length, and more preferably about 12-16 amino acid residues
in length.
Immunogenic components of the invention can be obtained, for example, by
screening polypeptides recombinantly produced from the corresponding fragment
of the
nucleic acid encoding the full-length H. pylori protein. In addition,
fragments can be
chemically synthesized using techniques known in the art such as conventional
Merrifield solid phase f Moc or t-Boc chemistry.
In one embodiment, immunogenic components are identified by the ability of the
peptide to stimulate T cells. Peptides which stimulate T cells, as determined
by, for
example, T cell prol-iferation or cytokine secretion are defined herein as
comprising at
least one T cell enitc pe. T cell epitopes are believed to be involved in
initiation and
perpetuation of the immune response to the protein allergen which is
responsible for the
clinical symptoms of allergy. These T cell epitopes-are thought to trigger
early events at
the level of the T helper cell by binding to an appropriate HLA molecule on
the surface
of an antigen presenting cell, thereby stimulating the T cell subpopulation
with the
relevant T cell receptor for the epitope. These events lead to T cell
proliferation,
lymphokine secretion, local inflammatory reactions, recruitment of additional
immune
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cells to the site of antigen/T cell interaction, and activation of the B cell
cascade, leading
to the production of antibodies. A T cell epitope is the basic element, or
smallest unit of
recognition by a T cell receptor, where the epitope comprises amino acids
essential to
receptor recognition (e.g., approximately 6 or 7 amino acid residues). Amino
acid
sequences which mimic those of the T cell epitopes are within the scope of
this
invention.
In another embodiment, immunogenic components of the invention are identified
through genomic vaccination. The-basic protocol is based on the idea that
expression
libraries consisting of all or parts of a pathogen genome, e.g., an H. pylori
genome, can
confer protection when used to genetically immunize a host. This expression
library
immunization (ELI) is analogous to expression cloning and involves reducing a
genomic
expression library of a pathogen, e.g., H. pylori, into plasmids that can act
as genetic
vaccines. The plasmids can also be designed to encode genetic adjuvants which
can
dramatically stimulate the humoral response. These genetic adjuvants can be
introduced
at remote sites and act as well extracelluraly as intraceIlularly.
This is a new approach to vaccine production that has many of the advantages
of
live/attenuated pathogens but no risk of infection. An expression library of
pathogen
DNA is used to immunize a host thereby producing the effects of antigen
presentation of
a live vaccine without the risk. For example, in-the present invention, random
fragments
from the H. pylori genome or from cosmid or plasmid clones, as well as PCR
products
from genes identified by genornic sequencing, can be used to immunize a host.
The
feasibility of this approach has been demonstrated with Mycoplasma pulmonis
(Barry et
al., Nature 377:632-635, 1995), where even partial expression libraries of
Mycoplasma
pulmonis, a natural pathogen in rodents, provided protection against challenge
from the
pathogen.
ELI is a technique that allows for production of a non-infectious multipartite
vaccine, even when little is known about pathogen's biology, because ELI uses
the
immune system to screen candidate genes. Once isolated, these genes can be
used as
genetic vaccines or for development of recombinant protein vaccines. Thus, ELI
allows
for production of vaccines in a systematic, largely mechanized fashion.
Screening immunogenic components can be accomplished using one or more of
several different assays. For example, in vitro, peptide T cell stimulatory
activity is
assayed by contacting a peptide known or suspected of being immunogenic with
an
antigen presenting cell which presents appropriate MHC molecules in a T cell
culture.
Presentation of an immunogenic H. pylori peptide in association with
appropriate MHC
molecules to T cells in conjunction with the necessary costimulation has the
effect of
transmitting a signal to the T cell that induces the production of increased
levels of
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cytokines, particularly of interleukin-2 and interleukin-4. The culture
supernatant can be
obtained and assayed for interleukin-2 or other known cytokines. For example,
any one
of several conventional assays for interleukin-2 can be employed, such as the
assay
described in Proc. Natl. Acad. Sci USA, 86: 1333 (1989) the pertinent portions
of which
are incorporated herein by reference. A kit for an assay for the production of
interferon
is also available from Genzyme Corporation (Cambridge, MA).
Alternatively, a common assay for T cell proliferation entails measuring
tritiated
thymidine incorporation. The proliferation of T cells can be measured in vitro
by
determining the amount of 3H-labeled thymidine incorporated into the
replicating DNA
of cultured cells. Therefore, the rate of DNA synthesis and, in turn, the rate
of cell
division can be quantified_
Vaccine compositions or formulations of the invention containing one or more
immunogenic components (e.g., H. pylori polypeptide or fragment thereof or
nucleic
acid encoding an H. pylori polypeptide or fragment thereof) preferably include
a
1 S pharmaceutically acceptable earner. The term "pharmaceutically acceptable
carrier" is
intended to include any and all solvents, dispersion media, coatings,
antibacterial and
antifungal agents, isotonic and absorption delaying agents, and the like,
compatible with
pharmaceutical administration. Suitable pharmaceutically acceptable carriers
include,
for example, one or more of water, saline, phosphate buffered saline,
dextrose, glycerol,
ethanol and the like, as well as combinations thereof. Pharmaceutically
acceptable
earners may further comprise minor amounts of auxiliary substances such as
wetting or
emulsifying agents, preservatives or buffers, which enhance the shelf life or
effectiveness of the H. pylori nucleic acid or polypeptide. For vaccine
formulations of
the invention containing H. pylori polypeptides, the polypeptide is preferably
coadministered with a suitable adjuvant and/or a delivery system described
herein.
It will be apparent to those of skill in the art that the therapeutically
effective
amount of DNA or protein-of this invention will depend, inter alia, upon the
administration schedule, the unit dose of an H. pylori nucleic acid or
polypeptide
administered, whether the protein or nucleic acid is administered in
combination with
other therapeutic agents, the immune status and health of the patient, and the
therapeutic
activity of the particular protein or nucleic acid.
Vaccine formulations are conventionally administered parenterally, e.g., by
inj ection, either subcutaneously or intramuscularly. Methods for
intramuscular
immunization are described by Wolff et al. (1990) Science 247: 1465-1468 and
by
Sedegah et al. (1994) Immunology 91: 9866-9870. Other modes of administration
include oral and pulmonary formulations, suppositories, and transdermal
applications.
Oral immunization is preferred over parenteral methods for inducing protection
against
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infection by H. pylori. Czinn et. al. ( 1993) Vaccine 11: 637-642. Oral
formulations
include such normally employed excipients as, for example, pharmaceutical
grades of
mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose,
magnesium
carbonate, and the like.
In one embodiment; the vaccine formulation includes, as a pharmaceutically
acceptable carrier, an adjuvant. Examples of the suitable adjuvants for use in
the
vaccine formulations of the invention include, but are not limited, to
aluminum
hydroxide; N-acetyl-muramyl--L-threonyl-D-isoglutamine (thr-MDP); N-acetyl-nor-
muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP); N-
acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1'-2'-dipalmitoyl-sn-
glycero-3-
hydroxyphos-phoryloxy)-ethylamine (CGP 19835A, referred to a MTP-PE); RIBI,
which contains three components from bacteria; monophosphoryl lipid A;
trehalose
dimycoloate; cell wall skeleton (MPL + TDM + CWS) in a 2% squalene/Tween 80
emulsion; and cholera toxin. Others which may be used are non-toxic
derivatives of
cholera toxin, including its B subunit, and/or conjugates or genetically
engineered
fusions of the H. pylori polypeptide with cholera toxin or its B subunit,
procholeragenoid, fungal polysaccharides, including schizophyllan, muramyl
dipeptide,
muramyl dipeptide derivatives, phorbol esters, labile toxin of E. coli, non-H.
pylori
bacterial lysates, block polymers or saponins.
In another embodiment, the vaccine formulation includes, as a pharmaceutically
acceptable carrier, a delivery system. Suitable delivery systems for use in
the vaccine
formulations of the invention include biodegradable microcapsules or immuno-
stimulating complexes (ISCOMs), cochleates, or liposomes, genetically
engineered
attenuated live vectors such as viruses or bacteria, and recombinant
(chimeric) virus-like
particles, e.g., bluetongue. In another embodiment of the invention, the
vaccine
formulation includes both a delivery system and an adjuvant.
Delivery systems in humans may include enteric release capsules protecting the
antigen from the acidic environment of the stomach, and including H. pylori
polypeptide
in an insoluble form as fusion proteins. Suitable carriers for the vaccines of
the
invention are enteric coated capsules and polylactide-glycolide microspheres.
Suitable
- diluents are 0.2 N NaHC03 and/or saline.
Vaccines of the invention can be administered as a primary prophylactic agent
in
adults or in children, as a secondary prevention, after successful eradication
of H. pylori
- in an infected host, or as a therapeutic agent in the aim to induce an
immune response in
a susceptible host to prevent infection by H. pylori. The vaccines of the
invention are
administered in amounts readily determined by persons of ordinary skill in the
art.
Thus, for adults a suitable dosage will be in the range of 10 ~g to 10 g,
preferably 10 p.g
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to 100 mg, for example 50 ~g to 50 mg. A suitable dosage for adults will also
be in the
range of 5 pg to 500 mg. Similar dosage ranges will be'applicable for
children.
The amount of adjuvant employed will depend on the type of adjuvant used. For
example, when the mucosal adjuvant is cholera toxin, it is suitably used in an
amount of
5 ~g to 50 pg, for example 10 ~.g to 35 p.g. When used in the form of
microcapsules, the
amount used will depend on the amount employed in the matrix of the
microcapsule to
achieve the desired dosage. The determination of this amount is within the
skill of a
person of ordinary skill in the art.-
Those skilled in the art will recognize that the optimal dose may be more or
less
depending upon the patient's body weight, disease, the route of
administration, and other
factors. Those skilled in the art will also recognize that appropriate dosage
levels can be
obtained based on results with known oral vaccines such as, for example, a
vaccine
based on an E. coli lysate (6 mg dose daily up to total of 540 mg) and with an
enterotoxigenic E. coli purified antigen (4 doses of 1 mg) (Schulman et al.,
J. Urol.
150:917-921 (1993)); Boedecker et al., American Gastroenterological Assoc.
999:A-222
( 1993)). The number of doses will depend upon the disease, the formulation,
and
efficacy data from clinical trials. Without intending any limitation as to the
course of
treatment, the treatment can be administered over 3 'to 8 doses for a primary
immunization schedule over 1 month (Boedeker, American Gastroenterological
Assoc.
888:A-222 (1993)).
In a preferred embodiment, a vaccine composition of the invention can be based
on a killed whole E. coli preparation with an immunogenic fragment of an H.
pylori
protein of the invention expressed on its surface or it can be based on an E.
coli lysate,
wherein the killed E. coli acts as a carrier or an adjuvant.
It will be apparent to those skilled in the art that some of the vaccine
compositions of the invention are useful only for preventing H. pylori
infection, some
are useful only for treating H. pylori infection, and some are useful for both
preventing
and treating H. pylori infection. In a preferred embodiment, the vaccine
composition of-
the invention provides protection against H. pylori infection by stimulating
humoral
and/or cell-mediated immunity against H. pylori. It should be understood that
amelioratio l of any of the symptoms of H. pylori infection is a desirable
clinical goal,
including a lessening of the dosage of medication used to treat H. pylori-
caused disease,
or an increase in the production of antibodies in the serum or mucous of
patients.
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VII. Antibodies Reactive With H. pylori Polypeptides
The invention also includes antibodies specifically reactive with the subject
H.
pylori polypeptide. Anti-protein/anti-peptide antisera or monoclonal
antibodies can be
made by standard protocols (See, for example, Antibodies: A Laboratory Manual
ed. by
Harlow and Lane (Cold Spring Harbor Press: 1988)). A mammal such as a mouse, a
hamster or rabbit can be immunized with an immunogenic form of the peptide.
Techniques for conferring immunogenicity on a protein or peptide include
conjugation
to carriers or other techniques well known in the art. An immunogenic portion
of the
subject H. pylori polypeptide can be administered in the presence of adjuvant.
The
I 0 progress of immunization can be monitored by detection of antibody titers
in plasma or
serum. Standard ELISA or other immunoassays can be used with the-immunogen as
antigen to assess the levels of antibodies.
In a preferred embodiment, the subject antibodies are immunospecific for
antigenic determinants of the H. pylori polypeptides of the invention, e.g.
antigenic
determinants of a polypeptide of the invention contained in the Sequence
Listing, or a
closely related human or non-human mammalian homolog (e.g., 90% homologous,
more
preferably at least 95% homologous). In yet a further preferred embodiment of
the
invention, the anti-H. pylori antibodies do not substantially cross react
(i.e., react
specifically) with a protein which is for example, Iess than 80% percent
homologous to a
sequence of the invention contained in the Sequence Listing. By "not
substantially cross
react", it is meant that the antibody has a binding affinity for a non-
homologous protein
which is less than 10 percent, more preferably less than 5 percent, and even
more
preferably less than I percent, of the binding affinity for a protein of the
invention
contained in the Sequence Listing. In a most preferred embodiment, there is no
crossreactivity between bacterial and mammalian antigens.
The term antibody as used herein is intended to include fragments thereof
which
are also specifically reactive with H. pylori polypeptides. Antibodies can be
fragmented
using conventional techniques and the fragments screened for utility in the
same manner
as described above for whole antibodies. For example, F(ab')2 fragments can be
generated by treating antibody with pepsin. The resulting F(ab')2 fragment can
be
treated to reduce disulfide bridges to produce Fab' fragments. The antibody of
the
invention is further intended to include bispecific and chimeric molecules
having an
anti-H. pylori portion.
Both monoclonal and polyclonal antibodies (Ab) directed against H. pylori
polypeptides or H. pylori polypeptide variants, and antibody fragments such as
Fab' and
F(ab')2, can be used to block the action of H. pylori polypeptide and allow
the study of
the role of a particular H. pylori polypeptide of the invention in aberrant or
unwanted
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intracellular signaling, as well as the normal cellular function of the H.
pylori and by
microinjection of anti-H. pylori polypeptide antibodies of the present
invention.
Antibodies which specifically bind H. pylori epitopes can also be used in
immunohistochemical staining of tissue samples in order to evaluate the
abundance and
S pattern of expression of H. pylori antigens. Anti H. pylori polypeptide
antibodies can be
used diagnostically in immuno-precipitation and immuno-blotting to detect and
evaluate
H. pylori levels in tissue or bodily fluid as part of a clinical testing
procedure. Likewise,
the ability to monitor H. pylori polypeptide levels in an individual can allow
determination of the efficacy of a given treatment regimen for an individual
afflicted
with such a disorder. The level of an H. pylori polypeptide can be measured in
cells
found in bodily fluid, such as in urine samples or can be measured in tissue,
such as
produced by gastric biopsy. Diagnostic assays using anti-H. pylori antibodies
can
include, for example, immunoassays designed to aid in early diagnosis of H.
pylori
infections. The present invention can also be used as a method of detecting
antibodies
contained in samples from individuals infected by this bacterium using
specific H. pylori
antigens.
Another application of anti-H. pylori polypeptide antibodies of the invention
is
in the immunological screening of cDNA libraries constructed in expression
vectors
such as ~,gtl 1, ~.gtl8-23, 7~ZAP, and ~,ORF8. Messenger libraries of this
type, having
coding sequences inserted in the correct reading frame and orientation, can
produce
fusion proteins. For instance, ~,gt 11 will produce fusion proteins whose
amino termini
consist of !3-galactosidase amino acid sequences and whose carboxy termini
consist of a
foreign polypeptide. Antigenic epitopes of a subject H. pylori polypeptide can
then be
detected with antibodies, as, for example, reacting nitrocellulose filters
lifted from
infected plates with anti-H. pylori polypeptide antibodies. Phage, scored by
this assay,
can then be isolated from the infected plate. Thus, the presence of H. pylori
gene
homologs can be detected and cloned from other species, and alternate isoforms
(including splicing variants) can be detected and cloned.
VIII. Kits Containing Nucleic Acids. Polypeptides or Antibodies of the
Invention
- The nucleic acid, polypeptides and antibodies of the snv~ntion can be
combined
with other reagents and articles to form kits. Kits for diagnostic purposes
typically
comprise the nucleic acid, polypeptides or antibodies in vials or other
suitable vessels.
- Kits typically comprise other reagents for performing hybridization
reactions,
polymerise chain reactions (PCR), or for reconstitution of lyophilized
components, such
as aqueous media, salts, buffers, and the like. Kits may also comprise
reagents for
sample processing such as detergents, chaotropic salts and the like. Kits may
also
__~_~._.~. ~._.___~_ ___ __.__.r___..._~ .
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comprise immobilization means such as particles, supports, wells, dipsticks
and the like.
Kits may also comprise labeling means such as dyes, developing reagents,
radioisotopes,
fluorescent agents, luminescent or chemiluminescent agents, enzymes,
intercalating
agents and the like. With the nucleic acid and amino acid sequence information
provided
herein, individuals skilled in art can readily assemble kits to serve their
particular
purpose. Kits further can include instructions for use.
IX. Drue Screening Assays Usin~Hwlori Polypeptides
By making available purified and recombinant H. pylori polypeptides, the
I 0 present invention provides assays which can be used to screen for drugs
which are either
agoilists or antagonists of the normal cellular function, in this case, of the
subject H.
pylori polypeptides, or of their role in intracellular signaling. Such
inhibitors or
potentiators may be useful as new therapeutic agents to combat H. pylori
infections in
humans. A variety of assay formats will suffice and, in light of the present
inventions,
15 will be comprehended by the skilled artisan.
In many drug screening programs which test libraries of compounds and natural
extracts, high throughput assays are desirable in order to maximize the number
of
compounds surveyed in a given period of time. Assays which are performed in
cell-free
systems, such as may be derived with purified or semi-purified proteins, are
often
20 preferred as "primary" screens in that they can be generated to permit
rapid development
and relatively easy detection of an alteration in a molecular target which is
mediated by
a test compound. Moreover, the effects of cellular toxicity and/or
bioavailability of the
test compound can be generally ignored in the in vitro system, the assay
instead being
focused primarily on the effect of the drug on the molecular target as may be
manifest in
25 an alteration of binding affinity with other proteins or change in
enzymatic properties of
the molecular target. Accordingly, in an exemplary screening assay of the
present
invention, the compound of interest is contacted with an isolated and purified
H. pylori
polypeptide.
Screening assays can be constructed in vitro with a purified H. pylori
30 polypeptide or fragment thereof, such as an H. pylori polypeptide having
enzymatic
activity, such that the activity of .he polypeptide produces a detectable
reaction product.
The efficacy of the compound can be assessed by generating dose response
curves from
data obtained using various concentrations of the test compound. Moreover, a
control
assay can also be performed to provide a baseline for comparison. Suitable
products
35 include those with distinctive absorption, fluorescence, or chemi-
luminescence
properties, for example, because detection may be easily automated. A variety
of
synthetic or naturally occurring compounds can be tested in the assay to
identify those
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which inhibit or potentiate the activity of the N. pylori polypeptide. Some of
these
active compounds may directly, or with chemical alterations to promote
membrane
permeability or solubility, also inhibit or potentiate the same activity
(e.g., enzymatic
activity) in whole, live H. pylori cells.
This invention is further illustrated by the following examples which should
not
be construed as limiting. The contents of all references and published patent
applications cited throughout this application are hereby incorporated by
reference.
EXEMPLIFICATION
I. Cloning and Sequencing of H pylori DNA
H. pylori chromosomal DNA was isolated according to a basic DNA protocol
outlined in Schleif R.F. and Wensink P.C., Practical Methods in Molecular
Biology,
p.98, Springer-Verlag, NY., 1981, with minor modifications. Briefly, cells
were
pelleted, resuspended in TE ( 10 mM Tris, 1 mM EDTA, pH 7.6) and GES lysis
buffer
(5.1 M guanidium thiocyanate, 0.1 M EDTA, pH 8.0, 0.5% N-laurylsarcosine) was
added. Suspension was chilled and ammonium acetate (NH4Ac) was added to final
concentration of 2.0 M. DNA was extracted, first with chloroform, then with
phenol-
chloroform, and reextracted with chloroform. DNA was precipitated with
isopropanol,
washed twice with 70% EtOH, dried and resuspended in TE.
Following isolation whole genomic H. pylori DNA was nebulized (Bodenteich et
al., Automated DNA Seguencing and Analysis (J.C. Venter, ed.), Academic Press,
I 994)
to a median size of 2000 bp. After nebulization, the DNA was concentrated and
separated on a standard 1 % agarose gel. Several fractions, corresponding to
approximate sizes 900-1300 bp, 1300-1700 bp, 1700-2200 bp, 2200-2700 bp, were
excised from the gel and purified by the GeneCIean procedure (Bio101, Inc.).
The purified DNA fragments were then blunt-ended using T4 DNA polymerase.
The healed DNA was then ligated to unique BstXI-linker adapters in 100-1000
fold
molar excess. These linkers are complimentary to the BstXI-cut pMPX vectors,
while
tl- a overhang is not self complimentary. Therefore, the linkers will not
concatemerize
nor will the cut-vector religate itself easily. The linker-adopted inserts
were separated
from the unincorporated linkers on a 1 % agarose gel and purified using
GeneClean. The
linker-adopted inserts were then ligated to each of the 20 pMPX vectors to
construct a
series of "shotgun" subclone Libraries. The vectors contain an out-of frame
IacZ gene at
the cloning site which becomes in-frame in the event that an adapter-dimer is
cloned,
allowing these to be avoided by their blue-color.
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All subsequent steps were based on the multiplex DNA sequencing protocols
outlined in Church G.M. and Kieffer-Higgins S., Science 240:185-188, 1988.
Only
major modifications to the protocols are highlighted. Briefly, each of the 20
vectors was
then transformed into DHSa competent cells (GibcoBRL, DHSa transformation
S protocol). The libraries were assessed by plating onto antibiotic plates
containing
ampicillin, methicillin and IPTG/Xgal. The plates were incubated overnight at
37oC.
Successful transformants were then used for plating of clones and pooling into
the
multiplex pools. The clones were picked and pooled into 40 ml growth medium
cultures. The cultures were grown overnight at 37oC. DNA was purified using
the
Qiagen Midi-prep kits and Tip-100 columns (Qiagen, Inc.). In this manner, 100
~g of
DNA was obtained per pool. Fifteen 96-well plates of DNA were generated to
obtain a
5- I 0 fold sequence redundancy assuming 250-300 base average read-lengths.
These purified DNA samples were then sequenced using the multiplex DNA
sequencing based on chemical degradation methods (Church G.M. and Kieffer-
Higgins
S., Science 240:185-188, 1988) or by Sequithrem (Epicenter Technologies)
dideoxy
sequencing protocols. The sequencing reactions were electrophoresed and
transferred
onto nylon membranes by direct transfer electrophoresis from 40 cm gels
(Richterich P.
and Church G.M., Methods in Enrymology 218:187-222, 1993) or by
electroblotting
(Church, supra). 24 samples were run per gel. 45 successful membranes were
produced
by chemical sequencing and 8 were produced by dideoxy sequencing. The DNA was
covalently bound to the membranes by exposure to ultraviolet light, and
hybridized with
labeled oligonucleotides complimentary to tag sequences on the vectors
(Church, supra).
The membranes were washed to rinse off non-specifically bound probe, and
exposed to
X-ray film to visualize individual sequence ladders. After autoradiography,
the
hybridized probe was removed by incubation at 65° C, and the
hybridization cycle
repeated with another tag sequence until the membrane had been probed 3 8
times for
chemical sequencing membranes and 10 times for the dideoxy sequencing
membranes.
Thus, each gel produced a large number of films, each containing new
sequencing
information. Whenever a new blot was processed, it was initially probed for an
internal
standard sequence added to each of the pools.
Digital images of the films were generated using a laser-scanning densitomet
:r
(Molecular Dynamics, Sunnyvale, CA). The digitized images were processed on
computer workstations (VaxStation 4000's) using the program REPLICATM (Church
et
al., Automated DNA Sequencing and Analysis (J.C. Venter, ed.), Academic Press,
1994).
Image processing included lane straightening, contrast adjustment to smooth
out
intensity differences, and resolution enhancement by iterative gaussian
deconvolution.
The sequences were then automatically picked in REPLICATM and displayed for
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interactive proofreading before being stored in a project database. The
proofreading was
accomplished by a quick visual scan of the film image followed by mouse clicks
on the
bands of the displayed image to modify the base calls. Many of the sequence
errors
could be detected and corrected because multiple sequence reads covering the
same
portion of the genomic DNA provide adequate sequence redundancy for editing.
Each
sequence automatically received an identification number (corresponding to
microtiter
plate, probe information, and lane set number). This number serves as a
permanent
identifier of the sequence so it is always possible to identify the original
of any
particular sequence without recourse to a specialized database.
Routine assembly of H. pylori sequences was done using the program FALCON
(Church, Church et al., Automated DNA Sequenicng and Analysis (J.C. Venter,
ed.),
Academic Press, 1994). This program has proven to be fast and reliable for
most
sequences. The assembled contigs were displayed using a modified version of
GelAssemble, developed by the Genetics Computer Group (GCG) (Devereux et al.,
1 S Nucleic Acid Res. 12:387-95, 1984) that interacts with REPLICATM. This
provided for
an integrated editor that allows multiple sequence gel images to be
instantaneously
called up from the REPLICATM database and displayed to allow rapid scanning of
contigs and proofreading of gel traces where discrepancies occurred between
different
sequence reads in the assembly.
I1. Identification, cloning and expression of recombinant H. pylori DNA
sequences
To facilitate the cloning, expression and purification of membrane and
secreted
proteins from H. pylori a powerful gene expression system, the pET System
(Novagen),
for cloning and expression of recombinant proteins in E. coli, was selected.
Also, a
DNA sequence encoding a peptide tag, the His-Tag, was fused to the 3' end of
DNA
sequences of interest in order to facilitate purification of the recombinant
protein
products. The 3' end was selected for fusion in order to avoid alteration of
any 5'
terminal signal sequence. The exception to the above was ppiB, a gene cloned
for use as
a control in the expression studies. In this study, the sequence for H. pylori
ppiB
contains a DNA sequence encoding a His-Tag fused to the 5' end of the full
length gene,
because the protein product of this gene does not c~nt~.in a signal sequence
and is
expressed as a cytosolic protein.
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PCR Amplifrcation and cloning of DNA sequences containing ORF's for membrane
and
secreted proteins from the J99 Strain of Helicobacter pylori.
Sequences chosen (from the list of the DNA sequences of the invention) for
cloning from the J99 strain of H. pylori were prepared for amplification
cloning by
polymerase chain reaction (PCR). Synthetic oligonucleotide primers (Table 3)
specific
for the 5' and 3' ends of open reading frames (ORFs) were designed and
purchased
(GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers
(specific
for the 5' end of the sequence) were designed to include an NcoI cloning site
at the
extreme 5' terminus, except for HpSeq. 4821082 where NdeI was used. These
primers
were designed to permit initiation of protein translation at a methionine
residue followed
by a valine residue and the coding sequence for the remainder of the native H.
pylori
DNA sequence. An exception is H. pylori sequence 4821082 where the initiator
methionine is immediately followed by the remainder of the native H. pylori
DNA
sequence. All reverse primers (specific for the 3' end of any H. pylori ORF)
included a
EcoRI site at the extreme 5' terminus to permit cloning of each H. pylori
sequence into
the reading frame of the pET-28b. The pET-28b vector provides sequence
encoding an
additional 20 carboxy-terminal amino acids (only 19 amino acids in HpSeq.
26380318
and HpSeq.14640637) including six histidine residues (at the extreme C-
terminus),
which comprise the His-Tag. An exception to the above, as noted earlier, is
the vector
construction for the ppiB gene. A synthetic oligonucleotide primer specific
for the 5'
end of ppiB gene encoded a BamHI site at its extreme 5' terminus and the
primer for the
3' end of the ppiB gene encoded a XhoI site at its extreme 5' terminus.
TABLE 3
OIi~POnucleotide primers used for PCR amplification of H. pylori DNA sequences
Outer membrane Forward primer 5' Reverse Primer 5'
to 3' to 3'
Proteins
Protein 16225006 5'-TATACCATGGTGGG 5'-ATGAATTCGAGTA
CGCTAA-3' (SEQ ID AGGATTTTTG-3' (SEQ
_ N0:195) ID N0:196)
Protein 26054702 5'-TTAACCATGGTGA 5'-TAGAATTCGCATA
AAAGCGATA-3' (SEQ ACGATCAATC-3' (SEQ
ID
N0:197) ID N0:198)
Protein 7116626 5'-ATATCCATGGTGA 5'-ATGAATTCAATTT
GTTTGATGA-3' (SEQ TTTATTTTGCCA-3'
ID
N0:199) (SEQ ID N0:200)
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I Protein 29479681 5'-AATTCCATGGTGG 5'-ATGAATTCTCGAT
GGGCTATG-3' (SEQ AGCCAAAATC-3' (SEQ
ID
N0:201 ) ID N0:202)
Protein 14640637 5'-AATTCCATGGTG 5'-AAGAATTCTCTA
CATAACTTCCATT-3' GCATCCAAATGGA-3'
(SEQ ID N0:203) (SEQ ID N0:204)
Periplasmic/ Secreted
Proteins
Protein 30100332 5'-ATTTCCATGGTCATG 5'-ATGAATTCCATC
TCTCATATT-3' (SEQ TTTTATTCCAC-3'
ID
N0:205) (SEQ ID N0:206)
Protein 4721061 5'-AACCATGGTGATTT 5'-AAGAATTCCAC
TAAGCATTGAAAG-3' TCAAAATTTTTTAAC
(SEQ ID N0:207) AG-3' (SEQ ID N0:208)
'i
Other Surface Proteins
Protein 4821082 5'-GATCATCCATATGTT 5'-TGAATTCAACCA
ATCTTCTAAT-3' (SEQ TTTTAACCCTG-3'
ID N0:209) (SEQ ID N0:210)
Protein 978477 5'-TATACCATGGTGAA S'-AGAATTCAATT
ATTTTTTCTTTTA-3' GCGTCTTGTAAAAG-
(SEQ ID N0:211 ) 3' (SEQ ID N0:212)
Inner Membrane
Protein
Protein 26380318 5'-TATACCATGGTGAT 5'-ATGAATTCCCACTT
GGACAAACTC-3' (SEQ GGGGCGATA-3' (SEQ
ID N0:213) ID N0:214)
Cytoplasmic Protein
ppi 5'-TTATGGATCCAAAC 5'-TATCTCGAGTTATA
CAATTAAAACT-3' (SEQ GAGAAGGGC-3' (SEQ
ID N0:215) ID N0:216)
Genomic DNA prepared from the J99 strain of H. pylori (ATCC #55679;
deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA
02154) was used as the source of template DNA for PCR amplification reactions
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994). To amplify a DNA sequence containing an H. pylori ORF, genomic
DNA
(50 nanograms) was introduced into a reaction vial containing 2 mM MgCl2, 1
micromolar synthetic oligonucleotide primers (forward and reverse primers)
complementary to and flanking a defined H. pylori ORF, 0.2 mM of each
deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 2.5 units of heat
stable
___ ._~._._r. __.
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DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA)
in
a final volume of 100 microliters. The following thermal cycling conditions
were used
to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/
GeneAmp
PCR System 9600 thermal cycler:
Protein 26054702, Protein 7116626, Protein 29479681, Protein 30100332, and
Protein 4821082;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 1 S sec, 30°C for 15 sec and 72°C
for 1.5 min
23 cycles at 94°C for I S sec, 55°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes.
Protein 16225006;
Denaturation at 94°C for 2 min,
25 cycles at 95°C for I S sec, 55°C for 15 sec and
72°C for 1.5 min
Reaction was concluded at 72°C for 6 minutes.
Protein 4721061;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 36°C for 15 sec and 72°C
for 1.5 min
23 cycles at 94°C for 15 sec, 60°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes.
Protein 26380318;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 38°C for 15 sec and 72°C for
1.5 min
23 cycles at 94°C for 15 ses, 62°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes.
Protein 14640637;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 33°C for 15 sec and 72°C for
1.5 min
30 cycles at 94°C for 15 sec, SS°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes. -
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Conditions for amplification of H. pylori ppiB;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 32°C for 15 sec and 72°C for
1.5 min
25 cycles at 94°C for 1 S sec, 56°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes
Upon completion of thermal cycling reactions, each sample of amplified DNA
was washed and purified using the Qiaquick Spin PCR purification kit (Qiagen,
Gaithersburg, MD, USA). All amplified DNA samples were subjected to digestion
with
the restriction endonucleases, NcoI and EcoRI (New England BioLabs, Beverly,
MA,
USA), or in the case of HpSeq. 4821082 (SEQ ID NO: 1309), with NdeI and EcoRI
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994). DNA samples were then subjected to electrophoresis on 1.0 %
NuSeive
(FMC BioProducts, Rockland, ME USA) agarose gels. DNA was visualized by
1 S exposure to ethidium bromide and long wave uv irradiation. DNA contained
in slices
isolated from the agarose gel was purified using the Bio 101 GeneClean Kit
protocol
(Bio 101 Vista, CA, USA).
Cloning of H. pylori DNA sequences into the pET 28b prokaryotic expression
vector.
The pET-28b vector was prepared for cloning by digestion with NcoI and EcoRI,
or in the case of H. pylori protein 4821082 with NdeI and EcoRI (Current
Protocols in
Molecular Biology, 3ohn Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
In the case
of cloning ppiB, the pET-28a vector, which encodes a His-Tag that can be fused
to the
S' end of an inserted gene, was used and the cloning site prepared for cloning
with the
ppiB gene by digestion with BamHI and XhoI restriction endonucleases.
Following digestion, DNA inserts were cloned (Current Protocols in Molecular
Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) into the
previously
digested pET-28b expression vector, except for the amplified insert for ppiB,
which was
cloned into the pET-28a expression vector. Products of the ligation reaction
were then
used to transform the BL21 strain of E. coli (Current Protocols in Molecular
Biology,
John Wiley and Sons, Inc., F. Ausubel et al., ids., 1994) as described below.
Transformation of competent bacteria with recombinant plasmids
Competent bacteria, E coli strain BL21 or E. coli strain BL21(DE3), were
transformed with recombinant pET expression plasmids carrying the cloned H.
pylori
sequences according to standard methods (Current Protocols in Molecular, John
Wiley
and Sons, Inc., F. Ausubel et al., eds., 1994). Briefly, 1 microliter of
ligation reaction
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was mixed with 50 microliters of electrocompetent cells and subjected to a
high voltage
pulse, after which, samples were incubated in 0.45 milliliters SOC medium
(0.5% yeast
extract, 2.0 % tryptone, 10 mM NaCI, 2.5 mM KCI, 10 mM MgCl2, 10 mM MgS04 and
20, mM glucose) at 37oC with shaking for 1 hour. Samples were then spread on
LB
agar plates containing 25 microgram/ml kanamycin sulfate for growth overnight.
Transformed colonies of BL21 were then picked and analyzed to evaluate cloned
inserts
as described below.
Identification of recombinant pET expression plasmids carrying H. pylori
sequences
Individual BL21 clones transformed with recombinant pET-28b-H.pylori ORFs
were analyzed by PCR amplification of the cloned inserts using the same
forward and
reverse primers, specific for each H. pylori sequence, that were used in the
original PCR
amplification cloning reactions. Successful amplification verified the
integration of the
H. pylori sequences in the expression vector (Current Protocols in Molecular
Biology,
John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Isolation and Preparation of plasmid DNA from BL21 transformants
Individual clones of recombinant pET-28b vectors carrying properly cloned H.
pylori ORFs were picked and incubated in 5 mls of LB broth plus 25
microgram/ml
kanamycin sulfate overnight. The following day plasmid DNA was isolated and
purified using the Qiagen plasmid purification protocol (Qiagen Inc.,
Chatsworth, CA,
USA).
Expression of recombinant H. pylori sequences in E coli
The pET vector can be propagated in any E coli K-12 strain e.g. HMS174,
HB 101, JM109, DHS, etc. for the purpose of cloning or plasmid preparation.
Hosts for
expression include E. coli strains containing a chromosomal copy of the gene
for T7
RNA polymerise. These hosts are lysogens of bacteriophage DE3, a lambda
derivative
that carries the lacI gene, the lacUVS promoter and the gene for T7 RNA
polymerise.
T7 RNA polymerise is induced by addition of isopropyl-B-D-thiogalactoside
{IPTG),
and the T7 RN ~ polymerise transcribes any target plasmid, such as pET-28b,
carrying a
T7 promoter and a gene of interest. Strains used include: BL21 (DE3) (Studier,
F.W.,
Rosenberg, A.H., Dunn, J.J., ind Dubendorff, J.W. (1990) Meth. Enzymol. 185,
60-89).
To express recombinant H. pylori sequences, 50 nanograms of plasmid DNA
isolated as described above was used to transform competent BL21 (DE3)
bacteria as
described above {provided by Novagen as part of the pET expression system
kit). The
IacZ gene (beta-galactosidase) was expressed in the pET-System as described
for the H.
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pylori recombinant constructions. Transformed cells were cultured in SOC
medium for
1 hour, and the culture was then plated on LB plates containing 25
micrograms/ml
kanamycin sulfate. The following day, bacterial colonies were pooled and grown
in LB
medium containing kanamycin sulfate (25 micrograms/ml) to an optical density
at 600
nM of 0.5 to 1.0 O.D. units, at which point, 1 millimolar IPTG was added to
the culture
for 3 hours to induce gene expression of the H. pylori recombinant DNA
constructions.
After induction of gene expression with IPTG, bacteria were pelleted by
centrifugation in a Sorvall RC-3B centrifuge at 3500 x g for 15 minutes at
4°C. Pellets
were resuspended in 50 milliliters of cold 10 mM Tris-HCI, pH 8.0, 0.1 M NaCI
and 0.1
mM EDTA (STE buffer). Cells were then centrifuged at 2000 x g for 20 min at
4oC.
Wet pellets were weighed-and frozen at -80°C until ready for protein
purification.
III. Purification of recombinant proteins from E toll
Analytical Methods
The concentrations of purified protein preparations were quantified
spectrophotometrically using absorbance coefficients calculated from amino
acid
content (Perkins, S.J. 1986 Eur. J. Biochem. 157, 169-180). Protein
concentrations were
also measured by the method of Bradford, M.M. ( 1976) Anal. Biochem. 72, 248-
254,
and Lowry, O.H., Rosebrough, N., Farr, A.L. & Randall, R.J. ( 1951 ) J. Biol.
Chem. 193,
pages 265-275, using bovine serum albumin as a standard.
SDS-polyacrylamide gels ( 12% or 4.0 to 25 % acrylamide gradient gels) were
purchased from BioRad (Hercules, CA, USA), and stained with Coomassie blue.
Molecular weight markers included rabbit skeletal muscle myosin (200 kDa), E.
toll (-
galactosidase ( 116 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine
serum
albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anhydrase (31 kDa),
soybean
trypsin inhibitor (21.5 kDa), egg white lysozyme ( 14.4 kDa) and bovine
aprotinin (6.5
kDa). -
1. Purification of soluble proteins
All steps were carried out at 4oC. Frozen cells were thawed, resuspended in 5
volumes of lysis buffer (20 mM Tris, pH 7.9, 0.5 M NaCI, 5 mM imidazole with
10%
glycerol, 0.1 % 2-mercaptoethanol, 200 fig/ ml lysozyme, 1 mM
phenylmethyIsulfonyl
fluoride (PMSF), and 10 ug/ml each of leupeptin, aprotinin, pepstatin, L-1-
chloro-3-[4-
tosylamido]-7-amino-2-heptanone (TLCK), L-1-chloro-3-[4-tosylamidoJ-4-phenyl-2-
butanone (TPCK), and soybean trypsin inhibitor, and ruptured by several
passages
through a small volume microfluidizer (Model M-1 l OS, Microfluidics
International
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Corporation, Newton, MA). The resultant homogenate was made 0.1 % Brij 35, and
centrifuged at 100,000 x g for 1 hour to yield a clear supernatant (crude
extract).
Following filtration through a 0.8 ~m Supor filter (Gelman Sciences, FRG) the
crude extract was loaded directly onto a Ni2+- nitrilotriacetate-agarose (NTA)
with a 5
milliliter bed volume (Hochuli, E., Dbeli, H., and Schacheer, A. (1987) J.
Chromatography 411, 177-184) pre-equilibrated in lysis buffer containing 10
glycerol, 0.1 % Brij 35 and 1 mM PMSF. The column was washed with 250 ml (50
bed
volumes) of lysis buffer containing 10 % glycerol, 0.1 % Brij 35, and was
eluted with
sequential steps of lysis buffer containing 10 % glycerol, 0.05 % Brij 35, 1
mM PMSF,
and 20, 100, 200, and 500 mM imidazole in succession. Fractions were monitored
by
absorbance at OD280 nm, and peak fractions were analyzed by SDS--PAGE.
Fractions
containing the recombinant protein eluted at 100 mM imidazole.
Recombinant protein 14640637 and proteins, beta-galactosidase (IacZ) and
peptidyl-
prolyl cis-traps isomerase (ppiB)
Fractions containing the recombinant proteins from the Ni2+-NTA-agarose
columns were pooled and then concentrated to approximately 5 ml by centrifugal
filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 180-ml
column (1.6
X 91 cm) of Sephacryl S-100 HR gel filtration medium equilibrated in Buffer A
(10 mM
Hepes, pH 7.5, 150 mM NaCI, 0.1 mM EGTA) and run in Buffer A at 18 ml/h.
Fractions containing the recombinant protein were identified by absorbance at
280 nm
and analyzed by SDS-PAGE. Fractions were pooled and concentrated by
centrifugal
filtration.
Recombinant protein 7116626
Fractions containing the recombinant protein from the Ni2+ -NTA-agarose
column were pooled and dialyzed overnight against 1 liter of dialysis buffer (
10 mM
MOPS, pH 6.5, 50 mM NaCI, 0.1 mM EGTA, 0.02% Brij 35 and 1 mM PMSF). In the
morning, a fine white precipitate was removed by centrifugation and the
resulting
supernatant was loaded onto an 8 ml (8 x 75 mm) MonoS high performance liquid
chromatography column (Pharmacia Biotechnology, Inc., Piscataway, NJ; USA)
equilibrated in buffer B (I O mM MOPS, pH 6.5, 0.1 mM EGTA) containing 50 mM
NaCI. The column was washed with 10 bed volumes of buffer B containing 50 mM
NaCI, and developed with a 50-ml linear gradient of increasing NaCI (50 to 500
mM).
Recombinant protein 7116626 eluted as a sharp peak at 300 mM NaCI.
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2. Purifrcation of insoluble proteins from inclusion bodies
The following steps were carried out at 4oC. Cell pellets were resuspended in
lysis buffer with 10% glycerol 200 p.g/ ml lysozyme, 5 mM EDTA, i mM PMSF and
0.1
-mercaptoethanol. After passage through the cell disrupter, the resulting
homogenate
was made 0.2 % deoxycholate, stirred 10 minutes, then centrifuged at 20,000 x
g, for 30
min. The pellets were washed with lysis buffer containing 10 % glycerol, 10 mM
EDTA, 1 % Triton X-100, 1 mM PMSF and 0.1 % -mercaptoethanol, followed by
several
washes with lysis buffer containing 1 M urea, 1 mM PMSF and 0.1 % 2-
mercaptoethanol. The resulting white pellet was composed primarily of
inclusion
bodies, free of unbroken cells and membranous materials.
Recombinant proteins 26054702, 16225006, 30100332, 4721061
The following steps were carried out at room temperature. Purified inclusion
bodies were dissolved in 20 ml 8.0 M urea in lysis buffer with 1 mM PMSF and
0.1
2-mercaptoethanol, and incubated at room temperature for 1 hour. Materials
that did not
dissolve were removed by centrifugation. The clear supernatant was filtered,
then
loaded onto a Ni2~ -NTA agarose column pre-equilibrated in 8.0 M urea in Lysis
Buffer. The column was washed with 250 ml (50 bed volumes) of lysis buffer
containing 8 M urea, 1.0 mM PMSF and 0.1 % 2-mercaptoethanol, and developed
with
sequential steps of lysis buffer containing 8M urea, 1 mM PMSF, 0.1 % 2-
mercaptoethanol and 20, 100, 200, and 500 mM imidazole in succession.
Fractions
were monitored by absorbance at OD2g0 nm, and peak fractions were analyzed by
SDS-
PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
Recombinant proteins 29479681, 26380318
The pellet containing the inclusion bodies was solubilized in buffer B
containing
8 M urea, I mM PMSF and 0.1 % 2-mercaptoethanol, and incubated for 1 hour at
room
temperature. Insoluble materials were removed by centrifugation at 20,000 x g
for 30
min, and the cleared supernatant was loaded onto a 15 ml ( 1.6 x 7.5 cm ) SP-
Sepharose
column pre-equilibrated in buffer B, 6 M urea, 1 mM PMSF, 0.1 % 2-
mercaptoethanol.
- After washing the column with 1~ bid volumes, the column was developed with
a linear
gradient from 0 to 500 mM NaCI.
Dialysis and concentration of protein samples
Urea was removed slowly from the protein samples by dialysis against Tris-
buffered saline (TBS; 10 mM Tris pH 8.0, 150 mM NaCI) containing 0.5
deoxycholate (DOC) with sequential reduction in urea concentration as follows;
6M,
_. ..._~__.._.._ _ .__ _._._____. ......r...__._ .._.. . .
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4M, 3M, 2M, 1 M, 0.5 M and finally TBS without any urea. Each dialysis step
was
conducted for a minimum of 4 hours at room temperature.
After dialysis, samples were concentrated by pressure filtration using Amicon
stirred-cells. Protein concentrations were measured using the methods of
Perkins ( 1986
Eur. J. Biochem. 157, 169-180), Bradford ((1976) Anal. Biochem. 72, 248-254)
and
Lowry ((1951) J. Biol. Chem. 193, pages 265-275))
The recombinant proteins purified by the methods described above are
summarized in Table 4 below.
TABLE 4
J99 Homolog Gene Bacterial Method RelativeFinal Composit
Sequenceidentifiedsymbolcell of MW on concentratioionof
Identifierby Blastof fraction purificationSDS- n of buffer
used to purified
purify
Homologrecombinant PAGE protein
gel
protein
s
vuacmcmva auc t a a»cum
16225006P28635 YEAC inclusion His-Tag 18 kDa 5 mg/mlB
bodies
26054702P15929 tlgH Inclusion His-Tag 37 kDa 1.18 B
bodies mg/ml
---- as dry
pellet
71 16626P26093 e(P4) Soluble His-Tag 29 kDa 0.8 A
fraction mg/ml
1.85 C
mg/ml
29479681P13036 fecA InclusionsSP- 23 kDa 2.36 B
bodies Sepharose mglml
0.5 B
mg
ml
---- as dry
pellet
14640637P16665 TPFI Soluble His-Tag 17 kDa 2.4 A
fraction mg/ml
gel filtration
S100
HR
Periplasmic/Secreted
Protein
~
_ ~~ P23847 dppA Inclusion His-Tag I1 kDa 2.88 B
~032 bodies mg/ml
4721061 P36175 GCP Inclusion His-Tag 38 kDa 2.8 B
bodies mg/ml
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Other Surface Proteins
4821082 P08089 M Inciusion His-Tag20 kDa 1.16 B
proteinbodies mg/ml
978477 L28919 FBP54 Inclusion SP- 44 kDa 2.56 B
bodies Sepharose mg/ml
-
[ I 0.3 mg/mlB ~~
loner Membrane Yrotems
26380318 P15933 flit Inclusion SP- 11 kDa 22 mg/mlB
bodies
Sepharose
l;ontrol Yrotems Wth tl~s-l a~
P00722 IacZ Soluble His-Tag 116 10 mg/mlA
fraction kDa
gel
filtration
5200
HR
ppiB Soluble His-Tag 21 4.4 A
fraction kDa mg/ml
gel
filtration
S100
HR
Buffer
composition
s:
A=10
mM Hepes
pH 7.5,
150
mM NaCI,
0.1
mM EGTA
B= 10
mM Tris
pH 8.0,
150
mM NaCI,
0.5
% DOC
C= 10
mM MOPS
pH 6.5,
300
mM NaCI,
0.1
EGTA
I
IV. Analysis of H pylori proteins as Vaccine candidates
To analyze H. pylori proteins for use in the vaccine formulations of the
invention, several H. pylori proteins were expressed, characterized
immunologically and
tested in animal efficacy studies as outlined below. Specifically, the
immunomodulatory
effects of H. pylori proteins were investigated in a mouse/H. pylori model
which mimics
the human H. pylori infection in humans. In these studies, the effect of oral
immunization of selected H. pylori poiypeptides in H. pylori infected mice was
determined.
-- Identification, cloning and expression of recombinant Helicobacter pylori
seguences.
1 S To facilitate the cloning, expression and purification of membrane andlor
secreted proteins from H. pylori, the pET gene expression system (Novagen),
for cloning '-
and expression of recombinant proteins in Escherichia coli was selected.
Further, for
proteins that have a signal sequence at their amino-terminal end, a DNA
sequence
encoding a peptide tag (His-tag) was fused to the 5' end of the H. pylori DNA
sequences
of interest in order to facilitate purification of the recombinant protein
products.
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PCR amplification and cloning of DNA sequences containing ORFs for membrane
and
secreted proteins from the J99 strain of Helicobacter pylori.
The sequences selected (from the list of the DNA sequences of the invention)
for
S cloning from H. pylori strain J99 were prepared for amplification cloning by
the
polymerase chain reaction (PCR). All of the selected sequences encode for
outer
membrane H. pylori proteins, with vac9 (SEQ ID N0:125), vacl0 (SEQ ID N0:147),
vac22 (SEQ ID N0:121 ) and vac41 (SEQ ID N0:176) sequences all sharing a
terminal
phenylalanine residue. Likewise, the vac32 (SEQ ID N0:108), vac36 (SEQ ID
N0:149)
and vac37 (SEQ ID N0:139) sequences all share a terminal phenylalanine residue
and a
tyrosine cluster at the C-terminus. Synthetic oligonucleotide primers for each
ORF of
interest (Table 5) specific for the predicted mature 5' end of the ORF and
downstream
(3') of the predicted translational termination codon were designed and
purchased
(GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers
{specific
for the 5' terminus of the region of ORF of interest) were designed to include
a BamIII
restriction site followed by a NdeI restriction site. These primers were
designed to
permit the initiation of protein translation at a methionine residue encoding
within the
NdeI restriction site sequence (in the case of producing a non His-tagged
recombinant
protein) or to fuse in frame with the DNA sequence encoding the His-tag (for
producing
His-tagged recombinant protein), followed by the coding sequence for the
remainder of
the native H. pylori DNA. All reverse oligonucleotide primers (specific for
downstream
(3') of the predicted translational termination codon of the ORF) were
designed to
include an EcoRI restriction site at the 5' terminus. This combination of
primers would
enable each ORF-of interest to be cloned into pET28b (to produce a His-tagged
recombinant protein) or pET30a (to produce a non His-tagged or native
recombinant
protein). The pET28b vector provides sequence encoding an additional 20 amino-
terminal amino acids (plus the methionine in the NdeI restriction site)
including a stretch
of six histidine residues which makes up the His-tag.
Genomic DNA prepared from H. pylori strain J99 (ATCC 55679) was used as
the source of template DNA for the PCR amplification reactions (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausube~ et al., eds., 1994).
To
amplify a DNA sequence containing a specific H. pylori ORF, genomic DNA (50
nanograms) was introduced into a reaction tube containing 200 nanograms of
both the
forward and reverse synthetic oligonucleotide primer specific for the ORF of
interest,
and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies,
Gaithersburg, MD, USA) in a total of 50 microliters. The PCR SuperMix is
supplied in
1.1X concentrations and contains 22mM Tris-HCl (pH 8.4), SSmM KCI, 1.65 mM
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MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22 units recombinant
Taq polymerase/ml and stabilizers. The following thermal cycling conditions
were used
to obtain amplified DNA products for each ORF using a Perkin-Elmer Cetus/Gene
Amp
PCR System thermal cycler.
Table 5: Oligonucleotide primers
Gene Forward primer Reverse primer
vac9 CGCGGATCCATATGGCTGAAA CCGGAATTCATCAGTATTCAA
(nt SEQ AAACGCCTTTTTTTAAAACTAA TGGGAATAAAGCC (SEQ ID
ID
N0:28) AAACCAC (SEQ ID NO: 257) NO: 258)
(aa SEQ
ID
NO: 125)
vacl0 CGCGGATCCATATGAAAGAAG CCGGAATTCGCTTAAAAGAAA
(nt SEQ AAGAAAAAGAAGAAAAAAAG ATAGTCCCCCAAACGC (SEQ
ID
NO:50) ACAGAAAGG (SEQ ID NO: 259) ID NO: 260)
(aa SEQ
ID
NO: 147)
vac22 CGCCGGATCCATATGAAAGAG CCGGAATTCATATAAATATCA
(nt SEQ GTCATTCCACCCCTTCAACCCC TATAGGCAGAAAAAC (SEQ ID
ID
N0:24) (SEQ ID NO: 261 ) NO: 262)
(aa SEQ
ID
NO: 121)
vac32 CGCGGATCCATATGGAGGCAG CCGGAATTCGATTGATTTTGTC
(nt SEQ AGCTTGATGAAAAATC (SEQ ID AAATCTAAAATCCC (SEQ ID
ID
NO:11 NO: 263) NO: 264)
)
(aa SEQ
ID
NO: 108)
vac36 TATTATACATATGGAAGAAGA TAATCTCGAGTTTAGAAGGCG
(hop
B) TGGG (SEQ ID NO: 265) TA (SEQ ID NO: 266)
(nt SEQ
ID
N0:52)
(aa SEQ
ID
N0:149)
_.._.___ __ _.____T . . ... . .
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vac37 TTATATTCATATGGAAGACGAT AATTCTCGAGCCTCTTTATAA
(i-hop) GGC (SEQ ID NO: 267) GCC (SEQ ID NO: 268)
(nt SEQ
ID
N0:42)
(aa SEQ
ID
NO: 139)
vac41 CGCGGATCCATATGGTAGAAG CCGGAATTCGGAGCCAATAGG
(nt SEQ CCTTTCAAAAACACCAAAAAG GAGCTAAAGCC (SEQ ID NO:
ID
N0:79) ACGG (SEQ ID NO: 269) 270)
(aa SEQ
ID
NO: 176)
Sequences for Vac32, Vac9 and Vac22
Denaturation at 94°C for 30 sec
35 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C
for 1.5 min
Reactions were concluded at 72°C for 8 minutes
Sequences for VaclO and Vac41
Denaturation at 94°C for 30 sec
35 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C
for 2.5 min
I0 Reactions were concluded at 72°C for 8 minutes
Sequences for Vac36 and Vac37
Denaturation at
2 cycles at 94°C for 15 sec, 30°C for 15 sec, and 72°C
for 1.5 min
23 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes
Upon completion of the thermal cycling reactions, each sample of amplified
DNA was subjected to electrophoresis on 1.0% agarose gels. The DNA was
visualized
''0 by exposure to ethidium bromide and long wave UV irradiation, and cut out
in gel
slices. DNA was purified using the Wizard PCR Preps Kit (Promega Corp.,
Madison,
WI, USA), and then subj ected to digestion with BamHI and EcoRI (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
The
digested PCR amplicon was then re-electrophoresed and purified as before.
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Ligation of H. pylori DNA sequences into cloning vectors
The pOKl2 vector (J. Vieira and J. Messing, Gene 100:189-194, 1991) was
prepared for cloning for digestion with BamHI and EcoRI in the case of Vac9,
10, 22, 31
and 32, whereas the pSU21 vector (B. Bartolome et al., Gene 102:75-78, 1991 )
was
prepared for cloning by digestion with BamHI and EcoRI in the case of Vac 41
(Current
Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al.,
eds.,
1994). The vectors were subjected to electrophoresis on 1.0% agarose gels and
purified
using the Wizard PCR Preps kit (Promega Corp., Madison, WI, USA). Following
ligation of the purified, digested vector and the purified, digested amplified
H. pylori
ORF, the products of the ligation reaction were transformed into E. coli JM109
competent cells according to standard methods (Current Protocols in Molecular
Biology,
John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Individual
bacterial colonies
were screened for those containing the correct recombinant plasmids by
incubating in
LB broth overnight (plus 25ug/ml kanamycin sulfate for the pOKl2 based
plasmids or
25ug/ml chloramphenicol for the pSU21 based plasmids) followed by plasmid DNA
preparation using the Magic Minipreps system (Promega Corp., Madison, WI,
USA),
and then analyzed by restriction digestion (Current Protocols in Molecular
Biology, John
Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Cloning of H. pylori DNA sequences into the pET28b and pET30a prokaryotic
expression vectors
Both the pET28b and pET30a expression vectors were prepared for cloning by
digestion with NdeI and EcoRI (Current Protocols in Molecular Biology, John
Wiley
and Sons, Inc., F. Ausubel et al., eds., 1994). The H. pylori DNA sequences
were
removed from pOKl2 (Vac9,10,23,31 and 32) or pSU21 (Vac41 ) plasmid backbones
by
digestion with NdeI and EcoRI (Current Protocols in Molecular Biology, John
Wiley
and Sons, Inc., F. Ausubel et al.) eds., 1994). The pET28b, pET30a and H.
pylori DNA
sequences were ali electrophoresed on a 1 % agarose gel and purified using the
Wizard
PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the
purified,
digested expression vector and the purified, digest H. pylori DNA sequences,
the
products of the ligation reaction were transformed into E. col i JM 109
competes _ cells
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994). Individual bacterial colonies were screened for those containing
the correct
recombinant plasmids by preparing plasmid DNA as described above followed by
3 S analysis by restriction digestion profiles and DNA sequencing (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
These
recombinant plasmids were then used to transform specific E. coli expression
strains.
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Transformation of competent bacteria with recombinant expression plasmids
Competent bacterial strains (BL21 (DE3), BL21 (DE3)pLyS, HMS 174(DE3) and
HMS 174(DE3)pLysS were prepared and transformed with the recombinant pET28b
expression plasmids carrying the cloned H. pylori sequences according to
standard
methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F.
Ausubel et al., eds., 1994). These expression host strains contain a
chromosomal copy
of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage
DE3, a
lambda derivate that carries the lacl gene, the IacUV~ promoter and the gene
for T7
RNA polymerase. T7 RNA polymerase expression is induced by the addition of
isopropyl-(3-D thiogalactoside ( 1 PTG), and the T7 RNA polymerase then
transcribes any
target plasmid, such as pET28b, that carries a T7 promoter sequence and a gene
of
Interest.
Expression of recombinant H. pylori sequences in E. coli
Transformants were collected from LB agar plates containing 25ug/ml
kanamycin sulfate (ensures maintenance of the pET28b-based recombinant
plasmids)
and used to inoculate LB broth containing 25ug/ml kanamycin sulfate and grown
to an
optical density at 600nm of 0.5 to 1.0 OD units, at which point 1 mM 1 PTG was
added
to the culture for one to three hours to induce gene expression of the H.
pylori
recombinant DNA constructions. After induction of gene expression with 1 PTG,
bacteria were pelleted by centrifugation and resuspended in SDS-PAGE
solubilization
buffer and subjected to SDS-PAGE (Current Protocols in Molecular Biology, John
Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Proteins were visualized
by staining
with Coomassie Brilliant Blue or detected by western immunoblotting using the
specific
anti-His tag monoclonal antibody (Clontech, Palo Alto, CA, USA) using standard
methods (Current Protocols-in Molecular Biology, John Wiley and Sons, Inc., F.
Ausubel et al., eds., 1994). The host strain that provided the highest level
of
recombinant protein production was then chosen for use in a large-scale
induction in
order to purify the recombinant protein. All of the following proteins listed
were
expressed recombinantly and the strain giving the highest level of expression
listed:
BL21 (DE3) (vac31, vac26, vac37); BL21 (DE3) pLysS (vac 9, 32); HMS 174(DE3)
(vac 10,11 ).
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Purifrcation of recombinant proteins and generation of specific antiserum
Large scale cultures were inoculated and grown as above, and induced with 1mM
1 PTG for 3 hours. After induction, bacteria were pelleted by centrifugation
in a Sorvall
centrifuge at 3500 x g for 15 min at 4°C. All of the expressed
recombinant proteins
S were present in the insoluble inclusion body fraction. Inclusion bodies were
purified
according to standard protocols (Antibodies, Cold Spring Harbor Laboratory
Press, E.
Harlow and D. Lane, eds., 1988). The recombinant protein produced by vac32 was
solubilized in 8M urea and partially purified by nickel chromatography (REF
here).
Denatured recombinant proteins were purified by electrophoresis on SDS-PAGE
gels,
and after visualization with Coomassie Brilliant Blue, the protein was excised
from the
gel and the gel slices homogenized. This material was used to raise specific
polyclonal
antibodies in mice or rabbits according to standard protocols (Antibodies,
Cold Spring
Harbor Laboratory Press, E. Harlow and D. Lane, eds., 1988).
Immunological characterization of recombinant proteins
In all cases where antibody was attempted to be raised, high titre antisera
was
generated, confirming the immunogenicity of the recombinant proteins. Further,
these
specific antisera were used to analyze whether the protein encoded by the
cloned gene
was expressed in H. pylori. Western immunoblot analysis using standard
protocols
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994) confirmed that the H. pylori strain J99 did express proteins of
the expected
molecular weight that reacted with the vacl0, vac32, vac3l, vac36 antiserum.
The
specific antiserum was also used to determine the level of antigenic
conservation
between a large number of H. pylori isolates that had been obtained from
distinct
geographical sites around the world, and from all types of clinical
manifestations,
including gastritis, duodenal ulcer, gastric ulcer and gastric cancer. It was
found that
every strain produced a protein that reacted specifically with each antiserum.
Further, H. pylori cells from strains J99, 17874, AH244 and SS 1-were
fractionated into different cellular compartments (Doig and Trust 1994 Infect.
Immun.
62:4526-4533: O'Toole et al. 1995 J. Bacteriol. 177:6049-6057). The specific
antiserum
was used to probe .hese fractions by western immunoblot to identify in which
fraction
the protein was localized. In all cases, the immunoreactive protein was
present in the
outer membrane as had been predicted by the sequence features and motif
searches
described herein.
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Demonstration of protein effrcacy as a vaccine
Purification of vac36 for efficac~studies
All the following steps were carried out at 4°C. Cell pellets were
resuspended in
volumes per gram of cell of lysis buffer (50mM Sodium Phosphate pH 8.0, 0.5 M
5 NaC 1, 5mM Imidazole) with 1 OmM EDTA, 1 mM phenylmethylsulfonyl fluoride
(PMSF) and 0.1 % (3-mercaptoethanol, and ruptured by several passages through
a small
volume microfluidizer (Model M-1 lOS, Microfluidics International Corporation,
Newton, MA). The resulting homogenate was made 0.2% sodium deoxycholate (DOC),
stirred 20 minutes, then centrifuged ( 10,000 g x 30 min). The pellets were
washed twice
with Lysis Buffer containing 1 OmM EDTA, 1 % Triton X-100, 1 mM PMSF and 0.1 %
~i
-mercaptoethanol, then with lysis buffer containing 1 M urea, 1 mM PMSF and
0.1 % (3-
mercaptoethanol. The resulting white pellet is composed primarily of inclusion
bodies,
free of unbroken cells and membranous materials.
The inclusion bodies were dissolved in 20 ml 6M guanidine-HC 1 in lysis buffer
with 1 mM PMSF and 0.1 % ~-mercaptoethanol, and incubated on ice for 1 hour.
Materials that did not dissolve were removed by centrifugation {100,000 g x 30
min.)
The clear supernatant was filtered through a 0.8 pm Supor filter (Gelman
Sciences,
FRG) and then load directly onto a 10 ml Ni2+ - NTA agarose column (Hochuli et
al.
1987) pre-equilibrated in 6M guanidine-HCl in Lysis Buffer containing 1 mM
PMSF
and 0.1 % (3-Mercaptoethanol. The column was washed with 20m1 (2 bed volumes)
of
Lysis Buffer containing 6M guanidine-HCI, 1 mM PMSF and 0.1 %~3-
mercaptoethanol,
then guanidine-HCl was removed slowly with a 100 ml linear gradient (from 6M
to 0 M
Guanidine-HCl) of lysis buffer containing 0.5% Brij 35, 1 mM PMSF, 0.1 % ~i-
mercaptochanol. Next, the column was developed with a 25 ml linear gradient of
increasing imidazole (5 to 500 mM) in Lysis buffer containing 0.5% Brij 35, 1
mM
PMSF and 0.1 % (3-mercaptoethanol. The recombinant proteins elute as a peak
centered
at 100mM imidazole.
Fractions containing the recombinant proteins were pooled and then
concentrated
to approximately 8 ml by centrifugal filtration (Centriprep-10, Amicon, MA),
and
loaded directly onto a 350-ml column (2.2 X 91 cm) of Sephacyl S-100 HR gel
filtration
medium equilibrated in Buffer A (50mM Sodium Phosphate, pH 8.0, 500 mM NaC 1,
0.1 mM EGTA, 1 mM PMSF, 0.1 %(3-mercaptoethanol, 0.5% Brij 35) and ran in
Buffer
A at 30 ml/h. Fractions containing the recombinant protein were identified by
absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled,
concentrated to 1.5 to 2 mg/ml and dialysed overnight against 10 mM Potassium
Phosphate pH 7.5, 150 mM NaCI, 0.1 mM EGTA and 0.5% Brij 35. The concentration
of protein in the dialysate was quantified, then aliquoted prior to freezing
at - 20°C.
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Mouse model of Heliocobacterpylori infection
A marine model of H. pylori infection was produced by infection of C57BL/6
mice with with H. pylori Sydney strain SS l and was used to assess the
efficacy of
recombinant H. pylori vac36. This mouse-adapted H. pylori strain is cagA+
vacA+,
shows colonization levels in C57BL/6 mice equivalent to those observed in
humans,
forms adhesion pedestals, colonizes for at least 8 months, and elicits a
chronic-active
gastritis and mucosal atrophy (Lee et al., Gastroenterology, 112:1386-1397,
1997).
Dose-response studies have shown 100% infection rates of inbred C57BL/6 and
Balb/C
mice at 8 weeks post-challenge with a single inoculation of 106 organisms.
Assessment of gastric H. pylori infection
The presence of H. pylori organisms in gastric tissue was determined by
culture
of gastric tissue and by a quantitative urease assay. In the latter method, a
longitudinal
segment of antrum, representing approximately '/4 of the total antral region
was placed in
1 ml of urea broth. After 4 hr, the extent of color change resulting from urea
hydrolysis
and increased pH was quantiated by spectrophotometric measurement of A550 (Fox
et
al., Immunol. 88:400-406, I996). The assay sensitivity is ~ 103 H. pylori
organisms. A
positive (H pylori-infected) gastric tissue was defined as that sample showing
2
standard deviations above the mean A550 value derived from a group of
unchallenged
uninfected age-matched control mice.
Assessment of local immune response to immunization in gastric tissue
Longitudinal sections of gastric tissues from the esophageal to the duodenal
junction were embedded in OCT embedding compound, frozen in liquid nitrogen,
and
cryosections immunostained with monoclonal antibodies recognizing CD4+ or
CD8+T
cells or with antisera against mouse IgA for identification of IgA containing
(IgACC)
plasma cells (Pappo et al., Infect. Immun. 63:1246-1252, 1995). The degree of
local
gastric immune response was expressed quantitatively as the number of CD4+~
CD8+ or
IgACC cells per mm2 of gastric region examined.
Protective activity of purified recombinant Hwlori vac36 antigen
The ability of purified recombinant vac36 antigen derived from H. pylori to
interfere with the establishment of an H. pylori infection was examined in
mice. Groups
(n=I O) of 6-8 week-old female C57BL/6 mice were immunized orally 4 times at
weekly
intervals as follows: 1 ) 100 ~g of recombinant vac36 antigen and 10 ~g
cholera toxin
(CT) adjuvant, 2) I mg H. pylori lysate antigens and 10 ~.g CT, and 3) 0.2 M
._.._. ._ ~. __ .~.._...T _
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bicarbonate buffer and 10 ug CT adjuvant. The mice were challenged 2 weeks
later on 3
consecutive days by oral administration of 108 H. pylori organisms. The
experiment
was terminated 2 weeks post-challenge, and the H. pylori infection level
assessed by
bacterial colony counts and by quantitative urease assays.
Oral immunization with vac36 antigen interfered with the establishment of H.
pylori infection upon challenge with live H. pylori organisms. Mice immunized
with
purified recombinant vac36 antigen exhibited a significantly lower level of
colonization
by H. pylori, as assessed by gastric urease activity and bacterial count
assays (Table 6).
Oral immunization with vac36 antigen also resulted in the generation of a
local
protective gastric immune response. Greater numbers of CD4+T cells and of
IgACC
were recruited in the gastric tissues of vac36-immunized mice when compared
with
unirnmunized H. pylori-infected mice (Table 7).
Table 6
Recombinant vac36 antigen protects mice from challenge with H. nvlnri
Y'accine Urease p H. pylori p
Treatment Activitya burden
Group
vac36 0.1990.080 0.0022 55,800112,5990.0125
H. pylori 0.0570.007 0.0002 2,3601955 0.0002
lysate
buffer 1.65510.420 - 131,00018,39-
1
a Urease activity is expressed as mean A550~ SEM of duplicate antral samples
from n=10 mice/group.
b by Wilcoxon Rank Sum Test compared with mice immunized with CT adjuvant
alone
c The level of H. pylori in gastric tissue was assessed by bacterial counts,
and
shown as mean colony forming units~SEM
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Table 7
vac36-immunized mice generate a local gastric immune response upon challenge
with
H. pylori
Vaccine
TreatmeCD4+ CD8+ IgACC
nt
Group
cardi corpu antru cardi corpu antru cardi corpu antru
as s m a s m a s m
vac36 33 54 31 3 0 1 24 79 67
8 2 1
9a 8* 12 16 13
pylori 31 36 248 42 2I 21 319 73 79
lysate 13 19 13* I5
buffer
122 278 184 1 0 0 42 30 46
1
13 14
a Mean number of cells/mm~ of gastric region ~ SEM
* p<0.05 by Wilcoxon Rank Sum Test when compared with unimmunized H.
pylori infected mice
V. Seauence Variance Analysis of~enes in Helicobacterpvlori strains
Four genes were cloned and sequenced from several strains of H. pylori to
compare the DNA and deduced amino acid sequences. This information was used to
determine the sequence variation between the H. pylori strain, J99, and other
H. pylori
strains isolated from human patients.
Preparation of Chromosomal DNA.
Cultures of H. pylori strains (as listed in Table 10) were grown in BLBB ( 1
Tryptone, 1 % Peptamin 0.1 % Glucose, 0.2% Yeast Extract 0.5% Sodium Chloride,
5%
Fetal Bovine Serum) to an OD600 of 0.2. Cells were centrifuged in a Sorvall RC-
3B at
3500 x g at 4°C for 15 minutes and the pellet resuspended in 0.95 mls
of 10 mM Tris-
HCI, 0.1 mM EDTA (TE). Lysozyme was added to a final concentration of 1 mg/ml
along with, SDS to 1 % and RNAse A + T 1 to 0.5mg/ml and 5 units/mI
respectively, and
incubated at 37°C for one hour. Proteinase K was then added to a final
concentration of
0.4mg/ml and the sample was incubated at 55 C for more than one hour. NaCI was
added to the sample to a concentration of 0.65 M, mixed carefully, and 0.15 mI
of 10%
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CTAB in 0.7M NaCL (final is 1 % CTAB/70mM NaCL) was added followed by
incubation at 65°C for 20 minutes. At this point, the samples were
extracted with
chloroform:isoamyl alcohol, extracted with phenol, and extracted again with
chloroform:isoamyl alcohol. DNA was precipitated with either EtOH (I.5 x
volumes) or
isopropanol (0.6 x volumes) at -70°C for l Ominutes, washed in 70%
EtOH and
resuspended in TE.
PCR Amplification and cloning.
Genomic DNA prepared from twelve strains of Helicobacter pylori was used as
the source of template DNA for PCR amplification reactions (Current Protocols
in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors;
1994). To
amplify a DNA sequence containing an H. pylori ORF, genomic DNA (10 nanograms)
was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar
synthetic
oligonucleotide primers (forward and reverse primers, see Table 8)
complementary to
and flanking a defined H. pylori ORF, 0.2 mM of each deoxynucleotide
triphosphate;
dATP, dGTP, dCTP, dTTP and 0.5 units of heat stable DNA polymerase (Amplitaq,
Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 20
microliters in duplicate reactions.
Table 8
Oligonucleotide primers used for PCR amplification of H. pylori DNA sequences.
Outer membrane Forward primer 5' Reverse Primer 5'
to 3' to 3'
Proteins _
Protein 26054702 5'-TTAACCATGGTGAAAA 5'-TAGAATTCGCCTCTAA
(for strains AH4, GCGATA-3' (SEQ ID AACTTTAG-3' (SEQ
AH15, ID
AH61, 5294, 5640, N0:217) N0:218)
AH18,
and AH244)
Protein 26054702 5'-TTAACCATGGTGAAAA 5'-TAGAATTCGCATAA
(for strains AHS, GCGATA-3' (SEQ ID CGATCAATC-3' (SEQ
5155, ID
7958, AH24,and J99)N0:219) N0:220)
Protein 7116626 5'-ATATCCATGGTGAGTT S'-ATGAATTCAATTTT
TGATGA-3' (SEQ ID TTATTTTGCCA-3' (SEQ
ID
_ N0:221 ) N0:222)
Protein 29479681 S'-AATTCCATGGCTATC 5'-ATGAATTCGCCAAAA
CAAATCCG-3' (SEQ TCGTAGTATT-3' (SEQ
ID ID
N0:223) N0:224)
Protein 346 5'-GATACCATGGAATTT 5'-TGAATTCGAAAAAGTG
ATGAAAAAG-3' (SEQ TAGTTATAC-3' (SEQ
ID ID
N0:225) N0:226)
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The following thermal cycling conditions were used to obtain amplified DNA
products for each ORF using a Perkin Elmer Cetus/ GeneAmp PCR System 9600
thermal cycler:
Protein 7116626 and Protein 346;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 15 sec and 72°C for
1.5 min
23 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C
for 1.5 min
Reactions were concluded at 72°C for 6 minutes.
Protein 26054702 for strains AHS, 5155, 7958, AH24,and J99;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 15 sec and 72°C for
1.5 min
25 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C
for 1.5 min
Reaction was concluded at 72°C for 6 minutes.
Protein 26054702 and Protein 294796813 for strains AH4, AH15, AH61, 5294,
5640,
AH 18, and Hp244 ;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 20 sec and 72°C for
2 min
cycles at 94°C for 15 sec, 55°C for 20 sec and 72°C for 2
min
Reactions were concluded at 72°C for 8 minutes.
Upon completion of thermal cycling reactions, each pair of samples were
25 combined and used directly for cloning into the pCR cloning vector as
described below.
Cloning of H. pylori DNA sequences into the pCR TA cloning vector.
All amplified inserts were cloned into the pCR 2.1 vector by the method
described in the Original TA cloning kit (Invitrogen, San Diego, CA). Products
of the
ligation reaction were then used to transform the TOP10F' (INVaF' in the case
ofH.
- pylori sequence 350) strain of E coli as described below.
Transformation of competent bacteria with recombinant plasmids
- Competent bacteria, E coli strain TOP10F' or E. coli strain INVaF' were
transformed with recombinant pCR expression plasmids carrying the cloned H.
pylori
sequences according to standard methods (Current Protocols in Molecular
Biology, John
Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). Briefly, 2
microliters of 0.5
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micromolar BME was added to each vial of 50 microliters of competent cells.
Subsequently, 2 microliters of ligation reaction was mixed with the competent
cells and
incubated on ice for 30 minutes. The cells and ligation mixture were then
subjected to a
"heat shock" at 42°C for 30 seconds, and were subsequently placed on
ice for an
additional 2 minutes, after which, samples were incubated in 0.45 milliliters
SOC
medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCI, 2.5 mM KCI, 10 mM
MgCl2, 10 mM MgS04 and 20, mM glucose) at 37°C with shaking for 1 hour.
Samples
were then spread on LB agar plates containing 25 microgram/ml kanamycin
sulfate or
100 micrograms/ml ampicillan for growth overnight. Transformed colonies of
TOP10F'
or INVaF' were then picked and analyzed to evaluate cloned inserts as
described below.
Identification of recombinant PCR plasmids carrying H. pylori sequences
Individual TOP10F' or INVaF' clones transformed with recombinant pCR-
H.pylori ORFs were analyzed by PCR amplification of the cloned inserts using
the same
forwardand reverse primers, specific for each H. pylori sequence, that were
used in the
original PCR amplification cloning reactions. Successful amplification
verified the
integration of the H. pylori sequences in the cloning vector (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors,
1994).
Individual clones of recombinant pCR vectors carrying properly cloned H.
pylori
ORFs were picked for sequence analysis. Sequence analysis was performed on ABI
Sequencers using standard protocols (Perkin Elmer) using vector-specific
primers (as
found in PCRII or pCR2.l, Invitrogen, San Diego, CA) and sequencing primers
specific
to the ORF as listed in Table 9 below.
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Table 9
Oli~onucleotide primers used for sequencin~of X_pylori DNA sequences
Outer membraneForward primers 5' Reverse Primers 5' to
Proteins to 3' 3'
Protein 260547025'CCCTTCATTTTAGAAATC 5'CTTTGGGTAAAAACGCATC
G-3' (SEQ ID N0:227) -3' (SEQ ID N0:234)
S'ATTTCAACCAATTCAAT 5'CGATCTTTGATCCTAATTC
GCG-3' (SEQ ID N0:228)A-3' (SEQ ID N0:235)
5'GCCCCTTTTGATTTGAA 5'ATCAAGTTGCCTATGCTGA
GCT-3' (SEQ ID N0:229)-3' (SEQ ID N0:236)
5'TCGCTCCAAGATACCAA
GAAGT-3' (SEQ ID N0:230)
5'CTTGAATTAGGGGCAAA
GATCG-3' (SEQ ID N0:231
)
5'ATGCGT"T'TT'TACCCAAA
GAAGT-3' (SEQ ID N0:232)
S'ATAACGCCACTTCCTTA
TTGGT-3' (SEQ ID N0:233)
Protein 71166265'TTGAACACTTTTGATTAT S'GTCTTTAGCAAAAATGGCG
GCGG-3' (SEQ ID N0:237)TC-3' (SEQ ID N0:239)
5'GGATTATGCGATTGTTTT 5'AATGAGCGTAAGAGAGCC
ACAAG-3' (SEQ ID N0:238)TTC-3' (SEQ ID N0:240)
Protein 5'CTTATGGGGGTATTGTC S'AGGTTGTTGCCTAAAGACT
29479681 A-3' (SEQ ID N0:241 -3' (SEQ ID N0:243)
)
S'AGCATGTGGGTATCCAG 5'-CTGCCTCCACCTTTGATC-
C-3' (SEQ ID N0:242) 3' (SE(j ID N0:244)
Protein 346 5'ACCAATATCAATTGGCA 5'CTTGCTTGTCATATCTAGC-
CT-3' (SEQ ID N0:245)3' (SEQ ID N0:247)
5'ACTTGGAAAAGCTCTGC S'-GTTGAAGTGTTGGTGCTA-
A-3' (SEQ ID N0:246) 3' (SEQ ID N0:248)
5'CAAGCAAGTGGTTTGGT 5'GCCCATAATCAAAAAGCC
TTTAG-3' (SEQ ID N0:249)CAT-3' (SEQ ID N0:251
)
5'TGGAAAGAGCAAATCAT 5'CTAAAACCAAACCACTTGC
TGAAG-3' (SEQ ID N0:250)TTGTC-3' (SEQ ID N0:252)
Vector Primers5'-GTAAAACGACGGCCAG- 5'-CAGGAAACAGCTATGAC-
I
3' (SEQ ID N0:253) 3' (SEQ ID N0:254)
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Results
To establish the PCR error rate in these experiments, five individual clones
of
Protein 26054702, prepared from five separate PCR reaction mixtures from H.
pylori
strain J99, were sequenced over a total length of 897 nucleotides for a
cumulative total
of 4485 bases of DNA sequence. DNA sequence for the five clones was compared
to a
DNA sequence obtained previously by a different method, i.e., random shotgun
cloning
and sequencing. The PCR error rate for the experiments described herein was
determined to be 2 base changes out of 4485 bases, which is equivalent to an
estimated
error rate of less than or equal to 0.04%.
l 0 DNA sequence analysis was performed on four different open reading frames
identified as genes and amplified by PCR methods from a dozen different
strains of the
bacterium Helicobacter pylori. The deduced amino acid sequences of three of
the four
open reading frames that were selected for this study showed statistically
significant
BLAST homology to defined proteins present in other bacterial species. Those
ORFs
included: Protein 26054702, homologous to the val A & B genes encoding an ABC
transporter in F. novicida; Protein 7116626, homologous to lipoprotein a (P4)
present in
the outer membrane of H. influenzae; Protein 29479681, homologous to fecA, an
outer
membrane receptor in iron (III) dicitrate transport in E. toll. Protein 346
was identified
as an unknown open reading frame, because it showed low homology with
sequences in
the public databases.
To assess the extent of conservation or variance in the ORFs across various
strains of H. pylori, changes in DNA sequence and the deduced protein sequence
were
compared to the DNA and deduced protein sequences found in the J99 strain of
H.
pylori (see Table 10 below). Results are presented as percent identity to the
J99 strain of
H. pylori sequenced by random shotgun cloning. To control for any variations
in the
J99 sequence each of the four open reading frames were cloned and sequenced
again
from the J99 bacterial strain and that sequence information was compared to
the
sequence information that had been collected from inserts cloned by random
shotgun
sequencing of the J99 strain. The data demonstrate that there is variation in
the DNA
sequence ranging from as little as 0.12 % difference (Protein 346, J99 strain)
to
approximately 7% change (Protein 26054702, strain AHS). The deduced protein
sequences show either no variation ( Protein 346, strains AH 18 and AH24) or
up to as
much as 7.66% amino acid changes (Protein 26054702, Strain AHS).
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Table 10
Multiple Strain DNA Sequence analysis of H. pylori Vaccine Candidates
J99 Protein #: 26054702 26054702 7116626 7116626 29479681 29479681 346 346
Length of Region
Sequenced: 248 a.a. 746 nt. 232 a.a. 96 nt. 182 a.a. 548 nt. 273 a.a. 819 nt.
Strain Tested
AA Nuc. AA Nuc. AA Nuc. AA Nuc.
identity identityidentityidentityidentityidentityidentityidentity
J99 100.00% 100.00%100.00%100.00%100.00%100.00%99.63%99.88%
AH244 95.16% 95.04%n.d. n.d. 99.09% 96.71%98.90%96.45%
AH4 95.97% 95.98%97.84%95.83%n.d. n.d. 97.80%95.73%
AHS 92.34% 93.03%98.28%96.12%98.91% 96.90%98.53%95.73%
AH 1 95.16% 94.91 97.41 95.98%99.82% 97.99%99.63%96.09%
S % %
AH61 n.d. n.d. 97.84%95.98%99.27% 97.44%n.d. n.d.
5155 n.d. n.d. n.d. n.d. 99.45% 97.08%98.53%95.60%
5294 94.35% 94.37%'98.28%95.40%99.64% 97.26%97.07%95.48%
7958 94.35% 94.10%97.84%95.40ion.d. n.d. 99.63%96.46%
5640 95.16% 94.37%97.41%95.69%99.09% 97.63%98.53%95.48%
AH 18 n._d. n.d. 98.71 95.69%99.64% 97.44%I 00.00%95.97%
%
AH24 94.75% 95.04%97.84%95.40%99.27% 96.71%100.00%96.46%
n.d.= not done.
VI. Experimental Knock-Out Protocol for the Determination of Essential H.
pylori
Genes as Potential Ther~eutic Tarp
Therapeutic targets are chosen from genes wh ose protein products appear to
play
key roles in essential cell pathways such as cell envelope synthesis, DNA
synthesis,
transcription, translation, regulation and colonization/virulence.
The protocol for the deletion of portions of H. pylori genes/ORFs and the
insertional mutagenesis of a kanamycin-resistance cassette in order to
identify genes
which are essential to the cell is modified from previously published methods
(Labigne-
Roussel et al., 1988, J. Bacteriology 170, pp. 1704-1708; Cover et a1.,1994,
J. Biological
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Chemistry 269, pp. 10566-10573; Reyrat et al., 1995, Proc. Natl. Acad. Sci.
92, pp
8768-8772). The result is a gene "knock-out."
Identification and Cloning of H. pylori Gene Sequences
The sequences of the genes or ORFs (open reading frames) selected as knock-out
targets are identified from the H. pylori genomic sequence and used to design
primers to
specifically amplify the genes/ORFs. All synthetic oligonucleotide primers are
designed
with the aid of the OLIGO program (National Biosciences, Inc., Plymouth, MN
55447,
USA), and can be purchased from Gibco/BRL Life Technologies (Gaithersburg, MD,
USA). If the ORF is smaller than 800 to 1000 base pairs, flanking primers are
chosen
outside of the open reading frame.
Genomic DNA prepared from the Helicobacter pylori HpJ99 strain (ATCC
55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street,
Waitham,
MA 02154) is used as the source of template DNA for amplification of the ORFs
by
PCR (polymerase chain reaction) (Current Protocols in Molecular Biology, John
Wiley
and Sons, Inc., F. Ausubel et al., editors, 1994). For the preparation of
genomic DNA
from H. pylori, see Example I. PCR amplification is carried out by introducing
10
nanograms of genomic HpJ99 DNA into a reaction vial containing 10 mM Tris pH
8.3,
50 mM KCI, 2 mM MgCl2, 2 microMolar synthetic oligonucleotide primers
(forward=F 1 and reverse=R 1 ), 0.2 mM of each deoxynucleotide triphosphate
(dATP,dGTP, dCTP, dTTP), and 1.25 units of heat stable DNA polymerase
(Amplitaq,
Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 40
microliters. The PCR is carried out with Perkin Elmer Cetus/GeneAmp PCR System
9600 thermal cyclers.
Upon completion of thermal cycling reactions, each sample of amplified DNA is
visualized on a 2% TAE agarose gel stained with Ethidium Bromide (Current
Protocols
in Molecular Biology, John_Wiley and Sons, Inc., F. Ausubel et al., editors,
1994) to
determine that a single product of the expected size had resulted from the
reaction.
Amplified DNA is then washed and purified using the Qiaquick Spin PCR
purification
-- 30 kit (Qiagen, Gaithersburg, MD, USA).
PCR products a.e cloned into the pT7Blue T-Vector (catalog#69820-1, Novagen,
Inc., Madison, WI, USA) using the TA cloning strategy (Current Protocols in
Molecular
Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). The
ligation of the
PCR product into the vector is accomplished by mixing a 6 fold molar excess of
the
PCR product, 10 ng of pT7Blue-T vector (Novagen), 1 microliter of T4 DNA
Ligase
Buffer (New England Biolabs, Beverly, MA, USA), and 200 units of T4 DNA Ligase
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(New England Biolabs) into a final reaction volume of 10 microliters. Ligation
is
allowed to proceed for 16 hours at 16°C.
Ligation products are electroporated (Current Protocols in Molecular Biology,
John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994) into
electroporation-
S competent XL-1 Blue or DHS-a E.coli cells (Clontech Lab., Inc. Palo Alto,
CA, USA).
Briefly, 1 microliter of ligation reaction is mixed with 40 microliters of
electrocompetent cells and subjected to a high voltage pulse (25 microFarads,
2.5 kV,
200 ohms) after which the samples are incubated in 0.45 ml SOC medium (0.5%
yeast
extract, 2% tryptone, 10 mM NaCI, 2.5 mM KCI, 10 mM MgCl2, 10 mM MgS04 and 20
mM glucose) at 37°C with shaking for 1 hour. Samples are then spread
onto LB ( 10 g/1
bacto tryptone, 5 g/1 bacto yeast extract, 10 g/1 sodium chloride) plates
containing 100
microgramlml of Ampicillin, 0.3% X-gal, and 100 microgram/ml IPTG. These
plates
are incubated overnight at 37°C. Ampicillin-resistant colonies with
white color are
selected, grown in 5 ml of liquid LB containing 100 microgramlml of
Ampicillin, and
plasmid DNA is isolated using the Qiagen miniprep protocol (Qiagen,
Gaithersburg,
MD, USA).
To verify that the correct H.pylori DNA inserts had been cloned, these pT7Blue
plasmid DNAs are used as templates for PCR amplification of the cloned
inserts, using
the same forward and reverse primers used for the initial amplification of the
J99
H.pylori sequence. Recognition of the primers and a PCR product of the correct
size as
visualized on a 2% TAE, ethidium bromide stained agarose gel are confirmation
that the
correct inserts had been cloned. Two to six such verified clones are obtained
for each
knock-out target, and frozen at -70°C for storage. To minimize errors
due to PCR,
plasmid DNA from these verified clones are pooled, and used in subsequent
cloning
steps.
The sequences of the genes/ORFs are again used to design a second pair of
primers which flank the region of H. pylori DNA to be either interrupted or
deleted (up
to 250 basepairs) within the ORFs but are oriented away from each other. The
pool of
circular plasmid DNAs of the previously isolated clones are used as templates
for this
round of PCR. Since the orientation of amplification of this pair of deletion
primers is
away from each other, the portion of the ORF between the prT mers is not
included in the
resultant PCR product. The PCR product is a linear piece of DNA with H. pylori
DNA
at each end and the pT7Blue vector backbone between them which, in essence,
resultes
in the deletion of a portion of the ORFs. The PCR product is visualized on a 1
% TAE,
ethidium bromide stained agarose gel to confirm that only a single product of
the correct
size has been amplified.
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A Kanamycin-resistance cassette (Labigne-Roussel et al., 1988 J. Bacteriology
170, 1704-1708) is ligated to this PCR product by the TA cloning method used
previously (Current Protocols in Molecular Biology, John Wiley and Sons, Inc.,
F.
Ausubel et al., editors, 1994). The Kanamycin cassette containing a
Campylobacter
kanamycin resistance gene is obtained by carrying out an EcoRI digestion of
the
recombinant plasmid pCTBB:kan (Cover et al.,1994, J. Biological Chemistry 269,
pp.
10566-10573). The proper fragment (1.4 kb) is isolated on a 1% TAE gel, and
isolated
using the QIAquick gel extractionkit (Qiagen, Gaithersburg, MD, USA). The
fragment
is end repaired using the Klenow fill-in protocol, which involved mixing 4ug
of the
DNA fragment, 1 microliter of dATP,dGTP, dCTP, dTTP at 0.5 mM, 2 microliter of
Klenow Buffer (New England Biolabs) and 5 units of Klenow DNA Polymerase I
Large
(Klenow) Fragment (New England Biolabs) into a 20 microliter reaction,
incubating at
30°C for 15 min, and inactivating the enzyme by heating to 75°C
for 10 minutes. This
blunt-ended Kanamycin cassette is then purified through a Qiaquick column
(Qiagen,
Gaithersburg, MD, USA) to eliminate nucleotides. The "T" overhang is then
generated
by mixing 5 micrograms of the blunt-ended kanamycin cassette, 10 mM Tris pH
8.3, SO
mM KCI, 2 mM MgCl2, S units of DNA Polymerase (Amplitaq, Roche Molecular
Systems, Inc., Branchburg, NJ, USA), 20 microliters of S mM dTTP, in a 100
microliter
reaction and incubating the reaction for 2 hours at 37°C. The "Kan-T"
cassette is
purified using a QIAquick column (Qiagen, Gaithersburg, MD, USA). The PCR
product of the deletion primers (F2 and R2) is ligated to the Kan-T cassette
by mixing
10 to 25 ng of deletion primer PCR product, SO - 75 ng Kan-T cassette DNA, 1
microliter l Ox T4 DNA Ligase reaction mixture, 0.5 microliter T4 DNA Ligase
(New
England Biolabs, Beverly, MA, USA) in a 10 microliter reaction and incubating
for 16
hours at 16°C.
The ligation products are transformed into XL-1 Blue or DHS-a E. col i cells
by
electroporation as described previously. After recovery in SOC, cells are
plated onto LB
plates containing 100 microgram/ml Ampicillin and grown overnight at
37°C. These
plates are then replica plated onto plates containing 25 microgram/mI
Kanamycin and
allowed to grow overnight. Resultant colonies have both the Ampicillin
resistance gene
present in the pT7Blue vector, .uud the newly introduced Kanamycin resistance
gene.
Colonies are picked into LB containing 25 microgram/ml Kanamycin and plasmid
DNA
is isolated from the cultured cells using the Qiagen miniprep protocol
(Qiagen,
Gaithersburg, MD, USA).
Several tests by PCR amplification are conducted on these plasmids to verify
that
the Kanamycin is inserted in the H. pylori gene/ORF, and to determine the
orientation of
the insertion of the Kanamycin-resistance gene relative to the H. pylori
gene/ORF. To
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verify that the Kanamycin cassette is inserted into the H. pylori sequence,
the plasmid
DNAs are used as templates for PCR amplification with the set of primers
originally
used to clone the H. pylori gene/ORFs. The correct PCR product is the size of
the
deleted gene/ORF but increased in size by the addition of a 1.4 kilobase
Kanamycin
cassette. To avoid potential polar effects of the kanamycin resistance
cassette on H.
pylori gene expression, the orientation of the Kanamycin resistance gene with
respect to
the knock-out gene/ORF is determined and both orientations are eventually used
in H.
pylori transformations (see below). To determine the orientation of insertion
of the
kanamycin resistance gene, primers are designed from the ends of the kanamycin
resistance gene ("Kan-1" S'-ATCTTACCTATCACCTCAAAT-3' (SEQ ID N0:255)),
and "Kan-2" 5'-AGACAGGAACATCTTTGTGAA-3' (SEQ ID N0:256)). By using
each of the cloning primers in conjunction with each of the Kan primers (4
combinations
of primers), the orientation of the Kanamycin cassette relative to the
H.pylori sequence
is determined. Positive clones are classified as either in the "A" orientation
(the same
direction of transcription is present for both the H. pylori gene and the
Kanamycin
resistance gene), or in the "B" orientation (the direction of transcription
for the H.pylori
gene is opposite to that of the Kanamycin resistance gene). Clones which share
the
same orientation (A or B) are pooled for subsequent experiments and
independently
transformed into H. pylori.
Transformation of Plasmid DNA into H. pylori cells
Two strains of H. pylori are used for transformation: ATCC 55679, the clinical
isolate which provided the DNA from which the H. pylori sequence database is
obtained, and AH244, an isolate which had been passaged in, and has the
ability to
colonize the mouse stomach. Cells for transformation are grown at 37°C,
10% C02,
100% humidity, either on Sheep-Blood agar plates or in Brucella Broth liquid.
Cells are
grown to exponential phase, and examined microscopically to determine that the
cells
are "healthy" (actively moving cells) and not contaminated. If grown on
plates, cells are
- 30 harvested by scraping cells from the plate with a sterile loop, suspended
in 1 ml of
'3rucella Broth, spun down ( 1 minute, top speed in eppendorf microfuge) and
resuspended in 200 microliters Brucella Broth. If grown in Brucella Broth
liquid, cells
are centrifuged (15 minutes at 3000 rpm in a Beckman TJ6 centrifuge) and the
cell pellet
. resuspended in 200 microliters of Brucella broth. An aliquot of cells is
taken to
determine the optical density at 600 nm, in order to calculate the
concentration of cells.
An aliquot ( 1 to 5 OD6oo units/25 microliter) of the resuspended cells is
placed onto a
prewarmed Sheep-Blood agar plate, and the plate is further incubated at
37°C, 6% C02,
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100% humidity for 4 hours. After this incubation, 10 microliters of plasmid
DNA ( 100
micrograms per microliter) is spotted onto these cells. A positive control
(plasmid DNA
with the ribonuclease H gene disrupted by kanamycin resistance gene) and a
negative
control (no plasmid DNA) are done in parallel. The plates are returned to
37°C, 6% C02
for an additional 4 hours of incubation. Cells are then spread onto that plate
using a
swab wetted in Brucella broth, and grown for 20 hours at 37°C, 6% C02.
Cells are then
transferred to a Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin,
and
allowed to grow for 3 to S days at 37°C, 6% C02, I 00% humidity. If
colonies appear,
they are picked and regrown as patches on a fresh Sheep-Blood agar plate
containing 25
micrograms/ml Kanamycin.
Three sets of PCR tests are done to verify that the colonies of transformants
have
arisen from homologous recombination at the proper chromosomal location. The
template for PCR (DNA from the colony) is obtained by a rapid boiling DNA
preparation method as follows. An aliquot of the colony (stab of the colony
with a
I S toothpick) is introduced into 100 microliters of 1% Triton X-100, 20 mM
Tris, pH 8.5,
and boiled for 6 minutes. An equal volume of phenol : chloroform (1:1 ) is
added and
vortexed. The mixture is microfuged for 5 minutes and the supernatant is used
as DNA
template for PCR with combinations of the following primers to verify
homologous
recombination at the proper chromosomal location.
TEST 1. PCR with cloning primers originally used to amplify the gene/ORF. A
positive result of homologous recombination at the correct chromosomal
location should
show a single PCR product whose size is expected to be the size of the deleted
gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin
cassette. A
PCR product of just the size of the gene/ORF is proof that the gene had not
been
knocked out and that the transformant is not the result of homologous
recombination at
the correct chromosome location.
TEST 2. PCR with F3 (primer designed from sequences upstream of the
gene/ORF and not present on the plasmid), and either primer Kan-1 or Kan-2
(primers
designed from the ends of the kanamycin resistance gene), depending on whether
the
plasmid DNA used was of "A" or "B" orientation. Homologous recombination at
the
correct chromosomal location will result in a single PCR product of the
expected s~ze
(i.e., from the location of F3 to the insertion site of kanamycin resistance
gene). No
PCR product or PCR products) of incorrect sizes) will prove that the plasmid
had not
integrated at the correct site and that the gene had not been knocked out.
TEST 3. PCR with R3 (primer designed from sequences downstream of the
gene/ORF and not present on the plasmid) and either primer Kan-1 or Kan-2,
depending
on whether the plasmid DNA used was of "A" or "B" orientation. Homologous
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recombination at the correct chromosomal location will result in a single PCR
product of
the expected size (i.e., from the insertion site of kanamycin resistance gene
to the
downstream location of R3). Again, no PCR product or PCR products) of
incorrect
sizes) will prove that the plasmid had not integrated at the correct site and
that the gene
had not been knocked out.
Transformants showing positive results for all three tests above indicate that
the
gene is not essential for survival in vitro.
A negative result in any of_the three above tests for each transformant
indicates
that the gene had not been disrupted, and that the gene is essential for
survival in vitro.
In the event that no colonies result from two independent transformations
while
the positive control with the disrupted ribonuclease H plasmid DNA produces
transformants, the plasmid DNA is further analyzed by PCR on DNA from
transformant
populations prior to plating for colony formation. This will verify that the
plasmid can
enter the cells and undergo homologous recombination at the correct site.
Briefly,
plasmid DNA is incubated according to the transformation protocol described
above.
DNA is extracted from the H. pylori cells immediately after incubation with
the plasmid
DNAs and the DNA is used as template for the above TEST 2 and TEST 3. Positive
results in TEST 2 and TEST 3 would verify that the plasmid DNA could enter the
cells
and undergo homologous recombination at the correct chromosomal location. If
TEST
2 and TEST 3 are positive, then failure to obtain viable transformants
indicates that the
gene is essential, and cells suffering a disruption in that gene are incapable
of colony
formation.
VII. High-throuehput drub screen assay
Cloning, expression and protein purification
Cloning, transformation, expression and purification of the H. pylori target
gene
and its protein product,e.g., an X. pylori enzyme, to be used in a high-
throughput drug
screen assay, is carned out essentially as described in Examples II and III
above.
Development and application of a screening assay for a particular H. pylori
gene
product, peptidyl-propyl cis-traps isomerase, is described below as a specific
example.
Enzymatic Assay
The assay is essentially as described by Fisher (Fischer, G., et.al. ( 1984)
Biomed.
Biochim. Acta 43:1101-1111). The assay measures the cis-traps isomerization
ofthe
Ala-Pro bond in the test peptide N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide
(Sigma # S-
7388, lot # 84H5805). The assay is coupled with a-chymotrypsin, where the
ability of
the protease to cleave the test peptide occurs only when the Ala-Pro bond is
in traps.
The conversion of the test peptide to the traps isomer in the assay is
followed at 390 nm
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on a Beckman Model DU-650 spectophotometer. The data are collected every
second
with an average scanning of time of 0.5 second. Assays are carried out in 35
mM
Hepes, pH 8.0, in a final volume of 400 ul, with 10 p.M a,-chymotrypsin (type
I -5 from
bovine Pancreas, Sigma # C-7762, lot 23H7020) and 10 nM PPIase. To initiate
the
reaction, 10 p l of the substrate ( 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-
nitroanilide in
DMSO) is added to 390 ~l of reaction mixture at room temperature.
Enzymatic assay in crude bacterial extract.
A 50 ml culture of Helicobacter pylori (strain J99) in Brucella broth is
harvested
at mid-log phase (OD 60o nm ~ 1 ) and resuspended in lysis buffer with the
following
protease inhibitors: 1 mM PMSF, and 10 pg/ml of each of aprotinin; leupeptin,
pepstatine, TLCK, TPCK, and soybean trypsin inhibitor. The suspension is
subjected to
3 cycles of freeze-thaw ( I 5 minutes at -70 ° C, then 30 minutes at
room temperature),
followed by sonication (three 20 second bursts). The lysate is centrifuged (
12,000 g x
30 minutes) and the supernatant is assayed for enzymatic activity as described
above.
Many H. pylori enzymes can be expressed at high levels and in an active form
in
E. coli. Such high yields of purified proteins provide for the design of
various high
throughput drug screening assays.
VIII. Truncated gene expression and protein production
Identification, cloning and expression of recombinant Helicobacter pylori
sequences.
To facilitate the cloning, expression and purification of membrane proteins
from
H. pylori, the pET gene expression system. (Novagen), for cloning and
expression of
recombinant proteins in Escherichia coli was selected. Further, for proteins
that have a
signal sequence at their amino-terminal end, a DNA sequence encoding a peptide
tag
(His-tag) was fused to the 5' end of the H. pylori DNA sequences of interest
in order to
facilitate purification of the recombinant protein products. In some cases,
the DNA
sequence was cloned in frame with the glutathione-S-transferase-protein to
produce a
GST-fusion protein. The vectors used in this case were the pGEX series from
Pharmacia LKB (Uppsala, Sweden).
PCR amplification and cloning of DNA sequences containing ORFs for membrane
and
secreted proteins from the J99 strain of Helicobacter pylori.
The sequences chosen (from the list of the DNA sequences of the invention) for
cloning from H. pylori strain J99 were prepared for amplification cloning by
the
polymerase chain reaction (PCR). Synthetic oligonucleotide primers for the ORF
of
interest (Table 11 ) specific for the predicted mature 5' end of the ORF and
either
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downstream (3') of the predicted translational termination codon or at
specific points
within the coding region were designed and purchased (GibcoBRL Life
Technologies,
Gaithersburg, MD, USA). All forward primers (specific for the 5' terminus of
the
region of ORF of interest) were designed to include either a BamHI or a NdeI
restriction
site. These primers within the NdeI restriction site sequence were designed to
permit the
initiation of protein translation at a methionine residue (encoded within the
Ndei
restriction site sequence, in the case of producing a non His-tagged
recombinant protein)
or to fuse in frame with the DNA sequence encoding the His-tag (for producing
His
tagged recombinant protein), followed by the coding sequence for the remainder
of the
native H. pylori DNA. The primer with the BamHI restriction site was produced
to fuse
the H. pylori specific sequence in-frame with the C-terminus of the
glutathione-S-
transferase gene in the pGEX vectors (Pharmacia LKB, Uppsala, Sweden}. All
reverse
oligonucleotide primers designed to include an EcoRI restriction site at the
5' terminus.
Several reverse oligonucleotide primers were selected that would cause a
truncation of
the polypeptide to remove certain portions of the C-terminus, and in these
cases the
EcoRI restriction site at the 5' end was followed by a translational
termination codon.
This combination of primers would enable the ORF of interest (or parts of the
ORF of
interest) to be cloned into pET28b (to produce a His-tagged recombinant
protein),
pET30a (to produce a non His tagged or native recombinant protein) or the pGEX-
4T or
pGEX-SX series (to produce a GST fusion protein). The pET28b vector provides
sequence encoding an additional 20 amino-terminal amino acids (plus the
methionine in
the NdeI restriction site) including a stretch of six histidine residues which
makes up the
His-tag, whereas the pGEX vectors fuse the H. pylori protein to a 26,OOODa
glutathione-
S-transferase protein.
Genomic DNA prepared from H. pylori strain J99 (ATCC 55679) was used as
the source of template DNA for the PCR amplification reactions (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
To
amplify a DNA sequence containing a specific H. pylori ORF, genomic DNA (50
nanograms) was introduced into a reaction tube containing 200 nanograms of
both the
forward and reverse synthetic oligonucleotide primer specific for the ORF of
interest,
and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies,
Gaithersburg, MD, USA) in a total of 50 microliters. The PCR SuperMix is
supplied in
1.1X concentrations and contains 22mM Tris-HCl (pH 8.4), SSmM KCI, 1.65mM
MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22units recombinant
Taq polymerase/mI and stabilizers. The following thermal cycling conditions
were used
to obtain amplified DNA products for each ORF using a Perkin Elmer
Cetus/GeneAmp
PCR System thermal cycler.
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Table 11: Oligonucleotide primers
Gene and location Sequence
Vac38- BamHI post signal sequence CGGGATCCGAAGGTGATGGTGTTTATA
TAGG (SEQ ID NO: 27I )
Vac38- Ndel post signal sequence CGCATATGGAAGGTGATGGTGTTTATA
TAGGG (SEQ ID NO: 272)
Vac38- EcoRI/stop codon (removes GCGAATTCTCACTCTTTCCAATAGTTTG
C-
terminal third of protein) CTGCAGAGC (SEQ ID NO: 273)
Vac38- EcoRt/stop codon (removes CCGGAATTCTTAATCCCGTTTCAAATG
C-
terminal 11 amino acids) GTAATAAAGG (SEQ ID NO: 274)
Vac38- EcoRI downstream of GCGAATTCCCTTTTATTTAAAAAGTGT
native stop
codon AGTTA1'ACC (SEQ ID NO: 275)
Sequences for Vac38 (full length or truncated)
Denaturation at 94°C for 30 sec
35 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C
for 1.5 min
Reactions were concluded at 72°C for 8 minutes
I 0 Upon completion of the thermal cycling reactions, each sample of amplified
DNA was subjected to electrophoresis on 1.0% agarose gels. The DNA was
visualized
by exposure to ethidium bromide and long wave UV irradiation, and cut out in
gel
slices. DNA was purified using the Wizard PCR Preps kit (Promega Corp.,
Madison
WI, USA), and then subjected to digestion with BamHI and EcoRI (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
The
digested PCR amplicon was then re-eIectrophoresed and purified as before.
Ligation of H. pylori DNA sequences into cloning vectors
The pOKl2 vector (J. Vieira and J. Messing, Gene 100:189-194, 1991) was
prepared for cloning by digestion with BamHI and EcoRI or NdeI and EcoRI in
the case
of Vac41 (Current Protocols in Molecular Biology, John Wiley and Sons, Inc.,
F.
Ausubel et al., eds., 1994). The vectors were subj ected to electrophoresis on
1.0%
agarose gels and purified using the Wizard PCR Preps kit (Promega Corp.,
Madison WI,
USA). Following ligation of the purified, digested vector and the purified,
digested
SUBSTITUTE SHEET (RULE 26)
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amplified H. pylori ORF, the products of the ligation reaction were
transformed into E.
col i JM 109 competent cells according to standard methods (Current Protocols
in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Individual
bacterial colonies were screened for those containing the correct recombinant
plasmids
by incubating in LB broth overnight (plus 25ug/ml kanamycin sulfate) followed
by
plasmid DNA preparation using the Magic Minipreps system (Promega Corp.,
Madison
WI, USA), and Then analyzed by restriction digestion (Current Protocols in
Molecular
Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Cloning of H. pylori DNA sequences into the pET28b, pET30a and pGEX4T 3
prokaryotic expression vectors
Both the pET28b and pET30a expression vectors were prepared for cloning by
digestion with NdeI and EcoRI, and the pGEX4T-3 vector was prepared for
cloning by
digestion with BamHI and EcoRI (Current Protocols in Molecular Biology, John
Wiley
and Sons, Inc., F. Ausubel et al., eds., 1994). The H. pylori DNA sequences
were
removed from pOKl2 plasmid backbones by digestion with NdeI and EcoRI or BamHI
and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc.,
F.
Ausubel et al., eds., 1994). The pET28b, pET30a, pGEX4T-3 and H. pylori DNA
sequences were all electrophoresed on a 1 % agarose gel and purified using the
Wizard
PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the
purified,
digested expression vector and the purified, digested H. pylori DNA sequences,
the
products of the ligation reaction were transformed into E. coli JM 109
competent cells
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994). Individual bacterial colonies were screened for those containing
the correct
recombinant plasmids by preparing plasmid DNA as described above followed by
analysis by restriction digestion profiles and DNA sequencing (Current
Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
These
recombinant plasmids were then used to transform specific E. coli expression
strains.
Transformation of competent bacteria with recombinant expression plasmids
Competent bacterial strains BL21 (I~~E3), BL21 (DE3)pLysS, HMS 174(DE3) and
HMS 174(DE3)pLysS were prepared and transformed with the recombinant pET28b
expression plasmids carrying the cloned H. pylori sequences according to
standard
methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F.
3 5 Ausubel et al., eds., 1994). These expression host strains contain a
chromosomal copy
of the gene for T7 RNA polymerise. These hosts are lysogens of bacteriophage
DE3, a
lambda derivative that carries the lacl gene, the IacUVS promoter and the gene
for T7
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RNA polymerase. T7 RNA polymerase expression is induced by the addition of
isopropyl-(3-D-thiogalactoside (IPTG), and the T7 RNA polymerase then
transcribes any
taget plasmid, such as pET28b, that carnes a T7 promoter sequence and a gene
of
interest.
Competent bacterial strains JM109 and DHSa were prepared and transformed
with the recombinant pGEX4T-3 expression plasmid carrying the cloned H. pylori
sequences according to standard methods (Current Protocols in Molecular
Biology, John
Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Expression of recombinant H. pylori sequences in E coli
Transformants were collected from LB agar plates containing 25ug/ml
kanamycin sulfate (ensures maintenance of the pET28b-based recombinant
plasmids) or
100ug/ml ampicillin (ensures maintenance of the pGEX4T-3-based recombinant
plasmids) and used to inoculate LB broth containing 25ug/ml kanamycin sulfate
or
1 OOug/ml ampicillin and grown to an optical density at 600nm of 0.5 to 1.0 OD
units, at
which point 1 mM IPTG was added to the culture for one to three hours to
induce gene
expression of the H. pylori recombinant DNA constructions. After induction of
gene
expression with IPTG, bacteria were pelleted by centrifugation and resuspended
in SDS-
PAGE solubilization buffer and subjected to SDS-PAGE (Current Protocols in
Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Proteins
were visualized by staining with Coomassie Brilliant Blue or detected by
western
immunoblotting using the specific anti-His tag monoclonal antibody (Clontech,
Palo
Alto, CA, USA) or the anti-GST tag antibody (Pharmacia LKB) using standard
methods
(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel
et al.,
eds., 1994)) The host strain that provided the highest level of recombinant
protein
production was then chosen for use in a large-scale induction in order to
purify the
recombinant protein. The strains used were HMS 174(DE3) (pET28b-based
constructs)
and DHSa (pGEX4T-3-based constructs).
Removal of the C-terminal regions appeared in both systems to improve the
level
of expression, although this increase was far more prominent in the GST-fusion
system.
All recombi~ pant proteins produced were of the predicted molecular weight
based on the
DNA sequence plus, if necessary, the size of the fusion tag. The truncated
portion of the
H. pylori protein contains some extremely hydrophobic stretches, and removal
of these
may be the reason for the increased expression.
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EQUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more
than
routine experimentation, many equivalents to the specific embodiments and
methods
described herein. Such equivalents are intended to be encompassed by the scope
of the
following claims.
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SEQUENCE LISTING
1) GENERAL INFORMATION:
S (i) APPLICANT:
(A) NAME: Astra Aktiebolag
(B) STREET: S-151 85
(C) CITY: Sodertalje
(D) STATE:
(E) COUNTRY: Sweden
(F) POSTAL CODE (ZIP)
(ii) TITLE OF INVENTION: NUCLEIC ACID AND AMINO ACID SEQUENCES
RELATING TO HELICOBACTER PYLORI AND
IS VACCINE COMPOSITIONS THEREOF
(iii) NUMBER OF SEQUENCES: 275
(iv) COMPUTER READABLE FORM-:
(A) MEDIUM TYPE: CD/ROM IS09660
(B) COMPUTER:
(C) OPERATING SYSTEM:
(D) SOFTWARE:
ZS (v) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER
(B) FILING DATE:
(vi) PRIOR APPLICATION DATA:
30 (A) APPLICATION NUMBER: US 08/759,625
(B) FILING DATE: 05-DEC-1996
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 08/823,745
3S (B) FILING DATE: 25-MAR-1997
(viii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 08/891,928
(B) FILING DATE: 14-JULY-1997
40 -
(ix) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: LAHIVE & COCKFIELD
(B) STREET: 28 State Street
(C) CITY: Boston
4S (D) STATE: Massachusetts
(E) COUNTRY: USA
(F) ZIP: 02109-1875
(x) ATTORNEY/AGENT INFORMATION:
S0 (A) NAME: Mandragouras, Amy E.
(B) REGISTRATION NUMBER: 36,207
(C) REFERENCE/DOCKET NUMBER: GTN-O11CP2PC
(xi) TELECOMMUNICATION INFORMATION:
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(A) TELEPHONE: (617)227-7400
(B) TELEFAX: (617)227-5941
S
(2) INFORMATION FOR SEQ ID NO:1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 687 base pairs
(B) TYPE: nucleic acid
(C} STRANDEDNESS: double
lO (D) TOPOLOGY: circular
1S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
( ix) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...687
2S (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:
ATGAGATTTA AGGGTTCAAGAGTGGAAGCGTTTTTAGGAGCGTTAGAATTTCAAGAGAAT60
GAATATGAAG AGTTTAAAGAGCTTTATGAGAGCTTAAAAACCAAGCAAAAGCCCCACACT120
TTGTTCATTT CTTGCGTGGATTCACGAGTCGTGCCTAATTTAATCACAGGCACCCAACCG180
3O GGCGAATTGTATGTGATCCGCAACATGGGCAATGTGATCCCCCCTAAAACAAGCTATAAA240
GAATCCCTTT CTACCATTGCGAGCGTTGAATACGCTATCGCGCATGTGGGCGTTCAAAAC300
TTAATCATTT GCGGGCATAGCGATTGTGGGGCTTGCGGGAGCATTCATTTAATCCATGAT360
GAAACCACCA AAGCTAAAACCCCTTACATTGCAAACTGGATACAATTTTTAGAGCCTATT420
AAAGAAGAAT TAAAAAACCACCCGCAATTCAGCAACCATTTCGCCAAGCGTTCATGGCTT480
3S ACAGAGCGTTTGAATGCGCGCTTGCAACTCAACAACCTCTTAAGCTATGATTTCATTCAA540
GAAAGAGTAA TAAATAACGAATTAAAAATTTTTGGTTGGCACTATATCATAGAAACAGGC600
AGGATTTATA ATTATAATTTTGAAAGCCATTTTTTTGAGCCGATTGAAGAAACCATTAAA660
CAAAGGATAA GTCATGAAAACTTCTAA 687
40 (2) INFORMATION FOR SEQ ID N0:2:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 666 base pairs
(B) TYPE: nucleic acid
4S (C) STRANDEDNESS: double
(D) TOPOLOGY: ~i:cular
(ii) MOLECULE TYPE: DNA (genomic)
SO (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
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(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
S (B) LOCATION 1...666
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:2:
GTGGAAGCGTTTTTAGGAGCGTTAGAATTTCAAGAGAATG 60
AATATGAAGA
GTTTAAAGAG
lO CTTTATGAGAGCTTAAAAACCAAGCAAAAGCCCCACACTTTGTTCATTTC TTGCGTGGAT120
TCACGAGTCGTGCCTAATTTAATCACAGGCACCCAACCGGGCGAATTGTA TGTGATCCGC180
AACATGGGCAATGTGATCCCCCCTAAAACAAGCTATAAAGAATCCCTTTC TACCATTGCG240
AGCGTTGAATACGCTATCGCGCATGTGGGCGTTCAAAACTTAATCATTTG CGGGCATAGC300
GATTGTGGGGCTTGCGGGAGCATTCATTTAATCCATGATGAAACCACCAA AGCTAAAACC360
IS CCTTACATTGCAAACTGGATACAATTTTTAGAGCCTATTAAAGAAGAATT AAAAAACCAC420
CCGCAATTCAGCAACCATTTCGCCAAGCGTTCATGGCTTACAGAGCGTTT GAATGCGCGC480
TTGCAACTCAACAACCTCTTAAGCTATGATTTCATTCAAGAAAGAGTAAT AAATAACGAA540
TTAAAAATTTTTGGTTGGCACTATATCATAGAAACAGGCAGGATTTATAA TTATAATTTT600
GAAAGCCATTTTTTTGAGCCGATTGAAGAAACCATTAAACAAAGGATAAG TCATGAAAAC660
ZO TTCTAA 666
(~) INFORMATION FOR SEQ ID N0:3:
(i) SEQUENCE CHARACTERISTICS:
2$ (A) LENGTH: 1008 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4O (A) NAME/KEY: misc_feature
(B) LOCATION 1...1008
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:3:
4S ATGTTAGTTACTCGTTTTAA ATTTCTTATTCTTTAGGCGTGCTTGTTGTT60'
AAAAGCCTTC
~CATTATTAT TGAATGTGTGCAACGCTTCAGCACAAGAAGTCAAAGTCAAGGATTATTTT120
GGGGAGCAAA CCATAAAGCTTCCTGTTTCCAAAATAGCCTATATAGGGAGTTATGTAGAA180
GTGCCTGCCA TGCTTAATGTTTGGGATAGGGTTGTAGGCGTTTCTGATTATGCCTTTAAG240
GATGACATTG TCAAAGCCACTCTCAAAGGCGAGGATCTTAAACGAGTCAAACACATGAGC300
SO ACCGATCATACAGCCGCGTTGAATGTGGAATTATTAAAAAAGCTTAGCCCTGATCTTGTG360
GTAACCTTTG TGGGTAACCCTAAAGCGGTAGAGCATGCGAAAAAATTTGGGATTTCATTC420
CTTTCTTTCC AAGAGACAACGATTGCAGAGGCCATGCAAGCTATGCAAGCTCAAGCCACG480
GTCTTAGAAA TTGACGCTTCCAAAAAATTCGCCAAAATGCAAGAAACTTTGGACTTTATT540
GCTGAGCGTT TGAAGGGCGTTAAAAAGAAAAAGGGGGTGGAGCTTTTCCATAAAGCCAAT600
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AAAATCAGCG GCCATCAAGC CATTAGCTCA GACATTTTAG AAAAAGGGGG TATAGATAAT 660
TTTGGCTTGA AATACGTTAA GTTTGGACGC GCTGACATTA GTGTGGAAAA AATCGTTAAA 720
GAAAACCCTG AAATCATTTT CATTTGGTGG GTAAGCCCAC TCACTCCTGA AGACGTGTTG 780
AACAACCCTA AATTTTCCAC TATCAAAGCC ATTAAAAATA AGCAAGTCTA TAAGCTCCCC 840
S ACGATGGATA TTGGCGGTCC TAGAGCCCCA CTCATTAGTC TTTTTATCGC TTTAAAAGCC 900
CACCCTGAAG CCTTTAAAGG CGTGGATATT AATGCGATAG TCAAAGATTA TTATAAAGTG 960
GTCTTTGATT TGAATGATGC GGAAATTGAG CCATTCTTAT GGCACTGA 1008
(2) INFORMATION FOR SEQ ID N0:4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
1S (D} TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO -
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...825
3O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:4:
ATGTTAGTTA CTCGTTTTAA AAAAGCCTTC ATTTCTTATT CTTTAGGCGT GCTTGTTGTT 60
TCATTATTAT TGAATGTGTG CAACGCTTCA GCACAAGAAG TCAAAGTCAA GGATTATTTT 120
GGGGAGCAAA CCATAAAGCT TCCTGTTTCC AAAATAGCCT ATATAGGGAG TTATGTAGAA 180
3S GTGCCTGCCA TGCTTAATGTTTGGGATAGGGTTGTAGGCGTTTCTGATTATGCCTTTAAG240
GATGACATTG TCAAAGCCACTCTCAAAGGCGAGGATCTTAAACGAGTCAAACACATGAGC300
ACCGATCATA CAGCCGCGTTGAATGTGGAATTATTAAAAAAGCTTAGCCCTGATCTTGTG360
GTAACCTTTG TGGGTAACCCTAAAGCGGTAGAGCATGCGAAAAAATTTGGGATTTCATTC420
CTTTCTTTCC AAGAGACAACGATTGCAGAGGCCATGCAAGCTATGCAAGCTCAAGCCACG480
4O GTCTTAGAAA TTGACGCTTCCAAAAAATTCGCCAAAATGCAAGAAACTTTGGACTTTATT540
GCTGATCGTT TGAAGGGCGTTAAAAAGAAAAAGGGGGTGGAGCTTTTCCATAAAGCCAAT600
AAAATCAGCG GCCATCAAGCCATTAACTCAGACATTTTACAACAAGGGGGTATTGATAAT660
TTTGGCTTGA AATACGTCAAGTTTGGACGCGCTGACATTAGTGTGGAAAAAATCGTTAAA720
GAAAACCCTG AAATCATTTTCATTAGGTGGGTAACCCCACTCACTCCTGATTACGTGTTG780
4S AACAACCCAA AATTTTCTACTATCAATGCCATTAAAAACATATAA P25
{2) INFORMATION FOR SEQ ID N0:5:
(i) SEQUENCE CHARACTERISTICS:
S~ (A) LENGTH: 1287 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
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(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
lO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1287
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:5:
1S
ATGAAGAAAA AATTTCTGTCATTAACCTTAGGTTCGCTTTTAGTTTCCGCTTTAAGCGCT60
GAAGACAACG GCTTTTTTGTGAGCGCCGGCTATCAAATCGGTGAATCCGCTCAAATGGTG120
AAAAACACCA AAGGCATTCAAGATCTTTCAGACAGCTATGAAAGATTGAACAACCTTTTA180
ACGAATTATA GCGTCCTAAACGCTCTCATCAGGCAGTCCGCCGACCCCAACGCCATCAAT240
ZO AACGCAAGGG GCAATTTGAACGCGAGCGCGAAGAATTTGATCAATGATAAAAAGAATTCC300
CCGGCGTATC AAGCCGTGCTTTTAGCCTTGAATGCGGCAGCGGGGTTGTGGCAAGTCATG360
AGCTATGCGA TCAGCCCTTGTGGTCCCGGTAAAGACACAAGCAAAAATGGGGGCGTTCAA420
ACTTTCCACA ACACGCCTTCAAATCAATGGGGAGGCACTACCATTACTTGTGGCACTACT480
GGTTATGAAC CAGGACCATACAGCATTTTATCCACTGAAAATTACGCGAAAATCAATAAA540
ZS GCTTATCAAA TCATCCAAAAGGCTTTTGGGAGCAGCGGAAAAGATATTCCTGCCTTAAGC600
GACACCAACA CAGAACTCAAATTCACAATCAATAAAAATAATGGAAACACGAATACGAAT660
AATAATGGAG AAGAAATTGTTACAAAAAATAACGCTCAAGTTCTTTTAGAACAGGCTAGC720
ACCATTATAA CTACCCTTAATAGCGCATGCCCATGGATCAACAATGGTGGTGCAGGTGGT780
GCGAGTAGTG GTAGTTTATGGGAAGGAATATATTTGAAAGGCGATGGGAGCGCTTGCGGG840
3O ATTTTTAAAA ATGAAATCAGCGCGATTCAAGACATGATCAAAAACGCTGCAATAGCCGTA900
GAGCAATCCA AGATCGTTGCTGCAAACGCGCAAAACCAGCGCAACCTAGACACCGGGAAG960
ACATTCAACC CCTATAAAGACGCCAACTTCGCCCAAAGCATGTTCGCTAACGCCAAAGCG1020
CAAGCGGAGA TTTTAAACCGCGCCCAAGCAGTGGTGAAAGACTTTGAAAGAATCCCTGCA1080
GAGTTCGTAA AAGACTCTTTAGGGGTGTGCCATGAAGTGCAAAACGGCCATCTCCGTGGC1140
3S ACGCCATCCG GCACGGTAACTGATAACACTTGGGGAGCCGGTTGCGCGTATGTGGGAGAG1200
ACCGTAACGA ATCTAAAAGACAGCATCGCTCATTTTGGCGACCAAGCCGAGCGAATCCAT1260
AACGCGCGCA ACCTCGCTACACTTTAG 1287
(2) INFORMATION
FOR SEQ ID N0:6:
40
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 537 base
pairs
(B) TYPE: nucleic
acid
(C) STRANDEDNESS: e
doubl
4S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
- SO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
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S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...537
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:6:
ATGAACCCCT TATTGCAAGA TTATGCGCGC ATCCTTTTAG AATGGAATCA AACGCACAAC 60
TTGAGCGGCG CGAGAAATTT AAGCGAATTA GAACCCCAGA TCACAGACGC TCTAAAGCCC 120
IO TTAGAATTTG TCAAAGATTT TAAAAGCTGC TTGGATATTG GGAGCGGGGC GGGACTTCCT 180
GCTATCCCTT TAGCCCTTGA 240
AAAACeTGAA
GCGCAATTCA
TTCTTTTAGA
GCCAAGGGTA
AAAAGAGCGG CTTTTTTAAACTACCTTAAA AGCGTTTTGC CTTTAAACAA CATTGAAATC300
ATTAAAAAGC GTTTAGAAGATTATCAAAAT CTTTTACAAG TGGATTTAAT CACTTCTAGA360
GCGGTCGCTA GCTCTTCTTTTTTGATAGAA AAAAGCCAAC GCTTCCTAAA AGATAAGGGG420
IS TATTTTTTATTCTATAAAGGCGAGCAGTTA AAGAATGAAA TCGCTTATAA AACCACTGAA480
TGCTTTATGC ATCAAAAGCGCGTTTATTTT TACAAATCAA AGGAAAGTTT ATGTTAA537
(2) INFORMATION FOR SEQ ID N0:7:
2O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 723 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
2S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3O (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...723
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:7:
TTGGGTCTTA AAAAACGAGC TATTTTATGGTCTTTAATGGGATTTTGTGCAGGATTGAGC60-
GCGCTTGATT ATGACACCCT AGACCCAAAATATTACAAATATATCAAGTATTATAAGGCT120
TATGAAGATA AAGAAGTTGA AGAATTGATCAGAGACTTGAAAAGGGCGAACGCTAAAAGC180
GGGCTTATTT TAGGGATCAA TACCGGTTTTTTTTATAACCATGAAATCATGGTCAAAACC240
4S AATAGCTCCA GTATCACC3GGAATATTTTAAATTATTTGTTCGCCTATGGCTTGCGTTTT300
GGCTATCAAA CTTTC..3.CC GTCGTTTTTTGCGCGCTTGGTTAAGCCCAATATCATTGGC360
AGGCGCATCT ATATTCAATA TTATGGAGGAGCTCCTAAGAAAGCGGGCTTTGGGAGCGTG420
GGGTTTCAAT CGGTCATGTT GAATGGGGATTTTTTATTAGACTTTCCTTTGCCCTTTGTG480
GGGAAATACC TTTATATGGG GGGGTATATGGGTTTAGGCTTGGGGGTTGTGGCGCATGGG540
SO GTGAATTATA CGGCGGAATGGGGGATGTCTTTTAACGCAGGATTGGCTCTAACGGTATTA600
GAAAAAAACC GCATTGAATT TGAATTTAAAATTTTGAATAATTTCCCTTTTTTGCAATCT660
AATTCTTCAA AAGAGACTTG GTGGGGAGCTATAGCAAGCATTGGGTATCAATATGTGTTC720
T~ 723
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(2) INFORMATION FOR SEQ ID N0:8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 942 base pairs
S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
IS (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...942
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:8:
TTGAAACTCA AGTTTATCTGGCGTTCATTATAGGACTTCAAGCGACAGAT60
AATACTGGTT
ZS TATGACAATTTAGAAGAAGAAAACCAACAATTAGACGAAAAAATAAACAATTTAAAGCGA120
CAGCTCACCGAAAA.AGGGGTTTCACCCAAAGAGATGGATAAGGATAAGTTTGAAGAAGAA180
TATTTAGAGCGAACTTACCCAAAGATTTCTTCAAAGAAAAGAAAAAAATTGCTCAAATCT240
TTTTCCATAGCCGATGATAAGAGTGGGGTGTTTTTAGGGG.GCGGGTATGCTTATGGGGAA300
CTTAACTTGTCTTATCAAGGGGAGATGTTAGACAGGTATGGCGCAAATGCCCCTAGCGCG360
3O TTTAA.AAACAATATCAATATTAACGCTCCTGTTTCTATGATTAGCGTTAAATTTGGGTAT420
CAAAA.ATACTTCGTGCCTTATTTTGGGACACGATTTTATGGGGATTTGTTGCTTGGGGGA480
GGGGCGTTAAAAGAGAACGCGCTCAAGCAGCCTGTAGGCTCGTTTTTTTATGTTTTAGGG540
GCTATGAATACCGATTTATTGTTTGACATGCCTTTAGATTTTAAGACTAAAAAGCATTTT600
TTAGGCGTTTATGCGGGTTTTGGGATAGGGCTTATGCTTTATCAAGACAAGCCTAATCAA660
3S AACGGGAGGAATTTGATAGTAGGGGGTTATTCAAGCCCTAATTTTTTATGGAAATCTTTG720
ATTGAAGTGGATTACACTTTTAATGTGGGCGTGAGTTTAACGCTTTATAGGAAACACCGC780
TTAGAGATTGGCACAAAATTACCGATTAGCTATTTGAGGATGGGAGTAGAAGAGGGAGCG840
ATTTATCACAATAAAGAAAATGATGAACGATTGTTGATTTCGGCTAACAACCAGTTCAAA900
CGATCCAGTTTTTTATTAGTGAATTATGCGTTCATTTTTTGA 942
40
(2) INFORMATION FOR SEQ ID N0:9:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1182 base pairs
--- ~S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
S0
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: Np
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(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
S (A) NAME/KEY: misc_feature
(B) LOCATION 1...1182
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:9:
lO ATGACTTCAG CTTCAAGCCATTCTTTTAAA GAACAAGATTTTCATATTCC TATCGCTTTC60
GCTTTTGATA AGAATTATCTCATTCCTGCG GGCGCATGCATTTATTCCTT GCTAGAAAGC120
ATCGCTAAAG CCAATAAAAAAATCCGTTAC ACCTTACACGCTTTAGTGGT AGGCTTGAAT180
GAAGAAGATA AAACAAAACTTAACCAAATC ACAGAGCCTTTTAAAGAATT TGCTGTTTTA240
GAAGTAAAAG ATATTGAACCTTTTTTAGAC ACTATCCCTAACCCTTTTGA TGAGGATTTC300
IS ACCAAGCGTT TTTCTAAAATGGTGTTAGTG AAGTATTTTCTAGCGGATTT ATTCCCCAAA360
TATTCTAAAA TGGTGTGGAGCGATGTGGAT GTTATCTTTTGTAATGAATT TAGCGCTGAT420
TTCTTAAACA TTAAAGAAGATGATGAGAAT TATTTTTATGGGGTTTATGA CAAAATATAC480
CCGTATGAAG GCTTTTTTTATTGCAACTTA ACTTACCAGCGAAAAAATCA ATTTTGTAAA540
AAAATATTAG AAATCATACGCGCACAAAAA ATAGATAAAGAACCGCAATT GACAGAATTT600
ZO TGTCGTTCAA AGATCGCGCCATTAAAAATA GAGTATTGTATTTTCCCACA CTATTATAGC660
CTTTCTGAAG AGCATTTAAAGGGCGTGGCC AATGCAATTTATCATAACAC CATTAAACAA720
GCCCTAAGAG AACCTATCGTTATACAATAT GAC'TCTCATCCTTATTTTCA AATCAAGCCT780
TGGACATATC CTTTTGGTTTGAAAGCGGAT TTATGGCTGAACGCTTTGGC TAAAACCCCA840
TTTATGAGCG ATTGGTCTTATTTGATCACA GGGGGTGGGGGGATAGGTGG AGAAAAATGG900
ZS CATTACTACC ATGGCATTGCCGCTTATCAT TACTACTTTCCTTTATGGAA AGCAGAAGAA960
CAGATTGCCC ATGACGCTCTTAAGACATTT TTAAAACATTATTTTTTGCA CATTCATGAG1020
ATTCCCCAAA ACGCAAGGCGAAGACTATTC AAATACTGCATTTCAATACC GCTTAAGAGC1080
TTTATTAGTA AAACCCTTAAATTTCTAAAA CTCCATGCATTGGTGAAAAA AATCCTAATC1140
CAACTCAAGC TCTTAAAAAAGAACCAGAGC CAAAACTTTTAA 1182
30
(2) INFORMATION FOR SEQ ID NO:10:
(1) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1308 base pairs
3S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
__4S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
SO (B) LOCATION 1...1308
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:
TTGATTTTCT TAAAAAP.ATC TCTTTGCGCG TTGTTAATTT CAGGTTTTTT CATACCACCC 60
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TTAATGAAAGCGGCTAGTTTTGTCTATGACTTGAAGTTTATGAGCTTTAATTTCAATCTG120
GCTTCCCCTCCAAATAACCCCTATTG~AATAGCCTAACCAAAATGCAAGGTCGTCTCATG180
CCTCAAATTGGCGTCCAATTAGACAAAAGACAGGCCTTGATGTTTGGGGCGTGGTTCATT240
CAAAATTTGCACACGCATTATAGCTATTTCCCTTATTCGTGGGGGGTTACCATGTATTAC300
S CAATACATAGGGAAAAATTTGAGATTTTTTTTAGGCATTGTGCCACGAAGCTATCAAATA360
GGGCATTACCCTTTAAGCGC'TTTTAAAAAACTTTTCTGGTTTATAGACCCTACTTTTAGG420
GGAGGAGCGTTCCAATTCAAACCGGCTTATGATCCCAATCGTTGGTGGAATGGGTGGTTT480
GAGGGCGTTGTGGATTGGTATGGGGGGCGTAATTGGAACAACCAGCCCAAAAAGAAAAAT540
TACGATTTTGATCAATTCTTGTATTTTGTTTCTTCAGAATTTCAGTTTCTTAAAGGGTAT600
lO TTAGGTTTGGGGGGACAGCTTGTCATTTTTCATAACGCCAACTCTCATAGTATGGGGGAT660
AACTACCCTTATGGCGGGAATTCCTACTTAAAACCAGGCGATGCAACCCCACAATGGCCT720
AATGGCTACCCTTATTTCAGCCAAAAAGATAACCCACAAGGCGGAGAAATAGGGAAATAC780
TCTAACCCTACCATTTTAGACAGGGTTTATTACCATGCTTATTTAAAAGCAGATTTTAAA840
AATCTCATGCCTTATATGGACAATATTTTCATGACCTTTGGCACGCAGTCGTCTCAAACC900
IS CATTATTGCGTGCGTTATGCTAGCGAGTGTAAAAACGCCCGATTTTATAACAGCTTTGGG960
GGGGAATTTTACGCTCAAGCGCAATACAAAGGCTTTGGGATCTTTAACAGATACTATTTT1020
TCCAACAAACCCCAAATGCATTTTTATGCCACTTATGGCCAATCCCTTTATACCGGATTG1080
CCATGGTATAGAGCCCCTAATTTTGACATGATAGGGCTTTATTATCTTTATAAAAACAAA1140
TGGTTAAGCGTGCGAGCGGATGCGTTTTTTAGCTTTGTGGGTGGGGGCGATGGGTACCAT1200
ZO TTGTATGGCAAGGGGGGTAAGTGGTTTGTGATGTATCAGCAATTTTTAACCCTAACCATA1260
GACACAAGAGAGTTGATTGATTTTGTCAAATCTAAAATCCCTAAATAA 1308
(2) INFORMATION FOR SEQ ID NO:11:
ZS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 663 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature -
(B) LOCATION 1...663
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:
4S
ATGAATAAAA CAACAATTAA G.:C~TGGCGTTATTATCATCGCTTCAAGCC60
AATATTAATG
GCAGAGGCAG AGCTTGATGAAAAATCAAAAAAACCTAAATTTGCGGATAGGAATACGTTT120
TATTTAGGGG TTGGGTATCAGCTTAGCGCGATCAACACGTCTTTTAGCACCAGTTCTATA180
GATAAATCGT ATTTCATGACCGGCAATGGTTTTGGCGTGGTGTTGGGGGGGAAATTTGTG240
SO GCTAAAACGCAAGCTGTAGAGCATGTGGGTTTTCGTTACGGGTTGTTTTATGATCAGACC300
TTTTCTTCTC ACAAATCCTATATTTCTACCTATGGTTTAGAATTTAGCGGTTTGTGGGAC360
GCTTTCAATT CGCCAAAGATGTTTTTGGGGTTGGAGTTTGGCTTAGGCATCGCTGGGGCG420
ACTTACATGC CAGGAGGGGCCATGCATGGGATTATCGCTCAATATTTAGGCAAAGAAAAT480
TCGCTTTTCC AATTGCTTGTGAAAGTGGGTTTTCGTTTTGGCTTTTTCCACAATGAAATC540
CA 02273199 1999-06-O1
WO 98124475 PCT/US97/22104
- 118 -
ACCTTTGGGT TGAAATTCCC TGTCATTCCT AACAAAAAAA CGGAAATCGT TGATGGCTTG 600
AGCGCGACCA CTTTATGGCA ACGCTTGCCG GTAGCCTATT TCAATTATAT CTATAATTTT 660
TAG 663
S (2) INFORMATION FOR SEQ ID N0:12:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 base pairs
(B) TYPE: nucleic acid
1~ (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
IS (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
2~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...351
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:12:
TTGAATCTCC ATTTTATGAA AGGATTTGTT ATGAGTGGATTAAGAACATT TAGTTGTGTA
60
GTGGTTTTAT GCGGTGCAAT GGTTAATGTA GCTGTAGCTGGTCCTAAAAT AGAGGCAAGG
120
3O GGTGAATTAG GCAAATTTGT AGGGGGAGCT GTTGGAAATTTTGTTGGTGA TAAAATGGGC
180
GGATTTGTTG GTGGTGCAAT AGGAGGATAT ATTGGGTCTGAAGTAGGCGA TAGGGTAGAA
240
GATTATATCC GTGGCGTTGA TAGAGAGCCA CAAAACAAAGAACCACAAAC CCCAAGAGAA
300
CCTATCCGTG ATTTTTATGA TTACGGCTAT AGTTTTGGGCATGCTTGGTG A 351
3S (2) INFORMATION FOR SEQ ID N0:13:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1311 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D} TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S (iii) HYFJTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
SD (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1311
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 119 -
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:13:
ATGTCAAGGGATTTTAAATTTGATTCTAACTATTTAAATGTCAATACCAATCCTAAATTA60
S GGCCCCGTTTATACCAATCAAAATTATCCAGGATTTTTTATCTTTGATCATTTAAGGCGT120
TATGTGATGAACGCTTTTGAGCCTAATTTGAACTTAGTTGTCAATACCAATAAAGTTAAG180
CAAACTTTTAATGTGGGCATGCGTTTTATGACAATGGATATGTTCATTAGATCCGATCAA240
AGCACATGCGAAAAAACAGATATTATCAATGGGGTGTGCCACATGCCTCCTTATGTCCTT300
TCTAAAACGCCTAACAATAATCAAGAAATGTTTAATAACTATACAGCGGTATGGTTGAGC360
lO GATAAAATAGAGTTTTTTGATTCTAAATTGGTGATAACTCCAGGGCTTAGATACACTTTT420
TTGAACTATAACAACAAAGAGCCAGAAAAGCATGATTTTTCCGTATGGACCAGTAAAAAA480
CAGCGTCAAAACGAATGGAGTCCTGCCCTTAATATTGGCTATAAACCTATGGAAAATTGG540
ATATGGTATGCGAACTACCGCCGCAGTTTTATCCCCCCACAACACACAATGGTAGGCATT600
ACTAGGACTAATTACAACCAAATTTTTAATGAAATTGAAGTGGGGCAGCGCTATAGTTAT660
IS AAAAATCTATTGAGTTTTAACACCAATTATTTTGTGATTTTTGCCAAGCGTTACTATGCG720
GGAGGCTATAGCCCACAGCCTGTGGATGCCAGAAGTCAAGGGGTGGAATTGGAATTGTAT780
TACGCGCCGATTAGGGGTTTGCAATTCCATGTGGCTTACACTTATATTGATGCGCGCATC840
ACTTCTAACGCTGATGATATTGCTTATTATTTTACAGGCATTGTCAATAAACCCTTTGAC900
ATTAAAGGGAAGCGCTTGCCCTATGTGAGTCCTAACCAATTCATATTTGACATGATGTAT960
ZO ACTTACAAGCACACGACTTTTGGTATCAGCAGCTATTTTTATAGCCGCGCTTATAGTTCC1020
ATGCTCAATCAAGCCAAAGATCAAACCGTATGCCTGCCCTTAAACCCAGAATACACAGGG1080
GGGTTAAAGTATGGTTGTAATTCAGTGGGGTTATTGCCCTTGTATTTTGTGTTGAATGTC1140
CAAGTAAGCTCAATCTTATGGCAAAGCGGTAGGCATAAAATCACAGGGAGTTTGCAAATC1200
AATAACCTTTTTAACATGAAGTATTATTTTAGGGGGATTGGCACAAGCCCTACAGGGAGA1260
ZS GAACCCGCGCCAGGGAGATCCATTACAGCGTATTTGAATTATGAGTTTTAA 1311
(2) INFORMATION FOR SEQ ID N0:14:
(i) SEQUENCE CHARACTERISTICS:
30 (A) LENGTH: 2304 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:-
4S (A) NAME/KEY: misc_feature
(B) LOCATION 1...2304
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:14:
SO ATGAAAAGAATTTTAGTTTC TTTGGCTGTTTTGAGTCATAGCGCGCATGCTGTCAAAACT60
CATAATTTGG AAAGGGTGGA AGCTTCAGGGGTGGCTAACGATAAAGAAGCGCCTTTAAGC120
TGGAGGAGCA AGGAAGTTAG AAATTATATGGGTTCTCGCACGGTGATTTCTAACAAGCAA180
CTCACTAAAA GCGCCAATCA AAGCATTGAAGAAGCTTTGCAAAATGTGCCAGGCGTGCAT240
ATTAGAAACT CTACCGGTAT TGGAGCTGTGCCTAGCATTTCCATTAGGGGGTTTGGTGCT300
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 120 -
GGAGGCCCAGGGCATTCTAATACGGGAATGATTCTAGTCAATGGGATTCCTATTTATGTC360
GCGCCCTATGTTGAAATTGGCACGGTTATTTTTCCTGTAACCTTTCAGTCTGTGGATAGA420
ATCAGCGTAACTAAGGGTGGGGAGAGCGTGCGTTATGGCCCTAACGCTTTTGGCGGTGTG480
ATCAACATCATCACCAAAGGCATTCCTACCAATTGGGAAAGTCAGGTGAGCGAGAGGACC540
S ACTTTTTGGGGCAAGTCTGAAAACGGGGGCTTTTTCAATCAAAATTCTAAAAACATTGAT600
AAAAGCTTAGTTAATAACATGCTTTTTAACACCTATTTAAGAACGGGGGGTATGATGAAT660
AAGCATTTTGGAATCCAAGCTCAAGTCAATTGGCTCAAAGGGCAAGGGTTTAGATACAAC720
AGCCCTACGGATATTCAAAATTACATGTTAGATTCATTGTATCAAATCAATGATAGCAAT780
AAAATCACCGCTTTTTTTCAATATTATAGTTATTTCTTGACAGACCCTGGATCTTTAGGC840
lO ATAGCCGCTTACAATCAAAATCGTTTTCAAAACAACCGCCCCAATAACGATAAAAGCGGG900
AGAGCGAAGCGATGGGGAGCTGTGTATCAAAACTTTTTTGGGGACACGGATAGGGTAGGG960
GGGGATTTCACTTTTAGCTACTATGGGCATGACATGTCAAGGGATTTTAAATTTGATTCT1020
AACTATTTAAATGTCAATACCAATCCTAAATTAGGCCCCGTTTATACCAATCAAAATTAT1080
CCAGGATTTTTTATCTTTGATCATTTAAGGCGTTATGTGATGAACGCTTTTGAGCCTAAT1140
IS TTGAACTTAGTTGTCAATACCAATAAAGTTAAGCAAACTTTTAATGTGGGCATGCGTTTT1200
ATGACAATGGATATGTTCATTAGATCCGATCAAAGCACATGCGAAAAAACAGATATTATC1260
AATGGGGTGTGCCACATGCCTCCTTATGTCCTTTCTAAAACGCCTAACAATAATCAAGAA1320
ATGTTTAATAACTATACAGCGGTATGGTTGAGCGATAAAATAGAGTTTTTTGATTCTAAA1380
TTGGTGATAACTCCAGGGCTTAGATACACTTTTTTGAACTATAACAACAAAGAGCCAGAA1440
2O AAGCATGATTTTTCCGTATGGACCAGTAAAAAACAGCGTCAAAACGAATGGAGTCCTGCC1500
CTTAATATTGGCTATAAACCTATGGAAAATTGGATATGGTATGCGAACTACCGCCGCAGT1560
TTTATCCCCCCACAACACACAATGGTAGGCATTACTAGGACTAATTACAACCAAATTTTT1620
AATGAAATTGAAGTGGGGCAGCGCTATAGTTATAAAAATCTATTGAGTTTTAACACCAAT1680
TATTTTGTGATTTTTGCCAAGCGTTACTATGCGGGAGGCTATAGCCCACAGCCTGTGGAT1740
2S GCCAGAAGTCAAGGGGTGGAATTGGAATTGTATTACGCGCCGATTAGGGGTTTGCAATTC1800
CATGTGGCTTACACTTATATTGATGCGCGCATCACTTCTAACGCTGATGATATTGCTTAT1860
TATTTTACAGGCATTGTCAATAAACCCTTTGACATTAAAGGGAAGCGCTTGCCCTATGTG1920
AGTCCTAACCAATTCATATTTGACATGATGTATACTTACAAGCACACGACTTTTGGTATC1980
AGCAGCTATTTTTATAGCCGCGCTTATAGTTCCATGCTCAATCAAGCCAAAGATCAAACC2040
3O GTATGCCTGCCCTTAAACCCAGAATACACAGGGGGGTTAAAGTATGGTTGTAATTCAGTG2100
GGGTTATTGCCCTTGTATTTTGTGTTGAATGTCCAAGTAAGCTCAATCTTATGGCAAAGC2160
GGTAGGCATAAAATCACAGGGAGTTTGCAAATCAATAACCTTTTTAACATGAAGTATTAT2220
TTTAGGGGGATTGGCACAAGCCCTACAGGGAGAGAACCCGCGCCAGGGAGATCCATTACA2280
GCGTATTTGAATTATGAGTTTTAA 2304
3S
(2) INFORMATION FOR SEQ ID N0:15:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 348 base pairs
40 (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
SO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc feature
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/LTS97/22104
-121-
(B) LOCATION 1...348
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:15:
S TTGCACCCTC TATGCGCACA CGGCCAATGT GGAAGCGAAG CGATTGCGTG TTTAGAAGCC 60
ATTAGCGTGG GGATTGTGCC TGTTATCGCTAATAGCCCTTTAAGCGCGACCAGGCAATTC 120
GCGCTAGATG AACGATCGTT ATTTGAGCCTAATAACGCTAAAGATTTGAGCGCTAAAATA 180
GACTGGTGGT TAGAAAACAA ACTTGAAAGAGAAAGAATGCAAAACGAATACGCTAAAAGC 240
GCTTTAAACT ACACTTTAGA AAATTCAGTCATTCAAATTGAAAAAGTTTATGAAGAAGCG 300
lO ATCAAAGATTTTAAAAACAA CCCCAACCTCTTTAAAACCTTATCGTAA 348
(2) INFORMATION FOR SEQ ID N0:16:
(i) SEQUENCE CHARACTERISTICS:
1S (A) LENGTH: 1170 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
20 (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
2S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
30 (A) NAME/KEY: misc_feature
(B) LOCATION 1...1170
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:16:
3S ATGGTTATTG TTTTAGTCGTGGATAGCTTT AAAGACACCAGTAATGGCACTTCTATGACA60
GCGTTTCGTT TTTTTGAAGCGCTGAAAAAA AGAGGGCATGCGATGAGAGTGGTCGCCCCT120
CATGTGGATA ATTTAGGGAGTGAAGAAGAG GGGTATTACAACCTTAAAGAGCGCTATATC180
CCCCTAGTTA CAGAAATTTCACACAAGCAA CACATTCTTTTTGCCAAACCGGATGAAAAA240
ATTCTACGAA AGGCTTTTAAGGGAGCGGAT ATGATCCATACTTACTTGCCTTTTTTGCTA300
4O GAAAAAACAG CCGTAAAAATCGCGCGAGAA ATGCGAGTGCCTTATATTGGCTCTTTCCAT360
TTACAGCCAG AGCATATTTCTTATAACATG AAATTGGGGCAATTTTCTTGGCTAAATACC420
ATGCTTTTTT CATGGTTTAAATCTTCGCAT TACCGCTATATCCACCATATCCATTGCCCA480
TCAAAATTCA TTGTAGAAGAATTGGAAAAA TACAACTATGGAGGAAAAAAATACGCTATC540
TCTAACGGCT TTGATCCCATGTTTAAGTTT GAGCACCCGCAAAAAAGCCTTTTTGACACC600
4S ACGCCCTTTA AAATCGCTATGGTAGGC~GC TATTCTAATGAAAAAAATCAAAGCGTTCTC660
ATTAAAGCGG TTGCTTTAAGCCGA~A:AAA CAAGACATTGTATTATTACTCAAAGGCAAG720
GGGCCTGATG AGAAAAAAATCAAACTTCTA GCCCAAAAACTAGGCGTAAAAACGGAGTTT780
GGGTTTGTCA ATTCCCATGAATTGTTAGAG ATTTTAAAAACTTGCACCCTCTATGCGCAC840
ACGGCCAATG TGGAAAGCGAAGCGATTGCG TGTTTAGAAGCCATTAGCGTGGGGATTGTG900
SO CCTGTTATCG CTAATAGCCCTTTAAGCGCG ACCAGGCAATTCGCGCTAGATGAACGATCG960
TTATTTGAGC CTAATAACGCTAAAGATTTG AGCGCTAAAATAGACTGGTGGTTAGAAAAC1020
AAACTTGAAA GAGAAAGAATGCAAAACGAA TACGCTAAAAGCGCTTTAAACTACACTTTA1080
GAAAATTCAG TCATTCAAATTGAAAAAGTT TATGAAGAAGCGATCAAAGATTTTAAAAAC1140
AACCCCAACC TCTTTAAAACCTTATCGTAA 1170
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 122 -
(2) INFORMATION FOR SEQ ID N0:17:
(i) SEQUENCE CHARACTERISTICS:
S (A) LENGTH: 939 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
IO (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
1S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
2O (A) NAME/KEY: misc_feature
(B) LOCATION 1...939
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:17:
2S TTGGCTTCTT ACGGGTTTTT TTTAGGAGCG TTGTTTATTT TAGCGAGCGG GATCGTGTGC 60
TTACAGACTG CCGGTAATCCCTTTGTAACCTTGCTTTCTA AGCCAGAAAC120
AAGGTAAAGA
TTGGTTTTAG TCCAGGCGTTCAATTCGCTTGGCACGACTTTAGGGCCTATTTTTGGGAGC180
TTGTTGATTT TTAGCGCGACCAAAACGAGCGATAATTTAAGCCTGATAGACAAGTTAGCG240
GACGCTAAAA GCGTTCAAATGCCTTATTTGGGTTTAGCGGTGTTTTCGCTTCTTTTAGCG300
3O CTTGTGATGT ATCTTTTAAAATTGCCTGATGTGGAAAAAGAAATGCCCAAAGAAACGACG360
CAAAAAAGCC TGTTTTCGCACAAACACTTTGTTTTTGGGGCTTTAGGGATCTTTTTCTAT420
GTGGGGGGAG AAGTGGCGATTGGATCATTCTTGGTGCTAAGCTTTGAAAAGCTTTTGAAT480
TTAGACGCTC AATCAAGCGCGCATTACTTGGTGTATTATTGGGGCGGCGCGATGGTAGGG540
CGTTTCTTAG GCAGCGCTTTGATGAATAAAATCGCTCCTAATAAATACCTGGCTTTCAAC600
3S GCCTTAAGCT CTATCATTCTTATCGCTTTGGCTATTCTTATTGGAGGCAAGATCGCTTTA660
TTCGCTCTGA CTTTTGTGGGCTTTTTCAACTCTATCATGTTCCCTACAATCTTTTCTTTG720
GCTACGCTCA ATTTAGGGCATCTCACTTCTAAGGCTTCTGGAGTGATTAGCATGGCGATT780
GTGGGAGGGG CGTTAATCCCCCCCATTCAAGGCGTGGTTACAGACATGCTCACAGCAACC840
GAATCGAATC TGCTCTACGCTTATAGCGTGCCGTTGTTGTGCTATTTTTATATCCTCTTC900
4O TTTGCACTTA AGGGGTATAAACAAGAAGAAAACTCCTAA 939
(2) INFORMATION FOR SEQ ID N0:18:
(i) SEQUENCE-CHARACTERISTICS:
4$ (A) LENGTH: 1224 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
$O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
_ _ ._._. _r_
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 123 -
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1224
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:18:
ATGCAAAAAA CTTCTAACACTTTAGCGCTGGGGAGTTTGACGGCGCTATTCTTTCTAATG60
GGTTTTATCA CGGTTTTAAACGACATTTTGATCCCGCATTTAAAGCCCATTTTTGACTTG120
ACCTATTTTG AAGCTTCGCTCATTCAATTTTGCTTTTTTGGGGCGTATTTCATCATGGGG180
GGAGTCTTTG GGAACGTGATCAGTAAAATCGGCTACCCTTTTGGCGTGGTGCTTGGTTTT240
IS GTGATCACAG CGAGCGGGTGCGCGTTGTTTTATCCGGCGGCGCATTTTGGCTCTTACGGG300
TTTTTTTTAG GAGCGTTGTTTATTTTAGCGAGCGGGATCGTGTGCTTACAGACTGCCGGT360
AATCCCTTTG TAACCTTGCTTTCTAAAGGTAAAGAAGCCAGAAACTTGGTTTTAGTCCAG420
GCGTTCAATT CGCTTGGCACGACTTTAGGGCCTATTTTTGGGAGCTTGTTGATTTTTAGC480
GCGACCAAAA CGAGCGATAATTTAAGCCTGATAGACAAGTTAGCGGACGCTAAAAGCGTT540
2O CAAATGCCTT ATTTGGGTTTAGCGGTGTTTTCGCTTCTTTTAGCGCTTGTGATGTATCTT600
TTAAAATTGC CTGATGTGGAAAAAGAAATGCCCAAAGAAACGACGCAAAAAAGCCTGTTT660
TCGCACAAAC ACTTTGTTTTTGGGGCTTTAGGGATCTTTTTCTATGTGGGGGGAGAAGTG720
GCGATTGGAT CATTCTTGGTGCTAAGCTTTGA~AAGCTTTTGAATTTAGACGCTCAATCA780
AGCGCGCATT ACTTGGTGTATTATTGGGGCGGCGCGATGGTAGGGCGTTTCTTAGGCAGC840
2S GCTTTGATGA ATAAAATCGCTCCTAATAAATACCTGGCTTTCAACGCCTTAAGCTCTATC900
ATTCTTATCG CTTTGGCTATTCTTATTGGAGGCAAGATCGCTTTATTCGCTCTGACTTTT960
GTGGGCTTTT TCAACTCTATCATGTTCCCTACAATCTTTTCTTTGGCTACGCTCAATTTA1020
GGGCATCTCA CTTCTAAGGCTTCTGGAGTGATTAGCATGGCGATTGTGGGAGGGGCGTTA1080
ATCCCCCCCA TTCAAGGCGTGGTTACAGACATGCTCACAGCAACCGAATCGAATCTGCTC1140
3O TACGCTTATA GCGTGCCGTTGTTGTGCTATTTTTATATCCTCTTCTTTGCACTTAAGGGG1200
TATAAACAAG AAGAAAACTCCTAA
1224
(2) INFORMATION FOR SEQ ID N0:19:
3S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 378 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
40 -
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
4S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S0 (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...378
(xi) SEQU'ENCE DESCRIPTION: SEQ ID N0:19:
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 124 -
ATGAATAAAA TCGCTCCTAATAAATACCTGGCTTTCGGCGCCTTAAGCTCTATCATTCTT60
ATCGCTTTGG CTATTCTTATTGGAGGCAAGATCGCTTTATTCGCTCTGACTTTTGTGGGC120
TTTTTCAACT CTATCATGTTCCCTACAATCTTTTCTTTGGCTACGCTCAATTTAGGCATC180
S TCACTTCTAA TGGCTTCTGGAGTGATTAGCATGGCGATTGTGGGAGGGGCGTTAATCCCC240
CCCATTCAAG GCGTGGTTACAGACATGCTCACAGCAACCGAATCGAATCTGCTCTACGCT300
TATAGCGTGC CGTTGTTGTGCTATTTTTATATCCTCTTCTTTGCACTTAA~GGGGTATAAA360
CAAGAAGAAA ACTCCTAA 378
lO (2) INFORMATION FOR SEQ ID N0:20:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 993 base pairs
(B) TYPE: nucleic acid
1S (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2O (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
2S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE: -
(A) NAME/KEY: misc_feature
(B) LOCATION 1...993
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:20:
TTGAAAAAAA TATTACCGGCTTTGTTAATGGGGTTTGTGGGATTGAATGCTAGTGATCGT60
TTGTTAGAAA TCATGCGCCTTTATCAAAAACAAGGCTTGGAAGTGGTGGGTCAAAAATTG120
3S GATTCTTATT TAGCGGATAAGTCTTTTTGGGCAGAAGAGCTTCAAAACAAGGACACGGAT180
TTTGGCTATT ATCAAAACAAGCAGTTTTTATTTGTGGCGGATAAATCCAAGCCCAGTTTG240
GAGTTTTATG AAATAGAAAATAACATGCTTAAAAAAATCAACAGCTCTAAAGCCCTTGTA300
GGCTCTAAAA AGGGCGATAAAACTTTAGAGGGCGATTTGGCCACGCCTATTGGAGTGTAT360
CGTATCACGC AGAAATTAGAGCGTTTGGATCAATATTATGGCGTTTTGGCTTTTGTAACG420
4O AATTACCCTA ATTTGTATGACACTTTGAAAAAACGCACCGGGCATGGCATTTGGGTGCAT480
GGAATGCCTT TAAATGGCGATAGGAATGAATTGAACACTAAGGGTTGCATTGCGATTGAA540
AACCCTATTC TAAGCTCTTATGACAAAGTGTTAAAAGGCGAAAAAGCGTTCCTTATCACT600
TATGAAGACA AGTTTTCCCCTAGCACTAAAGAAGAATTGAGCATGATTTTAAGCTCCCTT660
TTCCAATGGA AAGAAGCTTGGGCTAGGGGCGATTTTGAACGCTACATGCGTTTTTATAAC720
4S CCCAATTTCA CTCGCTATGACGGCATGAGTTTTAACGCTTTT~AAGAGTATAAAAAAAGG780
GTGTTTGCAA AAAATGAAAAAAAGAATATCGCTTTTTCCT~'.ATCAATGTGATCCCTTAC840
CCCAACTCTC AAAACAAACGCTTGTTTTATGTGGTATTTGACCAAGATTACAAAGCCTAC900
CAGCAAAACA AGCTCTCTTATAGCTCCAATTCTCAAAAAGAACTCTATGTAGAGATTGAA960
AACAATCAAG CGTCTATTATAATGGAAAAATAA 993
SO
(2) INFORMATION FOR SEQ ID N0:21:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 510 base pairs
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 12S -
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
1~
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
1S (A) NAME/KEY: misc_feature
(B) LOCATION 1...510
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:21:
2O TTGTTTGAGA AATGGATTGG TCTGACCTTA CTCCTTAGTTCCTTAGGCTA TCCATGCCAA60
AAGGTAAGTA TTAGTTTCAA GCAATACGAA AATCTTATCCATATCCATCA AAAAGGTTGC120
AACAATGAAG TGGTGTGCAG AACGCTCATC TCTATCGCTZTACTAGAAAG CTCTCTAGGG180
TTGAACAACA AGCGAGAAAA ATCCCTTAAA GACACTTCTTACTCCATGTT CCATATCACC240
TTAAACACCG CTAAAAAGTT CTACCCTACC TATTCTAAAACGCTCCTCAA AACCAAATTG300
2S TTAAATGATG TGGGTTTTGC GATCCAATTA GCCAAACAAATTTTAAAAGA AAATTTTGAT360
TATTACCACC AAAAACACCC CAACAAAAGC GTGTATCAATTAGTACAAAT GGCCATAGGC420
GCTTACAATG GGGGAATGAA ACACAACCCT AATGGCGCTTACATGAAGAA GTTTCGTTGC480
ATTTATTCTC AAGTGCGATA CAACGAATAA 510
3O (2) INFORMATION FOR SEQ ID N0:22:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 648 base pairs
(B) TYPE: nucleic acid
3S (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
4S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...648
SU
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:22:
ATGAAAAAAC CCTACAGAAA GATTTCTGAT TATGCGATCG TGGGTGGTTT GAGCGCGTTA 60
GTGATGGTAA GCATTGTGGG GTGTAAGAGC AATGCCGATG ACAAACCAAA AGAGCAAAGC 120
CA 02273199 1999-06-O1
WO 98/24475 PCTIUS97/22104
- 126 -
TCTTTAAGTC AAAGCGTTCA TTTGTGATTTTAGAAGAGCA 180
AAAAGGCGCG AAAGGATAAA
TCTTACAAGG TTGTTGAAGAATACCCCAGCTCAAGAACCCACATTGTAGTGCGCGATTTG240
CAAGGCAATG AACGCGTGTTGAGCAATGAAGAGATTCAAAAGCTCATCAAAGAAGAAGAA300
GCCAAAATTG ATAACGGCACGAGCAAGCTTGTCCAGCCTAATAATGGAGGGAGTAATGAA360
S GGATCAGGCT TTGGCTTGGGAAGCGCGATTTTAGGGAGCGCGGCGGGGGCGATTTTAGGG420
AGTTATATTG GCAATAAGCTTTTTAATAACCCTAATTATCAGCAAAACGCCCAACGGACC480
TACAAATCCC CACAAGCTTACCAACGCTCTCAAAATTCTTTTTCTAAAAGCGCACCCAGC540
GCTTCAAGCA TGGGCACAGCGAGTAAGGGACAGAGCGGGTTTTTTGGCTCTAGTAGGCCT600
ACTAGTTCGC CTGCAATAAGCTCTGGGACAAGGGGCTTTAACGCATAA 648
(2) INFORMATION FOR SEQ ID N0:23:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs
1S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
{ii) MOLECULE TYPE: DNA (genomic)
(iii} HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
2S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...762
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:23:
TTGAAAACTC TATTTAGTGT TTATCTCTTTTTGTCGTTGA ATCCACTCTT TTTAGAAGCT60
3S AAAGAAATCA CTTGGTCTCA ATTCTTGGAAAATTTTAAAA ACAAGAATGA AGACGACAAA120
CCTAAACCCC TAACCATTGA CAAAAACAATGAAAAACAGC AAATCCTAGA CAAAAACCAG180
CAAATCTTAA AAAGGGCTTT AGAAAAAAGCCTTAAATTTT TCTTTATTTT TGGATACAAC240
TATTCGCAAG CCGCTTATTC AACCACTAATCAAAACTTGA CTCTTACGGC GAATAGCATA300
GGGTTTAACA CCGCTACAGG CTTGGAGCATTTTTTAAGAA ACCACCCTAA AGTCGGTTTT360
4O AGAATCTTTA GCGTCTATAA CTATTTCCATTCCGTTTCGC TCTCCCAGCC TCAAATCCTA420
ATGGTGCAAA ATTACGGAGG CGCGTTAGATTTTTCTTGGA TTTTTGTGGA TAAAAAAACC480-
TATCGCTTTA GGAGTTATTT AGGAATCGCTTTAGAGCAAG GGGTGTTGTT AGTGGATACG540
ATTAAAACCG GCTCTTTCAC AACCATCATCCCAAGAACCA AGAAAACCTT TTTTCAAGCC600
CCTTTGCGTT TTGGTTTTAT CGTGGATTTTATCGGCTATT TGTCTTTGCA ATTAGGGATT660
4S GAAATGCCCT TAGTGAGGAA TGTTTTTTACACCTACAATA ACCATCAAGA AAGATTCAAA720
CCACGATTTA ACGCTAA~~." TTCTTTAATCGTTTCGTTTT AG 762
(2) INFORMATION FOR SEQ ID N0:24:
SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1011 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
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S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
1~
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1011
IS (xi) SEQUENCE DESCRIPTION: SEQ ID N0:24:
TTGTTTTTCA ATGTTTATCATTAGGAATATTTGCATGGGCAAAAGAGGTC60
AATTTATTTT
ATTCCCACCCCTTCAACCCCATTAACGCCCTCTAAACGCTATTCTATCAATTTGATGACT120
GAAAATGATGGTTATATCAATCCTTACATTGATGAGTATTACACGGCAGGCAATCAAATA180
2O GGCTTTTCTACTAAAGAGTTTGATTTTTCTAAAAATAAAGCGATGAAATGGTCTTCGTAT240
TTAGGGTTTTTCAATAAAAGCCCTAGGGTTACTCGTTTTGGCATTTCTCTCGCCCAAGAC300
ATGTATACCCCCTCACTTGCAAACAGAAhACTGGTGCATTTGCATGACAACCACCCTTAT360
GGGGGGTATTTGAGGGTGAATTTGAACGTGTATAACCGCCATCAAACTTTCATGGAGTTA420
TTCACGATTTCTTTAGGCACGACAGGGCAAGATTCTTTGGCCGCTCAAACGCAGCGTCTC480
2S ATTCATAAATGGGGTCATGATCCCCAATTTTATGGCTGGAACACGCAGCTCAAAAACGAA540
TTTATCTTTGAACTGCACTACCAATTGCTTAAAAAAGTCCCCCTTTTAAAGACTCGTTTT600
TTTTCTATGGAGTTGATGCCTGGGTTTAATGTGGAACTGGGTAATGCGAGGGATTATTTC660
CAACTCGGCTCGCTCTTTAGGGCTGGGTATAACTTGGACG-CTGATTATGGGGTCAATAAG720
GTCAATACCGCTTTTGATGGGGGCATGCCTTATAGCGATAAGTTTTCCATCTATTTTTTT780
3O GCAGGGGCTTTTGGGCGCTTCCAACCCCTTAACATCTTCATTCAAGGCAATAGCCCTGAA840
ACTAGGGGCATTGCCAATTTGGAATACTTTGTTTATGCCAGTGAAATAGGAGCGGCTATG900
ATGTGGCGTAGCCTCAGGGTGGCTTTTACAATCACTGATATTAGTAAAACCTTTCAGTCC960
CAGCCTAAGCACCATCAGATCGGCACCTTAGAATTGAATTTCGCCTTTTGA 1011
3S (2) INFORMATION FOR SEQ ID N0:25:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 327 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
-- 45 (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
S~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...327
CA 02273199 1999-06-O1
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- 128 -
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:25:
ATGAAACCAA TCTTTAGCCT CTTTTTCCTC CTTATTGTTT TAAAAGCGCA CCCCATAAAC 60
S CCCTTATTAG AGCCGTTATA TTTCCCCAGT TACACGCAAT TTTTAGATTT AGAACCTCAT 120
TTTGTCATTA AAAAAAAGCG CGCTTACAGG CCTTTTCAAT GGGGGAACAC TATTATTATC 180
AAACGCCATG ATTTAGAAGA GCGCCAGAGC AACCAACCAA GCGATATTTT CCGCCAGAAC 240
GCTGAAATCA ATGTGTCTTC TCAAACTTTT TTAAGAGGAA TCAGCAGCGC TTCTTCACGC 300
ATAGTGATCG ATTCGGTCGC TCAGTAA 327
(2) INFORMATION FOR SEQ ID N0:26:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 588 base pairs
1S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
2S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...588
(xi} SEQUENCE DESCRIPTION: SEQ ID N0:26:
ATGAGCAATA ACCCCTTTAA AAAAGTGGGC ATGATCAGCT CTCAAAACAA TAACGGCGCT 60
3S TTGAACGGGCTTGGCGTGCAAGTGGGTTATAAACAATTCTTTGGCGAAAGCAAAAGATGG120
GGGTTAAGGT ATTATGGTTTCTTTGATTACAACCACGGCTATATCAAATCCAGCTTTTTT180
AATTCTTCTT CTGATATATGGACTTATGGCGGTGGGAGCGATTTGTTAGTGAATTTTATC240
AACGATAGCA TCACAAGAAAGAACAACAAGCTTTCTGTGGGTCTTTTTGGTGGTATCCAA300
CTAGCAGGGA CTACATGGCTTAATTCTCAATACATGAATTTAACAGCGTTCAATAACCCT360
4O TACAGCGCGAAAGTCAATGCTTCCAATTTCCAATTTTTGTTCAATCTCGGCTTGAGGACG420
AATCTCGCTA CAGCTAAGAAAAAAGACAGCGAACGTTCCGCGCAACATGGCGTTGAACTG480
GGCATTAAAA TCCCTACCATTAACACCAATTATTATTCTTTTCTAGGCACTAAGCTAGAA540
TACAGAAGGC TTTATAGCGTGTATCTCAATTATGTGTTTGCTTATTAA 5gg
- 4S (2) INFORMATION FOR SEQ ID N0:27:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 684 base pairs
(B) TYPE: nucleic acid
S0 (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
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(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...684
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:27:
GTGCGTTTTGGTAAAATTGATTATTTGAACATGCTCCCTTTTGATGTGTTTATCAAATCC60
IS TACCCCACCCCTTGTTATTTCAAACAATTCTTACGGCTTAAAAAAACCTACCCCTCCAAA120
CTCAATGAGAGTTTTTTATTCAGGCGCATTGATGCGGGGTTTATTTCTTCTATCGCTGGC180
TATCCATTCGCTCTTTGTTCTTATTCTCTAGGCATTGTCGCTTATAAGGAAGTTTTAAGC240
GTGTTGGTTGTAAATAGAGAAAACGCTTTTGACAAAGAAAGCGCTTCTTCAAACGCCCTC300
TCTAAAGTGTTAGGGTTAAAAGGCGAGGTCTTAATCGGCAATAAAGCGCTGCAATTTTAT360
2O TATTCCAACCCTAAAAAAGATTTTATAGATTTAGCCGCTCTGTGGTATGAAAAAAAACGC420
TTGCCGTTTGTTTTTGGGCGTCTGTGCTATTATCAAAACAAGGATTTTTACAAACGCTTG480
TCTTTAGCCTTCAAACATCAAAAAACAAAAATCCCTCACTACATCCTTAAAGAAGCCGCT540
TTGAAAACCAACTTGAAACGCCAAGATATTCTAAACTACTTGCAAAAAATTTACTACACT600
TTAGGCAAAAAGGAACAATCAGGCCTTAAAGCGTTCTATCGTGAATTGTTGTTCAAACGC660
2S ATCCAAAAACCCAAGCGGTTTTAG
684
(2) INFORMATION FOR SEQ ID N0:28:
(i) SEQUENCE CHARACTERISTICS:
30 (A) LENGTH: 918 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4S (A) NAME/KEY: misc_feature
(B) LOCATION 1...918
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:28:
SO ATGGGTAGAA TTGAATCAAA GAGTTTGGGG60
AAAGCGTTTG AAAGCACTCA
TTTTTTTAGC
GTGTTGTGGG GCAATGCGGC TGAAAAAACGCCTTTTTTTA AAACTAAAAACCACATTTAT120
TTGGGTTTTA GGCTAGGCAC AGGGGCTACTACGCGCACAA GCATGTGGCA~1ACAAGCCTAT180
AAAGACAACC CCACTTGCCC TAGCAGCGTGTGTTATGGCG AGAAATTAGAAGCCCATTAT240
AAGGGGGGTA AAAACTTATC TTATACCGGGCAAATAGGCG ATGAAATAGCTTTTGATAAA300
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TACCATATTT TAGGCTTAAGGGTGTGGGGGGATGTAGAATACGCTAAGGCTCAATTAGGT360
CAAAAAGTGG GGGGTAACACCCTTTTATCCCAAGCGAATTATAACCCAAGCGCGATTAAA420
ACCTACGATC CTACTTCAAACGCTCAAGGCTCTTTAGTTTTGCAAAAAACCCCAAGCCCC480
CAAGATTTCC TTTTCAATAACGGGCATTTCATGGCGTTTGGTTTGAACGTGAACATGTTT540
S GTCAATCTCC CTATAGACACCCTTTTAAAACTCGCTTTAAAAACGGAAAAAATGCTGTTT600
TTTAAAATAG GCGTGTTTGGTGGGGGTGGGGTGGAATACGCAATCTTGTGGAGTCCTCAA660
TATAAAAATC AAAATACCCATCAAGACGATAAATTTTTTGCCGCAGGTGGGGGGTTTTTT720
GTGAATTTTG GAGGCTCTTTGTATATAGGCAAGCGCAACCGCTTCAATGTGGGGCTAAAA780
ATCCCTTATT ATAGCTTGAGCGCGCAAAGTTGGAAAAATTTTGGCTCTAGCAATGTGTGG840
lO CAGCAACAAACGATCCGACAAAACTTCAGCGTTTTTAGGAATAAAGAAGTTTTTGTCAGC900
TACGCGTTCT TGTTTTAG 918
(2) INFORMATION FOR SEQ ID N0:29:
1S (i) SEQUENCE CHARACTERISTICS: - -
(A) LENGTH: 777 base pairs
(8) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
2S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...777
3S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:29:
ATGTTTTTAA GATCATACCCAAAGCTTAGATACGCTTTATGTTTACCCCTACTCACTGAG60
ACTTGCTATA GCGAGGAGCGCACTTTAAATAAGGTTACCACCCAAGCTAAAAGGATTTTC120
ACTTACAATA ATGAGTTTAAGGTTACTTCTAAAGAATTGGATCAACGCCAAAGCAATGAA180
GTCAAAGACC TGTTTAGGACTAACCCTGATGTGAATGTGGGCGGAGGGAGCGTGATGGGG240
CAGAAAATCT ACGTGAGAGGCATTGAAGACAGGCTTTTAAGGGTTACGGTGGATGGGGCT300
GCGCAAAATG GCAACATCTACCACCACCAAGGCAACACCGTGATTGACCCTGGCATGCTC360
AAAAGCGTGG AAGTTACTAAAGGCGCGGCGAATGCGAGCGCGGGGCCAGGAGCGATCGCG420
GGAGTGATTA AAATGGAGACTAAAGGAGCGGCTGATTTTATCCCTAGGGGGAAAAATTAT480
GCAGCGAGTG GGGCGGTGAGTTTTTATACCAATTTTGGGGACAGAGAGACTTTTAGATCG540
4S GCCTATCAAA GC~~CGCATTTTGATATTATCGCTTACTACACGCACCAAAATATTTTCTAT600
TATAGGAGCG ~C3CCACAGTGATGAAAAACCTTTTCAAACCCACACAAGCCGATAAAGAG660
CCAGGAACTC CCAGCGAGCAAAACAACGCTTTGATTAAAATGAATGGCTATTTGAGCGAC720
AGAGACACGC TCACTTTCAGCTGGAACATGACACGAGATAACGCCACACGCCTTTAA 777
SO (2) INFORMATION FOR SEQ ID N0:30:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 579 base pairs
(B) TYPE: nucleic acid
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(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
lO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
15 (B) LOCATION 1...579
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:30:
ATGTTTTTAA GATCATACCCAAAGCTTAGATACGCTTTATGTTTACCCCTACTCACTGAG60
ZO ACTTGCTATAGCGAGGAGCGCACTTTAAATAAGGTTACCACCCAAGCTAAAAGGATTTTC120
ACTTACAATA ATGAGTTTAAGGTTACTTCTAAAGAATTGGATCAACGCCAAAGCAATGAA180
GTCAAAGACC 'IGTTTAGGACTAACCCTGATGTGAATGTGGGCGGAGGGAGCGTGATGGGG24G
CAGAAAATCT ACGTGAGAGGCATTGAAGACAGGCTTTTAAGGGTTACGGTGGATGGGGCT300
GCGCAAAATG GCAACATTTACCACCACCAAGGCAACACCGTGATTGACCCTGGCATGCTC360
ZS AAAAGCGTGGAAGTTACTAAAGGCGCGGCGAATGCGAGCGCGGGGCCAGGAGCGATCGCG420
GGAGTGATTA AAATGGAGACTAAAGGAGCGGCTGATTTTATCCCTAGGGGGAAAAATTAT480
GCAGCGAGTG GGGCGGTGAGTTTTTATACCAATTTTGGGGACAGAGAGACTTTTAGATCG540
GCCTATCAAA GCGCGCATTTTGATATTATCGCTTACTAG 579
3O (2) INFORMATION FOR SEQ ID N0:31:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 381 base pairs
(B) TYPE: nucleic acid
35 (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4O (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAIs SOURCE:
4$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...381
SO
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:31:
GTGCCCTTGA GTTTGGGAGG CAACCTCTTA AACCCTAACA ACAGTAGCGT GCTGAATTTA 60
AAAAACAGCC AGCTTGTTTT TAGCGATCAA GGGAGCTTGA ATATCGCTAA CATTGATTTA I20
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CTAAGCGATC TGAATGGTAATAAAAATCGTGTGTATAACATCATTCAAGC GGACATGAAT180
GGTAATTGGT ATGAGCGTATCAACTTCTTTGGCATGCGCATTAATGATGG GATTTATGAC240
GCTAAAAACC AAACTTATAGTTTCACTAACCCTCTCAATAACGCCGTAAA ATTCACCGAG300
AGCTTTTTCA TACACCGCCTGTGCGGTTCGCTCTCTCAAATACAAAAAAA AAAAAACACA360
S ATAGTCTCACCTCGGCTCTGA 381
(2) INFORMATION FOR SEQ ID N0:32:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1698 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
1S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
2S (A) NAME/KEY: misc_feature
(B) LOCATION 1...1698
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:32:
3O GTGTATTCTTATAGCGATGACGCACAAGGC GTGTTTTATCTCACGAGCAGCGTGAAAGGC60
TATTACAACCCCAACCAATCCTATCAAGCC AGCGGCAGCAATAACACCACGAAAAATAAC120
AATCTAACCTCTGAATCTTCTGTCATTTCG CAAACCTATAACGCGCAAGGCAACCCTATC180
AGCGCGTTACACGTCTATAACAAGGGCTAT AATTTCAGTAATATCAAAGCGTTAGGGCAA240
ATGGCGCTCAAACTCTACCCTGAAATCAAA AAGATATTAGGGAATGATTTTTCGCTTTCA300
3S AGTTTGAGCAATTTAAAAGGCGATGCGCTA AACCAGCTTACCAAGCTCATCACGCCTAGC360
GATTGGAAAAACATTAACGAGTTGATTGAT AACGCAAACAATTCGGTCGTGCAAAATTTC420
AATAACGGCACTTTGATTATAGGAGCGACT AAAATAGGGCAAACAGACACCAATAGTGCG480
GTGGTTTTTGGGGGCTTGGGCTATCAAAAG CCTTGCGATTACACTGATATTGTGTGCCAA540
AAATTTAGAGGCACTTATTTGGGGCAGCTT TTGGAGTCCAACTCCGCTGATTTGGGCTAT600
4O ATTGACACGACTTTTAACGCTAAAGAAATT TATCTTACCGGCACTTTAGGGAGCGGGAAC660
GCATGGGGGACTGGGGGGAGTGCGAGCGTA ACTTTTAACAGCCAAACTTCG~TCATTCTC720
AACCAAGCGAATATCGTAAGCTCGCAAACC GATGGGATTTTTAGCATGCTGGGTCAAGAG780
GGCATCAATAAGGTTTTCAATCAAGCCGGG CTCGCTAATATTTTGGGCGAAGTGGCAATG840
CAATCCATTAACAAAGCCGGGGGATTAGGG AATTTGATAGTAAATACGCTAGGGAGTGAT900
4S AGCGTGATTGGGGGGTATTTAACGCCTGAG CAAAAAAATCAAACCCTAAG~CAGCTTTTG960
GGGCAGAATAATTTTGATAACCTCATGAAC GATAGCGGTTTGAACACG..~GATTAAGGAT1020
TTGATCAGACAAAAATTAGGCTTTTGGACC GGGCTAGTGGGGGGATTAGCCGGACTGGGG1080
GGCATTGATTTGCAAAACCCTGAAAAGCTT ATAGGCAGCATGTCCATCAATGATTTATTG1140
AGTAAAAAGGGGTTGTTCAATCAGATCACC GGCTTTATTTCCGCTAACGATATAGGGCAA1200
SO GTCATAAGCGTGATGCTGCAAGATATTGTC AAGCCGAGCGACGCTTTAAAAAACGATGTA1260
GCCGCTTTGGGCAAGCAAATGATTGGCGAA TTTTTAGGCCAAGACACGCTCAATTCTTTA1320
GAAAGCTTGCTGCAAAACCAGCAGATTAAA AGCGTTTTAGACAAAGTCTTAGCGGCTAAA1380
GGATTAGGGTCTATTTATGAACAAGGTTTG GGGGATTTGATCCCTAATCTTGGTAAAAAG1440
GGGATTTTCGCTCCCTATGGCTTGAGTCAA GTGTGGCAAAAAGGGGATTTTAGTTTCAAC1500
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-133-
S
GCGCAAGGCA ATGTTTTTGT GCAAAATTQC ACTTTCTCTA ACGCTAATGG AGGCACGCTC 1560
AGTTTTAACG CAGGAAATTC GCTCATTTTT GCCGGAAACA ACCACATCGC TTTCACTAAC 1620
CATTCTGGAA CGCTCAATTT GTTGTCTAAT CAAGTTTCTA ACATTAACGT CACCATGCTT 1680
AACGCAGCAA CGGCCTAA 1698
(2) INFORMATION FOR SEQ ID N0:33:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 519 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
1S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
ZO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
ZS (B) LOCATION 1...519
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:33:
GTGTTTGGAT TGAGTTTGGC GGATATGATT TTAGAGCGTT TTAAAGATTT TATGAGAGAA 60
3O TACCCTGAGC CTTACAAGTT TTTACAGGTT TTTTACGCGC AAGAAAAAGA ACGCTTCTTA 120
AATCATAAAA TGAACGATTATATCAAGCAA AGGAAGAGGCTAGTATTTTG190
AATAAGAGCA
GCCAGACAAG GCTTTGTCAGCGTAATTGGAAGAGCGTTAGAAAAAATCATAGAACTTTTA240
TTAAAAGATT TTTGTATTAAAAACAATGTAAAAATGACGAACGATAAAACCTTAAGGGCT300
AAGCGCATTA ATGGCGAATTAGATAAGGTCAAACGGGCTTTATTGGTGCATTTTGGAGGA360
3S TATAGCGTTTTACCCGATATTATTCTTTATCAAACCAACAAAGATAATATCAAAATCCTA420
GCGATTTTAT CGGTAAAAAATTCGTTTAGAGAGCGTTTCACAAAAGACGCCTTATTGGAA480
ATTAAAACTT TTGCAATCGCCTGTAACTTCTCACATTAA 519
(2) INFORMATION FOR SEQ ID N0:34:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 996 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
4S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
SO
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
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(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...996
S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:34:
ATGAAAAGAT TTGTTTTATTCTTGTTATTCATATGTGTTTGCGTTTGCGTTCAAGCTTAC60
GCTGAGCAAG ATTACTTTTTTAGGGATTTTAAATCTATAGATTTGCCCCAAAAACTCCAC120
lO CTTGATAAAA AGCTCTCCCAAACAATACAGCCATGCGCGCAACTTAACGCATCAAAACAC180
TACACTGCTA CTGGGGTTAGAGAGCCTGATGCCTGCACCAAGAGTTTTAAAAAATCCGCT240
ATGGTTTCCT ATGATTTAGCGCTAGGCTATTTAGTGAGCCAAAACAAACCATACGGCTTA300
AAAGCTATAG AGATTTTAAACGCTTGGGCTAATGAGCTTCAAAGCGTGGATACTTATCAA360
AGCGAGGACA ATATCAATTTTTACATGCCTTATATGAACATGGCTTATTGGTTTGTCAAA420
IS AAAGAATTTC CTAGCCCAGAATATGAAGATTTCATTAGGCGGATGCGTCAGTATTCTCAA480
TCAGCTCTTA ACACTAACCATGGGGCGTGGGGGATTCTCTTTGATGTGAGCTCTGCACTA540
GCGCTAGATG ATCATGCCCTTTTGCAAAGTAGCGCTAATCGGTGGCAGGAGTGGGTGTTT600
AAAGCCATAG ATGAGAACGGGGTTATTGCTAGCGCGATCACTAGGAGCGATACGAGCGAT660
TATCATGGCG GCCCTACAAAGGGCATTAAGGGGATAGCTTATACCAATTTTGCGCTTCTT720
2O GCGATAACTA TATCAGGCGAATTGCTTTTTGAGAACGGGTATGATTTGTGGGGTAGTGGA780
GCCGGGCAAA GGCTCTCTGT_GGCGTATAACAAAGCCGCAACATGGATTCTAAACCCTGAA840
ACTTTCCCCT ATTTTCAGCCTAACCTCATTGGGGTGCATAACAACGCCTATTiCATTATT900
TTAGCCAAAC ATTATTCTAGCCCTAGCGCGGATGAGCTTTTAGAGCAAGGCGATTTGCAT960
GAAGATGGCT TCAGGCTGAAACTCCGATCGCCATGA 996
2S
(2) INFORMATION FOR SEQ ID N0:35:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 384 base pairs
30 (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
4S (B) LOCATION 1...384
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:35:
ATGCGTCAGT ATTCTCAATC AGCTCTTAAC ACTAACCATG GGGCGTGGGG GATTCTCTTT 60
SO GATGTGAGCT CTGCACTAGCGCTAGATGATCATGCCCTTTTGCAAAGTAGCGCTAATCGG120
TGGCAGGAGT GGGTGTTTAAAGCCATAGATGAGAACGGGGTTATTGCTAGCGCGATCACT180
AGGAGCGATA CGAGCGATTATCATGGCGGCCCTACAAAGGGCATTAAGGGGATAGCTTAT240
ACCAATTTTG CGCTTCTTGCGATAACTATATCAGGCGAATTGCTTTTTGAGAACGGGTAT300
GATTTGTGGG GTAGTGGAGCCGGGCAAAGGCTCTCTGTGGCGTATAACAAAGCCGCAACA360
_.._w. ~._.._ ___._.._ ___~...~_.__..__ .. .
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-135-
TGGATTCTAA ACCCTGAAAC TTTC 384
(2) INFORMATION FOR SEQ ID N0:36:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 738 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
lO
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...738
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:36:
TTGAGAACCT TGTTAAAAATGTTGGTTGGTGTGAGCTTACTAACACACGCTTTAATGGCT 60
ACAGAAGAAA GCGCTGCCCCTTCTTGGACAAAAAATTTGTATATGGGATTCAATTACCAA 120
ACAGGTTCTA TCAATTTAATGACTAATATTCATGAAGTTAGAGAAGTTACTAGCTATCAA 180
ACCGGTTACA CCAATGTAATGACTAGCATTAATAGCGTTAAAAAACTCACTAACATGGGT 240
3O TCTAATGGGATTGGCTTAGTCATGGGCTATAACCACTTTTTCCATCCGGATAAAGTCTTG 300
GGTTTGCGCT ATTTTGCTTTTTTAGATTGGCAAGGCTATGGCATGAGATACCCTAAAGGC 360
TATTATGGGG GCAATAACATGATCACTTATGGCGTGGGCGTGGATGCGATATGGAATTTC 420
TTCCAAGGGA GTTTTTATCAAGATGATATTGGCGTGGATATTGGCGTTTTTGGGGGGATT 480
GCGATTGCTG GGAATAGCTGGTATATTGGCAATAAAGGGCAGGAATTATTAGGCATCACC 540
3S AATAGTAGTGCGGTTGATAACACCTCTTTTCAATTCCTCTTTAACTTTGGTTTCAAAGCT 600
TTATTTGTAG ATGAACATGAATTTGAAATTGGGTTTAAATTCCCCACTCTTAACAACAAA 660
TACTACACCA CCGACGCGCTCAAGGTTCAAATGCGTAGGGTCTTTGCCTTTTATGTGGGG 720
TATAATTACC ACTTCTAA 738
4O (2) INFORMATION FOR SEQ ID N0:37:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 873 base pairs
(B) TYPE: nucleic acid
4S (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
SO (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/US97/22104
- 136 -
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
S (B) LOCATION 1...873
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:37:
ATGTTTGAAGAAATTACCCTAGCGCATAAGGACTTGTTTTCAAGGTTTTTACAAACTCAA60
lO AAAATCGTTTTATCGGATGTGAGTTTTACCAATTGCTTTTTATGGCAGCACGCAAGGCTC120
ATTCAAGTGGCTGTGATTAGGGATTGTTTGGTGATTCAAACCACTTATGAAAACCAAAAA180
CCCTTTTATTTCTATCCTATCGGTAAGAGGCCGCATGAATGCGTGAAAGAGCTTTTGGAA240
TTAGAAAAAAATTTAAGATTCCACTCCCTGACTTTAGAGCAAAAAGACGATTTGAAAGAC300
AATTTTGTAGGGGTGTTTGATTTCACTTACAACCGAGACAGGAGCGATTATGTTTATTCT360
IS ATTGAAGAACTAATCGCGCTCAAAGGGAAAAAATACCATAAGAAAAAAAACCACTTAAAC420
CAGTTTTTAACCAATCATGCGAATTTTGTTTATGAAAAAATTTCTCCTCAAAACAGAAAG480
GAAGTTTTAGAAGCCTCTAAAGCGTGGTTTTTAGAAAGCCAGACCGATGATATAGGGTTA540
ATCAACGAAAATAAGGGCATTCAAAGCGTTTTAGAAAATTATGAAAGCTTGGATTTAAAG600
GGGGGGCTTATTAGGGTTAATGGGGAAATAGTCTCGTTTAGTTTTGGGGAAGTTTTAAAC660
ZO GAAGAGAGCGCGCTCATCCACATTGAAAAAGCCCGCACAGATATTGCAGGCGCGTATCAA720
ATCATCAACCAACAATTGCTTTTGAATGAATTTAGCCATTTAACTTACGCTAACAGAGAA780
GAAGATCTAGGATTAGAGGGCTTAAGAAGGTCTAAAATGAGCTATAACCCGGTGTTTTTG840
ATAGACAAATACGAAGCGGTTGCTAGAAATTAA 873
ZS (2) INFORMATION FOR SEQ ID N0:38:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 333 base pairs
(B) TYPE: nucleic acid
30 (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S (iii) HYPOTHETICAL: NO
~(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
40 (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...333
4S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:38:
ATGATGTTCA TTGTAGCGGTTTTGATGCTG GCGTTTTTGA TCTTTGTCCATGAGTTAGGG60
CATTTCATTA TCGCTAGGATTTGTGGGGTG AAAGTGGAAG TGTTTAGCATTGGTTTTGGT120
SO AP.AAAACTCTGGTTTTTCAAGCTTTTTGGC ACGCAATTCG CTCTGTCTTTGATCCCGCTT180
GGGGGCTATG TGAAATTAAAGGGCATGGAT AAAGAAGAAA ATGAAGAAAATAAAATTAAT240
CAAGCGAATG ATAGCTACGCCAAAAAAGCC CTTTCCAAAA GCTATGGATATTGTTTGGTG300
GGGCGTTTTT TAATTTTCTTTTTGCGGTTT TAG 333
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 137 -
(2) INFORMATION FOR SEQ ID N0:39:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1056 base pairs
$ (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
1~
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO _
(iv) ANTI-SENSE: NO
IS (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
20 (B) LOCATION 1...1056
(xi) SEQUENCE DESCRIPTION: SEQ ID 140:39:
ATGATGTTCA TTGTAGCGGTTTTGATGCTGGCGTTTTTGATCTTTGTCCATGAGTTAGGG60
ZS CATTTCATTA TCGCTAGGATTTGTGGGGTGAAAGTGGAAGTGTTTAGCATTGGTTTTGGT120
AAAAAACTCT GGTTTTTCAAGCTTTTTGGCACGCAATTCGCTCTGTCTTTGATCCCGCTT180
GGGGGCTATG TGAAATTAAAGGGCATGGATAAAGAAGAAAATGAAGAAAATAAAATTAAT240
CAAGCGAATG ATAGCTACGCGCAAAAAAGCCCTTTCCAAAAGCTATGGATATTGTTTGGT300
GGGGCGTTTT TTAATTTTCTTTTTGCGGTTTTAGTGTATTTTTTTCTGGCATTGAGCGGG360
3O GAAAAAGTCT TACTGCCCGTCATTGGCGGTTTAGAAAAAAACGCGCTAGAAGCCGGGCTG420
TTAAAGGGGG ATAGAATCCTTTCTATCAACCATCAAAAAATAGCGAGTTTTAGAGAGATT480
AGAGAGATAG TGGCGCGTTCTCAAGGCGAGTTAATTTTAGAAATAGAGCGAAACAATCAG540
ATTT'TAGAAAAACGACTGACCCCCAAAATCGTGGCGGTGATAAGCGAGTCTAATGATCCT600
AATGAAATCA TCAAGTATAAAATAATAGGCATTAAACCGGACATGCAAAAAATGGGCGTT660
3S GTCTCTTATT CCGTGTTTCAAGCGTTTGAAAAGGCTTTGAGTCGGTTTAAAGAGGGCGTT720
GTTTTGATTG TGGATTCTTTAAGGCGTTTGATTATGGGGAGCGCTTCAGTTAAAGAATTG780
AGTGGGGTAA TAGGCATTGTGGGGGCGTTAAGCCATGCCAATAGCGTGAGCATGCTTTTG840
TTGTTTGGGG CGTTTTTATCTATCAATCTAGGGATTTTAAATTTATTACCCATTCCAGCC900
TTAGATGGGG CGCAAATGCTAGGGGTCGTTTTTAAAAATATTTTTCATATCGCTTTGCCA960
4O ACGCCCATAC AAAATGCGTTGTGGCTAGTGGGGGTGGGGTTTTTGGTTTTTGTCATGTTT1020
TTAGGGCTT"TTTAATGACATTACTCGTTTGCTATAA 1056
(2) INFORMATION FOR SEQ ID N0:40:
4S (i) SEQUENCE CHARA~TERISTICS:
(A) LENGTH. ~03 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
SU
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
CA 02273199 1999-06-O1
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- 138 -
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...303
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:40:
ATGCAAAAGA ATTTGGATAG TCTTTTAGAA AATTTAAGGGCTGAAATTGA TGCGTTGGAT
60
AATGAATTGA GCGATCTTTT AGACAAACGC TTAGGAATCGCTTTAAAAAT CGCTCTCATC
I20
AAACAAGAAA GCCCCCAAGA AAACCCCATT TATTGCCCTAAAAGAGAGCA AGAGATTTTA
180
IS AAACGACTCA GCCAAAGGGG TTTCAAGCAT TTGAATGGAGAAATCCTTGC AAGTTTTTAT
240
GCAGAGGTTT TTAAGATTTC TAGAAATTTT CAAGAAAACGCCCTAAAAGA GTTAAAAAAA
300
T~ 303
(2) INFORMATION FOR SEQ ID N0:43:
20
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 525 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
2S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
30
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
35
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...525
4O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:41:
GTGAAAATGC GTTTTTTTAG TGGTTTTGGG TTTGTTAATGAAAGCGTTTT GTTTGAAGAG
60
TGGCTTTTAA AAGGGGCTTA TGATGTGTCA GGCTTTTCTATGGGGGCGAT TAAGGCGATA
120
GAATACGCCT ATAATGAAGT CTTGCAACAA CGGCGCATCCATTCCTTATT GTTGTTTTCG
180
4S CCTTGCATGC TAGCGCATAA GAGTTTGGCG TTCAAACGCTTGCAACTTTT CTTGTTTCAA
240
AAAGATCCGC AAAGCTACAT GGATAACTTT TATAAGGAAGTGGGATTGGA CGCTCAATTG
300
GAGCGTTTTA AAAAAGAGGG TTCTTTAGAA GAATTGGAATTTTTATTGGA TTACAAGTAT
360
AGTGATTCTA TAATTAGATT TTTATTGGAA AAGGGCGTGAAGATTGAAGT GTTTATCGGT
420
TTAAAAGATA GAATCACTGA CATTCAAGCC CTTTTAGAATTTTTTATGCC CTTAGTTCAA
480
_
SO GTGTGGCAGT TTAAGGATTG TAACCATTTG TTGCAP.AAATCTTAA 525
(2) INFORMATION FOR SEQ ID N0:42:
(i) SEQUENCE CHARACTERISTICS:
_.____.~~.._.._ __..._~._.~T...... _...._._ _
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 139 -
(A) LENGTH: 1416 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
lO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IS (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1416
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:42:
ATGAAAAATACCAATACAAA TGAAAAAAGGTTATAGTCAA60
AGAGATAAAG
AATACAAGGA
TACCACACGCTCAAAAAAGGGCTTTTA:~AAACCGCTCTGCTTTTTAGCCTTCCTTTAAGC120
GTGGCGTTAGCTGAAGACGATGGCTTTTATATGGGAGTGGGCTATCAAATCGGCGGCGCG180
CAACAAAACATCAACAACAAAGGCAGCACCCTAAGGAATAATGTCATTGATGATTTCCGC240
2S CAAGTGGGCGTGGGTATGGCAGGGGGTAATGGGCTTTTAGCTTTAGCGACAAACACGACC300
ATGGACGCTCTTTTAGGGATAGGCAACCAAATTGTCAATACTAATACAACTGTTGGCAAC360
AACAACGCAGAGTTAACCCAGTTTAAAAAAATACTCCCCCAAATTGAACAACGCTTTGAG420
ACGAATAAAAACGCTTATAGCGTTCAAGCCTTGCAAGTGTATTTGAGTAATGTGCTTTAT480
AACTTGGTTAATAATAGTAATAATGGTAGCAATAATGGAGTCGTTCCTGAATATGTAGGG540
3O ATTATAAAAGTTCTCTATGGTTCTCAAAATGAATTCAGTCTCTTAGCCACGGAGAGTGTG600
GCGCTTTTAAACGCGCTCACGAGAGTGAATCTGGATAGTAATTCGGTGTTTTTAAAAGGG660
CTATTAGCCCAAATGCAGCTTTTTAATGACACTTCTTCAGCAAAGCTAGGTCAGATCGCA720
GAAAACTTGAAGAACGGTGGTGCAGGGGCCATGCTTCAAAAGGATGTGAAAACCATCTCG780
GATCGAATCGCTACTTACCAAGAGAATCTAAAACAGCTAGGAGGGATGTTAAAGAATTAC840
3S GATGAGCCATACCTACCCCAATTTGGGCCAGGCACAAGCTCTCAGCATGGGGTTATTAAT900
GGCTTTGGCATTCAAGTGGGCTATAAGCAATTTTTTGGGA.GCAAGAAGAATATAGGCTTA960
CGATATTACGCTTTCTTTGATTATGGCTTTACGCAATTGGGCAGTCTTAACAGTGCTGTT1020
AAAGCGAACATCTTTACTTATGGTGCTGGCACGGACTTTTTATGGAATATCTTTAGAAGG1080
GTTTTTAGCGATCAGTCCTTGAATGTGGGGGTGTTTGGGGGCATTCAAATAGCGGGTAAC1140
4O ACTTGGGATAGCTCTTTAAGAGGTCAAATTGAAAACTCGTTTAAAGAATACCCCACTCCC1200
ACGAATTTCCAATTTTTGTTTAATTTGGGCTTAAGGGCTCATTTTGCCAGCACCATGCAC1260
CGCCGGTTTTTGAGCGCGTCTCAAAGCATTCAGCATGGTATGGAATTTGGCGTGAAAATC1320
CCAGCTATCAATCAAAGGTATTTGAAAGCGAATGGGGCTGATGTGGATTACAGGCGTTTG1380
TATGCGTTCTATATCAATTACACGATAGGTTTTTAA 1416
-
4S
(2)INFORMATION FOR SEQ ID N0:43:
(i) SEQUENCE CHARACTERISTICS:
_ (A) LENGTH: 390 base pairs
SO (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
CA 02273199 1999-06-O1
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- 140 -
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...30
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:43:
IS ATGAAAAGCA TCAGAAGAGG CGATGGGCTG AATGTTGTCC CTTTCATTGA 60
TATTATGCTC
GTCTTACTAG CGATTGTGTT GAGTATTTCT ACTTTTATCG CGCAAGGTAA I20
GATTAAAGTC
AGTCTCCCTA ACGCTAAAAA TGCGGAAAAA TCCCAGCCAA ACGATCAAAA 180
AGTGGTGGTC
ATCTCTGTGG ATGAGCATGA CAATATTTTC GTAGATGACA AACCGACGAA 240
TTTAGAAGCT
TTGAGCGCTG TAGTCAAGCA AACAGACCCT AAAACCCTTA TAGATTTAAA 300
AAGCGACAAG
ZO AGCTCTCGTT TTGAAACTTT TATCAGCATT ATGGATATTT TAAAAGAGCA 360
TAATCATGAA
AATTTCTCCA TCTCCACGCA AGCTCAGTAA 390
(2) INFORMATION FOR SEQ ID N0:44:
ZS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 225 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
30
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...225
(xi) SEQUENCE
DESCRIPTION:
SEQ ID N0:44:
4S
ATGCTCGTCT TACTAGCGATTGTGTTGAGTATTT~r.CTT TTATCGCGCA AGGTAAGATT60
AAAGTCAGTC TCCCTAACGCTAAAAATGCGGAAAAATCCC GACCAAACGA TCAAAAAGTG120
GTGGTCATCT CTGTGGATGAGCATGACAATATTTTCGTAG ATGACAAACC GACGAATTTA180
GAAGCTTTGA GCGCTGTF~GTCAAGCAAACAGACCCTAAAA CCCTT 225
S0
(2) INFORMATION FOR SEQ ID N0:45:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 672 base pairs
CA 02273199 1999-06-O1
WO 98124475 PCT1US97/22104
-141-
(B) TYPE: nucleic acid
(C) STRANDEDNESS:' double
(D) TOPOLOGY: circular
S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
1S (A) NAME/KEY: misc_feature
(B) LOCATION 1...672
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:45:
ZO ATGTTTTCAC TTTCTTATGT TTCCAAGAAA TTTTTAAGCG TGTTGCTATT GATTTCGCTG 60
TTTTTAAGCG CTTGCAAATCCAACAATAAAGACAAATTGGATGAAAATCTTTTAAGCTCC120
GGCACTCAAA GCTCCAAAGAATTAAACGACAAGCGAGACAATATAGACAAAAAGAGCTAC180
GCTGGTTTAG AAGATGTTTTTTTAGACAACAAGTCCATTAGCCCTAATGATAAATACATG240
CTTTTAGTTT TTGGCCGTAATGGTTGCTCCTATTGTGAAAGGCTTAAAAAAGATCTCAAA300
ZS AATGTCAAAGAATTGCGCAACTATATTAAAGAGCATTTTAGTGCTTACTATGTCAATATC360
AGCTATTCTA AAGAGCATAATTTTAAAGTCGGCGATAAGGATAAAAATGATGAAAAAGAA420
ATCAAAATGT CCACAGAAGAATTAGCGCAAATTTATGCCGTCCAATCCACCCCTACGATT480
GTTTTATCCG ATAAAACCGGCAAAACCATCTATGAATTGCCGGGCTATATGCCTTCTGTG540
CAATTTTTAG CCGTGTTAGAATTTATCGGCGATGGGAAGTATCAAGACACGAAAAACGAT600
3O GAGGATCTCACTAAAAAATTAAAGGCTTACATCAAGTATAAAACCAACCTTTCTAAGAGC660
AAGTCCAGCT AG 672
(2) INFORMATION FOR SEQ ID N0:46: -
3S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
4S (iv) ANTI-SE'dSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
SO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...351
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:46:
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- I 42 -
TTGATGAAAT CTAAAATCAC TCATTTTATC GTTATCTCTTTTGTTTTAAG CGTGTTGAGC
60
GCCTGCAAAG ATGAGCCTAA AAAATCGTCC CAATCGCACCAAAACAACAC TAAAACCACT
120
CAAAACAATC AAATCAATCA ACCTAATAAG GATATAAAAAAGATTGAGCA TGAAGAAGAA
180
S GATGAAAAAG TCACCAAAGA AGTGAATGAT CTGATCAATAACGAAAATAA AATTGATGAA
240
ATCAATAATG AAGAAAACGC TGATCCTTCG CAAAAAAGAACGAACAATGT TTTGCAACGA
300
GCCACTAACC ACCAAGACAA TCTCAGTTCC CCACTCAACAGGAAGTATTA A 351
(2) INFORMATION FOR SEQ ID N0:47:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 240 base pairs
(B) TYPE: nucleic acid
(C) STR.ANDEDNESS: double
IS (D) TOPOLOGY: circular _
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...240
3O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:47:
ATGTTTGAAA AAATACGCAA GATTTTAGCG GATATTGAAGATTCGCAAAA TGAAATTGAA
60
ATGCTTTTAA AATTAGCGAA TTTGAGTTTG GGGGATTTTATTGAGATTAA AAGAGGGAGC
120
ATGGACATGC CAAAGGGCGT GAATGAAGCG TTTTTTACGCAATTAAGCGA AGAAGTGGAG
180
3S CGCCTAAAGG AGCTTATCAA CGCTTTGAAT AAAATCAAAAAAGGGTTATT GGTGTTTTAA
240
(2) INFORMATION FOR SEQ ID N0:48:
(i) SEQUENCE CHARACTERISTICS:
40 (A) LENGTH: 156 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
- 4S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
SO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
_..._.._..._.~_ ___. . _._......_._ . _..._..._r____..
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-143-
(A) NAME/KEY: misc_feature
(B) LOCATION 1...156
S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:48:
ATGTCTATGT TCATTTCTAA TCTGGCTTTC ACGAGCGAAC ATAAGGACGC TATGGAAGTG 60
GCAAAAATTG CGATTTTACT CGGATCTTTG ATTTCTGGGA TCATAGGGGC TTTATATTTA 120
TTCGCACTAG ATAAAAGAGC GGCTTTAAAG AAATAG 156
IO (2) INFORMATION FOR SEQ ID N0:49:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1350 base pairs
(B) TYPE: nucleic acid
IS (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
ZO (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
ZS (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1350
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:49:
ATGGGTTTGA TTTAAGGTTGTCTATGAATCTCAAAAAAACAGAAAACGCG60
AAATAAAAAT
CTCAGTTTGACGCTTAAAAACTTCATTAAAAGCGAGTCTTTTGGAGGGATTTTCCTCTTT120
3S TTGAACGCCGTTTTAGCGATGGTGGTGGCTAATTCGTTTTTAAAAGAAAGTTATTTTGCG180
CTATGGCACACCCCTTTTGGGTTTCAAGTAGGGGATTTTTTTATCGGCTTTAGTTTGCAC240
AACTGGATTGATGATGTCTTAATGGCGTTATTCTTTTTAATGATAGGCTTAGAGATCAAG300
CGAGAATTGTTGTTTGGGGAATTATCCAGTTTTAAAAAAGCTTCTTTCCCTGTGATCGCA360
GCCATAGGGGGCATGATAGCTCCAGGATTGATTTATTTTTTTCTTAACGCCAACACGCCC420
4O TCTCAGCATGGTTTTGGGATCCCTATGGCAACGGATATTGCGTTCGCTTTAGGCGTGATC480
ATGCTTTTAGGCAAGAGGGTGCCAACCGCCTTAAAGGTTTTTTTAATCACTCTAGCGGTG540
GCTGATGACTTAGGGGCTATTGTGGTGATCGCGCTCTTTTATACCACGAATTTAAAATTC600
GCATGGCTTTTAGGGGCTTTAGGGGTGGTTCTTGTTTTAGCCATATTGAACCGCCTGAAT660
ATCCGATCGCTCATC6CTTACTTGCTTTTAGGGGTGTTGCTTTGGTTTTGCGTGCATCAA720
4S AGCGGTATCCATGCGACGATCGCTGCGGTGGTTCTAGCTTTTATGATACCGG'.'GAAAATC780
CCTAAAGATTCTAAAAATGTAGAGCTTTTGGAATTAGGCAAACGATACGCaf.AGACGAGT840
TCAGGAGTGCTTTTAACCAAAGAGCAGCAAGAAATCTTGCATTCTATTGAAGAAAAAGCG900
AGTGCTTTACAAAGCCCCTTAGAAAGATTGGAGCATTTTCTAGCCCCCATCAGCGGGTAT960
TTCATCATGCCCTTATTCGCGTTTGCAAACGCTGGGGTGAGCGTTGATTCTAGCATCAAT1020
SO TTAGAAGTGGATAAGGTGCTTTTAGGGGTTATTTTAGGGCTTTGTTTGGGCAAGCCTTTA1080
GGGATTTTCTTAATCACTTTCATAAGCGAAAAGCTTAAAATCACTGCGCGCCCTAAAGGC1140
ATCGGCTGGTGGCATATTTTAGGGGCTGGGCTTTTAGCAGGGATTGGCTTTACCATGTCT1200
ATGTTCATTTCTAATCTGGCTTTCACGAGCGAACATAAGGACGCTATGGAAGTGGCAAAA1260
ATTGCGATTTTACTCGGATCTTTGATTTCTGGGATCATAGGGGCTTTATATTTATTCGCA1320
CA 02273199 1999-06-O1
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CTAGATAAAA GAGCGGCTTT AAAGAAATAG 1350
(2) INFORMATION FOR SEQ ID N0:50:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2448 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
lO
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
1S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...2448
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:50:
ATGAATGACAAGCGTTTTAGAAAATATTGTAGTTTTTCTATTTTTTTGTCCTTATTAGGA60
ACGTTTGAATTAGAGGCTAAAGAAGAAGAAAAAGAAGAAAAAAAGACAGAAAGGAACAAA120
GATAAAGAAAAGAACGCCCAACACACTTTGGGTAAAGTTACCACTCAAGCGGCTAAAATC180
TTTAATTACAACAACCAGACAACCATTTCAAGTAAAGAATTAGAAAGAAGGCAAGCCAAC240
3O CAAATCAGCGACATGTTTAGAAGAAACCCCAATATCAATGTGGGCGGTGGTGCGGTGATA300
GCGCAAAAAATTTACGTGCGCGGTATTGAAGACAGATTGGCTAGGGTTACGGTGGATGGC360
GTGGCGCAAATGGGCGCAAGCTATGGGCATCAAGGCAATACAATCATTGACCCTGGAATG420
CTCAAAAGCGTGGTGGTTACCAAGGGGGCGGCTCAAGCGAGCGCGGGGCCTATGGCTTTA480
ATTGGCGCGATCAAAATGGAGACTAGGAGCGCGAGCGATTTTATCCCTAAAGGCAAAGAC540
3S TACGCCATAAGTGGGGCTGCCACTTTTTTAACCAACTTTGGGGATAGGGAAACCATTATG600
GGCGCTTATCGTAACCATCATTTTGATGCGCTTTTGTATTACACGCACCAAAATATTTTT660
TATTATCGTGATGGGGATAACGCGATGAAAAATCTTTTTGACCCTAAAGCGGATAATAAA720
GTTACAGCAAGCCCTAGCGAACAAAACAATGTGATGGCTAAGATCAATGGTTATTTGAGC780
GAAAGGGATACCTTAACGCTCAGTTATAACATGACTAGAGATAACGCCAATCGCCCTTTA840
4O AGAGCGAATTTTACCGGCACTTTTTTACCCTATTCTTGTGGTGATTTCAACGCTTTCCCT900
AACGAGAAAAACCCTAGCGATTGTTTGTTTGAAAATGACGCCAGTTTGTTTAAAACTTAT960
AGCGTCAATTTAGTGCATAACGTGAGCTTGAATTATGAAAGGGAAGGGGGGAGTCGCTTT1020
GGCGATCCTAAATTAAAAATCAATGGCTACACGAGCATTAGGAATGTCCAAATTGATCCG1080
CTTTTCAGACCTAGCGATATAGCGACTACCATTCCTTTCACCCCAAACCCGCAGCTCTCT1140
4S CAAGGCGAAGAAAATCAATGCGTGGCGCAAGGGGGCATTTATGACGCTCTTAAACAAACT1200
TGCTCCATCACTTTTAAAAGCCTTGGAG~CGGTTCTGTTGTCGCTAATAAAAATTTATTC1260
ATCATCAATTCTGGGTTTAATGCGAACGTGATCCACACCATAGACCACAAGAATGACAAT1320
CTTTTGGAATACGGGTTGAATTACCAGAATTTAACCACTTTTGATAAAGCGATCCCTGAT1380
AGCGAATTAGTCAAGCCCGGCGATGCCCCTGATGCGTGCTTAAGAGTTACAGGACCTGAT1440
SO GATCCTAACATGAACGGGCGCTGCCAACGGAATGGCGCTACGGCGAATGTGGTTGGGGTG1500
TATGCGCAAGCGAATTACACCTTGCACCCTATGGTAACTTTAGGGGCAGGGACTCGTTAT1560
GACGTTTATACTTTAGTGGATAAAGACTGGCAATTGCACGTAACTCAAC;GTTTAGCCCT1620
AGCGCGGCTTTAAACGTCTCGCCTTTAGAAAATTTGAATTTCAGGCTTTCTTACGCGTAT1680
GTAACTAGAGGCCCTATGCCTGGAGGTTTGGTGTGGATGCGTCAAGACAATTTGCGCTAT1740
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/US97/22104
-14S-
AACCGCAATT TAAAGCCAGA AATTGGGCAA AATGCGGAAT TTAACACCGA ATACAGCAGT 1800
CAGTATTTTG ATTTCAGAGC CGCCGGTTTT GTCCAATTGA TTTCTAATTA CATCAATCAA 1860
TTTTCTTCAA CGCTTTTTGT CACCAACTTG CCCGCACAAG ATATTATTTA TGTGCCTGGC 1920
TATGAAGTTT CAGGGACGGC TAAATACAAG GGTTTTTCTT TAGGCTTGAG CGTGGCGCGA 1980
S TCATGGCCTT CTTTAAAAGG GCGTTTGATC GCTGACGTGT ATGAATTGGC GGCTACGACA 2040
GGCAATGTGT TTATTTTAAC GGCAAGCTAT ACAATCCCAC GCACCGGCCT TAGCATCACT 2100
TGGCTTTCAC GCTTTGTTAC TAATTTGAGT TATTGCTCTT ATAGCCCTTA TCGTAACGGC 2160
CCTACGGATA TTGACAGAAG GCCTAGTAAT TGCCCTAAAA CGCCCGGGAT TTTTCATGTG 2220
CATAAACCCG GCTATGGGGT GAGCAGTTTC TTTATCACTT ACAAGCCTAC TTATAAGAAA 2280
lO CTCAAAGGGT TGAGCCTGAA CGCGGTGTTT AATAATGTTT TTAACCAACA ATATATTGAT 2340
CAAGCAAGCC CGGTGATGAG CCCTGATGAA CCCAATCAAG ACAAATACGC AAGGGGCATG 2400
GCAGAGCCTG GCTTTAACGC TAGGTTTGAA ATTTCTTATA AGTTTTAA 2448
1S
(2) INFORMATION FOR SEQ ID N0:51:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2445 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
20 (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...2445
3S (xi) SEQUENCE DESCRIPTION: SEQ ID NO:51:
ATGACAAGCG TTTTAGAAAA ATATTGTAGT TTTTCTATTT TTTTGTCCTT ATTAGGAACG 60
TTTGAATTAG AGGCTAAAGA AGAAGAAAAA GAAGAAAAAA AGACAGAAAG GAACAAAGAT 120
AAAGAAAAGA ACGCCCAACA CACTTTGGGT AAAGTTACCA CTCAAGCGGC TAAAATCTTT 180
4O AATTACAACA ACCAGACAAC CATTTCAAGT AAAGAATTAG AAAGAAGGCA AGCCAACCAA 240
ATCAGCGACA TGTTTAGAAGAAACCCCAATATCAATGTGGGCGGTGGTGCGGTGATAGCG300
CAAAAAATTT ACGTGCGCGGTATTGAAGACAGATTGGCTAGGGTTACGGTGGATGGCGTG360
GCGCAAATGG GCGCAAGCTATGGGCATCAAGGCAATACAATCATTGACCCTGGAATGCTC420
AAAAGCGTGG TGGTTACCAAGGGGGCGGCTCAAGCGAGCGCGGGGCCTATGGCTTTAATT480
4S GGCGCGAT~AAAATGGAGACTAGGAGCGCGAGCGATTTTATCCCTAAAGGCAAAGACTAC540
GCCAT~..=.~i'GGGGCTGCCACTTTTTTAACCAACTTTGGGGATAGGGAAACCATTATGGGC600
GCTTATCGTA ACCATCATTTTGATGCGCTTTTGTATTACACGCACCAAAATATTTTTTAT660
TATCGTGATG GGGATAACGCGATGAAAAATCTTTTTGACCCTAAAGCGGATAATAAAGTT720
ACAGCAAGCC CTAGCGAACAAAACAATGTGATGGCTAAGATCAATGGTTATTTGAGCGAA780
SO AGGGATACCTTAACGCTCAGTTATAACATGACTAGAGATAACGCCAATCGCCCTTTAAGA840
GCGAATTTTA CCGGCACTTT TTTACCCTAT TCTTGTGGTG ATTTCAACGC TTTCCCTAAC 900
GAGAAAAACC CTAGCGATTG TTTGTTTGAA AATGACGCCA GTTTGTTTAA AACTTATAGC 960
GTCAATTTAG TGCATAACGT GAGCTTGAAT TATGAAAGGG AAGGGGGGAG TCGCTTTGGC 1020
GATCCTAAAT TAAAAATCAA TGGCTACACG AGCATTAGGA ATGTCCAAAT TGATCCGCTT 1080
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 146 -
TTCAGACCTAGCGATATAGCGACTACCATTCCTTTCACCCCAAACCCGCAGCTCTCTCAA1140
GGCGAAGAAAATCAATGCGTGGCGCAAGGGGGCATTTATGACGCTCTTAAACAAACTTGC1200
TCCATCACTTTTAAAAGCCTTGGAGGGGGTTCTGTTGTCGCTAATAAAAATTTATTCATC1260
ATCAATTCTGGGTTTAATGCGAACGTGATCCACACCATAGACCACAAGAATGACAATCTT1320
S TTGGAATACGGGTTGAATTACCAGAATTTAACCACTTTTGATAAAGCGATCCCTGATAGC1380
GAATTAGTCAAGCCCGGCGATGCCCCTGATGCGTGCTTAAGAGTTACAGGACCTGATGAT1440
CCTAACATGAACGGGCGCTGCCAACGGAATGGCGCTACGGCGAATGTGGTTGGGGTGTAT1500
GCGCAAGCGAATTACACCTTGCACCCTATGGTAACTTTAGGGGCAGGGACTCGTTATGAC1560
GTTTATACTTTAGTGGATAAAGACTGGCAATTGCACGTAACTCAAGGGTTTAGCCCTAGC1620
lO GCGGCTTTAAACGTCTCGCCTTTAGAAAATTTGAATTTCAGGCTTTCTTACGCGTATGTA1680
ACTAGAGGCCCTATGCCTGGAGGTTTGGTGTGGATGCGTCAAGACAATTTGCGCTATAAC1740
CGCAATTTAAAGCCAGAAATTGGGCAAAATGCGGAATTTAACACCGAATACAGCAGTCAG1800
TATTTTGATTTCAGAGCCGCCGGTTTTGTCCAATTGATTTCTAATTACATCAATCAATTT1860
TCTTCAACGCTTTTTGTCACCAACTTGCCCGCACAAGATATTATTTATGTGCCTGGCTAT1920
IS GAAGTTTCAGGGACGGCTAAATACAAGGGTTTTTCTTTAGGCTTGAGCGTGGCGCGATCA1980
TGGCCTTCTTTAAAAGGGCGTTTGATCGCTGACGTGTATGAATTGGCGGCTACGACAGGC2040
AATGTGTTTATTTTAACGGCAAGCTATACAATCCCACGCACCGGCCTTAGCATCACTTGG2100
CTTTCACGCTTTGTTACTAATTTGAGTTATTGCTCTTATAGCCCTTATCGTAACGGCCCT2160
ACGGATATTGACAGAAGGCCTAGTAATTGCCCTAAAACGCCCGGGATTTTTCATGTGCAT2220
ZO AAACCCGGCTATGGGGTGAGCAGTTTCTTTATCACTTACAAGCCTACTTATAAGAAACTC2280
AAAGGGTTGAGCCTGAACGCGGTGTTTAATAATGTTTTTAACCAACAATATATTGATCAA2340
GCAAGCCCGGTGATGAGCCCTGATGAACCCAATCAAGACAAATACGCAAGGGGCATGGCA2400
GAGCCTGGCTTTAACGCTAGGTTTGAAATTTCTTATAAGTTTTAA 2445
ZS (2) INFORMATION FOR SEQ ID N0:52:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1584 base pairs
(B) TYPE: nucleic acid
30 (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
4O (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1584
4S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:52:
ATGAAACAAA ATTTAAAGCC ATTCAAAATGATTAAGGAAA ACAATCTCAA60
ATTTAATGAC
AAAGTAAGAT TCTTAGCCCCTTTGAGCCTAGCGTTAAGCTTGAGCTTCAATCCAGTGGGC120
SO GCTGAAGAAG ATGGGGGCTTTATGACCTTTGGGTATGAATTAGGTCAGGTGGTCCAGCAA180
GTGAAAAACC CGGGTAAAATCAAAGCCGAAGAATTAGCGGGCCTGTTAAACTCTACCACG240
ACAAACAACA CCAATATCAATATTGCAGGCACAGGAGGGAATGTCGCCGGGACTTTGGGC300
AACCTTTTTA TGAACCAATTGGGCAATTTGATTGATTTGTATCCTACTTTGAAAACTAAT360
AATCTTCACC AATGCGGTAGCACTAATAGCGGTAATGGCGCTACTGCTGCCGCTGCTACT420
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 147 -
AACAATAGCC CTTGTTTCCAAGGTAACCTGGCTCTTTATAACGAAATGGTTGACTCTATC480
AAAACTTTGA GTCAAAACATCAGCAAGAACATCTTTCAAGGCGACAACAACACCACGAGC540
GCTAATCTCT CCAACCAGCTCAGTGAGTTGAACACCGCTAGCGTTTATTTGACTTACATG600
AACTCGTTCT TAAACGCCAACAACCAAGCGGGTGGGATTTTTCAAAACAACACCAATCAA660
S GCTTACGAGA ATGGTGTTACCGCTCAACAAATCGCTTATGTCCTAAAGCAAGCTTCAATC720
ACTATGGGGC CAAGCGGTGATAGTGGGGCTGCGGGAGCGTTTTTAGACGCCGCTTTAGCC780
CAACATGTTT TCAACTCGGCTAACGCTGGGAACGATTTGAGCGCTAAGGAATTCACTAGC840
TTGGTGCAAA ACATCGTCAATAATTCTCAAAACGCTTTAACGCTAGCCAACAACGCTAAC900
ATCAGCAATT CAACAGGCTATCAAGTGAGCTATGGTGGGAATATTGATCAAGCGCGCTCT960
lO ACCCAACTGT TAAACAACACCACAAACACTTTGGCTAAAGTTACCGCTCTAAACAACGAG1020
CTTAAAGCTA ACCCATGGCTTGGGAATTTCGCTGCTGGTAACAGCTCTCAAGTGAATGCG1080
TTTAACGGGT TTATCACTAAAATCGGTTATAAGCAATTCTTCGGGGAAAACAAGAATGTG1140
GGCTTACGCT ACTACGGGTTCTTCAGCTATAACGGCGCGGGCGTGGGTAATGGCCCCACT1200
TACAATCAAG TCAATCTGCTCACTTATGGGGTGGGGACTGATGTGCTTTACAATGTGTTT1260
IS AGCCGCTCTT TTGGCAGTAGGAGTCTTAATGCGGGCTTCTTTGGGGGGATCCAACTCGCA1320
GGGGACACTT ACATCAGCACGCTAAGAAACAGCCCTCAGCTTGCGAGCAGACCTACAGCG1380
ACAAAATTCC AATTCTTGTTTGATGTGGGCTTACGCATGAACTTTGGTATCTTGAAAAAA1440
GACCTAAAAA GCCATAACCAGCATTCTATAGAAATCGGTGTGCAAATCCCTACGATTTAC1500
AACACTTACT ATAAAGCTGGTGGCGCTGAAGTGAAATACTTCCGCCCTTATAGCGTGTAT1560
ZO TGGGTCTATG GCTACGCCTTCTAA 1584
(2) INFORMATION FOR SEQ ID N0:53:
(i) SEQUENCE CHARACTERISTICS:
2$ (A) LENGTH: 1380 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4O (A) NAME/KEY: misc_feature
(B) LOCATION 1...1380
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:53:
4S GTGGTGTTATTAACAATGACAAAACGACTTTTTAAAGGGTTGTTAG';GAT TTCTCTTGCG60
GTGAGTTTGC ATGGTGGTGAAGTTAAGGAAAAAAAGCCGGTCA..3~;CGGT CAAAGAAGAT120
CCGCAAGAAT TAGCGGCTAAAAGGGTGGAAGCGTTCAGTCGTTTCTCTAA TGTGGTTACA180
GAAATTGAAA AAAAGTATGTGGATAAGATCAGTATTTCTGAGATCATGAC TAAAGCGATT240
GAAGGCTTAC TCTCTAATTTGGACGCGCATTCAGCGTATTTGAATGAAAA GAAGTTTAAG300
SO GAATTTCAGGCCCAAACCGAGGGCGAATTTGGGGGGCTTGGGATCACGGT GGGCATGCGC360
GATGGCGTTT TGACCGTTATTGCACCTTTAGAGGGCACTCCAGCTTACAA GGCTGGGGTT420
AAATCAGGCG ATAGCATTTTAAAAATCAATAACGAAAGCACGCTGAGCAT GAGCATTGAT480
GATGCGGTTA ATCTCATGCGCGGCAAGCCAAAAACCTCTATTCAGATCAC TGTTGTTAGG540
AAAAATGAGC CAAAACCCTTGGTATTTAATATCGTTAGGGATATTATCAA GATCCCCTCT600
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/US97/22104
- 148 -
GTCTATGTGA AAAAGATTAA AGACACACCT TATTTGTACG TGAGAGTCAA TTCTTTTGAT 660
AAAAATGTTA CCAAATCGGT TTTAGACGGC TTGAAGGCTA ACCCTAACAT TAAGGGCGTT 720
GTGTTGGATT TGAGGGGGAA TCCTGGAGGG CTATTAAACC AGGCGGTAGG CTTGTCTAAC 780
CTTTTCATTA AAGAGGGGGT TTTAGTCTCT CAAAGAGGCA AAAATAAGGA GGAAAACTTA 840
S GAATACAAGG CTAATGGCAG AGCCCCTTAT ACCAATTTAC CTGTTGTGGT GTTAGTCAAT 900
GGCGGTTCAG CGAGCGCGAG CGAGATCGTC GCAGGGGCAC TGCAAGATCA CAAGCGAGCC 960
ATCATTATCG GTGAAAAAAC CTTTGGTAAG GGAAGCGTGC AAGTGTTGCT CCCTGTCAAT 1020
AAAGACGAAG CCATTAAAAT CACGACCGCG CGCTATTATT TGCCGAGCGG GCGCACCATT 1080
CAAGCTAAGG GGATCACGCC TGATATTGTG ATTTATCCGG GTAAAGTGCC AGAAAATGAA 1140
lO AATAAATTCA GTTTGAAAGA AGCGGATTTA AAACACCATT TAGAGCAAGA GCTTAAAAAA 1200
CTTGATGATA AAACCCCTAT TTCCAAAGAG GCGGATAAAG ACAAGAAAAG CGAAGAGGAA 1260
AAAGAGGTTA CTCCTAAAAT GATCAATGAT GATATTCAGC TAAAAACCGC TATTGACAGC 1320
TTGAAAACCT GGTCTATCGT AGATGAGAAA ATGGATGAAA AAGTGCCTAA GAAGAAATAA 1380
1S (2) INFORMATION FOR SEQ ID N0:54:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 315 base pairs
(B) TYPE: nucleic acid
ZO (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
ZS (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO -
(vi) ORIGINAL SOURCE:
3O (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...315
3S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:54:
TTGCTTTTGC ACCCCTTGCATGCTCATGCACAAGTGCTTGGCTTCACAAACCACGATCAC60
GCCCCTTGGC TCTATGATTTCATCAAAAGTTTCTGCAATTTGAGTGGTCAGCCTTTCTTG120
4O GATTTGCAGGCGTTTGCTATAAATTTCAATGAGTTTAGCGATCGCGCTAATGCCTACAAT180
CTTTTCCTTA GGGATATATCCCACGCTAATATTCCCAAAAAAAGGGAGCAAATGGTGCTC240
GCAAGTGGAG TAAAATTCAATGTTTTGAGCCACTATCATTTCATCGCAAACGCCTTGAAA300
ATACGCGCTT TTTAA 315
4S (2) INFORMATION FOR SEQ Ir> N0:55:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 498 base pairs
(B) TYPE: nucleic acid
SO (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
CA 02273199 1999-06-O1
WO 98124475 PCT/US97I22104
- 149 -
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...498
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:55:
ATGATTGAAC TAATCTTACA CAATAAGTCC ATACAAATTG ATGAAACATT GCTGAATGTA 60
IS AAAGAGCATTTAGAAAAGTTTTATTCAAAC AAAGAACAAGAGACAATCGCAAAAACCTTA120
GAGAGCCAAA CAGAGCTTACTTGCAGTTAT TTATTGGATAAAGATTTTTCATTGCTAGAA180
AAGCATTTAG AAAATAGCTTAGGGCATTTT ACTTTTGAGAGTGAGTTTGCCCTACTAAAA240
GACAAAGAGC CTTTGAATTTAGCTCAAATC AAACAAATCGGTGTTTTAAAGGTTATTACC300
TATGAAATGA CACAAGCCTTAAAAAATCAA ATCATTCATTTAACGCAAATTGTCAATGAA360
2O GAAAATTTAGAGTTTGATGAAGAACTTGTT ATTTATCACTTAAATTTTAAGCTCAATCAA420
AATACTTACA AAGTGTTAGCGAAATTTTGC GTATTAAAAAAGAAAGGAACATTGCATGAA480
AAATTTAAGG CATTTTAG 4gg
2S
(2) INFORMATION FOR SEQ ID N0:56:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 642 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
30 (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...642
4S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:56:
ATGGATACCG GCGTATTTGTTTGAAAAAGC TTTACAAAAA60
AAACACAAGA
AAAGTTTTTA
AATCTACAAG CTTATTGGAT AACAACAACTGAAACTAAGAATGAATTAAC AAGAGAAGAG120
TTTTCAAATT TAATAAGAAA AACAATGATTGAACTAATCTTACACAATAA GTCCATACAA180
SO ATTGATGAAACATTGCTGAA TGTAAAAGAGCATTTAGAAAAGTTTTATTC AAACAAAGAA240
CAAGAGACAA TCGCAAAAAC CTTAGAGAGCCAAACAGAGCTTACTTGCAG TTATTTATTG300
GATAAAGATT TTTCATTGCT AGAAAAGCATTTAGAAAATAGCTTAGGGCA TTTTACTTTT360
GAGAGTGAGT TTGCCCTACT AAAAGACAAAGAGCCTTTGAATTTAGCTCA AATCAAACAA420
ATCGGTGTTT TAAAGGTTAT TACCTATGAAATGACACAAGCCTTAAAAAA TCAAATCATT480
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 150 -
CATTTAACGC AAATTGTCAA TGAAGAAAAT TTAGAGTTTG ATGAAGAACT TGTTATTTAT 540
CACTTAAATT TTAAGCTCAA TCAAAATACT TACAAAGTGT TAGCGAAATT TTGCGTATTA 600
AAAAAGAAAG GAACATTGCA TGAAAAATTT AAGGCATTTT AG 642
S (2) INFORMATION FOR SEQ ID N0:57:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
IS (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: -
20 (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...762
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:57:
ATGGCGATCT CTATTAAAAGCCCAAAAGAA TAAGAAAAGCCGGGGAATTA60
ATCAAAGCCC
ACCGCTCAAG CGTTAGCCCTTTTAGAGCGAGAAGTAAGGCCTGGGGTTTCACTTTTAGAG120
3O CTGGATAAAA TGGCTGAAGATTTTATCAAATCCTCGCATGCTAGGCCTGCTTTTAAGGGG180
CTCTATGGTT TCCCTAACTCTGTGTGCATGTCCTTAAATGAGGTGGTTATTCATGGTATT240
CCTACGGATT ATGTTTTACAAGAAGGGGATATTATAGGCTTGGATTTGGGGGTGGAGGTG300
GATGGCTATT ATGGCGATTCAGCCCTCACGCTTCCCATAGGCGCGATAAGCCCGCAAGAT360
GAAAAATTGC TCGCTTGCTCTAAAGAGAGCTTGATGCATGCCATTAGCTCAATTAGAGTG420
3S GGCATGCATT TTAAAGAGTTGAGTCAGATTTTAGAGGGCGCTATTACAGAAAGGGGCTTT480
GTGCCTTTGA AGGGATTTTGCGGGCATGGCATTGGTAAAAAGCCCCATGAAGAGCCAGAA540
ATCCCCAACT ACCTAGAAAAAGGCGTCAAAGCTAATAGCGGCCCTAAAATCAAAGAGGGC600
ATGGTGTTTT GTTTAGAGCCTATGGTGTGTCAAAAACAAGGCGAGCCTAAAATACTAGCG660
GATAAGTGGA GCGTGGTTTCAGTGGATGGACTTAACACAAGCCACCATGAGCATACTATC720
4O GCCATAGTTG GCAATAAAGCAGTGATTCTTACGGAGCGTTAA 762
(2) INFORMATION FOR SEQ ID N0:58:
(i) SEQUENCE CHARACTERISTICS:
4S (A) LENGTH: 744 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S~ (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
__..-.~.. ___.. __ ...~ _ _ _.._._..r . .. . _
CA 02273199 1999-06-O1
WO 98/24475 PCTIUS97/22104
- 1S1 -
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S (ix) FEATURE:
(A) NAME/K.EY: misc_feature
(B) LOCATION 1...744
lO
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:58:
AAGCCCAAAA GAAATCAAAGCCCTAAGAAA TAACCGCTCAAGCGTTAGCC 60
AGCCGGGAAT
CTTTTAGAGC GAGAAGTAAGGCCTGGGGTTTCACTTTTAGAGCTGGATAAAATGGCTGAA 120
GATTTTATCA AATCCTCGCATGCTAGGCCTGCTTTTAAGGGGCTCTATGGTTTCCCTAAC 180
TCTGTGTGCA TGTCCTTAAATGAGGTGGTTATTCATGGTATTCCTACGGATTATGTTTTA 240
IS CAAGAAGGGGATATTATAGGCTTGGATTTGGGGGTGGAGGTGGATGGCTATTATGGCGAT 300
TCAGCCCTCA CGCTTCCCATAGGCGCGATAAGCCCGCAAGATGAAAAATTGCTCGCTTGC 360
TCTAAAGAGA GCTTGATGCATGCCATTAGCTCAATTAGAGTGGGCATGCATTTTAAAGAG 420
TTGAGTCAGA TTTTAGAGGGCGCTATTACAGAAAGGGGCTTTGTGCCTTTGAAGGGATTT 480
TGCGGGCATG GCATTGGTAAAAAGCCCCATGAAGAGCCAGAAATCCCCAACTACCTAGAA 540
ZO AAAGGCGTCAAAGCTAATAGCGGCCCTAAAATCAAAGAGGGCATGGTGTTTTGTTTAGAG 600
CCTATGGTGT GTCAAAAACAAGGCGAGCCTAAAATACTAGCGGATAAGTGGAGCGTGGTT 660
TCAGTGGATG GACTTAACACAAGCCACCATGAGCATACTATCGCCATAGTTGGCAATAAA ?20
GCAGTGATTC TTACGGAGCGTTAA 744
ZS (2) INFORMATION FOR SEQ ID N0:59:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1023 base pairs
(B) TYPE: nucleic acid
3O (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
4O (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1023
_4S
(xi) SEQUENCE DESCRIPTION: SEQ ID NC.:f 3:
ATGTATCGTA AAGATTTGGA TCCCTAAAGCGGTGTTTTTG60
TAATTACTTA AAACAGCGCC
TATGGGGAGT TTGATTTTTT CATCCATTATTATATTCAAACGATTAGCGCGCTTTTTAAA120
SO GGCAATAACC CTGACACAGA AACTTCGCTTTTTTATGCGAGCGATTATGAAA.AAAGCCAG180
ATTGCGACCC TTTTAGAGCA GGATTCTTTATTTGGAGGGAGCAGTTTAGTTATTTTAAAA240
CTGGATTTTG CATTGCATAA GAAATTTAAGGAAAATGATATCAATCCTTTTTTAAAAGCT300
TTAGAGCGGC CTAGCCATAA TAGGCTTATGATAGGGCTTTATAATGCTAAAAGCGACACC360
ACAAAATACA AATACACTAG CGAAATTATCGTTAAATTTTTCCAi4AAAAGCCCCTTGAAA420
CA 02273199 1999-06-O1
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- 152 -
GATGAAGCCA TTTGCGTGCG CTTTTTTACC CCTAAAGCGT GGGAGAGTTT GAAATTCTTG 480
CAAGAAAGGG CTAATTTTTT GCATTTAGAC ATCAGCGGCC ATCTTTTAAA CGCTCTTTTT 540
GAAATTAATA ACGAAGATTT AAGCGTTTCG TTTAACGATT TAGACAAGCT AGCGGTTTTA 600
AACGCGCCCA TCACTTTAGA AGACATTCAA GAATTAAGCT CCAATGCGGG GGATATGGAT 660
S TTGCAAAAGC TCATTTTAGG GCTTTTTTTG AAAAAAAGCG TCCTTGATAT TTATGATTAT 720
TTGTTAAAAG AGGGCAAAAA GGATGCGGAT ATTTTAAGGG GGTTAGAGCG CTATTTTTAC 780
CAGCTTTTTT TATTTTTCGC CCACATTAAA ACGACCGGTT TAATGGACGC TAAAGAGGTC 840
TTAGGCTACG CTCCTCCTAA AGAGATTGTA GAAAATTACG CTAAAAACGC CCTGCGTTTG 900
AAAGAAGCCG GCTATAAGAG GGTTTTTGAA ATTTTTAGGT TATGGCACCT TCAAAGCATG 960
IO CAAGGGCAAA AGGAATTGGG CTTTTTGTAT TTGACCCCCA TTCAAAAAAT CATTAACCCT 1020
TGA _ 1023
(2) INFORMATION FOR SEQ ID N0:60:
IS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 603 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
2S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...603
3S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:60:
GTGTTTATGA CAAGCGCTCTGTTAGGCTTACAAATTGTTTTAGCGGTATTGATTGTGGTG60
GTGGTTTTGT TGCAAAAAAGTTCTAGCATCGGCTTAGGGGCTTATAGCGGAAGCAACGAT120
TCTTTATTTG GCGCTAAAGGGCCCGCAAGCTTTATGGCGAAATTGACCATGTTTTTAGGT180
TTATTGTTTG TCATCAACACCATCGCTTTGGGCTATTTTTACAACAAAGAATACGGCAAG240
4O AGCGTTTTAGATGAAACTAAAACCAATAAAGAGCTTTCGCCCTTAGTCCCTGCCACCGGC300
ACGCTCAACC CTACGCTTAATCCCACATTAAACCCAACGCTCAACCCTTTAGAGCAAGCC360
CCCACTAATC CTTTAATGCCTACACAAACGCCTAAAGAGCTTCCTAAAGAGCCAGCCAAA420
ACGCCTTTTG TTGAAAGCCCCAAACAGAATGAAAAGAATGAAAAGAATGATGCCAAAGAA480
AATGGTATAA AGGGTGTTGAAAAP.Ai~ICAAAGAGAACGCCAAAACGCCCCCAACCACCCAC540
4S CAAAAGCCTAAAACGCP'rGCGACAACCAACGCCCATACCAACCAAAAAAAGGATGAAAAA600
Z''~'~' 6
0
3
(2) INFORMATION FOR SEQ ID N0:61:
SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 4B0 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
CA 02273199 1999-06-O1
WO 98/24475 PCT/ITS97/22104
-153-
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
{iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...480
IS (xi) SEQUENCE DESCRIPTION: SEQ ID N0:61:
ATGCGTTCTC CAAATTTAGA AAAAGAAGAA ACTGAAATCA TAGAAACGCT TCTTGTGCGT 60
GAAAAAATGC GTTTATGCCC CTTGTATTGG CGCATCTTAG CGTTTTTAAT CGATAGTTTA 120
TTGGTGGCGT TTTTATTGAG CGATCTTTTA AGGGCATGCG CTTTTTTACA TTCTTTATAT 180
ZO TGGCTGACTA ACCCCATTTA TTACAGCGCG TTTGTTGTGA TGGGTTTTAT CATCTTGTAT 240
GGCGTTTATG AAATCTTTTT TGTGTGTTTG TGCAAGATGA GTTTGGCTAA ACTGGTTTTT 300
AGGATTAAGA TCATTGATAT TTATTTAGCG GATTGCCCCA GTAGGGCTAT TTTATTGAAG 360
CGTTTAGGGT TAAAAATCGT GGTTTTTCTA TGCCCCTTTT TATGGTTTGT GGTGTTTAAA 420
AACCCCTATC ATAGGGCATG GCATGAAGAA AAAAGCAAAA GTCTTTTGGT GTTGTTTTAA 480
(2) INFORMATION FOR SEQ ID N0:62:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 705 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO.
(iv) ANTI-SENSE: NO
4O (vi) ORIGINAL SOURCE:
{A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc
feature
_
(B) LOCATION 1...705
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:62:
TTGAATACGG ACTTTAGCCA TATCACCGAT ATTGAGGGCATGCGTTTTGT TAATGAAGAA60
SO GACGCTTTAA ACAAATTGAT TAATGAAATC CACACGCGCCACATTGATTT
AAAAGATTCC120
ATCATGCTCG CTTTGAGTTT TAACGCCTTG TATTTAGCTAACGCTTTAGC GCAAAAATTT180
GGGGCGACTT ATGATATACT TTTTTTAGAA CCTATCTTAGCCCCTTTAAA CTCAAAGTGT240
GAAATCGCTT TAGTGAGTGA AAGCATGGAT ATAGTGATGAATGAAAGTTT AATCAATTCC300
TTTGACATCG CTTTAGACTA TGTTTATGGG GAAGCCAAGCGGGCTTATGA AGAAGACATT360
CA 02273199 1999-06-O1
WO 98124475 PCT/US97/22104
- 1 S4 -
CTGTCTCACA TCTATCAGTA TCGCAAAGGC AATGCGATCA 420
AAAGCCTAAA AGATAAAAAT
ATTTTTATCG TAGATAGGGG GATTGAGACC GGGTTTAGAGCAGGGTTAGG CGTGCAAACT480
TGTTTGAAAA AAGAATGCCA AGACATTTAT ATTTTAACCCCCATTCTCGC GCAAAATGTC540
GCTCAAGGCT TAGAAAGCTT GTGCGATGGG GTGATTAGCGTGTATCGCCC TGAATGTTTT600
S GTCTCTGTGG AACACCATTATAAAGAACTC AAGCGATTAAGCAATGAAGA AATTGAAAAA660
TACTTGGGCG CTAACAACGC GCCCAATCTC AAAAAGGAACATTAA 705
(2) INFORMATION FOR SEQ ID N0:63:
IO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 864 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
1S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
ZO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
ZS (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...864
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:63:
TTGAAACAAA CATGGAATTTAATGATCCTAGGATGCGTTTTTTTATTGGC60
GCGAAATGGC
GATGTCAGGGATTTAGAACGCTTGAATTACGCTTTAGAGGGCGTGGATATTTGTATCCAT120
GCGGCCGCGCTCAAGCATGTGCCTATCGCTGAATACAACCCCCTAGAATGCATTAAAACT180
AACATCATGGGAGCGAGCAATGTGATTAACGCATGCTTAAAAAATGAAATCAGCCAGGTT240
3S ATTGCCCTAAGCACCGATAAAGCCGCTAACCCCATTAACCTCTACGGCGCAACCAAATTG300
TGCAGCGACAAGCTCTTTGTGAGCGCGAACAACTTTAAAGGCCCTTCTCAAACGCAATTT360
GGCGTGGTGCGTTATGGTAATGTGGTGGGGAGTCGTGGGAGCGTGGTGCCGTTTTTTAAA420
AAATTAGTCCAAAACAAAGCGAGTGAAATCCCCATTACCGATATTCGCATGACACGATTT480
TGGATCACCTTAGATGAGGGGGTTTCTTTTGTGCTTAAAAGCTTGAAAAGAATGCATGGG540
4O GGGGAAATTTTTGTGCCTAAAATCCCCAGCATGAAAATGATTGATCTCGCCAAAGCCCTA600
GCCCCCAATATCCCTACTAAAATCATAGGGATTCGCCCGGGCGAAAAACTCCATGAAGTG660
ATGATCCCTAAAGATGAAAGCCATTTAGCCCTAGAATTTGAAGACTTTTTTATTATTCAG720
CCCACTATAAGCTTCCAAACGCCTAAAGATTACACGCTCACCAAACTCCATGAAAAAGGC780
CAAAAAGTCGCCCCTGATTTTGAATACAGCAGCCATACTAATAACCAATGGCTAGAGCCT840
4S GATGATTTGTTAAAATTATTATGA 864
(2) INFORMATION FOR SEQ ID N0:64:
(i) SEQUENCE CHARACTERISTICS:
SO (A) LENGTH: 606 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-1SS-
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...606
1S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:64:
ATGCGTTTGC ACACTGCCTTTTTTGGTATT TTGTCGCCACTCTTTTGATA60
AATTCGTTGC
AGCGGTTGCA GTCTCTTTAAAAAGCGTAACACTAACGCTCAGCTAATCCCCCCTTCAGCT120
AACGGGTTGC AAGCCCCCATTTATCCCCCAACCAATTTCACCCCCAGAAAGAGCATTCAG180
CCTCTCCCAA GCCCTCGCCTTGAGAATAACGATCAGCCCATCATTAGCTCTAATCCCACT240
ZO AACGCTATCCCTAACACCCCCATTCTCACGCCCAATAATGTCATTGAGTTGAATGCGGTG300
GGCATGGGTG TGGCTCCAGAATCCACCATTTCGCCCTCTCAAGCTCTAGCTTTAGCTAAG360
CGAGCGGCTA TTGTTGATGGCTACCGCCAGTTGGGTGAAAAAATGTATGGCATCAGAGTG420
AACGCTCAAG ACACCGTCAAAGACATGGTTTTACAAAATTCCGTGATTAAAACGAGAGTG480
AATGCCCTCA TTCGTAACGCTGAAATCACTGAGACTATCTATAAAGACGGCTTGTGCCAG540
ZS GTAAGCATGGAGCTTAAATTAGACGGCAGGATTTGGTATCGTATTTTGAGCGGATCGAGA600
GGATAA 606
(2) INFORMATION FOR SEQ ID N0:65:
3O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1068 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double -
(D) TOPOLOGY: circular
3S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
4O (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4S (ix) FEATURE:
(A) NAME/KEY: misw_.eature
(B) LOCATION 1...1068
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:65:
SO
ATGAGTTATA CTATTAATAA ACGCTTTTCT GTGGGTGTGG GTTTAAGGGG GCTTTATGCG 60
ACCGGGAGCT TTAATAACAC CGTTTATGTG CCTTTAGAGG GCGCTTCAGT TTTGAGCGCG 120
GAGCAAATCT TAAACTTACC CAACAATGTT TTTGCCGATC AAGTGCCAAG TAACATGATG 180
ACTTTATTAG GCAATATTGG CTACCAACCA GCGCTTAATT GCCAAAAAGC CGGTGGGGAC 240
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 1S6 -
ATGAGTGATCAGAGCTGTCAAGAGTTTTACAACGGCTTGA GGGTTATAGC300
AAAAAATCAT
GGTTTAATCAAAGCGAGCGCGAATCTTTATGGCACGACTCAAGTCGTGCAAAAATCTAAC360
GGACAAGGCGTATCGGGGGGGTATAGAGTGGGTTCGAGTTTGCGTGTGTTTGATCATGGC420
ATGTTTTCTGTGGTGTATAATTCTTCAGTTACCTTTAACATGAAAGGCGGTTTGGTGGCT480
S ATCACAGAGCTTGGCCCTTCTTTAGGGAGCGTTTTGACTAAAGGCAGCTTGAATATCAAT540
GTTTCACTCCCCCAAACTTTAAGCTTAGCCTACGCCCACCAATTTTTTAAAGATCGCCTA600
AGGGTTGAAGGGGTGTTTGAGCGCACTTTTTGGAGTCAAGGGAATAAATTTTTAGTCACC660
CCTGATTTTGCGAACGCCACTTACAAGGGCTTGAGCGGGACGGTGGCTTCCTTGGACTCT720
GAAACGCTTAAAAAAATGGTAGGCCTAGCGAATTTTAAAAGCGTGATGAACATGGGGGCT780
lO GGCTGGAGGGACACCAACACCTTTAGATTAGGGGTAACTTACATGGGTAAAAGCTTGCGT840
TTAATGGGCGCTATTGATTATGATCAAGCCCCAAGCCCCCAAGACGCGATAGGCATTCCG900
GACTCTAATGGCTATACCGTGGCTTTTGGGACTAAATACAATTTTAGGGGCTTTGATTTG960
GGCGTAGCGGGGAGTTTCACTTTTAAGAGCAACCGCTCCAGTTTGTATCAATCCCCAACT1020
ATTGGGCAATTGAGAATCTTTAGCGCCTCTTTAGGCTATCGCTGGTAA 1068
1S
(2) INFORMATION FOR SEQ ID N0:66:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1764 base pairs
2O (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
30 (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
35 (B) LOCATION 1...1764
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:66:
ATGAAAAACTTTTCCCCACTCTATTGTCTT TTTAATCGCT60
AAAAAGCTCA
AAAAACGCCA
4O CTGAGTCTGCCCTTGCTTTCTTATGCGAATGGCTTTAAAATCCAAGAGCAAAGCTTGAAT120
GGCACGGCTTTAGGCTCGGCGTATGTCGCTGGGGCTAGGGGTGCTGACGCTTCTTTTTAC180
AACCCGGCTAACATGGGCTTTACTAACGATTGGGGCGAAAACAGAAGCGAATTTGAAATG240
ACCACCACCGTGATCAATATCCCGGCCTTTAGCTTTAAAGTCCCTACGACCAATCAAGGC300
TTATATTCGGTAACAAGTTTAGAA.ATTGATAAAAGCCAACAAAATATTTTAGGCATCATC360
-- 4S AACACTATAGGGTTAGGCAATATCCTTAAAGCGCTTGGCAATACGGCCGCTACCAATGGC420
TTA.C.CAAGCTATCAATCGTGTTCAAGGGCTTATGAACTTAACCAATCAAAAAGTCGTA480
ACCCTCGCTTCAAAACCTGACACTCAAATCGTGAATGGCTGGACAGGCACGACTAATTTT540
GTTTTACCTAAATTCTTTTATAAAACGCGCACGCATAACGGCTTCACTTTTGGGGGGAGT600
TTTACCGCTCCTAGTGGGTTGGGTATGAAATGGAATGGTAAGGGGGGGGAATTTTTGCAT660
SO GACGTGTTTATCATGATGGTAGAGCTTGCCCCTAGCATGAGTTATACTATTAATAAACGC720
TTTTCTGTGGGTGTGGGTTTAAGGGGGCTTTATGCGACCGGGAGCTTTAATAACACCGTT780
TATGTGCCTTTAGAGGGCGCTTCAGTTTTGAGCGCGGAGCAAATCTTAAACTTACCCAAC840
AATGTTTTTGCCGATCAAGTGCCAAGTAACATGATGACTTTATTAGGCAATATTGGCTAC900
CAACCAGCGCTTAATTGCCAAAAAGCCGGTGGGGACATGAGTGATCAGAGCTGTCAAGAG960
_ ._ _..__ _.... . _._ _~_T..._ _... . _....
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/US97/22104
- 1S7-
TTTTACAACG GCTTGAAAAA TATAGCGGTTTAATCAAAGCGAGCGCGAAT1020
AATCATGGGT
CTTTATGGCA CGACTCAAGTCGTGCAAAAATCTAACGGACAAGGCGTATCGGGGGGGTAT1080
AGAGTGGGTT CGAGTTTGCGTGTGTTTGATCATGGCATGTTTTCTGTGGTGTATAATTCT1140
TCAGTTACCT TTAACATGAAAGGCGGTTTGGTGGCTATCACAGAGCTTGGCCCTTCTTTA1200
S GGGAGCGTTT TGACTAAAGGCAGCTTGAATATCAATGTTTCACTCCCCCAAACTTTAAGC1260
TTAGCCTACG CCCACCAATTTTTTAAAGATCGCCTAAGGGTTGAAGGGGTGTTTGAGCGC1320
ACTTTTTGGA GTCAAGGGAATAAATTTTTAGTCACCCCTGATTTTGCGAACGCCACTTAC1380
AAGGGCTTGA GCGGGACGGTGGCTTCCTTGGACTCTGAAACGCTTAAAAAAATGGTAGGC1440
CTAGCGAATT TTAAAAGCGTGATGAACATGGGGGCTGGCTGGAGGGACACCAACACCTTT1500
IOAGATTAGGGG TAACTTACATGGGTAAAAGCTTGCGTTTAATGGGCGCTATTGATTATGAT1560
CAAGCCCCAA GCCCCCAAGACGCGATAGGCATTCCGGACTCTAATGGCTATACCGTGGCT1620
TTTGGGACTA AATACAATTTTAGGGGCTTTGATTTGGGCGTAGCGGGGAGTTTCACTTTT1680
AAGAGCAACC GCTCCAGTTTGTATCAATCCCCAACTATTGGGCAATTGAGAATCTTTAGC1740
GCCTCTTTAG GCTATCGCTGGTAA 1764
1S
(2) INFORMATION FOR SEQ ID N0:67:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 618 base pairs
20 {B) TYPE: nucleic acid
{C) STRANDEDNESS: double
(D) TOPOLOGY: circular
2S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
3O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
3S (B) LOCATION 1...618
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:67:
TTGATTTTTAGATTTTTCTT CTTTTAAAAGGGGTTTTACTGGCCAAAAAG60
AATCTTAAGC
4O GATTGGAATTTTTTCAAACCTTTAGAGCCTACTAAAAAATATTTTGGCTCTTTTAAAATC120
GGCTATCTTTACCAACATGCAGAAACGACTAAAAGATTCCCCATCCGCCCTAAAAACCGC180
CCGCCTATTTTAATGGATAAAATTTACCATGACGCTTCTTTGGGTTTTGACGCAGGGTAT240
GTTTTGAAAAAGAAAGCTTTATTGGGGGGGTATTTGGATGCAGGAATGGGCGATTCGTAT300
TTCATGAGCGCTGGGCTAGTCGCTGGGGTGAGGCTTTTTAAGGGGTGGGTTATCCCTAAA360
4S ATCGCCTTAGGCTATCAGCTTCAAATTTTAGGGGCTAAGATTGATAAGTATCAATTCAAT420
ATCCAATCAGCGGTGGGGAGTGTGGGCTTGTTTTTCAATGCGGCTAAAAATTTTGGCTTG~~C
AGTATAGAAGCAAGGGGCGGTATCCCTTTTTATTTCATTCAGAGCAGGTTTTCTAAGGCT540
TTCGGCACGCCACGATTGAATATCTATTCTGTTGGTATCACATTCACTTTTTATGACTTT600
ACGAGATTTTTAGGGTAA 618
SO
(2) INFORMATION FOR SEQ ID N0:68:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 1S8 -
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
1~
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
1S (A) NAME/KEY: misc_feature
(B) LOCATION 1...762
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:68:
ZO TTGTGGCATG CTGCCTTTAG CGTTGGCGAG TGGGGATGGA ACGGCGATGA AATCCCCTAT 60
AGGGATTGCG ATGAGTGGGGGCTTGATGATTTCTATGGTGTTAAGCCTACTGATTGTGCC 120
GGTGTTTTAT CGTTTGCTCG-CTCCCATAi~ACGACAAAATCAAGCGGTTTTATCAAAACCA 180
AAAAGCTTTA GAATGAAAAAAATTGCTTTCATTTTGGCTTTATGGGTGGGCTTGTTAGGG 240
GCGTTTGAGC CTAAAAAAAGTCATATTTATTTTGGGGCTATGGTGGGTTTAGCCCCTGTT 300
ZS AAAATAACCCCAAAACCGGCTAGTGATTCTTCTTATACGGCTTTTTTATGGGGGGCTAAA 360
GGGGGGTATC AATTCGCTTTTTTTAAAGCTCTAGCGTTAAGGGGTGAATTTTCCTACCTT 420
ATGGCGATCA AACCCACCGCACTGCACACGATTAACACTTCTTTATTGAGTTTAAATATG 480
GATGTGTTGA GCGATTTTTACACTTATAAAAAATACAGCTTTGGGGTGTATGGGGGGCTT 540
GGGATAGGGT ATTTTTATCAAAGCAACCATTTAGGCATGAAAAATAGTTCGTTTATGGGT 600
3O TATAACGGCTTGTTTAATGTGGGGCTTGGCAGCACGATCGATCGCCACCACCGCGTAGAG 660
CTTGGGGCTA AGATCCCTTTTTCAAAGACTAGAAATTCTTTTAAAAATTCTTATTTTTTA 720
GAGAGCGTTT TTATCCATGCGGCTTATAGTTATATGTTTTAA 762
3S
(2) INFORMATION FOR SEQ ID N0:69:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1239 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
4~ (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S~
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1239
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 1 S9 -
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:69:
ATGGAATCAGTAAAAACAGT AAAGTTGGCA GACAGCTAAC60
AAAAACAAAT AAAACACAGA
ACAGAGGCAAGTAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATACGCTCCGA120
S TCAATTGGTGGGATTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTGAAAAAACAT180
CCCAAGAAAAGCAGTGTGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAGGGCAAAA240
GAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT300
TGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGCACT360
GGTGATATTGATAAACAAATAGAACTAGAACAAGAA.AAA.AAGGAAGCAAATAAGAGTGGG420
IO ATAAAGTTAGAACAAGAAAGACAGAAAACAGAACAAGAAAGACAGAAGACAAATAAGAGT480
GAGATAGAGTTAGAACAAGAAAGACAAAAAACAAACAAGAGTGGGATAGAACTCGCTAAT540
AGTCAAATAAAAGCAGAACAAGAAAGACAAAAGACAGAACAAGAAAAACAAAAAGCAAAT600
AAGAGTGAGATAGAGTTAGAACAGCAAAAACAAAAGACAATTAATACACAAAGAGATTTG660
ATTAAAGAACAGAAAGATTTCATTAAAGAAACAGAACAAAATTGCCAAGAAAAACATGGC720
IS CAATTGTTTATTAAAAAAGCAAGAATTAAGACCGGTATTACTACTGGTATTGCCATAGAA780
ATAGAAGCTGAATGCAAAACCCCTAAACCTGCAAAAACCAATCAAACCCCTATCCAGCCA840
AAACACCTCCCAAACTCTAAACAACCCCGCTCTCAAAGAGGATCAAAAGCGCAAGAGCTT900
ATCGCTTATTTGCAAAAAGAGCTAGAATCTCTGCCCTATTCGCAAAAAGCTATCGCTAAA960
CAAGTGGATTTTTATAAACCAAGTTCTATCGCTTATTTAGAACTAGACCCTAGAGATTTT1020
ZO AAGGTTACAGAAGAATGGCAAAAAGAAAATTTAAAAATACGCTCTAAAGCTCAAGCTAAA1080
ATGCTTGAAATGAGAAACCCACAAGCCCACCTTCCAACCTCTCAAAGCCTTTTGTTCGTT1140
CAAAAAATATTTGCTGATATTAA'rAAAGAAATAGAAGCAGTTGCTAATACTGAAAAGAAA1200
ACAGAAAAAGCGGGTTATGGTTATAGTAAAAGGATGTAG 1239
ZS (2) INFORMATION FOR SEQ ID N0:70:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 450 base pairs
(B) TYPE: nucleic acid
3O (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
4O (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
-- (B) LOCATION 1...450
4S
(xi} SEQUENCE DE..:C:IPTION: SEQ ID N0:70:
TTGAATTGGG AGCATTTGATGAAAAAATTA GCGTTTTCTTTATTATTTAC AGGGACTTTT60
TTGGGGCTTT TTTTGAATGCGAGTGATTTT AAGAGCATGGATAACAAGCA ACTATTAGAG120
SO CAAGCAGGGAAAGTCGCTCCTAGCGAAGTT CCAGAGTTTCGCACAGAAGT CAATAAACGA180
TTAGAAGCGA TGAAAGAAGAAGAGCGTCAA AAATATAAAGCGGATTTTAA GAAAGCGATG240
GATAAGAATT TGGCTTCTTTAAGCCAAGAA GATCGCAACAAGCGTAAAAA AGAAATCCTT300
GAAGTCATTG CTAACAAAAAGAAAACAATG ACCATGAAAGAGTATCGTGA AGAGGGGTTG360
GATTTGCATG ATTGCGCATGCGAAGGCCCT TTTCATGATCATGAAAAAAA GGGGCAAAAA420
CA 02273199 1999-06-O1 -
WO 98/24475 PCT/US97/22104
- 160 -
GGGAAAAAAC CAAGCCATCA TAAGCATTAG 450
(2) INFORMATION FOR SEQ ID N0:71:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATIGN 1...615
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:71:
2S
ATGCAAGCAG TGATTTTAGC GAATGGGGAG TTTCCTAAATCTAAAAAATG CTTAGACATT
60
TTACAAAACG CTCCCTTTTT AATCGCATGC GATGGGGCTGTTATATCATT GCATGCGCTT
120
CAATTCAAAC CCAGCGTTGT TATAGGCGAT TTGGATAGCATTGATTCGCA TTTGAAAGCC
180
TTGTATAACC CTATACGCGT GAGCGAACAA GACAGCAACGATTTGTCCAA AGCCTTTTTT
240
3O TATGCTTTGA ATAGGGGTTG TGATGATTTT ATTTTTTTAGGGTTGAATGG CAAGCGAGAA
300
GACCACGCTT TAGCGAACAC TTTTTTATTG TTGGAGTATTTTAAATTTTG CAAP.AAAATC
360
CAATCCGTAA GCGATTATGG CCTTTTTAGG GTGTTAGAAACCCCTTTTAC TTTGCCCAGT
420
TTTAAGGGGG AGCAAATCTC GCTTTTTAGC TTGGATCTTAAAGCCCGATT CACTTCTAAA
480
AACCTCAAAT ACCCCTTAAA AGACTTGCGT CTAAAAACGCTCTTTTCCGG CTCGCTCAAT
540
3S GAAGCCACTA ATCATTGTTT TAGCCTTAGC TCTGAACCTAAATCGGTGGT GCTAGTGTAT
600
CAAAAATTCT CATGA 615
(2) INFORMATION FOR SEQ ID N0:72:
40 (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 843 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
4S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
SO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
CA 02273199 1999-06-O1
WO 98/24475 PCT/LJS97/22104
-161-
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...843
S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:72:
GTGTTTGACT CATTGGGCGGATTTTTGGGGTATAAAACTTTTAAGCCGATAGTGGATAAG60
GTTAAAAATA TAAACGCTTGGATAAAAAATTACGATAATAAAAAAGCTCAAGAGATTATG120
GGTTTTATAG AAAATCCTACGCCTGATTTCCAAAATAATAAGTTTTTGTGTGTTTTAAAC180
lO CGACAAGGAA CAAGGCACAACAATTATCTTGGTTTAACCTCTACAAACCTTCTAATCGGC240
GCGATCTATT TCTCCATCCGCCATT6CATCAAAGCCACATGGCAAAACGATAGGGATCAA300
TTCTACGCCC CTTATGATGACGCTTTCCAAGACGACAGCGAGTTTAAAAACAATTGTTTG360
GCGTTCATGC TTTTTCACACCCAAAACCGCATCACTGCCACTCAAGGGACTAACCATTTT420
ATCCCCTTTA GCGAAGATGAAGTTGATTCTAAAGAAAGGTATTTGAGCCATGCTTTATTA480
IS GACTTTTTAA AAGGCGAAATCAAAGAACCTAAAAAGAGCGATAGCCTCTTTTTAAACGCC540
AAAAAAGAAA ACAAGCCCCTAAAATTCAGCTCGAGCGCTTCAAAGGTGTTTGACGCTGGC600
AGAGAGATTT ATCGCTATTACCACACACAAGATTTCATCCACACCCCCTATAACGCTAAC660
GCAAGCCTTT ATGACATCAAAGAATTTTTTCAAGGCCGTAACAAGCAAGGCAGATTAAAC720
TCACCCACCA AAGCCAAAGATGAATATTACAAACAGCTTTACGCTAACTTGCAATACGCC780
ZO CTAAAAGATC TCGCCAAAGAAATACAGCCTAAAGTCTATGAATACGGATTTTTAAGGGAG840
TAG 843
(2) INFORMATION FOR SEQ ID N0:73:
ZS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 930 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (Henomic)
( i i i ) H'IPOTHETI CAL : NO
3S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...930
4S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:73:
TGTGACAGGG CAATTCCCCA TTGGCTTTTTAGTCTGGGATACCGCTACCC CCCCCCwr'.A60
AAACCAACCA ACGCGTTCAA TTTAGAAGTGTTTGACTCATTGGGCGGATT TTTGGGGTAT120
AAAACTTTTA AGCCGATAGT GGATAAGGTTAAAAATATAAACGCTTGGAT AAAAAATTAC180
GATAATAAAA AAGCTCAAGA GATTATGGGTTTTATAGAAAATCCTACGCC TGATTTCCAA240
SO AATAATAAGTTTTTGTGTGT TTTAAACCGACAAGGAACAAGGCACAACAA TTATCTTGGT300
TTAACCTCTA CAAACCTTCT AATCGGCGCGATCTATTTCTCCATCCGCCA-TTGCATCAAA360
GCCACATGGC AAAACGATAG GGATCAATTCTACGCCCCTTATGATGACGC TTTCCAAGAC420
GACAGCGAGT TTAAAAACAA TTGTTTGGCGTTCATGCTTTTTCACACCCA AAACCGCATC480
ACTGCCACTC AAGGGACTAA CCATTTTATCCCCTTTAGCGAAGATGAAGT TGATTCTAAA540
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 162 -
GAAAGGTATT TGAGCCATGCTTTATTAGAC TTTTTAAAAGGCGAAATCAA AGAACCTAAA600
AAGAGCGATA GCCTCTTTTTAAACGCCAAA AAAGAAAACAAGCCCCTAAA ATTCAGCTCG660
AGCGCTTCAA AGGTGTTTGACGCTGGCAGA GAGATTTATCGCTATTACCA CACACAAGAT720
TTCATCCACA CCCCCTATAACGCTAACGCA AGCCTTTATGACATCAAAGA ATTTTTTCAA780
S GGCCGTAACAAGCAAGGCAGATTAAACTCA CCCACCAAAGCCAAAGATGA ATATTACAAA840
CAGCTTTACG CTAACTTGCAATACGCCCTA AAAGATCTCGCCAAAGAAAT ACAGCCTAAA900
GTCTATGAAT ACGGATTTTTAAGGGAGTAG 930
(2) INFORMATION FOR SEQ ID N0:74:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 564 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
1S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO -
{iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...564
3O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:74:
TTGGAAACTT TGCAGATAATATAGATGGGGATTTATTTTTCTATAATCTT60
ATATCATTGA
ACTAGAAACA GCAATGATTTTTCCATGTTGCCCGTTTTTGAACTCGATCGCATTGCCCAA120
AAAATTAGAA ATATTCTTAAAAAACATGGCAGTAGAAAAGACATTATTTTAAAACACAAT180
3S GAAATTAAAGAAGCCTTTTTTAGCCCGTTCAAACCGCAGCTAAAAACCGTTCAAGTGTTC240
CTCTCGCACT CGCATGCGGATAAAAATAAGGCTTTAGGGGTTAAGGACTATTTGGAAAGC300
AAAACAAAAC GCAAAGTGTTTATCGATTCGCTTTTTTGGGATTATAAAGACGATGTTTTA360
AACAAATTGG CAAAACACGATGATATAAGCAAGATTGAAGACGCTTTCACGCTCATTCTC420
AGAAAATCTT TACAAGATATGATTGAAAAATGCCCTTATTTTGTGTTTTTACAAAGCAAG480
4O AACAGCGTTTCTAATCAAGGGCTATCACGCATCACTTATTCCGCATGGATTTATGAAGAA540
TTAAAAATCG CTTCATTCTATTAG 564
(2) INFORMATION FOR SEQ ID N0:75:
4S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 597 base pairs
(B) TYPE: nucleic acid
(C1 STRANDEDNESS: double
(D) TOPOLOGY: circular
SO
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-163-
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...597
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:75:
TTGGAAACTT ATATCATTGATGCAGATAATATAGATGGGGATTTATTTTTCTATAATCTT60
ACTAGAAACA GCAATGATTTTTCCATGTTGCCCGTTTTTGAACTCGATCGCATTGCCCAA120
AAAATTAGAA ATATTCTTAAAAAACATGGCAGTAGAAAAGACATTATTTTAAAACACAAT180
IS GAAATTAAAGAAGCCTTTTTTAGCCCGTTCAAACCGCAGCTAAAAACCGTTCAAGTGTTC240
CTCTCGCACT CGCATGCGGATAAAAATAAGGCTTTAGGGGTTAAGGACTATTTGGAAAGC300
AAAACAAAAC GCAAAGTGTTTATCGATTCGCTTTTTTGGGATTATAAAGACGATGTTTTA360
AACAAATTGG CAAAACACGATGATATAAGCAAGATTGAAGACGCTTTCACGCTCATTCTC420
AGAAAATCTT TACAAGATATGATTGAAAAATGCCCTTATTTTGTGTTTTTACAAAGCAAG480
ZO AACAGCGTTTCTAATCAAGGGCTATCACGCATCACTTATTCCGCATGGATTTATGAAGAA540
TTAAAAATCG CTTCATTTCTATTAGCGCTATTAACGAGAGTCGCCCAATTCCAATGA 597
(2) INFORMATION FOR SEQ ID N0:76:
ZS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 570 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...570
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:76:
_ 4S
ATGATGACTA A~P.~CGCTTATGCGTTTGTCGTGATTGAAAAAAGTATTAT GGTGTTTAAA60
TGCGCCAAAG ACAAGGGGCTAATCCCTATCACTGAAGGCTTTGTGCCGTT AAAAGAGGGC120
TTTTTGAGAA GTTTTAAAGAGCGTTGCAATCTGGATTTTTTAGAAAATTT AGACCTTTTG180
TTTTTGTATG ACTACCAATTTCCAAGCGAGGTTTTTTCATTGTGTAAGGA TTTGAAAAAT240
SO TCCATTTGGG ACAGAAAGCTTGTGGTAGTGCTAGTGGAGGCTTTGGAGGG TTTTAAGGGT300
TTGAATTTGT CTCTTAAGATAGAAGATAGGCATTCTAATAGCTTGGGTAA TGGCGTTCAA360
AAATTGCTCA CCAACGCTGATTTGGGGAGCAACCACAAACCAATCGTAAT AGACAGCATG420
AAAACATACC ACCAAAGCCAGCAAGAAAAATACAAAAGAGAAAGAGGCGA AACGCTAGAG480
GTTCGCCCCA CAACACCCCCTAGCTATGGGGGTGGGAGCATTAGAATCAG CGGCGATAAA540
CA 02273199 1999-06-O1
WO 98/24475 PCT/L1S97/22104
- 164 -
AAGCCTGATT CCAATGAAGA AAATTTTTAA _ 570
(2) INFORMATION FOR SEQ ID N0:77:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1773 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
lO
(ii) MOLECULE TYPE: DNA_(genomic)
(iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1773
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:77:
ATGAAAGCGA TAAAPATACTTCTTATAATG ACACTCAGTT TAAACGCTATCAGCGTGAAT60
AGGGCGTTGT TTGATTTAAAAGATTCGCAA TTAAAAGGGG AATTAACGCCAAAAATAGTG120
GATTTTGGGG GTTATAAAAGCAACACCACA GAGTGGGGAG CTACGGCTTTAAACTATATC180
AATGCGGCTA ATGGCGATGCGAAAAAATTC AGCGCGTTAG TGGAAAAAATGCGTTTTAAC240
3O TCTGGTATCT TGGGGAATTTTAGAGCGCAT GCACATTTGA GGCAAGCCCTAAAATTGCAA300
AAGAATTTGA AATATTGCCTTAAAATCATC GCTAGGGATT CTTTTTATAGTTACCGCACC360
GGTATTTATA TCCCCTTAGGCATTTCTTTA AAAGATCAAA AAACGGCTCAAAAAATGCTC420
GCTGATTTGA GCGTGGTAGGGGCGTATCTT AAAAAGCAAC AGGAGAATGAAAAGGCTCAA480
AGCCCTTATT ACAGGAGCAACAACTATTAC AACTCCTACT ATAGCCCTTATTATGGCATG540
3S TATGGCATGT ATGGAATGGGCATGTATGGA ATGTATGGCA TGGGCATGTATGATTTTTAT600
GACTTTTATG ATGGCATGTATGGGTTCTAC CCTAACATGT TTTTCATGATGCAAGTTCAA660
GACTACTTGA TGTTAGAAAATTACATGTAT GCACTCGATC AAGAAGAGATTTTAGACCAT720
GACGCTTCCA TCAACCAACTTGATACGCCT ACTGATGATG ACAGAGACGATAAAGACGAT780
AAATCTTCGC AACCAGCGAATCTCATGAGC TTTTATCGTG ATCCCAAATTCAGCAAAGAC840
4O ATTCAAACCA ACCGCTTGAATAGCGCCTTA GTCAATTTAG ACAACAGCCACATGCTCAAA900
GACAATTCGC TCTTCCACACTAAAGCCATG CCCACTAAAA GCGTGGATGCGATCACTTCT960.
CAAGCTAAAG AGCTTAACCATTTGGTGGGG CAAATCAAAG AGATGAAGCAAGACGGGGCG1020
AGTCCTAATA AGATTGATTCAGTGGTCAAT AAAGCTATGG AGGTTAGGGACAAATTAGAC1080
AACAACCTCA ACCAACTAGACAATGACTTA AAAGATCAAA AAGGGCTTTCAAGCGAGCAG1140
4S CAAGCCCAAG TGGATAAAGCCTTAGACAGC GTGCAACAAT TAAGCCATAGCAGCGATGTG1200
GTAGGGAATT ATTTAGACGGGAGTTTGAAA ATTGATGGCG ATGACAGAGACGATTTGAAT1260
GATGCGATCA ATAACCCTATGCAACAACCT GCGCAACAAA CGCCTATTAACAACATGGAC1320
AACACCCATG CAAATGACAGCAAAGATCAA GGGGGTAACG CGCTCATAAACCCTAACAAC1380
GCCACCAACG ATGATCACAACGATGATCAC ATGGACACTA ACACCACTGACACTAGCAAC1440
SO GCAAACGACA CCCCCACTGATGATAAAGAT GCTAGCGGCA ACAATACCGGCGATATGAAT1500
AACACCGACA CCGGCAATACGGACACTGGC AACACCGACA CCGGTAACACTGATGATATG1560
AGCAACATGA ACAACGGCAACGATGATACG GGTAACACTA ACGACGACATGGGTAATAGC1620
AACGACATGG GCGATGACATGAATAACGCG.AACGACATGA ACGACGACATGGGTAACAGC1680
AACGATGACA TGGGCGATATGGGGGACATG AACGATGACA TGGGTGGCGATATGGGAGAC1740
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-16S-
ATGGGGGATA TGGGTGGCGA TATGGGGAAT TGA 1773
(2) INFORMATION FOR SEQ ID N0:78:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 588 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
l~
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...588
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:78:
2S
TTGAATTTAC GATTGGCTGG AGCAAGCGTT TTAACGGCTTGTGTCTTTTC GGGGTGTTTT
60
TTTTTAAAAA TGTTTGACAA AAAACTTTCT AGCAACGATTGGCATATCCA AAAAGTAGAA
120
ATGAACCATC AAGTGTATGA CATTGAAACC ATGCTCGCTGATAGCGCTTT TAGAGAGCAT
180
GAAGAAGAGC AAGACTCCTC TTTAAATACC GCTTTGCCTGAAGATAAAAC AGCGATTGAA
240
3O GCCAAAGAGC AAGAGCAAAA AGAAAAAAGG AAACACTGGTATGAGCTTTT TAAAAAGAAG
300
CCAAAGCCCA AAAGCTCTAT GGGAGAGTTT GTGTTTGATCAAAAAGAAAA TCGTATTTAT
360
GGGAAAGGCT ATTGCAACCG GTATTTTGCT AGCTACACATGGCAGGGCGA TAGGCACATC
420
GCAATTGAAG ATAGCGGGAT TTCAAGAAAA GTGTGTAGAGATGAGCATTT GATGGCGTTT
480
GAATTGGAAT TTATGGAGAA TTTTAAGGGT AATTTTGCGGTAACTAAGGG CAAGGACACG
540
3S CTCATTTTAG ACAACCAAAA AATGAAAATT TATTTGAAAACGCCATGA 588
{2) INFORMATION FOR SEQ ID N0:79:
(i) SEQUENCE CHARACTERISTICS:
40 (A) LENGTH: 2235 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
4S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
SU
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
CA 02273199 1999-06-O1
WO 98/24475 PCTlUS97/22104
- 166 -
(A) NAME/ICEY: misc_feature
(B) LOCATION 1...2235
S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:79:
ATGTTAAAAC TCGCCAGTAA TTGTCCCTAATCAGCTCATTCACGGCTGTA60
AACGATTTGT
GAAGCCTTTC AAAAACACCAAAAAGACGGCTTTTTCATAGAAGCCGGCTTTGAAACCGGG120
CTATTACAAG GCACACAAACCCAAGAACAAACCATAGCCACCACTCAAGAAAAACCCAAA180
CCCAAACCCA AACCAAAACCCATTACCCCTCAAAGCACCTATGGGAAATACTACATCTCC240
CAAAGCACCA TTTTAAAGAATGCGACTGAGTTGTTTGCAGAGGATAATATCACCAACTTA300
ACCTTTTACT CTCAAAACCCTGTGTATGTAACCGCTTATAACCAAGAAAGCGCTGAAGAA360
GCTGGCTATG GTAATAACAGCTTGATTATGATACAAAACTTCTTGCCTTATAACTTGAAC420
AACATTGAGC TGAGTTACACGGACGATCAAGGCAATGTGGTCAGTTTGGGCGTGATAGAG480
ACTATCCCTA AACAATCTCAAATCATTCTGCCCGCAAGCTTGTTTAACGACCCACAGCTT540
IS AACGCCGATG GCTTCCAACAACTCCAAACCAACACCACACGATTTTCTGATGCCAGCACG600
CAGAATCTGT TTAACAAGCTCAGCAAGGTTACAACCAATCTTCAAATGACTTATATCAAT660
TACAACCAAT TTTCTAGCGGTAACGGCAGTGGCTCTAAACCCCCATGCCCCCCATACGAA720
AACCAAGCAA ATTGTGTGGCTAAAGTGCCGCCTTTCACCTCTCAAGACGCTAAAAATTTG780
ACCAATTTAA TGCTGAACATGATGGCGGTGTTTGATTCTAAATCTTGGGAAGACGCCGTC840
ZO TTAAACGCTC CTTTCCAATTCAGCGACAACAACCTGTCAGCGCCATGTTATTCTGATTAC900
CTTACATGCG TGAATCCTTACAACGATGGGCTTGTTGATCCTAAATTGATCGCCAAAAAT960
AAAGGAGATG AATACAATATAGAAAACGGGCAAACAGGCTCAGTGATATTAACGCCGCAA1020
GATGTTATCT ATAGCTATAGAGTCGCTAATAATATTTATGTGAATCTCTTGCCCACAAGA1080
GGAGGGGATT TAGGGTTAGGGTCTCAATATGGTGGCCCGAATGGCCCAGGCGATGATGGC1140
ZS ACCAATTTTG GCGCTTTAGGGATATTGTCCCCTTTCTTAGACCCTGAAATATTGTTTGGC1200
AAAGAATTGA ATAAAGTCGCCATCATGCAATTAAGAGACATCATCCATGAATACGGCCAT1260
ACTTTAGGCT ATACGCATAACGGGAACATGACTTATCAAAGAGTGCGCATGTGCGAAGAA1320
AACAATGGGC CAGAAGAGCGCTGTCAGGGCGGAAGGATAGAGCAAGTGGATGGGAAAGAA1380
GTGCAAGTGT TTGACAACGGGCATGAAGTGCGAGACACCGATGGCTCTACCTATGATGTG1440
3O TGTTCTCGTT TTAAAGATAAGCCCTATACAGCGGGCAGCTATCCTAATTCCATCTATACC1500
GATTGCTCTC AAGTCCCCGCTGGGCTTATAGGCGTTACCAGCGCTGTTTGGCAACAACTC1560
ATTGATCAAA ACGCCCTACCGGTGGATTTTACTAATTTGAGCAGCCAAACCAACTATTTG1620
AACGCCAGCT TGAACACGCAAGACTTTGCGACCACCATGCTTAGCGCGATCAGTCAAAGC1680
CTTTCATCTT CTAAATCTAGCGCCACTACTTATCGCACTTCAAAAACCTCACGGCCCTTT1740
3S GGAGCCCCCC TATTAGGCGTTAATCTTAAAATGGGCTATCAAAAATATTTTAATGATTAT1800
CTAGGGTTGT CTTCTTATGGCATTATCAAATACAACTACGCTCAAGCCAACAACGAAAAA1860
ATCCAGCAAT TAAGCTATGGCGTGGGAATGGATGTGCTGTTTGATTTCATCACCAATTAC1920
ACTAACGAAA AGAACCCCAAAAGCAATCTAACCAAGAAAGTTTTCACTTCCTCTCTTGGG1980
GTGTTTGGGG GGTTAAGGGGCTTATACAACAGCTATTATTTGTTGAACCAATACAAAGGG2040
4O AGCGGTAATT TAAATGTGACCGGTGGGTTGAATTACCGCTACAAGCATTCCAAATATTCT2100
ATAGGCATTA GCGTTCCTTTGGTCCAGTTGAAATCTAGGATCGTTTCTAGCGATGGTGCT2160
TATACCAATT CTATCACCCTCAATGAAGGGGGCAGTCATTTTAAAGTGTTTTTTAATTAC2220
GGGTGGATTT TCTAA 2235
4S (2) INFORMATION FOR SEQ ID N0:8(':
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1590 base pairs
(B) TYPE: nucleic acid
SD (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
CA 02273199 1999-06-O1
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- 167 -
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
S (vi) ORIGINAL SOURCE:
(A) ORGANISN~' Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
1~ (B) LOCATION 1...1590
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:80:
ATGACTTATATCAATTACAACCAATTTTCTAGCGGTAACGGCAGTGGCTCTAAACCCCCA60
IS TGCCCCCCATACGAAAACCAAGCAAATTGTGTGGCTAAAGTGCCGCCTTTCACCTCTCAA120
GACGCTAAAAATTTGACCAATTTAATGCTGAACATGATGGCGGTGTTTGATTCTAAATCT180
TGGGAAGACGCCGTCTTAAACGCTCCTTTCCAATTCAGCGACAACAACCTGTCAGCGCCA240
TGTTATTCTGATTACCTTACATGCGTGAATCCTTACAACGATGGGCTTGTTGATCCTAAA300
TTGATCGCCAAAAATAAAGGAGATGAATACAATATAGAAAACGGGCAAACAGGCTCAGTG360
ZO ATATTAACGCCGCAAGATGTTATCTATAGCTATAGAGTCGCTAATAATATTTATGTGAAT420
CTCTTGCCCACAAGAGGAGGGGATTTAGGGTTAGGGTCTCAATATGGTGGCCCGAATGGC480
CCAGGCGATGATGGCACCAATTTTGGCGCTTTAGGGATATiGTCCCCTTTCTTAGACCCT540
GAAATATTGTTTGGCAAAGAATTGAATAAAGTCGCCATCATGCAATTAAGAGACATCATC600
CATGAATACGGCCATACTTTAGGCTATACGCATAACGGGAACATGACTTATCAAAGAGTG660
ZS CGCATGTGCGAAGAAAACAATGGGCCAGAAGAGCGCTGTCAGGGCGGAAGGATAGAGCAA720
GTGGATGGGAAAGAAGTGCAAGTGTTTGACAACGGGCATGAAGTGCGAGACACCGATGGC780
TCTACCTATGATGTGTGTTCTCGTTTTAAAGATAAGCCCTATACAGCGGGCAGCTATCCT840
AATTCCATCTATACCGATTGCTCTCAAGTCCCCGCTGGGCTTATAGGCGTTACCAGCGCT900
GTTTGGCAACAACTCATTGATCAAAACGCCCTACCGGTGGATTTTACTAATTTGAGCAGC960
3O CAAACCAACTATTTGAACGCCAGCTTGAACACGCAAGACTTTGCGACCACCATGCTTAGC1020
GCGATCAGTCAAAGCCTTTCATCTTCTAAATCTAGCGCCACTACTTATCGCACTTCAAAA1080
ACCTCACGGCCCTTTGGAGCCCCCCTATTAGGCGTTAATCTTAAAATGGGCTATCAAAAA1140
TATTTTAATGATTATCTAGGGTTGTCTTCTTATGGCATTATCAAATACAACTACGCTCAA1200
GCCAACAACGAAAAAATCCAGCAATTAAGCTATGGCGTGGGAATGGATGTGCTGTTTGAT1260
3S TTCATCACCAATTACACTAACGAAAAGAACCCCAAAAGCAATCTAACCAAGAAAGTTTTC1320
ACTTCCTCTCTTGGGGTGTTTGGGGGGTTAAGGGGCTTATACAACAGCTATTATTTGTTG1380
AACCAATACAAAGGGAGCGGTAATTTAAATGTGACCGGTGGGTTGAATTACCGCTACAAG1440
CATTCCAAATATTCTATAGGCATTAGCGTTCCTTTGGTCCAGTTGAAATCTAGGATCGTT1500
TCTAGCGATGGTGCTTATACCAATTCTATCACCCTCAATGAAGGGGGCAGTCATTTTAAA1560
4O GTGTTTTTTAATTACGGGTGGATTTTCTAA 1590
(2) INFORMATION FOR SEQ ID N0:81:
(i) SEQUENCE CHARACTERISTICS:
4S (A) LENGTH: 564 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S~ (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-168-
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...564
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: B1:
lO
TTGGGTTGCG TATCAATGACTCTAGGTATT GATGAAGCGGGGAGGGGGTGTTTGGCCGGT60
TCGCTTTTTG TGGCGGGGGTGGTGTGTAAT GAAAAAATAGCCTTAGAATTTCTAAAAATG-120
GGTCTTAAGG ATAGCAAGAAGCTCAGCCCC AAAAAGCGCTTTTTCTTAGAAGATAAAATC180
AAAACGCATG GTGAGGTGGGGTTTTTCGTG GTTAAAAAAAGCGCGAATGAAATTGATCAT240
IS TTGGGCTTAG GGGCGTGTTTGAAACTCGCT ATTGAAGAAATTGTAGAAAA~'GGTTGCTCT300
TTAGCCAATG AAATAAAAATAGATGGCAAC ACGGCGTTTGGCTTGAACAAACGCTACCCC360
AACATACAAA CCATCATCAAGGGCGATGAA ACAATCGCTCAAATCGCTATGGCGTCTGTT420
TTGGCGAAAG CTTCTAAGGATAGGGAAATG TTAGAACTGCACGCTTTGTTTAAGGAATAC480
GGCTGGGATA AGAATTGCGGGTATGGGACT AAACAACATATAGAAGCGATCAATAAGCTA540
ZO GGGGCTACGC TTTCATCGGCATAG
564
(2) INFORMATION FOR SEQ ID N0:82:
(i) SEQUENCE CHARACTERISTICS:
2S (A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4O (A) NAME/KEY: misc_feature
(B) LOCATION 1...615
(xi} SEQUENCE DESCRIPTION: SEQ ID N0:82:
4S ATGACTCTAG GTATTGATGA AGCGGGGAGG GGGTGTTTGG TTTTGTGGCG 60
CCGGTTCGCT
GGGGTGGTGT GTAATGAAAA AATAGCCTTA GAATTTCTAA AAATGGGTCTTAAGGATAGC 12~
AAGAAGCTCA GCCCCAAAAA GCGCTTTTTC TTAGAAGATA AAATCAAAACGCATGGTGAG 180
GTGGGGTTTT TCGTGGTTAA AAAAAGCGCG AATGAAATTG ATCATTTGGGCTTAGGGGCG 240
TGTTTGAAAC TCGCTATTGA AGAAATTGTA GAAAATGGTT GCTCTTTAGCCAATGAAATA 300
SO AAAATAGATG GCAACACGGC GTTTGGCTTG AACAAACGCT ACAAACCATC 360
ACCCCAACAT
ATCAAGGGCG ATGAAACAAT CGCTCAAATC GCTATGGCGT CTGTTTTGGCGAAAGCTTCT 420
AAGGATAGGG AAATGTTAGA ACTGCACGCT TTGTTTAAGG AATACGGCTGGGATAAGAAT 480
TGCGGGTATG GGACTAAACA ACATATAGAA GCGATCAATA AGCTAGGGGCTACGCCTTTT 540
CATCGGCATA GCTTCACGCT TAAAAACCGC ATCTTAAATC CCAAACTCTTAGAGGTGGAA 600
__._ _~..___ .. _.. .~_.._re___ T....
CA 02273199 1999-06-O1
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- 169 -
CAACGCCTTG TTTAA 615
(2) INFORMATION FOR SEQ ID N0:83:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 579 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...579
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:83:
ATGAATGCAT TGAAAP~AATT AAGTTTTTGCGCCTTGTTATCCCTAGGCCTCTTCGCTCAA60
ACAGTGCATG CTCAGCATTT AAAGGACACGATTAACTATCCTGATTGGCTTAAAATCAAT120
CTTTTTGATA AAAAGAACCC GCCCAATCAATATGTCGGATCGGCTTCAATTTCTGGTAAA180
AGGAACGATT TTTATTCCAA TTACATCCCCTATGATGACAAATTGCCCCCTGAAAAGAAC240
3O GCTGAAGAAATCGCTCTTTT AAGGGCCAGAATGAACGCTTACAGCACTTTAGAAAGCGCT300
TTACTCACTA AAATGTGCAA TCGCATTGTTAAAGCGCTTCAAGTTAAAAATAATGTTATC360
AGCCATTTAT TCGGGTTTGT TGATTTTTTAACGTCTAAATCCATTTTGGCTAAAAGGTTC420
GTGGATACCA CCAACCATCG TGTGTATGTCATGGTGCAATTCCCTTTCATTCAGCCTGAA480
GACTTAATCG CTTACTTTAA AGCCAAACGCATCGACCTTTCTTTAGCGAGCGCTACCAAT540
3S CTCAGCGCCATTTTAAACAA GGCGTTGTTCCACCTCTAA 579
(2) INFORMATION FOR SEQ ID N0:84:
(i) SEQUENCE CHARACTERISTICS:
40 (A) LENGTH: 261 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
4S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
SO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
CA 02273199 1999-06-O1
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(A) NAME/KEY: misc_feature
(B) LOCATION 1...261
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:84:
S
ATGAATGCAT TGAAAAAATT AAGTTTTTGC GCCTTGTTAT CCCTAGGCCT CTTCGCTCAA 60
ACAGTGCATG CTCAGCATTT AAAGGACACG ATTAACTATC CTGATTGGCT TAAAATCAAT 120
CTTTTTGATA AAAAGAACCC GCCCAATCAA TATGTCGGAT CGGCTTCAAT TTCTGGTAAA 180
AGGAACGATT TTTATTCCAA TTACATCCCC TATGATGACA AATTGCCCCC TGAAAGAACG 240
lO CTGAAGAAAT CGCTCTTTTA A 261
(2) INFORMATION FOR SEQ ID N0:85:
(i) SEQUENCE CHARACTERISTICS:
1S (A) LENGTH: 228 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
20 (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
2S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
30 (A) NAME/KEY: misc_feature
(B) LOCATION 1...228
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:85:
3S TTGAAAATTT TAACCCTTTT TTTGATAGGT TTAAACGCATTGTTCGCCCT AGATTTGAAC60
GCGCTTAAAA CAGAAATCAA AGAAACCTAT CTCAAAGAATACAAAGACTT AAAATTGGAA120
ATTGAAACAA TTAATTTAGA AATCCCAGAG CGTTTTTCTCACGCTTCCAT TTTAAGCTAT180
GAATTGAACG CTTCTAACAA GCTTAAAAAA GATGGGTCGTGTTTTTAA 228
4O (2) INFORMATION FOR SEQ ID N0:86:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 636 base pairs
(B) TYPE: nucleic acid
4S (C) STRANDEDNESS: double
(D) TOPOLOG'-: circular
(ii) MOLECULE TYPE: DNA (genomic)
SO (iii) HYPOTHETICAL: NO
(iv} ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
CA 02273199 1999-06-O1 -
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-171-
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
S (B) LOCATION 1...636
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:86:
ATGTTTTCAA TAATTCTGGG GGGGGGGGGG GGTAATACCC CATGCGGCTT GACATGGCAA 60
lO CACTTCAAATTAGGGGATTTGTTTGAAATTGAAAAAACCTTAAGCTTTAATAAAGACGCT120
TTAACGCAAGGACAAGATTACGATTATATTACAAGAACTTCGCAAAATCAAGGCGTTTTG180
CAAACTACAGGATTTGTCAATGCAGAAAATTTAAACCCACCATTTACTTGGAGTTTAGGG240
CTTTTGCAAATGGATTTTTTCTATCGTAAAAAGTCATGGTATGCGGGACAATTCATGCGA300
AAAATCACACCAAAAACTGAAATTAAAAATAAAATTAATTCACGCATAGCCCACTATTTC360
IS ACAACGCTTTTAAACGCCTTAAAACGCCCTTTATTGAGTGTATTAGTTAGGGATATTGAT420
AAAACTTTTAGGGAGCAAAAAATCCAACTACCCCTAAAACCCACCGCTAAAACTCAAAGC480
CTTGATGGTATTGATTTTGATTTCATGCACACCCTAATCAACGCCCTGATGAAGCAAACC540
ATTCAAGGCGTGGTTCAATACTGCGACGCTAAAATACAGGCTACAAAAGAAGTTATCAGC600
CAAGAAACGCCTATTCAAAAAGACTCGTTATTTTGA 636
20
(2) INFORMATION FOR SEQ ID N0:87:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1221 base pairs
2S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
3S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1221
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:87:
GTGATTGGCC CCCTTAGCAGCCAACTCAACGCTATTAAGTGGGGCGAGTTCAAATTAGGG60
4S GATTTGTTTGAAGCGAGTAACGGCGATTTTGACATTCAAAAACGCCACATCAATCATAAG120
GGCGAATTTG TCATCACCGCAGGGCTTAGCAATAATGGCGTTTTAGGGCAAAGCGATATA180
AAAGCAAAAG TTTTTGAAAGCCATACCATTACTATTGACATGTTTGGTTGCGCGTTTTAT240
CGCAGTTTTG CTTATAAAATGGTAACACATGCTAGGGTATTTTCTCTCAAACCTAAATTT300
GAAATCAACC ATAAAATCGGCTTGTTTTTATCCACGCTATTTTTTGGTTACCATAAAAAA360
SO TTCGGCTATGAAAACATGTGTTCATGGGCAAAAATTAAAAACGATAAAGTCATTCTACCC420
CTAAAACCCA CCGCTAACACTCAAACCCTTGAGGGTATTGATTTTGATTTCATGGAAAAA480
TTCATAGCCG AACTTGAGCAGTGTCGGCTCGCCGAACTTCAGGCTTATTTAAAAGCTACA540
GGGCTAGAAA ACACCACCCTTTCTAACGATGAAGAAAATGCCCTTAATGTTTTCAATAAT600
TCTGGGGGGG GGGGGGGTAATACCCCATGCGGCTTGACATGGCAACACTTCAAATTAGGG660
SO AAAATAGATG GCAACACGGC GTTTGGCTTG AACAAACGCT ACAAACCATC 360
ACCCCAACAT
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GATTTGTTTG AAATTGAAAA AACCTTAAGC TTTAATAAAG ACGCTTTAAC GCAAGGACAA 720
GATTACGATT ATATTACAAG AACTTCGCAA AATCAAGGCG TTTTGCAAAC TACAGGATTT 780
GTCAATGCAG AAAATTTAAA CCCACCATTT ACTTGGAGTT TAGGGCTTTT GCAAATGGAT 840
TTTTTCTATC GTAAAAAGTC ATGGTATGCG GGACAATTCA TGCGAAAAAT CACACCAAAA 900
S ACTGAAATTA AAAATAAAAT TAATTCACGC ATAGCCCACT ATTTCACAAC GCTTTTAAAC 960
GCCTTAAAAC GCCCTTTATT GAGTGTATTA GTTAGGGATA TTGATAAAAC TTTTAGGGAG 1020
CAAAAAATCC AACTACCCCT AAAACCCACC GCTAAAACTC AAAGCCTTGA TGGTATTGAT 1080
TTTGATTTCA TGCACACCCT AATCAACGCC CTGATGAAGC AAACCATTCA AGGCGTGGTT 1140
CAATACTGCG ACGCTAAAAT ACAGGCTACA AAAGAAGTTA TCAGCCAAGA AACGCCTATT 1200
lO CAAAAAGACT CGTTATTTTG A 1221
(2) INFORMATION FOR SEQ ID N0:8B:
(i) SEQUENCE CHARACTERISTICS:
15 (A) LENGTH: 828 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
2O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
3O (A) NAME/KEY: misc_feature
(B) LOCATION 1...828
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:88:
3S ATGAGTAAGA GTTTATACCA AACTTTAAAC GTGAGCGAAA 60
ACGCCAGCCA AGATGAAATC
AAAAAATCCT ACCGCCGTTT AGCCAGGCAA TACCACCCGGATTTGAATAAAACCAAAGAA120
GCCGAAGAGA AATTCAAAGA AATCAACGCC GCTTATGAAATTTTGAGCGATGAAGAAAAA180
CGCCGCCAAT ACGATCAATT TGGCGACAAC ATGTTTGGCGGGCAGAATTTCAGCGATTTT240
GCCAGAAGCC GTGGTCCTAG TGAAGATTTA GATGATATTTTAAGCTCTATTTTTGGGAAA300
4O GGAGGCTTTT CGCAAAGATT TTCTCAAAAT TCGCAAGGCTTTTCTGGCTTTAATTTTTCC360
AATTTCGCCC CTGAAAATTT AGATGTAACC GCTATTTTAAATGTCTCTGTTTTAGACACC420
CTTTTAGGCA ATAAAAAACA AGTGAGCGTC AATAATGAGACTTTTAGCCTTAAAATCCCT480
ATCGGCGTGG AAGAGGGCGA AAAGATTAGG GTTCGCAACAAAGGGAAAATGGGGCGAACG540
GGTAGGGGCG ATTTGCTCTT ACAGATCCAT ATTGAAGAAGATGAAATGTATAGGCGCGAA600
4S AAAGACGATA TTATCCAAAT CTTTGATTTA CCCTTAAAAACGGCTCTTTTTGGAGGGAAA660
ATTGAAATCG CTACTTGGCA TAAAACCTTA ACCCTAACCATTCCCCCTAACACCAAAC..:C720
ATGCAAAAAT TCCGCATCAA AGACAAAGGG ATCAAAAGCAGAAAAACTTCGCATGTGGGG780
GATTGTATTG CAAGCTCGTT TGATCTGCTA AAATTGAAACGCTTCTAA g2g
SO (2) INFORMATION FOR SEQ ID N0:89:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 837 base pairs
(B) TYPE: nucleic acid
CA 02273199 1999-06-O1
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(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
IO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
1S (B) LOCATION 1...837
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:89:
ATGAGTAAGA GTTTATACCA AACTTTAAAC GTGAGCGAAA ACGCCAGCCA AGATGAAATC 60
ZOAAAAAATCCT ACCGCCGTTTAGCCAGGCAA ATTTGAATAA 120
TACCACCCGG AACCAAAGAA
GCCGAAGAGA AATTCAAAGAAATCAACGCCGCTTATGAAATTTTGAGCGATGAAGAAAAA180
CGCCGCCAAT ACi~ATCAATTTGGCGACAACATGTTTGGCGGGCAGAATTTCAGCGATTTT240
GCCAGAAGCC GTGGTCCTAGTGAAGATTTAGATGATATTTTAAGCTCTATTTTTGGGAAA300
GGAGGCTTTT CGCAAAGATTTTCTCAAAATTCGCAAGGCTTTTCTGGCTTTAATTTTTCC360
ZSAATTTCGCCC CTGAAAATTTAGATGTAACCGCTATTTTAAATGTCTCTGTTTTAGACACC420
CTTTTAGGCA ATAAAAAACAAGTGAGCGTCAATAATGAGACTTTTAGCCTTAAAATCCCT480
ATCGGCGTGG AAGAGGGCGAAAAGATTAGGGTTCGCAACAAAGGGAAAATGGGGCGAACG540
GGTAGGGGCG ATTTGCTCTTACAGATCCATATTGAAGAAGATGAAATGTATAGGCGCGAA600
AAAGACGATA TTATCCAAATCTTTGATTTACCCTTAAAAACGGCTCTTTTTGGAGGGAAA660
3OATTGAAATCG CTACTTGGCATAAAACCTTAACCCTAACCATTCCCCCTAACACCAAAGCC720
ATGCAAAAAT TCCGCATCAAAGACAAAGGGATCAAAAGCAGAAAAACTTCGCATGTGGGG780
GATTGTATTG CAAGCTCGTTTGATCTGCCTAAAATTGAAACGCTTCTAATGAGTTGA 837
3S
(2) INFORMATION FOR SEQ ID N0:90:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 699 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
4O (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
' (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
SO
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...699
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(xi) SEQUENCE DESCRIPTION: SEQ ID N0:90:
GTGGTTCAAA TTATAAGACAGGTGGCATGCGTTTAAAACATTTTAAGACA60
AATTTAATTT
TTCCTTTTTA TCACAATGGCGGTGATTGTGATAGGCACTGGTTGTGCGAATAAAAAGAAA120
S AAAAAAGATG AATACAACAAACCGGCGATCTTTTGGTATCAAGGGATTTTGAGAGAAATT1B0
CTTTTTGCTA ATTTAGAAACAGCGGACAATTACTATTCTTCCTTACAGAGCGAACACATC240
AATTCCCCCC TTGTCCCAGAAGCTATGCTAGCTTTAGGGCAAGCGCACATGAAAAAGAAA300
GAGTATGTTT TAGCGTCTTTTTACTTTGATGAATACATCAAGCGCTTTGGGACGAAGGAC360
AATGTGGATT ATTTGACCTTTTTGAAACTGCAATCGCATT.ATTACGCTTTCAAAAACCAT420
IOTCTAAAGACC AGGAATTTATCTCTAATTCTATTGTGAGTTTAGGCGAATTTATAGAAAAA480
TACCCTAACA GCCGTTACCGCCCCTATGTAGAATACATGCAAATCAAATTCATTTTAGGG540
CAAAATGAGC TCAATCGCGCGATCGCGAATGTCTATAAAAAACGCCACAAGCCCGAGGGC600
GTGAAACGCT ATTTAGAAAGGATAGATGAGACTTTAGAAAAAGAGACTAAACCCAAACCA660
TCGCACATGC CTTGGTATGTGTTAATTTTTGATTGGTAG Egg
1S
(2) INFORMATION FOR SEQ ID N0:91:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 345 base-pairs
2O (B) TYPE: nucleic acid
(C) STR.ANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2S
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
3O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
3S (B) LOCATION 1...345
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:91:
ATGCGTTTTT TGAATAACAA ACATAGAGAA AAGGGCTTAA AGAAGCTTGC60
AGGCTGAAGA
4O GGGTTTTTAA AAACGCTGGG TTTTGAAATG ATAGAGAGGAACTTTTTTTCACAATTTGGT120
GAAATTGATA TTATCGCTTT GAAAAAAGGG GTTTTGCATTTCATTGAAGTCAAAAGCGGG180
GAAAATTTTG ATCCCATTTA TGCGATCACG CCGAGCAAATTAAAAAAGATGATTAAAACG240
ATCCGCTGTT ATTTGTCTCA AAAAGATCCC AATAGCGATTTTTGCATTGACGCTCTTATT300
GTGAAAAATG GTAAATTTGA GCTTTTAGAA AATATCACTTTTTAG 345
4S
(2) INFORMATIC_: 'OR SEQ ID N0:92:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 306 base pairs _
SO (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
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(iii) HYPOTHETICAL: NO
S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
IO (A) NAME/KEY: misc_feature
(B) LOCATION 1...306
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:92:
IS ATGGGCAGCATTGGGGCTATGACTAAAGGGAGCTCTGATAGGTATTTTCAAGAGGGCGTG60
GCGAGTGAAA AATTAGTCCCAGAAGGCATTGAGGGGCGTGTGCCTTATCGTGGTAAGGTT120
TCGGATATGA TTTTCCAATTAGTAGGGGGCGTGCGTTCTTCTATGGGGTATCAGGGGGCG180
AAGAATATTT TGGAATTGTATCAAAACGCTGAATTTGTAGAAATCACTAGCGCGGGGTTA240
AAAAAAAGCC ATGTGCATGGCGTGGATATTACTAAAGAAGCCCCTAATATTATGGGTGAA300
ZO TTTTAA 306
(2) INFORMATION FOR SEQ ID N0:93:
(i) SEQUENCE CHARACTERISTICS:
ZS (A) LENGTH: 1446 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3O (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4O (A) NAME/KEY: misc_feature
(B) LOCATION 1...1446
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:93:
~S ATGAGAATTT TACAAAGGGC TTTGACTTTT GAAGACGTGT TGATGGTGCC TAGAAAATCC 60
AGCGTTTTAC CTAAAGATGTGAGCTTAAAGTCTCGCCTAACCAAAAACATTGGTTTGAAT 120
ATCCCTTTTA TTAGTGCGGCTATGGATACGGTTACAGAGCATAAAACCGCTATCGCTATG 180
GCGCGCCTTG GGGGTATTGGCATCGTGCATAAAAACATGGATATTCAAACGCAAGTCAAA 240
GAAATCACTA AAGTTAAAAAAAGCGAGAGCGGGGTGATTAATGATCCTATTTTTATCCAT 300
- SO GCGCACAGGA CGCTAGCGGACGCTAAAGTCATAACGGATAATTATAAGATTTCAGGCGTG 360
CCTGTGGTAG ATGATAAGGG GTTGTTGATT GGGATTTTAA CCAACAGAGA CGTGCGTTTT 420
GAAACCGATT TGAGTAAAAA AGTGGGCGAT GTGATGACTA AAATGCCTTT AGTTACCGCT 480
CATGTGGGCA TTAGCTTAGA TGAAGCGAGC GATTTGATGC ACAAGCATAA GATTGAAAAA 540
TTGCCCATTG TGGATAAAGA TAATGTTTTA AAAGGCTTGA TCACGATCAA AGACATTCAA 600
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AAACGCATTG GGCCAATAAA GATGATTTTGGGAGGTTGAGAGTGGGGGCG660
AATACCCTGA
GCTATTGGAGTGGGGCAGTTGGATAGGGCT GAAATGTTAGTTAAAGCGGGGGTGGATGCG720
TTGGTGTTAGACAGCGCGCATGGGCATTCA GCCAATATTTTACACACTTTAGAAGAGATT780
AAAAAAAGCTTGGTAGTGGATGTGATTGTG GGGAATGTGGTTACTAAAGAAGCCACAAGCB40
S GATTTGATTAGCGCGGGAGCGGACGCTGTT AAAGTGGGTATTGGGCCAGGAAGCATTTGC900
ACCACTAGGATTGTGGCCGGGGTGGGAATG CCCCAAGTGAGCGCAATTGATAATTGCGTG960
GAAGTGGCGTCTAAATTTGATATTCCTGTG ATTGCCGATGGAGGGATCCGCTATTCAGGC1020
GATGTGGCTAAGGCTCTAGCTTTAGGAGCA TCAAGCGTGATGATAGGCTCTTTACTCGCT1080
GGCACAGAAGAATCTCCAGGGGATTTTATG ATTTACCAAGGGAGGCAATATAAAAGCTAT1140
lO AGGGGCATGGGCAGCATTGGGGCTATGACT AAAGGGAGCTCTGATAGGTATTTTCAAGAG1200
GGCGTGGCGAGTGAAAAATTAGTCCCAGAA GGCATTGAGGGGCGTGTGCCTTATCGTGGT1260
AAGGTTTCGGATATGATTTTCCAATTAGTA GGGGGCGTGCGTTCTTCTATGGGGTATCAG1320
GGGGCGAAGAATATTTTGGAATTGTATCAA AACGCTGAATTTGTAGAAATCACTAGCGCG1380
GGGTTAAAAGAAAGCCATGTGCATGGCGTG GATATTACTAAAGAAGCCCCTAATTATTAT1440
1S GGGTGA 1446
(2) INFORMATION FOR SEQ ID N0:94:
(i) SEQUENCE CHARACTERISTICS:
20 (A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS:double
(D) TOPOLOGY: circular
ZS (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
3S (A) NAME/KEY: misc_feature
(B) LOCATION 1...615
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:94:
4O ATGCAAGGGT TTCTTTTACA AACACAAAGC ATAAGAGATG CGTGCACGTT 60
AAGATTTGAT
TTAACCAAAA ACCAGCTCAA AACCCTCTAT CGTTTCTATG CAGCGTGCTG 120
GCAAACGCCA
AATGTGGGTC GTAAAATTGA TTTTGAAGAA GAAAACGATG ACCCAAGTTA 180
ATAAATTTTT
AGGAATATTT TGCATTTAGG CTATATTTGG GAAAGAGAAA GTTTTTTTGG 240
TGGAGCGCTT
CAACGCTTTT GCGCTCTTTT GTTCAAGCAT TTAGAGGGCG AGATAGCATC 300
TGCATTCTTT
4S TATTTTGACA CTTTAGATGA TGGGGCTAGC AAACTCTCCA CTT~AGAGTG 360
AACAGCACCC
ATTTTAGAAA TGTATGCAGT CCTTTTGAAT TTTGAAGGGC _T.CAATTCT 420
GCTTGCAAAG
TGTTTTTTAT GCGATGCAAA ATTAGAGCGT TCTGTCGCTT GTTTATTTTA 480
TAGCGCAAGG
GCGCACCCCT CTTGCTTGAA AGCTAAAAGC TTGGATTTAG AGCTTTTTTC 540
AAi~.AAATCCA
CGCACTCAAA GCACGATTGA TCTAGAAACA GAAGAAGTGG GCGCACGCTG 600
AAGAATTATG
SO AATTTAGGGT TTTGA 615
(2) INFORMATION FOR SEQ ID N0:95:
(i) SEQUENCE CHARACTERISTICS:
.._._._~_ , .._. . ____..__..~a~ T_..
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(A) LENGTH: 249 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
lO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IS (ix) FEATURE: _
(A) NAME/KEY: misc_feature
(B) LOCATION 1...249
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:95:
20
ATGGGCGTCG GACGGGTCGG CAATATGGCA CTGTTGGCGTGTGCAGGTCC GATGGGCATC
60
GGCGCTATTG CTATCGCCAT TAACGGCGGC AGACAACGGTCGCGGF~TGTT GGTGGTCGAT
120
ATAGACGACA AACGTCTGGA GCAGGTACAG AAGATGCTGCCGGGGAATTG GCGGCCAGTA
180
ACGGCATTGA GCTGGTGTCT GTGCATACCA AAGCGAGGAGCGATCCGTGC CAGATGCTGC
240
25 GAGCGCTGA 249
(2) INFORMATION FOR SEQ ID N0:96:
(i) SEQUENCE CHARACTERISTICS:
30 (A) LENGTH: 204 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3$ (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
{iv) ANTI-SENSE: NO
40
(vi) ORIGINAL SOURCE:
{A) ORGANISM: Helicobacter pylori
- {ix) FEATURE:
--- 4$ (A) NAME/KEY: misc_featvre
(B) LOCATION 1...204
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:96:
SO TTGTCCGGTA CAGCCGTGAG TTGCCGGTGC ACATGCCGCATACAGTTGGT ATTGGTGCGC
60
ACCAGCATCC CGGTTGTTAT CGGGTGCTCA TGCCCATTCCTTTCCAGTAT TGGGTTCACA
120
ACGGGAACCC ACCAATCACC CGTTAAACGC TGCGGGGTTAACGCCGGAAA AACACCGTCA
180
AAAAAACATT TGCATTTAAA CTAA 204
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(2) INFORMATION FOR SEQ ID N0:97:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 345 base pairs
S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii} MOLECULE TYPE: DNA (genomic)
1~
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
IS (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...345
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:97:
GTGTGGCTGG CGGCGCTGGG CTTCCTGATCACCGCGGTGGGGCTGCCGGTGATCACCGTG60
ZS ATCGCCCTGG CCAAGGTCGG CGGTTCGTCGACGCCCTCAGCCATCCGATCGGCAGGTATG120
CCGGCGGCCT GCTGGCGGCG GTCTGCTACCTGGCGGTCGGCCCGCTGTTCGCCATTCCGC180
GCACCGCCAC GGTGTCCTTC GAAGGTCAGCGTGGTGCCGCTGCTCGGCGAAGAAGCGGCA240
CGGCGCTGTT CGTCTACAGC CTGGCGTACTTCCTCCTCGCCCTGGCCATCTCCCTCTACC300
CCGGTCGCCT GCTGGACACC GTCGGACGCTTCCTCGCCCCGCTGA 345
30
(2) INFORMATION FOR SEQ ID
N0:98:
(i) SEQUENCE CHARACTERISTICS :
(A) LENGTH: 228 amino a cids
3S (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
4O (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
_4S (ix) ?EATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...228
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:98:
S~
Met Arg Phe Lys Gly Ser Arg Val Glu Ala Phe Leu Gly Ala Leu Glu
1 5 10 15
Phe Gln Glu Asn Glu Tyr Glu Glu Phe Lys Glu Leu Tyr Glu Ser Leu
20 25 30
_... ...._ _.... .. ...w..-___ _.__._~._~___ __ .....
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Lys ThrLys GlnLysPro HisThr LeuPheIle SerCysVal AspSer
35 ~ 45
40
Arg ValVal ProAsnLeu IleThr GlyThrGln ProGlyGlu LeuTyr
50 55 60
$ Val IleArg AsnMetGly AsnVal IleProPro LysThrSer TyrLys
65 7~ 75 80
Glu SerLeu SerThrIle AlaSer ValGluTyr AlaIleAla HisVal
85 90 95
Gly ValGln AsnLeuIle IleCys GlyHisSer AspCysGly AlaCys
loo 105 llo
Gly SerIle HisLeuIle HisAsp GluThrThr LysAlaLys ThrPro
115 120 125
Tyr IleAla AsnTrpIle GlnPhe LeuGluPro IleLysGlu GluLeu
130 135 140
1$ Lys AsnHis ProGlnPhe SerAsn HisPheAla LysArgSer TrpLeu
145 150 155 160
Thr GluArg LeuAsnAla ArgLeu GlnLeuAsn AsnLeuLeu SerTyr
165 170 175
Asp PheIle GlnGluArg ValIle AsnAsnGlu LeuLysIle PheGIy
180 185 190
Trp HisTyr IleIleGlu ThrGly ArgIleTyr AsnTyrAsn PheGlu
195 200 205
Ser HisPhe PheGluPro IleGlu GluThrIle LysGlnArg IleSer
210 215 220
2$ His GluAsn Phe
225
(2) INFORMATION FOR SEQ ID N0:99:
3O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 221 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear ,
3$ (ii) MOLECULE TYPE: protein
- (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
4~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...221
4$
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:99:
Val Glu Ala Phe Leu Gly Ala Leu Glu Phe Gln Glu Asn Glu Tyr Glu
1 5 10 15
$0 Glu Phe Lys Glu Leu Tyr Glu Ser Leu Lys Thr Lys Gln Lys Pro His
25 30
Thr Leu Phe Ile Ser Cys Val Asp Ser Arg Val Val Pro Asn Leu Ile
35 40 45
Thr Gly Thr Gln Pro Gly Glu Leu Tyr Val Ile Arg Asn Met Gly Asn
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50 55 60
Val Ile ProProLys ThrSer TyrLysGlu SerLeuSer ThrIle Ala
65 70 75 80
Ser Val GluTyrAla IleAla HisValGly ValGlnAsn LeuIle Ile
S 85 90 95
Cys Gly HisSerAsp CysGly AlaCysGly SerIleHis LeuIle His
100 105 110
Asp Glu ThrThrLys AlaLys ThrProTyr IleAlaAsn TrpIle Gln
17.5 120 125
Phe Leu GluProIle LysGlu GluLeuLys AsnHisPro GlnPhe Ser
130 135 140
Asn His PheAlaLys ArgSer TrpLeuThr GluArgLeu AsnAla Arg
145 150 155 160
Leu Gln LeuAsnAsn LeuLeu SerTyrAsp PheIleGln GluArg Val
1S 165 170 _ 17~
Ile Asn AsnGluLeu LysIle PheGlyTrp HisTyrIle IleGlu Thr
180 185 190
Gly Arg IleTyrAsn TyrAsn PheGluSer HisPhePhe GluPro Ile
195 200 205
Glu Glu ThrIleLys GlnArg IleSerHis GluAsnPhe
210 215 220
(2) INFORMATION FOR SEQ ID NO:100:
ZS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 335 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
3S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...335
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:100:
Met Leu Val Thr Arg Phe Lys Lys Ala Phe Ile Ser Tyr Ser Leu Gly
1 5 10 15
-- 4$ Val Leu Val Val Ser Leu Leu Leu Asn Val Cys Asn Ala Ser Ala Gln
20 25 30
Glu Val Lys Val Lys Asp Tyr Phe Gly Glu Gln Thr Ile Lys Leu Pro
35 40 45
Val Ser Lys Ile Ala Tyr Ile Gly Ser Tyr Val Glu Val Pro Ala Met
S0 50 55 60
Leu Asn Val Trp Asp Arg Val Val Gly Val Ser Asp Tyr Ala Phe Lys
65 70 75 80
Asp Asp Ile Val Lys Ala Thr Leu Lys Gly Glu Asp Leu Lys Arg Val
85 90 95
r..__ __n..__... _~~.._.T....
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Lys HisMet SerThrAsp HisThrAla AlaLeu AsnValGlu LeuLeu
100 105 110
Lys LysLeu SerProAsp LeuValVal ThrPhe ValGlyAsn ProLys
115 120 125
S Ala ValGlu HisAlaLys LysPheGly IleSer PheLeuSer PheGln
130 135 140
Glu ThrThr IleAlaGlu AlaMetGln AlaMet GlnAlaGln AlaThr
145 150 155 160
Val LeuGlu IleAspAla SerLysLys PheAla LysMetGln GluThr
165 170 175
Leu AspPhe IleAlaGlu ArgLeuLys GlyVal LysLysLys LysGly
180 185 190
Val GluLeu PheHisLys AlaAsnLys IleSer GlyHisGln AlaIle
195 200 205
1S Ser SerAsp IleLeuGlu LysGlyGly IleAsp AsnPheGly LeuLys
210 215 220
Tyr ValLys PheGlyArg AlaAspIle SerVai GluLysIle ValLys
225 230 235 240
Glu AsnPro GluIleIle PheIleTrp TrpVal SerProLeu ThrPro
245 250 255
Glu AspVal LeuAsnAsn ProLysPhe SerThr IleLysAla IleLys
260 - 265 270
Asn LysGln ValTyrLys LeuProThr MetAsp IleGlyGly ProArg
275 280 285
2$ Ala ProLeu IleSerLeu PheIleAla LeuLys AlaHisPro GluAla
290 295 300
Phe LysGly ValAspIle AsnAlaIle ValLys AspTyrTyr LysVal
305 310 315 320
Val PheAsp LeuAsnAsp AlaGluIle GluPro PheLeuTrp His
325 330 335
(2) INFORMATION FOR SEQ ID NO:101:
(i) SEQUENCE CHARACTERISTICS:
3$ (A) LENGTH: 274 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL- SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...274
SO (xi) SEQUENCE DESCRIPTION: SEQ ID NO:101:
Met Leu Val Thr Arg Phe Lys Lys Ala Phe Ile Ser Tyr Ser Leu Gly
1 5 10 15
Val Leu Val Val Ser Leu Leu Leu Asn Val Cys Asn Ala Ser Ala Gln
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20 25 30
Glu Va1 Lys VaI Lys Asp Tyr Phe Gly Glu Gln Thr Ile Lys Leu Pro
35 40 45
Val Ser Lys Ile Ala Tyr Ile Gly Ser Tyr Val Glu Val Pro Ala Met
50 _ 55 60
Leu Asn Val Trp Asp Arg Val Val Gly Val Ser Asp Tyr Ala Phe Lys
65 70 75 80
Asp Asp Ile Val Lys Ala Thr Leu Lys Gly Glu Asp Leu Lys Arg Val
85 90 95
1~ Lys His Met Ser Thr Asp His Thr Ala Ala Leu Asn Val Glu Leu Leu
100 105 110
Lys Lys Leu Ser Pro Asp Leu Val Val Thr Phe Val Gly Asn Pro Lys
115 120 125
Ala Val Glu His Ala Lys Lys Phe Gly Ile Ser Phe Leu Ser Phe Gln
IS 130 135 140
Glu Thr Thr Ile Ala Glu Ala Met Gln Ala Met Gln Ala Gln Ala Thr
145 150 155 160
Val Leu Glu Ile Asp Ala Ser Lys Lys Phe Ala Lys Met Gln Glu Thr
165 170 175
2~ Leu Asp Phe Ile Ala Asg Arg Leu Lys Gly Val Lys Lys Lys Lys Gly
180 185 190
Val Glu Leu Phe His Lys Ala Asn Lys Ile Ser Gly His Gln Ala Ile
195 200 205
Asn Ser Asp Ile Leu Gln Gln Gly Gly Ile Asp Asn Phe Gly Leu Lys
25 210 215 220
Tyr Val Lys Phe Gly Arg Ala Asp Ile Ser Val Glu Lys Ile Val Lys
225 230 235 240
Glu Asn Pro Glu Ile Ile Phe Ile Arg Trp Val Thr Pro Leu Thr Pro
245 250 255
30 Asp Tyr Val Leu Asn Asn Pro Lys Phe Ser Thr Ile Asn Ala Ile Lys
260 265 270
Asn Ile
3S (2} INFORMATION FOR SEQ ID N0:102:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 428 amino acids
(B) TYPE: amino acid
4~ (D) TOPOLOGY: linear
(ii} MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
S~ (A) NAME/KEY: misc_feature
(B) LOCATION 1...428
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:102:
__ _~.....r....
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Met LysLys LysPheLeu SerLeu ThrLeuGly SerLeu LeuValSer
1 5 10 15
Ala LeuSer AlaGluAsp AsnGly PhePheVal SerAla GlyTyrGln
20 25 30
S Ile GlyGlu SerAlaGln MetVal LysAsnThr LysGly IleGlnAsp
35 40 45
Leu SerAsp SerTyrGlu ArgLeu AsnAsnLeu LeuThr AsnTyrSer
50 55 60
Val LeuAsn AlaLeuIle ArgGln SerAlaAsp ProAsn AlaIleAsn
1~ 65 70 75 80
Asn AlaArg GlyAsnLeu AsnAla SerAlaLys AsnLeu IleAsnAsp
85 90 95
Lys LysAsn SerProAla TyrGln AlaValLeu LeuAla LeuAsnAla
100 105 110
15 Ala AlaGly LeuTrpGln ValMet SerTyrAla IleSer ProCysGly
115 120 125
Pro GlyLys AspThrSer LysAsn GlyGlyVal GlnThr PheHisAsn
130 135 140
Thr ProSer AsnGlnTrp GlyGly ThrThrIle ThrCys GlyThrThr
20 145 150 155 160
Gly TyrGlu ProGlyPro TyrSer IleLeuSer ThrGlu AsnTyrAla
165 170 175
Lys IleAsn LysAlaTyr GlnIle IleGlnLys AlaPhe GlySerSer
180 185 190
25 Gly LysAsp IleProAla LeuSer AspThrAsn ThrGlu LeuLysPhe
195 200 205
Thr IleAsn LysAsnAsn GiyAsn ThrAsnThr AsnAsn AsnGlyGlu
210 215 220
Glu IleVal ThrLysAsn AsnAla GlnValLeu LeuGlu GlnAlaSer
3~ 225 230 235 240
Thr IleIle ThrThrLeu AsnSer AlaCysPro TrpIle AsnAsnGly
245 250 255
Gly AlaGly GlyAlaSer SerGly SerLeuTrp GluGly IleTyrLeu
260 265 270
3S Lys GlyAsp GlySerAla CysGly IlePheLys AsnGlu IleSerAla
275 280 285
Ile GlnAsp MetIleLys AsnAla AlaIleAla ValGlu GlnSerLys
290 295 300
Ile ValAla AlaAsnAla GlnAsn GlnArgAsn LeuAsp ThrGlyLys
4fl305 310 315 320
Thr PheAsn ProTyrLys AspAla AsnPheAia GlnSer MetPheAla
325 330 335
Asn AlaLys AlaGlnAla GluIle LeuAsnArg AlaGln AlaValVal
340 345 350
4S Lys AspPhe GluArgIle ProAla GluPheVal LysAsp SerLeuGly
355 360 365
Val CysHis GluValGln AsnGly HisLeuArg GlyThr ProSerGly
370 375 380
Thr ValThr AspAsnThr TrpGly AlaGlyCys AlaTyr ValGlyGlu
385 390 395 400
Thr ValThr AsnLeuLys AspSer IleAlaHis PheGly AspGlnAla
405 410 415
Glu ArgIle HisAsnAla ArgAsn LeuAlaThr Leu
420 425
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(2) INFORMATION FOR SEQ ID N0:103:
(i) SEQUENCE CHARACTERISTICS:
$ (A) LENGTH: 178 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
1~
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
1$
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...178
ZO (xi)SEQUENCE SEQID
DESCRIPTION: N0:103:
Met Asn -ProLeuLea GlnAspTyr AlaArgIle LeuLeu GluTrpAsn
1 5 10 15
Gln Thr HisAsnLeu SerGlyAla ArgAsnLeu SerGlu LeuGluPro
~$ 20 25 30
Gln Ile ThrAspAla LeuLysPro LeuGluPhe ValLys AspPheLys
35 40 45
Ser Cys LeuAspIle GlySerGly AlaGlyLeu ProAla IleProLeu
50 55 60
Ala Leu GluLysPro GluAlaGln PheIleLeu LeuGlu ProArgVal
65 70 75 80
Lys Arg AlaAlaPhe LeuAsnTyr LeuLysSer ValLeu ProLeuAsn
85 90 95
Asn Ile GluIleIle LysLysArg LeuGluAsp TyrGln AsnLeuLeu
3$ 100- 105 I10
Gln Val AspLeuIle ThrSerArg AlaValAla SerSer SerPheLeu
115 120 125
Ile Glu LysSerGln ArgPheLeu LysAspLys GlyTyr PheLeuPhe
130 135 140
4~ Tyr Lys GlyGluGln LeuLysAsn GluIleAla TyrLys ThrThrGlu
145 150 155 160
Cys Phe MetHisGln LysArgVal TyrPheTyr LysSer LysGluSer
165 170 175
Leu Cys
4$
(2) INFORMATION FOR SEQ ID N0:104:
(i) SEQUENCE CHARACTERISTICS:
$~ (A) LENGTH: 240 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...240
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:104:
Leu GlyLeu LysLysArg AlaIleLeu TrpSer LeuMetGly PheCys
1 5 10 15
IS Ala GlyLeu SerAlaLeu AspTyrAsp ThrLeu AspProLys TyrTyr
20 25 30
Lys TyrIle LysTyrTyr LysAlaTyr GluAsp LysGluVal GluGlu
35 40 45
Leu IIeArg AspLeuLys ArgAlaAsn AlaLys SerGlyLeu IleLeu
50 55 60
Gly IleAsn ThrGlyPhe PheTyrAsn HisGlu IleMetVal LysThr
65 70 75 80
Asn SerSer SerIleThr GlyAsnIle LeuAsn TyrLeuPhe AlaTyr
85 90 95
2.5Gly LeuArg PheGlyTyr GlnThrPhe ArgPro SerPhePhe AlaArg
100 105 110
Leu ValLys ProAsnIle IleGlyArg ArgIle TyrIleGln TyrTyr
115 120 125
Gly GlyAla ProLysLys AlaGlyPhe GlySer ValGlyPhe GlnSer
130 135 140
Val MetLeu AsnGlyAsp PheLeuLeu AspPhe ProLeuPro PheVal
145 150 155 160
Gly LysTyr LeuTyrMet GlyGlyTyr MetGly LeuGlyLeu GlyVal
165 170 175
35 Val AlaHis GlyValAsn TyrThrAla GluTrp GlyMetSer PheAsn
180 185 190
Ala GlyLeu AlaLeuThr ValLeuGlu LysAsn ArgIleGlu PheGlu
195 200 205
Phe LysIle LeuAsnAsn PheProPhe LeuGln SerAsnSer SerLys
4~ 210 215 220
Glu ThrTrp TrpGlyAla IleAlaSer IleGly TyrGlnTyr ValPhe
225 230 235 240
(2) INFORMATION FOR SEQ ID N0:105:
( i ) SEQUENC..~ .:HARACTERISTICS
(A) LENGTH: 313 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
Sfl
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
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(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
$ (A) NAME/KEY: misc_feature
(B) LOCATION 1...313
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:105:
Ifl Leu Lys Leu Lys Tyr Trp Leu Val Tyr Leu Ala Phe Ile Ile Gly Leu
1 5 10 15
Gln Ala Thr Asp Tyr Asp Asn Leu Glu Glu Glu Asn Gln Gln Leu Asp
20 25 30
Glu Lys Ile Asn Asn Leu Lys Arg Gln Leu Thr Glu Lys Gly Val Ser
1$ 35 40 45
Pro Lys Glu Met Asp Lys Asp Lys Phe Glu Glu Glu Tyr Leu Glu Arg
50 55 60
Thr Tyr Pro Lys Ile Ser Ser Lys Lys Arg Lys Lys Leu Leu Lys Ser
65 70 75 80
20 Phe Ser Ile Ala Asp Asp Lys Ser Gly Val Phe Leu Gly Gly Gly Tyr
85 90 95
Ala T~.~r Gly Glu Leu Asn Leu Ser Tyr Gln Gly Glu Met Leu Asp Arg
100 105 110
Tyr Gly Ala Asn Ala Pro Ser Ala Phe Lys Asn Asn Ile Asn Ile Asn
2$ 115 120 125
Ala Pro Val Ser Met Ile Ser Val Lys Phe Gly Tyr Gln Lys Tyr Phe
130 135 140
Val Pro Tyr Phe Gly Thr Arg Phe Tyr Gly Asp Leu Leu Leu Gly Gly
145 150 155 160
Gly Ala Leu Lys Glu Asn Ala Leu Lys Gln Pro Val Gly Ser Phe Phe
165 170 175
Tyr Val Leu Gly Ala Met Asn Thr Asp Leu Leu Phe Asp Met Pro Leu
180 185 190
Asp Phe Lys Thr Lys Lys His Phe Leu Gly Val Tyr Ala Gly Phe Gly
3$ 195 200 205
Ile Gly Leu Met Leu Tyr Gln Asp Lys Pro Asn Gln Asn Gly Arg Asn
2-10 215 2 2 0
Leu Ile Val Gly Gly Tyr Ser Ser Pro Asn Phe Leu Trp Lys Ser Leu
225 230 235 240
Ile Glu Val Asp Tyr Thr Phe Asn Val Gly Val Ser Leu Thr Leu Tyr
245 250 255
Arg Lys His Arg Leu Glu Ile Gly Thr Lys Leu Pro Ile Ser Tyr Leu
260 265 270
Arg Met Gly Val Glu Glu Gly Ala Ile Tyr His Asn Lys Glu Asn Asp
4$ 275 280 285
Glu Arg Leu Leu Ile Ser Ala Asn Asn Gln Phe Lys Arg Ser Ser Phe
290 295 300
Leu Leu Val Asn Tyr Ala Phe Ile Phe
305 310
$~
(2) INFORMATION FOR SEQ ID N0:106:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 393 amino acids
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(B) TYPE: amino acid _
(D) TOPOLOGY: linear
S
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...393
IS (xi) SEQUENCE DESCRIPTION: SEQ ID N0:106:
Met Thr SerAla SerSerHis SerPheLys GluGlnAsp PheHis Ile
1 5 10 15
Pro Ile AlaPhe AlaPheAsp LysAsnTyr LeuIlePro AlaGly Ala
20 25 30
Cys Ile TyrSer LeuLeuGlu SerIleAla LysAlaAsn LysLys Ile
35 40 45
Arg Tyr ThrLeu HisAlaLeu ValValGly LeuAsnGlu GluAsp Lys
50 55 60
2S Thr Lys LeuAsn GlnIleThr GluProPhe LysGluPhe AlaVal Leu
65 70 75 80
Glu Val LysAsp IleGluPro PheLeuAsp ThrIlePro AsnPro Phe
85 90 95
Asp Glu AspPhe ThrLysArg PheSerLys MetValLeu ValLys Tyr
loo l05 llo
Phe Leu AlaAsp LeuPhePro LysTyrSer LysMetVal TrpSer Asp
115 120 125
Val Asp ValIle PheCysAsn GluPheSer AlaAspPhe LeuAsn Ile
130 135 140
3S Lys Glu AspAsp GluAsnTyr PheTyrGly ValTyrAsp LysIle Tyr
145 150 155 160
Pro Tyr GluGly PhePheTyr CysAsnLeu ThrTyrGln ArgLys Asn
165 170 175
Gln Phe CysLys LysIleLeu GluIleIle ArgAlaGln LysIle Asp
180 185 190
Lys Glu ProGln LeuThrGlu PheCysArg SerLysIle AlaPro Leu
195 200 205
Lys Ile GluTyr CysIlePhe ProHisTyr TyrSerLeu SerGlu Glu
210 215 220
4S His Leu LysGly ValAlaAsn AlaIleTyr HisAsnThr IleLys '~ln
225 230 235 240
Ala Leu ArgGlu ProIleVaI IleGlnTyr AspSerHis ProTyr Phe
245 250 255
Gln Ile LysPro TrpThrTyr ProPheGly LeuLysAla AspLeu Trp
S0 260 265 270
Leu Asn AlaLeu AlaLysThr ProPheMet SerAspTrp SerTyr Leu
275 280 285
Ile Thr GlyGly GlyGlyIle GlyG.lyGlu LysTrpHis TyrTyr His
290 295 300
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Gly Ile Ala Ala Tyr His Tyr Tyr Phe Pro Leu Trp Lys Ala Glu Glu
305 310 315 320
Gln Ile Ala His Asp Ala Leu Lys Thr Phe Leu Lys His Tyr Phe Leu
325 330 335
S His Ile His Glu Ile Pro Gln Asn Ala Arg Arg Arg Leu Phe Lys Tyr
340 345 350
Cys Ile Ser Ile Pro Leu Lys Ser Phe Ile Ser Lys Thr Leu Lys Phe
355 360 365
Leu Lys Leu His Ala Leu Val Lys Lys Ile Leu Ile Gln Leu Lys Leu
370 375 380
Leu Lys Lys Asn Gln Ser Gln Asn Phe
385 390
(2) INFORMATION FOR SEQ ID N0:107:
1S
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 435 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
2S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...435
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:107:
Leu IlePheLeu LysLysSer LeuCysAla LeuLeu IleSerGly Phe
1 s to is
Phe IleProPro LeuMetLys AlaAlaSer PheVal TyrAspLeu Lys
20 25 30
Phe MetSerPhe AsnPheAsn LeuAlaSer ProPro AsnAsnPro Tyr
35 40 45
Trp AsnSerLeu ThrLysMet GlnGlyArg LeuMet ProGlnIle Gly
50 55 60
Val GlnLeuAsp LysArgGln AlaLeuMet PheGly AlaTrpPhe Ile
65 70 75 80
Gln AsnLeuHis ThrHisTyr SerTyrPhe ProTyr SerTrpGly Val
~S 85 90 95
Thr MetTyrTyr GlnTyrIle GlyLy:Asn LeuArg PhePheLeu Gly
100 105 110
Ile ValProArg SerTyrGln IleGlyHis TyrPro LeuSerAla Phe
115 120 125
_ _
S0 Lys LysLeuPhe TrpPheIle AspProThr PheArg GlyGlyAla Phe
130 135 140
Gln PheLysPro AlaTyrAsp ProAsnArg TrpTrp AsnGlyTrp Phe
145 I50 155 160
Glu GlyValVal AspTrpTyr GlyGlyArg AsnTrp AsnAsnGln Pro
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165 170 175
Lys Lys LysAsnTyr AspPhe AspGlnPhe LeuTyrPhe ValSerSer
180 185 190
Glu Phe GlnPheLeu LysGly TyrLeuGly LeuGlyGly GlnLeuVal
$ 195 200 205
Ile Phe HisAsnAla AsnSer HisSerMet GlyAspAsn TyrProTyr
210 215 220
Gly Gly AsnSerTyr LeuLys ProGlyAsp AlaThrPro GlnTrpPro
225 230 235 2.40
Asn Gly TyrProTyr PheSer GlnLysAsp AsnProGln GlyGlyGlu
245 250 255
Ile Gly LysTyrSer AsnPro ThrIleLeu AspArgVal TyrTyrHis
260 265 270
Ala Tyr LeuLysAla AspPhe LysAsnLeu MetProTyr MetAspAsn
1$ 275 280 285 _ -
Ile Phe MetThrPhe GlyThr GlnSerSer GlnThrHis TyrCysVal
290 295 300
Arg Tyr AlaSerGlu CysLys AsnAlaArg PheTyrAsn SerPheGly
305 310 315 320
Gly Glu PheTyrAla GlnAla GlnTyrLys GlyPheGly IlePheAsn
325 330 335
Arg Tyr TyrPheSer AsnLys ProGlnMet HisPheryr AlaThrTyr
340 345 350
Gly Gln SerLeuTyr ThrGly LeuProTrp TyrArgAla ProAsnPhe
Z$ 355 360 365
Asp Met IleGlyLeu TyrTyr LeuTyrLys AsnLysTrp LeuSerVal
370 375 380
Arg Ala AspAlaPhe PheSer PheValGly GlyGlyAsp GlyTyrHis
385 390 395 400
Leu Tyr GlyLysGly GlyLys TrpPheVal MetTyrGln GlnPheLeu
405 410 415
Thr Leu ThrIleAsp ThrArg GluLeuIle AspPheVal LysSerLys
420 425 430
Ile Pro Lys
3$ 435
(2) INFORMATION FOR SEQ ID N0:108:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 220 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
-- 4$
(iii) _i~ ?OTHETICAL: YES
(vi) ORIGINAL SOURCE: w
(A) ORGANISM: Helicobacter pylori
$0
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...220
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(xi) SEQUENCE DESCRIPTION: SEQ ID N0:108:
Met AsnLysThr ThrIleLys IleLeu MetGly MetAlaLeu LeuSer
1 5 10 15
Ser LeuGlnAla AlaGluAla GluLeu AspGlu LysSerLys LysPro
20 25 30
Lys PheAlaAsp ArgAsnThr PheTyr LeuGly ValGlyTyr GlnLeu
35 40 45
Ser AlaIleAsn ThrSerPhe SerThr SerSer IleAspLys SerTyr
50 55 60
Phe MetThrGly AsnGlyPhe GlyVal ValLeu GlyGlyLys PheVal
65 70 75 gp
Ala LysThrGln AlaValGlu HisVal GlyPhe ArgTyrGly LeuPhe
85 90 95
Tyr AspGlnThr PheSerSer HisLys SerTyr IleSerThr TyrGly
100 105 110
Leu GluPheSer GlyLeuTrp AspAla PheAsn SerProLys MetPhe
115 120 325
Leu GlyLeuGlu PheGlyLeu GlyIle AlaGly AlaThrTyr MetPro
130 135 140
Gly GlyAlaMet HisGlyIle IleAla GlnTyr LeuGlyLys GluAsn
145 150 1~5 160
Ser LeuPheGln LeuLeuVal LysVal GlyPhe ArgPheGly PhePhe
165 170 175
His AsnGluIle ThrPheGly LeuLys PhePro ValIlePro AsnLys
180 185 190
Lys ThrGluIle ValAspGly LeuSer AlaThr ThrLeuTrp GlnArg
195 200 205
Leu ProValAla TyrPheAsn TyrIle TyrAsn Phe
210 215 220
(2) INFORMATION FOR SEQ ID N0:209:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 116 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...116
- SO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:109:
Leu Asn Leu His Phe Met Lys Gly Phe Val Met Ser Gly Leu Arg Thr
1 5 10 15
Phe Ser Cys Val Val Val Leu Cys Gly Ala Met Val Asn Val Ala Val
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20 25 30
Ala Gly Pro Lys Ile Glu Ala Arg Gly Glu Leu Gly Lys Phe Val Gly
35 40 45
Gly Ala Val Gly Asn Phe Val Gly Asp Lys Met Gly Gly Phe Val Gly
S 50 55 60
Gly Ala Ile Gly Gly Tyr Ile Gly Ser Glu Val Gly Asp Arg Val Glu
65 70 75 80
Asp Tyr Ile Arg Gly Val Asp Arg Glu Pro Gln Asn Lys Glu Pro Gln
B5 90 95
Thr Pro Arg Glu Pro Ile Arg Asp Phe Tyr Asp Tyr Gly Tyr Ser Phe
100 105 110
Gly His Ala Trp
115
IS (2) INFORMATION FOR SEQ ID NO:110:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 436 amino acids
(B) TYPE: amino acid
2~ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
2S
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...436
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:110:
3S Me.tSer ArgAspPhe LysPhe AspSerAsn TyrLeu AsnValAsn Thr
1 5 10 15
Asn Pro LysLeuGly ProVal TyrThrAsn GlnAsn TyrProGly Phe
20 25 30
Phe Ile PheAspHis LeuArg ArgTyrVal MetAsn AlaPheGlu Pro
35 40 45
Asn Leu AsnLeuVal ValAsn ThrAsnLys ValLys GlnThrPhe Asn
50 55 60
Val Gly MetArgPhe MetThr MetAspMet PheIle ArgSerAsp Gln
65 70 75 80
4S Ser Thr CysGluLys ThrAsp IleIleAsn GlyVal CysFisMet Pro
85 90 95
Pro Tyr ValLeuSer LysThr ProAsnAsn AsnGln GluMetPhe Asn
100 105 110
Asn Tyr ThrAlaVal TrpLeu SerAspLys IleGlu PhePheAsp Ser
S~ 115 120 125
Lys Leu ValIleThr ProGly LeuArgTyr ThrPhe LeuAsnTyr Asn
130 135 140
Asn Lys GluProGlu LysHis AspPheSer ValTrp ThrSerLys Lys
145 150 155 160
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Gln Arg GlnAsn GluTrpSer ProAlaLeu AsnIle GlyTyrLys Pro
165 170 175
Met Glu AsnTrp IleTrpTyr AlaAsnTyr ArgArg SerPheIle Pro
180 185 190
$ Pro Gln HisThr MetValGly IleThrArg ThrAsn TyrAsnGln Ile
195 200 205
Phe Asn GluIle GluValGly GlnArgTyr SerTyr LysAsnLeu Leu
210 215 220
Ser Phe AsnThr AsnTyrPhe ValIlePhe AlaLys ArgTyrTyr Ala
1~ 225 230 235 240
Gly Gly TyrSer ProGlnPro ValAspAla ArgSer GlnGlyVal Glu
245 250 255
Leu Glu LeuTyr TyrAlaPro IleArgGly LeuGln PheHisVal Ala
260 265 270
1$ Tyr Thr TyrIle AspAlaArg IleThrSer AsnAla AspAsgI1e Ala
275 280 285
Tyr Tyr PheThr GlyIleVal AsnLysPro PheAsp IleLysGly Lys
290 295 300
Arg Leu ProTyr ValSerPro AsnGlnPhe IlePhe AspMetMet Tyr
2~ 305 310 315 320
Thr Tyr LysHis ThrThrPhe GlyIleSer SerTyr PheTyrSer Arg
325 330 335
Ala Tyr SerSer MetLeuAsn GlnAlaLys AspGln ThrValCys Leu
340 345 350
25 Pro Leu AsnPro GluTyrThr GlyGlyLeu LysTyr GlyCysAsn Ser
355 360 365
Val Gly LeuLeu ProLeuTyr PheValLeu AsnVal GlnValSer Ser
370 375 380
Ile Leu TrpGln SerGlyArg HisLysIle ThrGly SerLeuGln Ile
385 390 395 400
Asn Asn LeuPhe AsnMetLys TyrTyrPhe ArgGly IleGlyThr Ser
405 410 415
Pro Thr GlyArg GluProAIa ProGlyArg SerIle ThrAlaTyr Leu
420 425 430
35 Asn Tyr GluPhe
435
(2) INFORMATION FOR SEQ ID NO:111:
4O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 767 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
4S (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...767
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(xi) SEQUENCE DESCRIPTION: SEQ ID NO:111:
Met LysArgIle LeuVal SerLeu AlaValLeu SerHisSer AlaHis
1 5 10 15
Ala ValLysThr HisAsn LeuGlu ArgValGlu AlaSerGly ValAla
20 25 30
Asn AspLysGlu AlaPro LeuSer TrpArgSer LysGluVal ArgAsn
35 40 45
Tyr MetGlySer ArgThr ValIle SerAsnLys GlnLeuThr LysSer
50 55 60
Ala AsnGlnSer IleGlu GluAla LeuGlnAsn ValProGly ValHis
65 70 75 80
Ile ArgAsnSer ThrGly IleGly AlaValPro SerIleSer IleArg
85 90 95
Gly PheGlyAla GlyGly ProGly HisSerAsn ThrGlyMet IleLeu
100 105 110
Val AsnGlyIle ProIle TyrVal AlaProTyr ValGluIle GlyThr
115 120 125
Val IlePhePro ValThr PheGln SerValAsp ArgIleSer ValThr
130 135 140
Lys GlyGlyGlu SerVal AigTyr GlyProAsn AlaPheGly GlyVal
145 150 155 160
Ile AsnIleIle ThrLys GlyIle ProThrAsn TrpGluSer GlnVal
165 170 175
Ser GluArgThr ThrPhe TrpGly LysSerGlu AsnGlyGly PhePhe
180 185 190
Asn GlnAsnSer LysAsn IleAsp LysSerLeu ValAsnAsn MetLeu
195 200 205
Phe AsnThrTyr LeuArg ThrGly GlyMetMet AsnLysHis PheGly
210 215 220
Ile GlnAlaGln ValAsn TrpLeu LysGlyGln GlyPheArg TyrAsn
225 230 235 240
Ser ProThrAsp IleGln AsnTyr MetLeuAsp SerLeuTyr GlnIle
- 245 250 255
Asn AspSerAsn LysIle ThrAla PhePheGln TyrTyrSer TyrPhe
260 265 270
Leu ThrAspPro GlySer LeuGly IleAlaAla TyrAsnGln AsnArg
275 280 285
Phe GlnAsnAsn ArgPro AsnAsn AspLysSer GlyArgAla LysArg
290 295 300
Trp GlyAlaVal TyrGln AsnPhe PheGlyAsp ThrAspArg ValGly
305 310 315 320
Gly AspPheThr PheSer TyrTyr GlyHisAsp MetSerArg AspPhe
325 330 335
Ll: PheAspSer AsnTyr LeuAsn ValAsnThr AsnProLys LeuGly
340 345 350
Pro ValTyrThr AsnGln AsnTyr ProGlyPhe PheIlePhe AspHis
355 360 365
5~ Leu ArgArgTyr ValMet AsnAla PheGluPro AsnLeuAsn LeuVal
370 375 380
Val AsnThrAsn LysVal LysGln ThrPheAsn ValGlyMet ArgPhe
3B5 390 395 400
Met ThrMetAsp MetPhe IleArg SerAspGln SerThrCys GluLys
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405 410 415
Thr Asp Ile Ile Asn Gly Val ~Cys His Met Pro Pro Tyr Val Leu Ser
420 425 430
Lys Thr Pro Asn Asn Asn Gln Glu Met Phe Asn Asn Tyr Thr Ala Val
435 440 445
Trp Leu Ser Asp Lys Ile Glu Phe Phe Asp Ser Lys Leu Val Ile Thr
450 455 460
Pro Gly Leu Arg Tyr Thr Phe Leu Asn Tyr Asn Asn Lys Glu Pro Glu
465 470 475 480
I~ Lys His Asp Phe Ser Val Trp Thr Ser Lys Lys Gln Arg Gln Asn Glu
485 490 495
Trp Ser Pro Ala Leu Asn Ile Gly Tyr Lys Pro Met Glu Asn Trp Ile
500 505 510
Trp Tyr Ala Asn Tyr Arg Arg Ser Phe Ile Pro Pro Gln His Thr Met
IS 515 520 525
Val Gly Ile Thr Arg Thr Asn Tyr Asn Gln Ile Phe Asn Glu Ile Glu
530 535 540
Val Gly Gln Arg Tyr Ser Tyr Lys Asn Leu Leu Ser Phe Asn Thr Asn
545 550 555 560
Tyr Phe Val Ile Phe Ala Lys Arg Tyr Tyr Ala Gly Gly Tyr Ser Pro
565 570 575
Gln Pro Val Asp Ala Arg Ser Gln Gly Val Glu Leu Glu Leu Tyr Tyr
580 585 590
Ala Pro Ile Arg Gly Leu Gln Phe His Val Ala Tyr Thr Tyr Ile Asp
2$ 595 600 605
Ala Arg Ile Thr Ser Asn Ala Asp Asp Ile Ala Tyr Tyr Phe Thr Gly
610 615 620
Ile Val Asn Lys Pro Phe Asp Ile Lys Gly Lys Arg Leu Pro Tyr Val
625 630 635 640
Ser Pro Asn Gln Phe Ile Phe Asp Met Met Tyr Thr Tyr Lys His Thr
645 650 655
Thr Phe Gly Ile Ser Ser Tyr Phe Tyr Ser Arg Ala Tyr Ser Ser Met
660 665 -- 670
Leu Asn Gln Ala Lys Asp Gln Thr Val Cys Leu Pro Leu Asn Pro Glu
35 675 680 685
Tyr Thr Gly Gly Leu Lys Tyr Gly Cys Asn Ser Val Gly Leu Leu Pro
690 695 700
Leu Tyr Phe Val Leu Asn Val Gln Val Ser Ser Ile Leu Trp Gln Ser
705 710 715 720
4~ Gly Arg His Lys Ile Thr Gly Ser Leu Gln Ile Asn Asn Leu Phe Asn
725 730 735
Met Lys Tyr Tyr Phe Arg Gly Ile Gly Thr Ser Pro Thr Gly Arg Glu
740 745 750
Pro Ala Pro Gly Arg Ser Ile Thr Ala Tyr Leu Asn Tyr Glu Phe
45 755 760 765
(2) INFORMATION FOR SEQ ID N0:112:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 115 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
CA 02273199 1999-06-O1
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{iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...115
(xi)SEQUENCE SEQID
DESCRIPTION: N0:112:
Leu HisProLeu CysAlaHis GlyGlnCys GlySer GluAlaIle Ala
1 5 10 15
1$ Cys LeuGluAla IleSerVal GlyIleVal ProVal IleAlaAsn Ser
20 25 30
Pro LeuSerAla ThrArgGln PheAlaLeu AspGlu ArgSerLeu Phe
35 40 45
Glu ProAsnAsn AlaLysAsp LeuSerAla LysIle AspTrpTrp Leu
50 55 60
Glu AsnLysLeu GluArgGlu ArgMetGln AsnGlu TyrAlaLys Ser
65 70 75 80
Ala LeuAsF~Tyr ThrLeuGlu AsnSerVal IleGln IleGluLys Val
85 90 95
2$ Tyr GluGluAla IleLysAsp PheLysAsn AsnPro AsnLeuPhe Lys
100 105 110
Thr LeuSer -
115
(2) INFORMATION FOR SEQ ID N0:113:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 389 amino acids
(B) TYPE: amino acid
3$ (D) TOPOLOGY: linear
--(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4$ (A) NAME/KEY: misc_feature
(B) LOCATION 1...389
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:113:
$0 Met Val Ile Val Leu Val Val Asp Ser Phe Lys Asp Thr Sex Asn Gly
1 5 10 15
Thr Ser Met Thr Ala Phe Arg Phe Phe Glu Ala Leu Lys Lys Arg Gly
20 25 30
His Ala Met Arg Val Val Ala Pro His Val Asp Asn Leu Gly Ser Glu
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35 40 45
Glu Glu Gly Tyr Tyr Asn Leu Lys Glu Arg Tyr Ile Pro Leu Val Thr
50 , 55 60
Glu Ile SerHis LysGlnHis IleLeuPhe AlaLys ProAspGlu Lys
65 70 75 g0
Ile Leu ArgLys AlaPheLys GlyAlaAsp MetIle HisThrTyr Leu
85 90 95
Pro Phe LeuLeu GluLysThr AlaValLys IleAla ArgGluMet Arg
100 105 110
1~ Val Pro TyrIle GlySerPhe HisLeuGln ProGlu HisIleSer Tyr
115 120 125
Asn Met LysLeu GlyGlnPhe SerTrpLeu AsnThr MetLeuPhe Ser
130 135 140
Trp Phe LysSer SerHisTyr ArgTyrIle HisHis IleHisCys Pro
15 145 150 155 160
Ser Lys PheIle ValGluGlu LeuGluLys TyrAsn TyrGlyGly Lys
165 170 175
Lys Tyr AlaIle SerAsnGly PheAspPro MetPhe LysPheGlu His
180 185 190
Pro Gln LysSer LeuPheAsp ThrThrPro PheLys IleAlaMet Val
195 200 205
Gly Arg TyrSer AsnGruLys AsnGlnSer ValLeu IleLysAla Val
210 215 220
Ala Leu SerArg TyrLysGln AspIleVal LeuLeu LeuLysGly Lys
25 225 230 235 240
Gly Pro AspGlu LysLysIle LysLeuLeu AlaGln LysLeuGly Val
245 250 255
Lys Thr GluPhe GlyPheVal AsnSerHis GluLeu LeuGluIle Leu
260 265 270
Lys Thr CysThr LeuTyrAla HisThrAla AsnVal GluSerGlu Ala
275 280 285
Ile Ala CysLeu GluAlaIle SerValGly IleVal ProValIle Ala
290 295 300
Asn Ser ProLeu SerAlaThr ArgGlnPhe AlaLeu AspGluArg Ser
35 305 310 315 320
Leu Phe GluPro AsnAsnAla LysAspLeu SerAla LysIleAsp Trp
325 330 335
Trp Leu GluAsn LysLeuGlu ArgGluArg MetGln AsnGluTyr Ala
340 345 350
Lys Ser AlaLeu AsnTyrThr LeuGluAsn SerVa1 IleGlnIle Glu
355 360 365
Lys Val TyrGlu GluAlaIle LysAspPhe LysAsn AsnProAsn Leu
370 375 380
Phe Lys ThrLeu Ser
45 385
(2) INFORMATION FOR SEQ ID N0:114:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 312 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...312
1~
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:114:
Leu AlaSer TyrGlyPhe PheLeu GlyAlaLeu PheIleLeu AlaSer
1 5 10 15
1$ Gly IleVal CysLeuGln ThrAla GlyAsnPro PheValThr LeuLeu
20 - 25 30
-
Ser LysGly LysGluAla ArgAsn LeuValLeu ValGlnAla PheAsn
35 40 45
Ser LeuGly ThrThrLeu GlyPro IlePheGly SerLeuLeu IlePhe
50 55 60
Ser AlaThr LysThrSer AspAsn LeuSerLeu IleAspLys LeuAla
65 70 75 gp
Asp AlaLys SerValGln MetPro TyrLeuGly LeuAlaVal PheSer
85 90 95
2$ Leu LeuLeu AlaLeuVal MetTyr LeuLeuLys LeuProAsp ValGlu
100 105 110
Lys GluMet ProLysGlu ThrThr GlnLysSer LeuPheSer HisLys
115 120 125
His PheVal PheGlyAla LeuGly IlePhePhe TyrValGly GlyGlu
3~ 130 135 140
Val AlaIle GlySerPhe LeuVal LeuSerPhe GluLysLeu LeuAsn
145 150 155 160
Leu AspAla GlnSerSer AlaHis TyrLeuVal TyrTyrTrp GlyGly
165 170 175
3$ Ala MetVal GlyArgPhe LeuGly SerAlaLeu MetAsnLys IleAla
180 185 190
Pro AsnLys TyrLeuAla PheAsn AlaLeuSer SerIleIle LeuIle
195 200 205
Ala LeuAla IleLeuIle GlyGly LysIleAla LeuPheAla LeuThr
210 - 215 220
Phe ValGly PhePheAsn SerIle MetPhePro ThrIlePhe SerLeu
225 230 235 240
Ala ThrLeu AsnLeuGly HisLeu ThrSerLys AlaSerGly ValIle
245. 250 255
4$ Ser MetAla IleValGly GlyAla LeuIlePro ProIleGln GlyVal
260 265 270
Val ThrAsp MetLeuThr AlaThr GluSerAsn LeuLeuTyr AlaTyr
275 280 285
Ser ValPro LeuLeuCys TyrPhe TyrIleLeu PhePheAla LeuLys
$~ 290 295 300
Gly TyrLys GlnGluGlu AsnSer
305 310
(2) INFORMATION FOR SEQ ID N0:115:
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(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 407 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...407
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:115:
Met Gln Lys Thr Ser Asn Thr Leu Ala Leu Gly Ser Leu Thr Ala Leu
1 5 10 15
Phe Phe Leu Met Gly Phe Ile Thr Val Leu Asn Asp Ile Leu Ile Pro
20 25 30
His Leu Lys Pro Ile Phe Asp Leu Thr Tyr Phe Glu Ala Ser Leu Ile
35 40 45
Gln Phe Cys Phe Phe Gly Ala Tyr Phe Ile Met Gly Gly Val Phe Gly
50 55 60
Asn Val Ile Ser Lys Ile Gly Tyr Pro Phe Gly Val Val Leu Gly Phe
65 70 75 80
Val Ile Thr Ala Ser Gly Cys Ala Leu Phe Tyr Pro Ala Ala His Phe
85 90 95
Gly Ser Tyr Gly Phe Phe Leu Gly Ala Leu Phe Ile Leu Ala Ser Gly
100 105 110
Ile Val Cys Leu Gln Thr Ala Gly Asn Pro Phe Val Thr Leu Leu Ser
115 120 125
Lys Gly Lys Glu Ala Arg Asn Leu Val Leu Val Gln Ala Phe Asn Ser
330 135 140
Leu Gly Thr Thr Leu Gly Pro Ile Phe Gly Ser Leu Leu Ile Phe Ser
145 150 155 160
4~ Ala Thr Lys Thr Ser Asp Asn Leu Ser Leu Ile Asp Lys Leu Ala Asp
165 170 175
Ala Lys Ser Val Gln Met Pro Tyr Leu Gly Leu Ala Val Phe Ser Leu
180 185 190
Leu Leu Ala Leu Val Met Tyr Leu Leu Lys Leu Pro Asp Val Glu Lys
4$ 195 200 205
Glu Met Pro Lys Glu Thr Thr Gln Lys Ser Leu Phe Ser His Lys _a s
210 215 220
Phe Val Phe Gly Ala Leu Gly Ile Phe Phe Tyr Val Gly Gly Glu Val
225 230 235 240
Ala Ile Gly Ser Phe Leu Val Leu Ser Phe Glu Lys Leu Leu Asn Leu
245 250 255
Asp Ala Gln Ser Ser Ala His Tyr Leu Val Tyr Tyr Trp Gly Gly Ala
260 265 270
Met Val Gly Arg Phe Leu Gly Ser Ala Leu Met Asn Lys Ile Ala Pro
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275 280 _ 285
Asn Lys TyrLeuAla PheAsnAla LeuSer SerIleIle LeuIleAla
290 295 300
Leu Ala IleLeuIle GlyGlyLys IleAla LeuPheAla LeuThrPhe
$ 305 310 315 320
Val Gly PhePheAsn SerIleMet PhePro ThrIlePhe SerLeuAla
325 330 335
Thr Leu AsnLeuGly HisLeuThr SerLys AlaSerGly ValIleSer
340 345 350
Met Ala IleValGly GlyAlaLeu IlePro ProIleGln GlyValVal
355 _360 365
Thr Asp MetLeuThr AlaThrGlu SerAsn LeuLeuTyr AlaTyrSer
370 375 380
Val Pro LeuLeuCys TyrPheTyr IleLeu PhePheAla LeuLysGly
385 390 395 400
Tyr Lys GlnGluGlu AsnSer
405
(2) INFORMATION FOR SEQ ID N0:116:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 125 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
2$
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
3O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
3$ (B) LOCATION 1...125
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:116:
Met Asn Lys Ile Ala Pro Asn Lys Tyr Leu Ala Phe Gly Ala Leu Ser
40 1 s to is
Ser Ile IleLeu IleAlaLeu AlaIleLeu IleGly GlyLysIleAla
20 25 30
Leu Phe AlaLeu ThrPheVal GlyPhePhe AsnSer IleMetPhePro
35 40 45
4$ Thr Ile PheSer LeuAlaThr LeuAsnLFU GlyIle SerLeuLeuMet
50 55 60
Ala Ser GlyVal IleSerMet AlaIleVal GlyGly AlaLeuIlePro
65 70 75 80
Pro Ile GlnGly ValValThr AspMetLeu ThrAla ThrGluSerAsn
$~ 85 90 95
Leu Leu TyrAla TyrSerVal ProLeuLeu CysTyr PheTyrIleLeu
100 105 110
Phe Phe AlaLeu LysGlyTyr LysGlnGlu GluAsn Ser
115 120 125
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(2) INFORMATION FOR SEQ ID N0:117:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 330 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...330
2O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:117:
Leu Lys Lys Ile Leu Pro Ala Leu Leu Met Gly Phe Val Gly Leu Asn
1 5 10 15
Ala Ser Asp Arg Leu Leu Glu Ile Met Arg Leu Tyr Gln Lys Gln Gly
20 25 30
Leu Glu Val Val Gly Gln Lys Leu Asp Ser Tyr Leu Ala Asp Lys Ser
40 45
Phe Trp Ala Glu Glu Leu Gln Asn Lys Asp Thr Asp Phe Gly Tyr Tyr
50 55 60
30 Gln Asn Lys Gln Phe Leu Phe Val Ala Asp Lys Ser Lys Pro Ser Leu
65 70 75 80
Glu Phe Tyr Glu Ile Glu Asn Asn Met Leu Lys Lys Ile Asn Ser Ser
85 90 95
Lys Ala Leu Val Gly Ser Lys Lys Gly Asp Lys Thr Leu Glu Gly Asp
35 loo l05 llo
Leu Ala Thr Pro Ile Gly Val Tyr Arg Ile Thr Gln Lys Leu Glu Arg
115 120 125
Leu Asp Gln Tyr Tyr Gly Val Leu Ala Phe Val Thr Asn Tyr Pro Asn
130 135 140
Leu Tyr Asp Thr Leu Lys Lys Arg Thr Gly His Gly Ile Trp Val His
145 150 155 160
Gly Met Pro Leu Asn Gly Asp Arg Asn Glu Leu Asn Thr Lys Gly Cys
165 170 175
Ile Ala Ile Glu Asn Pro Ile Leu Ser Ser Tyr Asp Lys Val Leu Lys
4$ 1~t0 185 190
Gly Glu Lye Ila Phe Leu Ile Thr Tyr Glu Asp Lys Phe Ser Pro Ser
195 200 205
Thr Lys Glu Glu Leu Ser Met Ile Leu Ser Ser Leu Phe Gln Trp Lys
210 215 220
5Q Glu Ala Trp Ala Arg Gly Asp Phe Glu Arg Tyr Met Arg Phe Tyr Asn
225 230 235 240
Pro Asn Phe Thr Arg Tyr Asp Gly Met Ser Phe Asn Ala Phe Lys Glu
245 250 255
Tyr Lys Lys Arg Val Phe Ala Lys Asn Glu Lys Lys Asn Ile Ala Phe
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260 265 270
Ser Ser Ile Asn Val Ile Pro Tyr Pro Asn Ser Gln Asn Lys Arg Leu
275 280 285
Phe Tyr Val Val Phe Asp Gln Asp Tyr Lys Ala Tyr Gln Gln Asn Lys
S 290 295 300
Leu Ser Tyr Ser Ser Asn Ser Gln Lys Glu Leu Tyr Val Glu Ile Glu
305 310 315 320
Asn Asn Gln Ala Ser Ile Ile Met Glu Lys
325 330
(2) INFORMATION FOR SEQ ID N0:118:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 169 amino acids
1S (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...169
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:118:
Leu Phe Glu Lys Trp Ile Gly Leu Thr Leu Leu Leu Ser Ser Leu Gly
1 5 10 15
Tyr Pro CysGlnLys ValSer IleSerPhe LysGlnTyr GluAsnLeu
20 25 30
3S Ile His IleHisGln LysGly CysAsnAsn GluValVal CysArgThr
35 40 45
Leu Ile SerIleAla LeuLeu GluSerSer LeuGlyLeu AsnAsnLys
50 55 60
Arg Glu LysSerLeu LysAsp ThrSerTyr SerMetPhe HisIleThr
65 70 75 80
Leu Asn ThrAlaLys LysPhe TyrProThr TyrSerLys ThrLeuLeu
85 90 95
Lys Thr LysLeuLeu AsnAsp ValGlyPhe AlaIleGln LeuAlaLys
100 105 110
--~S Gln Ile LeuLysGlu AsnPhe AspTyrTyr HisGlnLys HisProAsn
115 120 125
Lys Ser ValTyrGln LeuVal GlnMetAla IleGlyAla.TyrAsnGly
130 135 140
Gly Met LysHisAsn ProAsn GlyAlaTyr MetLysLys PheArgCys
_ 145 150 155 160
S0
Ile Tyr SerGlnVal ArgTyr AsnGlu
165
(2) INFORMATION FOR SEQ ID N0:119:
CA 02273199 1999-06-O1
WO 98/24475 PCT/LTS97/22I04
- 202 -
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 215 amino acids
(B) TYPE: amino acid
$ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: _
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
1$ (A) NAME/KEY: misc_feature
(B) LOCATION 1...215
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:119:
Met Lys LysPro TyrArgLys IleSerAsp TyrAla IleValGly Gly
1 5 10 15
Leu Ser AlaLeu ValMetVal SerIleVal GlyCys LysSeiAsn Ala
20 25 30
Asp Asp LysPro LysGluGln SerSerLeu SerGln SerValGln Lys
2$ 35 40 45
Gly Ala PheVal IleLeuGlu GluGlnLys AspLys SerTyrLys Val
50 55 60
Val Glu GluTyr ProSerSer ArgThrHis IleVal ValArgAsp Leu
65 70 75 80
Gln Gly AsnGlu ArgValLeu SerAsnGlu GluIle GlnLysLeu Ile
85 90 95
Lys Glu GluGlu AlaLysIle AspAsnGly ThrSer LysLeuVal Gln
100 105 110
Pro Asn AsnGly GlySerAsn GluGlySer GlyPhe GlyLeuGly Ser
3$ 115 120 125
Ala Ile LeuGly SerAlaAla GlyAlaIle LeuGly SerTyrIle Gly
130 135 140
Asn Lys LeuPhe AsnAsnPro AsnTyrGln GlnAsn AlaGlnArg Thr
145 150 155 160
Tyr Lys SerPro GlnAlaTyr GlnArgSer GlnAsn SerPheSer Lys
165 170 175
Ser Ala ProSer AlaSerSer MetGlyThr AlaSer LysGlyGln Ser
180 185 190
Gly Phe PheGly SerSerArg ProThrSer SerPro AlaIleSer Ser
4$ 195 200 205
Gly Thr ArgGly PheAsnAla
210 215
(2) INFORMATION FOR SEQ ID N0:120:
$0
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 253 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97l22104
- 203 -
(ii) MOLECULE TYPE: protein
S
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...253
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:120:
IS Leu Lys Thr Leu Phe Ser Val Tyr Leu Phe Leu Ser Leu Asn_ Pro Leu
1 5 10 15
Phe LeuGluAla LysGlu IleThrTrp SerGlnPhe LeuGluAsn Phe
20 25 30
Lys AsnLysAsn GluAsp AspLysPro LysProLeu ThrIleAsp Lys
35 40 45
Asn AsnGluLys GlnGln IleLeuAsp LysAsnGln GlnIleLeu Lys
50 55 60
Arg AlaLeuGlu LysSer LeuLysPhe PhePheIle PheGlyTyr Asn
65 70 75 80
2$ Tyr SerGlnAla AlaTyr SerThrThr AsnGlnAsn LeuThrLeu Thr
85 90 95
Ala AsnSerIle GlyPhe AsnThrAla ThrGlyLeu GluHisPhe Leu
100 105 110
Arg AsnHisPro LysVal GlyPheArg IlePheSer ValTyrAsn Tyr
115 120 125
Phe HisSerVal SerLeu SerGlnPro GlnIleLeu MetValGln Asn
130 135 140
Tyr GlyGlyAla LeuAsp PheSerTrp IlePheVal AspLysLys Thr
145 150 155 160
3S Tyr ArgPheArg SerTyr LeuGlyIle AlaLeuGlu GlnGlyVal Leu
165 170 175
Leu ValAspThr IleLys ThrGlySer PheThrThr IleIlePro Arg
180 185 190
Thr LysLysThr PhePhe GlnAlaPro LeuArgPhe GlyPheIle Val
195 200 205
Asp PheIleGly TyrLeu SerLeuGln LeuGlyIle GluMetPro Leu
210 - 215 220
Val ArgAsnVal PheTyr ThrTyrAsn AsnHisGln GluArgPhe Lys
225 230 235 240
- 4S Pro ArgPheAsn AlaAsn LeuSe'-Leu IleValSer Phe
245 250
(2) INFORMATION FOR SEQ ID N0:121:
SO (i} SEQUENCE CHARACTERISTICS:
(A) LENGTH: 336 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
CA 02273199 1999-06-O1
WO 98/24475 PCT/LTS97/22104
-204-
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...336
(xi)--SEQUENCE DESCRIPTION. SEQ ID N0:121:
Leu Phe Phe Lys Phe Ile Leu Cys Leu Ser Leu Gly Ile Phe Ala Trp
IS 1 5 to is
Ala Lys Glu Val Ile Pro Thr Pro Ser Thr Pro Leu Thr Pro Ser Lys
20 25 30
Arg Tyr Ser Ile Asn Leu Met Thr Glu Asn Asp Gly Tyr Ile Asn Pro
35 40 45
20 Tyr Ile Asp Glu Tyr Tyr Thr Ala Gly Asn Gln Ile Gly Phe Ser Thr
50 55 60
Lys Glu Phe Asp Phe Ser Lys Asn Lys Ala Met Lys Trp Ser Ser Tyr
65 70 75 80
Leu Gly Phe Phe Asn Lys Ser Pro Arg Val Thr Arg Phe Gly Ile Ser
2S 85 90 95
Leu Ala Gln Asp Met Tyr Thr Pro Ser Leu Ala Asn Arg Lys Leu Val
100 105 110
His Leu His Asp Asn His Pro Tyr Gly Gly Tyr Leu Arg Val Asn Leu
115 120 125
30 Asn Val Tyr Asn Arg His Gln Thr Phe Met Glu Leu Phe Thr Ile Ser
130 135 140
Leu Gly Thr Thr Gly Gln Asp Ser Leu Ala Ala Gln Thr Gln Arg Leu
145 150 155 160
Ile His Lys Trp Gly His Asp Pro Gln Phe Tyr Gly Trp Asn Thr Gln
3S 165 170 175
Leu Lys Asn Glu Phe Ile Phe Glu Leu His Tyr Gln Leu Leu Lys Lys
180 185 190
Val Pro Leu Leu Lys Thr Arg Phe Phe Ser Met Glu Leu Met Pro Gly
195 200 205
40 Phe Asn Val Glu Leu Gly Asn Ala Arg Asp Tyr Phe Gln Leu Gly Ser
210 215 220
Leu Phe Arg Ala Gly Tyr Asn Leu Asp Ala Asp Tyr Gly Val Asn Lys
225 230 235 240
Val Asn Thr Ala Phe Asp Gly Gly Met Pro Tyr Ser Asp Lys Phe Ser
-4S 245 250 255
Ile :~r Phe Phe Ala Gly Ala Phe Gly Arg Phe Gln Pro Leu Asn Ile
260 265 270
Phe Ile Gln Gly Asn Ser Pro Glu Thr Arg Gly Ile Ala Asn Leu Glu
275 280 285
S0 Tyr Phe Val Tyr Ala Ser Glu Ile Gly Ala Ala Met Met Trp Arg Ser
290 295 300
Leu Arg Val Ala Phe Thr Ile Thr Asp Ile Ser Lys Thr Phe Gln Ser
305 310 315 320
Gln Pro Lys His His Gln Ile Gly Thr Leu Glu Leu Asn Phe Ala Phe
...___._r.~._ _T
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97122104
-205-
325 330 335
(2) INFORMATION FOR SEQ ID N0:122:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 108 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
(vi)ORIGINAL SOURCE:
IS (A) ORGANISM: Helicobacter
pylori
(ix)FEATURE:
(A) NAME/ItEY: misc_feature
(B) LOCATION 1...108
(xi)SEQUENCE DESCRIPTION: SEQ
ID N0:122:
Met Lys Pro Ile Phe Ser Leu Phe Leu Ile Val Leu Lys
Phe Leu Ala
1 5 10 15
2S His Pro Ile Asn Pro Leu Leu Glu Tyr Phe Pro Ser Tyr
Pro Leu Thr
20 25 30
Gln Phe Leu Asp Leu Glu Pro His Ile Lys Lys Lys Arg
Phe Val Ala
35 40 45
Tyr Arg Pro Phe Gln Trp Gly Asn Ile Ile Lys Arg His
Thr Ile Asp
50 55 60
Leu Glu Glu Arg Gln Ser Asn Gln Asp Ile Phe Arg.Gln
Pro Ser Asn
65 70 75 80
Ala Glu Ile Asn Val Ser Ser Gln Leu Arg Gly Ile Ser
Thr Phe Ser
85 90 95
3S Ala Ser Ser Arg Ile Val Ile Asp Ala Gln
Ser Val
100 105
(2) INFORMATION
FOR
SEQ
ID
N0:123:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 195 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
4S (ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
(vi)ORIGINAL SOURCE:
_ 50 (A) ORGANISM: Helicobacter
pylori
(ix)FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...195
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-206-
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:123:
Met Ser AsnAsn ProPheLys LysVal GlyMetIle SerSerGln Asn
S 1 5 10 15
Asn Asn GlyAla LeuAsnGly LeuGly ValGlnVal GlyTyrLys Gln
20 25 30
Phe Phe GlyGlu SerLysArg TrpGly LeuArgTyr TyrGlyPhe Phe
35 40 45
Asp Tyr AsnHis GlyTyrIle LysSer SerPhePhe AsnSerSer Ser
50 55 60
Asp Ile TrpThr TyrGlyGly GlySer AspLeuLeu ValAsnPhe Ile
65 70 75 8p
Asn Asp SerIle ThrArgLys AsnAsn LysLeuSer ValGlyLeu Phe
IS 85 90 95
Gly Gly IleGln LeuAlaGly ThrThr TrpLeuAsn SerGlnTyr Met
100 105 110
Asn Leu ThrAla PheAsnAsn ProTyr SerAlaLys ValAsnAla Ser
115 120 125
Asn Phe GlnPhe LeuPheAsn LeuGly LeuArgThr AsnLeuAla Thr
130 135 140
Ala Lys LysLys AspSerGlu ArgSer AlaGlnHis GlyValGlu Leu
145 150 155 160
Gly Ile LysIle ProThrIle AsnThr AsnTyrTyr SerPheLeu Gly
ZS 165 170 175
Thr Lys LeuGlu TyrArgArg LeuTyr SerValTyr LeuAsnTyr Val
180 185 190
Phe Ala Tyr
195
(2) INFORMATION FOR SEQ ID N0:124:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 227 amino acids
3S (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...227
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:124:
S0
Val Arg Phe Gly Lys Ile Asp Tyr Leu Asn Met Leu Pro Phe Asp Val
1 5 10 15
Phe Ile Lys Ser Tyr Pro Thr Pro Cys Tyr Phe Lys Gln Phe Leu Arg
20 25 30
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22144
-207-
Leu Lys LysThr TyrProSer LysLeu AsnGluSer PheLeuPhe Arg
35 40 45
Arg Ile AspAla GlyPheIle SerSer IleAlaGly TyrProPhe Ala
50 55 60
$ Leu Cys SerTyr SerLeuGly IleVal AlaTyrLys GluValLeu Ser
65 70 75 80
Val Leu ValVal AsnArgGlu AsnAla PheAspLys GluSerAla Ser
85 90 95
Ser Asn AlaLeu SerLysVal LeuGly LeuLysGly GluValLeu Ile
100 105 110
Gly Asn LysAla LeuGlnPhe TyrTyr SerAsnPro LysLysAsp Phe
115 120 125
Ile Asp LeuAla AlaLeuTrp TyrGlu LysLysArg LeuProPhe Val
130 135 140
1$ Phe Gly ArgLeu CysTyrTyr GlnAsn LysAspPhe TyrLysArg Leu
145 150 155 160
Ser Leu AlaPhe LysHisGln LysThr LysIlePro HisTyrIle Leu
165 170 175
Lys Glu AlaAla LeuLysThr AsnLeu LysArgGln AspIleLeu Asn
lso las 190
Tyr Leu GlnLys IleTyrTyr ThrLeu GlyLysLys GluGlnSer Gly
195 20G 205
Leu Lys AlaPhe TyrArgGlu LeuLeu PheLysArg IleGlnLys Pro
210 215 220
2$ Lys Arg Phe
225
(2) INFORMATION FOR SEQ ID N0:125:
3O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 305 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
3$ (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
40 (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...305
4$
(xi) SEQUENCE DE..~.'.IPTION: SEQ ID N0:125:
Met Gly Arg Ile Glu Ser Lys Lys Arg Leu Lys Ala Leu Ile Phe Leu
1 5 10 15
$0 Ala Ser Leu Gly Val Leu Trp Gly Asn Ala Ala Glu Lys Thr Pro Phe
20 25 30
Phe Lys Thr Lys Asn His Ile Tyr Leu Gly Phe Arg Leu Gly Thr Gly
35 40 45
Ala Thr Thr Arg Thr Ser Met Trp Gln Gln Ala Tyr Lys Asp Asn Pro
CA 02273199 1999-06-O1
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-208-
50 55 60
Thr Cys Pro Ser Ser Val Cys Tyr Gly Glu Lys Leu Glu Ala His Tyr
65 70 75 8p
Lys Gly Gly Lys Asn Leu Ser Tyr Thr Gly Gln Ile Gly Asp Glu Ile
85 90 95
Ala Phe Asp Lys Tyr His Ile Leu GIy Leu Arg Val Trp Gly Asp Val
100 105 110
Glu Tyr Ala Lys Ala Gln Leu Gly Gln Lys Val Gly Gly Asn Thr Leu
115 120 125
Leu Ser Gln Ala Asn Tyr Asn Pro Ser Ala Ile Lys Thr Tyr Asp Pro
130 135 140
Thr Ser Asn Ala Gln Gly Ser Leu Val Leu Gln Lys Thr Pro Ser Pro
145 150 155 160
Gln Asp Phe Leu Phe Asn Asn Gly His Phe Met Ala Phe Gly Leu Asn
165 170 175
Val Asn Met Phe Val Asn Leu Pro Ile Asp Thr Leu Leu Lys Leu Ala
180 185 190
Leu Lys Thr Glu Lys Met Leu Phe Phe Lys Ile Gly Val Phe Gly Gly
195 200 205
Gly Gly Val Glu Tyr Ala Ile Leu Trp Ser Pro Gln Tyr Lys Asn Gln
210 215 220
Asn Thr His Gln Asp Asp Lys Phe Phe Ala Ala Gly Gly Gly Phe Phe
225 230 235 240
Val Asn Phe Gly Gly Ser Leu Tyr Ile Gly Lys Arg Asn Arg Phe Asn
245 250 255
Val Gly Leu Lys Ile Pro Tyr Tyr Ser Leu Ser Ala Gln Ser Trp Lys
260 265 270
Asn Phe Gly Ser Ser Asn Val Trp Gln Gln Gln Thr Ile Arg Gln Asn
275 280 285
Phe Ser Val Phe Arg Asn Lys Glu Val Phe Val Ser Tyr Ala Phe Leu
290 295 300
Phe
305
3$ (2) INFORMATION FOR SEQ ID N0:126:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 258 amino acids
(B} TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
$0 (A) NAME/KEY: misc_feature
(B) LOCATION 1...258
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:126:
CA 02273199 1999-06-O1
WO 98124475 PCT/US97/22104
-209-
Met Phe LeuArgSer TyrProLys LeuArgTyr AlaLeu CysLeuPro
1 5 10 15
Leu Leu ThrGluThr CysTyrSer GluGluArg ThrLeu AsnLysVal
20 25 30
S Thr Thr GlnAlaLys ArgIlePhe ThrTyrAsn AsnGlu PheLysVal
35 40 45
Thr Ser LysGluLeu AspGlnArg GlnSerAsn GluVal LysAspLeu
50 55 60
Phe Arg ThrAsnPro AspValAsn ValGlyGly GlySer ValMetGly
65 70 75 80
Gln Lys IleTyrVal ArgGlyIle GluAspArg LeuLeu ArgValThr
85 90 95
Val Asp GlyAlaAla GlnAsnGly AsnIleTyr HisHis GlnGlyAsn
100 105 110
1S Thr Val IleAspPro GlyMetLeu LysSerVal G1uVa1 ThrLysGly
115 120 125
Ala Ala AsnAlaSer AlaGlyPro GlyAlaIle AlaGly ValIleLys
130 135 140
Met Glu ThrLysGly AlaAlaAsp-PheIlePro ArgGly LysAsnTyr
145 150 155 160
Ala Ala SerGlyAla ValSerPhe TyrThrAsn PheGly AspArgGlu
165 170 175
Thr Phe ArgSerAla TyrGlnSer AlaHisPhe AspIle IleAlaTyr
180 185 190
2S Tyr Thr HisGlnAsn IlePheTyr TyrArgSer GlyAla ThrValMet
195 200 205
Lys Asn LeuPheLys ProThrGln AlaAspLys GluPro GlyThrPro
210 215 220
Ser Glu GlnAsnAsn AlaLeuIle LysMetAsn GlyTyr LeuSerAsp
30 225 230 235 240
Arg Asp ThrLeuThr PheSerTrp AsnMetThr ArgAsp AsnAlaThr
245 250 255
Arg Leu
3S
(2) INFORMATION FOR SEQ ID N0:127:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 192 amino acids
(B) TYPE: amino acid
{D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
4S (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
SO ( ix) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...192
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:127:
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-210-
Met Phe Leu Arg Ser Tyr Pro Lys Leu Arg Tyr Ala Leu Cys Leu Pro
1 5 10 15
Leu Leu Thr Glu Thr Cys Tyr Ser Glu Glu Arg Thr Leu Asn Lys Val
S 20 25 30
Thr Thr Gln Ala Lys Arg Ile Phe Thr Tyr Asn Asn Glu Phe Lys Val
35 40 45
Thr Ser Lys Glu Leu Asp Gln Arg Gln Ser Asn Glu Val Lys Asp Leu
50 55 60
Phe Arg Thr Asn Pro Asp Val Asn Val Gly Gly Gly Ser Val Met Gly
65 70 75 80
Gln Lys Ile Tyr Val Arg Gly Ile Glu Asp Arg Leu Leu Arg Val Thr
B5 90 95
Val Asp Gly Aia Ala Gln Asn Gly Asn Ile Tyr His His Gln Gly Asn
1S 100 105 110
Thr Val Ile Asp Pro Gly Met Leu Lys Ser Val Glu Val Thr Lys Gly
115 120 125
Ala Ala Asn Ala Ser Ala Gly Pro Gly Ala Ile Ala Gly Val Ile Lys
130 135 140
Met Glu Thr Lys Gly Ala Ala Asp Phe Ile Pro Arg Gly Lys Asn Tyr
145 150 155 160
Ala Ala Ser Gay Ala Val Ser Phe Tyr Thr Asn Phe Gly Asp Arg Glu
165 I70 175
Thr Phe Arg Ser Ala Tyr Gln Ser Ala His Phe Asp Ile Ile Ala Tyr
2S 180 185 190
(2) INFORMATION FOR SEQ ID N0:128:
(i) SEQUENCE CHARACTERISTICS:
3fl (A) LENGTH: 126 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
3$
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...126
4S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:128:
Val Pro Leu Ser Leu Gly Gly Asn Leu Leu Asn Pro Asn Asn Ser Ser
1 5 10 15
Val Leu Asn Leu Lys Asn Ser Gln Leu Val Phe Ser Asp Gln Gly Ser
S~ 20 25 30
Leu Asn Ile Ala Asn Ile Asp Leu Leu Ser Asp Leu Asn Gly Asn Lys
35 40 45
Asn Arg Val Tyr Asn Ile Ile Gln Ala Asp Met Asn Gly Asn Trp Tyr
55 60
CA 02273199 1999-06-O1
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-211-
Glu Arg Ile Asn Phe Phe Gly Met Arg Ile Asn Asp Gly Ile Tyr Asp
65 70 75 80
Ala Lys Asn Gln Thr Tyr Ser Phe Thr Asn Pro Leu Asn Asn Ala Val
85 90 95
$ Lys Phe Thr Glu Ser Phe Phe Ile His Arg Leu Cys Gly Ser Leu Ser
100 105 110
Gln Ile Gln Lys Lys Lys Asn Thr Ile Val Ser Pro Arg Leu
115 120 125
IO (2) INFORMATION FOR SEQ ID N0:129:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 565 amino acids
(B) TYPE: amino acid
~$ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
2$ (A) NAME/KEY: misc_feature
(B) LOCATION 1...565
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:129:
Val Tyr SerTyr SerAspAsp AlaGln GlyValPhe TyrLeuThr Ser
1 5 10 15
Ser Val LysGly TyrTyrAsn ProAsn GlnSerTyr GlnAlaSer Gly
20 25 30
Ser Asn AsnThr ThrLysAsn AsnAsn LeuThrSer GluSerSer Val
3$ 35 40 45
Ile Ser GlnThr TyrAsnAla GlnGly AsnProIle SerAlaLeu His
50 55 60
Val Tyr AsnLys GlyTyrAsn PheSer AsnIleLys AlaLeuGly Gln
65 70 75 80
Met Ala LeuLys LeuTyrPro GluIle LysLysIle LeuGlyAsn Asp
85 90 95
Phe Ser LeuSer SerLeuSer AsnLeu LysGlyAsp AlaLeuAsn Gln
100 105 110
Leu Thr LysLeu IleThrPro SerAsp TrpLysAsn IleAsnGlu Leu
4$ 115 720 125
Ile Asp AsnAla AsnAsnSEi ValVal GlnAsnPhe AsnAsnGly Thr
130 135 140
Leu Ile IleGly AlaThrLys IleGly GlnThrAsp ThrAsnSer Ala
145 150 155 160
$~ Val Val PheGly GlyLeuGly TyrGln LysProCys AspTyrThr Asp
165 170 175
Ile Val CysGln LysPheArg GlyThr TyrLeuGly GlnLeuLeu Glu
180 185 190
Ser Asn SerAla AspLeuGly TyrIle AspThrThr PheAsnAla Lys
CA 02273199 1999-06-O1
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-212-
195 200 205
Glu Ile Tyr Leu Thr Gly Thr Leu Gly Ser Gly Asn Ala Trp Gly Thr
210 215 220
Gly Gly Ser Ala Ser Val Thr Phe Asn Ser Gln Thr Ser Leu Ile Leu
$ 225 230 235 240
Asn Gln Ala Asn Ile Val Ser Ser Gln Thr Asp Gly Ile Phe Ser Met
245 250 255
Leu Gly Gln Glu Gly Ile Asn Lys Val Phe Asn Gln Ala Gly Leu Ala
260 265 270
1~ Asn Ile Leu Gly Glu Val Ala Met Gln Ser Ile Asn Lys Ala Gly Gly
275 280 285
Leu Gly Asn Leu Ile Val Asn Thr Leu Gly Ser Asp Ser Val Ile Gly
290 295 300
Gly Tyr Leu Thr Pro Glu Gln Lys Asn Gln Thr Leu Ser Gln Leu Leu
1$ 305 310 315 320
Gly Gln Asn Asn Phe Asp Asn Leu Met Asn Asp Ser Gly Leu Asn Thr
325 330 335
Ala Ile Lys Asp Leu Ile Arg Gln Lys Leu Gly Phe Trp Thr Gly Leu
340 - 345 350
Val Gly Gly Leu Ala Gly Leu Gly Gly Ile Asp Leu Gln Asn Pro Glu
355 360 365
Lys Leu Ile Gly Ser Met Ser Ile Asn Asp Leu Leu Ser Lys Lys Gly
370 375 380
Leu Phe Asn Gln Ile Thr Gly Phe Ile Ser Ala Asn Asp Ile Gly Gln
2$ 385 390 395 400
Val Ile Ser Val Met Leu Gln Asp Ile Val Lys Pro Ser Asp Ala Leu
405 410 415
Lys Asn Asp Val Ala Ala Leu Gly Lys Gln Met Ile Gly Glu Phe Leu
420 425 430
Gly Gln Asp Thr Leu Asn Ser Leu Glu Ser Leu Leu Gln Asn Gln Gln
435 440 445
Ile Lys Ser Val Leu Asp Lys Val Leu Ala Ala Lys Gly Leu Gly Ser
450 455 460
Ile Tyr Glu Gln Gly Leu Gly Asp Leu Ile Pro Asn Leu Gly Lys Lys
3$ 465 470 475 480
Gly Ile Phe Ala Pro Tyr Gly Leu Ser Gln Val Trp Gln Lys Gly Asp
485 490 495
Phe Ser Phe Asn Ala Gln Gly Asn Val Phe Val Gln Asn Ser Thr Phe
500 505 510
Ser Asn Ala Asn Gly Gly Thr Leu Ser Phe Asn Ala Gly Asn Ser Leu
515 520 525
Ile Phe Ala Gly Asn Asn His Ile Ala Phe Thr Asn His Ser Gly Thr
530 535 540
Leu Asn Leu Leu Ser Asn Gln Val Ser Asn Ile Asn Val Thr Met Leu
~$ 545 550 555 560
A~_~ Ala Ala Thr Ala
565
(2) INFORMATION FOR SEQ ID N0:130:
$~ _
(i} SEQUENCE CHARACTERISTICS:
(A) LENGTH: 172 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-213-
(ii) MOLECULE TYPE: protein
$
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...172
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:130:
1$ Val Phe GlyLeuSer LeuAla AspMetIle LeuGluArg PheLysAsp
1 5 10 15
Phe Met ArgGluTyr ProGlu ProTyrLys PheLeuGln ValPheTyr
20 25 30
Ala Gln GluLysGlu ArgPhe LeuAsnHis LysMetAsn AspTyrIle
35 40 45
Lys Gln AsnLysSer LysGlu GluAlaSer IleLeuAla ArgGlnGly
50 55 60
Phe Val SerValIle GlyArg AlaLeuGlu LysIleIle GluLeuLeu
65 70 75 g0
2$ Leu Lys AspPheCys IleLys AsnAsnVal LysMetThr AsnAspLys
B5 90 95
Thr Leu ArgAlaLys ArgIle AsnGlyGlu LeuAspLys ValLysArg
100 105 110
Ala Leu LeuValHis PheGly GlyTyrSer ValLeuPro AspIleIle
115 120 125
Leu Tyr GlnThrAsn LysAsp AsnIleLys IleLeuAla IleLeuSer
130 135 140
Val Lys AsnSerPhe ArgGlu ArgPheThr LysAspAla LeuLeuGlu
145 150 155 160
3$ Ile Lys ThrPheAla IleAla CysAsnPhe SerHis
165 170
(2) INFORMATION FOR SEQ ID N0:131:
4O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 331 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
4$ (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
- $~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...331
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(xi) SEQUENCE DESCRIPTION: SEQ ID N0:131:'
Met Lys Arg Phe Val Leu Phe Leu Leu Phe Ile Cys Val Cys Val Cys
$ 1 5 10 15
Val Gln Ala Tyr Ala Glu Gln Asp Tyr Phe Phe Arg Asp Phe Lys Ser
20 25 30
Ile Asp Leu Pro Gln Lys Leu His Leu Asp Lys Lys Leu Ser Gln Thr
35 40 45
Ile Gln Pro Cys Ala Gln Leu Asn Ala Ser Lys His Tyr Thr Ala Thr
50 55 _ 60
Gly Val Arg Glu Pro Asp Ala Cys Thr Lys Ser Phe Lys Lys Ser Ala
65 70 75 g0
Met Val Ser Tyr Asp Leu Ala Leu Gly Tyr Leu Val Ser Gln Asn Lys
1$ 85 90 95
Pro Tyr Gly Leu Lys Ala Ile Glu Ile Leu Asn Ala Trp Ala Asn Glu
100 105 110
Leu Gln Ser Val Asp Thr Tyr Gln Ser Glu Asp Asn Ile Asn Phe Tyr
115 120 125
Met Pro Tyr Met Asn Met Ala Tyr Trp Phe Val Lys Lys Glu Phe Pro
130 135 140
Ser Pro Glu Tyr Glu Asp Phe Ile Arg Arg Met Arg Gln 'fyr Ser Gln
145 150 155 160
Ser Ala Leu Asn Thr Asn His Gly Ala Trp Gly Ile Leu Phe Asp Val
2$ 165 170 175
Ser Ser Ala Leu Ala Leu Asp Asp His Ala Leu Leu Gln Ser Ser Ala
180 185 190
Asn Arg Trp Gln Glu Trp Val Phe Lys Ala Ile Asp Glu Asn Gly Val
195 200 205
Ile Ala Ser Ala Il.e Thr Arg Ser Asp Thr Ser Asp Tyr His Gly Gly
210 215 220
Pro Thr Lys Gly Ile Lys Gly Ile Ala Tyr Thr Asn Phe Ala Leu Leu
225 230 235 240
Ala Ile Thr Ile Ser Gly Glu Leu Leu Phe Glu Asn Gly Tyr Asp Leu
3$ 245 250 255
Trp Gly Ser Gly Ala Gly Gln Arg Leu Ser Val Ala Tyr Asn Lys Ala
260 265 270
Ala Thr Trp Ile Leu Asn Pro Glu Thr Phe Pro Tyr Phe Gln Pro Asn
275 280 285
Leu Ile Gly Val His Asn Asn Ala Tyr Phe Ile Ile Leu Ala Lys His
290 295 300
Tyr Ser Ser Pro Ser Ala Asp Glu Leu Leu Glu Gln Gly Asp Leu His
305 310 315 320
Glu Asp GIy Phe Arg Leu Lys Leu Arg Ser Pro
4$ 325 330
(2) INFORMATION FOR SEQ ID N0:132:
(i) SEQUENCE CHARACTERISTICS:
$~ (A) LENGTH: 128 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...128
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:132:
Mec Arg GlnTyrSer GlnSer AlaLeuAsn ThrAsn HisGlyAla Trp
1 5 10 15
1$ Gly Ile LeuPheAsp ValSer SerAlaLeu AlaLeu AspAsp_His_Ala
25 30
Leu Leu GlnSerSer AlaAsn ArgTrpGln GluTrp ValPheLys Ala
35 40 45
Ile Asp GluAsnGly ValIle AlaSerAla IleThr ArgSerAsp Thr
20 50 55 60
Ser Asp TyrHisGly GlyPro ThrLysGly IleLys GlyIleAla Tyr
65 70 75 g0
Thr Asn PheAlaLeu LeuAla IleThrIle SerGly GluLeuLeu Phe
B5 90 95
2$ Glu Asn GlyTyrAsp LeuTrp GlySerGly AlaGly GlnArgLeu Ser
100 105 110
Val Ala TyrAsnLys AlaAla ThrTrpIle LeuAsn ProGluThr Phe
115 120 125
(2) INFORMATION FOR SEQ ID N0:133:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 245 amino acids
(B) TYPE: amino acid
3$ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
- (ix) FEATURE:
__ 4$ (A) NAME/KE't: misc_feature
(B) LOCA_I~N 1...245
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:133: _
$0 Leu Arg Thr Leu Leu Lys Met Leu Val Gly Val Ser Leu Leu Thr His
1 5 10 15
Ala Leu Met Ala Thr Glu Glu Ser Ala Ala Pro Ser Trp Thr Lys Asn
20 25 30
Leu Tyr Met Gly Phe Asn Tyr Gln Thr Gly Ser Ile Asn Leu Met Thr
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35 40 45
Asn Ile His Glu Val Arg Glu Val Thr Ser Tyr Gln Thr Gly Tyr Thr
50 55 60
Asn Val MetThrSer IleAsn SerValLys LysLeuThr AsnMetGly
$ 65 70 75 g0
Ser Asn GlyIleGly LeuVal MetGlyTyr AsnHisPhe PheHisPro
85 90 95
Asp Lys ValLeuGly LeuArg TyrPheAla PheLeuAsp TrpGlnGly
100 105 110
I~ Tyr Gly MetArgTyr ProLys GlyTyrTyr GlyGlyAsn AsnMetIle
115 120 125
Thr Tyr GlyValGly ValAsp AlaIleTrp AsnPhePhe GlnGlySer
130 135 140
Phe Tyr GlnAspAsp IleGly ValAspIle GlyValPhe GlyGlyIle
15 145 150 155 160
Ala Ile AlaGlyAsn SerTrp TyrIleGly AsnLysGly GlnGluLeu
165 170 175
Leu Gly IleThrAsn SerSer AlaValAsp AsnThrSer PheGlnPhe
180 185 190
Leu Phe AsnPheGly PheLys AlaLeuPhe ValAspGlu HisGluPhe
195 200 205
Glu Ile GlyPheLys PhePro ThrLeuAsn AsnLysTyr TyrThrThr
210 215 220
Asp Ala LeuLysVal GlnMet ArgArgVal PheAlaPhe TyrValGly
25 225 230 235 240
Tyr Asn TyrHisPhe
245
(2} INFORMATION FOR SEQ ID N0:134:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 290 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
4' (B) LOCATION 1...290
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:134:
Met Phe Glu Glu Ile Thr Leu Ala His Lys Asp Leu Phe Ser Arg Phe
- 50 1 s l0 15
Leu Gln Thr Gln Lys Ile Val Leu Ser Asp Val Ser Phe Thr Asn Cys
20 25 30
Phe Leu Trp Gln His Ala Arg Leu Ile Gln Val Ala Val Ile Arg Asp
35 40 45
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Cys Leu ValIle GlnThrThr TyrGluAsn GlnLys ProPheTyr Phe
50 55 60
Tyr Pro IleGly LysArgPro HisGluCys ValLys GluLeuLeu Glu
65 70 75 80
S Leu Glu LysAsn LeuArgPhe HisSerLeu ThrLeu GluGlnLys Asp
85 ~~ 90 95
Asp Leu LysAsp AsnPheVal GlyValPhe AspPhe ThrTyrAsn Arg
100 105 110
Asp Arg SerAsp TyrValTyr SerIleGlu GluLeu IleAlaLeu Lys
IO 115 120 125
Gly Lys LysTyr HisLysLys LysAsnHis LeuAsn GlnPheLeu Thr
130 135 140
Asn His AlaAsn PheValTyr GluLysIle SerPro GlnAsnArg Lys
145 150 155 160
1$ Glu Val LeuGlu AlaSerLys AlaTrpPhe LeuGlu SerGlnThr Asp
165 170 175
Asp Ile GlyLeu IleAsnGlu AsnLysGly IleGln SerValLeu Glu
180 185 190
Asn Tyr GluSer LeuAspLeu LysGlyGly LeuIle ArgValAsn Gly
ZO 195 200 205
Glu Ile ValSer PheSerPhe GlyGluVal LeuAsn GluGluSer Ala
210 215 220
Leu Ile HisIle GluLysAla ArgThrAsp IleAla GlyAlaTyr Gln
225 230 235 240
2S Ile Ile AsnGln GlnLeuLeu LeuAsnGlu PheSer HisLeuThr Tyr
245 250 255
Ala Asn ArgGlu GluAspLeu GlyLeuGlu GlyLeu ArgArgSer Lys
260 265 270
Met Ser TyrAsn ProValPhe LeuIleAsp LysTyr GluAlaVal Ala
30 275 280 285
Arg Asn
290
3S
(2) INFORMATION FOR SEQ ID N0:135:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 110 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
SO (B) LOCATION 1...110
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:135:
Met Met Phe Ile Val Ala Val Leu Met Leu Ala Phe Leu Ile Phe Val
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1 5 10 15
His Glu Leu Gly His Phe Ile Ile Ala Arg Ile Cys Gly Val Lys Val
20 25 30
Glu Val Phe Ser Ile Gly Phe Gly Lys Lys Leu Trp Phe Phe Lys Leu
$ 35 40 45
Phe Gly Thr Gln Phe Ala Leu Ser Leu Ile Pro Leu Gly Gly Tyr Val
50 55 60
Lys Leu Lys Gly Met Asp Lys Glu Glu Asn Glu Glu Asn Lys Ile Asn
65 70 75 BO
Gln Ala Asn Asp Ser Tyr Ala Lys Lys Ala Leu Ser Lys Ser Tyr Gly
85 90 95
Tyr Cys Leu Val Gly Arg Phe Leu Ile Phe Phe Leu Arg Phe
100 105 110
IS (2) INFORMATION FOR SEQ ID N0:136:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
2$
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...351
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:136:
3$ Met MetPheIle ValAlaVal LeuMet LeuAlaPhe LeuIlePhe Val
1 5 10 15
His GluLeuGly HisPheIle IleAla ArgIleCys GlyValLys Val
20 25 30
Glu ValPheSer IleGlyPhe GlyLys LysLeuTrp PhePheLys Leu
35 40 45
Phe GlyThrGln PheAlaLeu SerLeu IleProLeu GlyGlyTyr Val
50 _ 55 60
Lys LeuLysGly MetAspLys GluGlu AsnGluGlu AsnLysIle Asn
65 70 75 80
-- 4$ Gln AlaAsnAsp SerTyrAla GlnLys Se'.ProPhe GlnLysLeu Trp
85 j 95
Ile LeuPheGly GlyAlaPhe PheAsn PheLeuPhe AlaValLeu Val
100 105 110
Tyr PhePheLeu AlaLeuSer GlyGlu LysValLeu LeuProVal Ile
$~ 115 120 125
Gly GlyLeuGlu LysAsnAla LeuGlu AlaGlyLeu LeuLysGly Asp
130 135 140
Arg IleLeuSer IleAsnHis GlnLys IleAlaSer PheArgGlu Ile
145 150 155 160
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Arg Glu IleVal AlaArg SerGlnGly GluLeuIle LeuGluIle Glu
165 170 175
Arg Asn AsnGln IleLeu GluLysArg LeuThrPro LysIleVal Ala
180 185 190
$ Val Ile SerGlu SerAsn AspProAsn GluIleIle LysTyrLys Ile
195 200 205
Ile Gly IleLys ProAsp MetGlnLys MetGlyVal ValSerTyr Ser
210 215 220
Val Phe GlnAla PheGlu LysAlaLeu SerArgPhe LysGluGly Val
225 230 235 240
Val Leu IleVal AspSer LeuArgArg LeuIleMet GlySerAla Ser
245 250 255
Val Lys GluLeu SerGly ValIleGly IleValGly AlaLeuSer His
260 265 270
1$ Ala Asn SerVal SerMet LeuLeuLeu PheGlyAla PheLeuSer Ile
275 280 285
Asn Leu GlyIle LeuAsn LeuLeuPro IleProAla LeuAspGiy Ala
290 295 300
Gln Met LeuGly ValVal PheLysAsn IlePheHis IleAlaLeu Pro
2~ 305 310 315 320
Thr Pro IleGln AsnAla LeuTrpLeu ValGlyVal GlyPheLeu Val
325- 330 335
Phe Val MetPhe LeuGly LeuPheAsn AspIleThr ArgLeuLeu
340 345 350
2$
(2) INFORMATION FOR 5EQ ID N0:137:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 100 amino acids
30 (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
3S (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...100
(xi) SEQUENCE_ DESCRIPTION: SEQ ID N0:137:
Met Gln Ly:. 7.sn Leu Asp Ser Leu Leu Glu Asn Leu Arg Ala Glu Ile
1 5 10 15
Asp Ala Leu Asp Asn Glu Leu Ser Asp Leu Leu Asp Lys Arg Leu Gly
20 25 30
$~ Ile Ala Leu Lys Ile Ala Leu Ile Lys Gln Glu Ser Pro Gln Glu Asn
35 40 45
Pro Ile Tyr Cys Pro Lys Arg Glu Gln Glu Ile Leu Lys Arg Leu Ser
55 60
Gln Arg Gly Phe Lys His Leu Asn Gly Glu Ile Leu Ala Ser Phe Tyr
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65 70 75 gp
Ala Glu Val Phe Lys Ile Ser Arg Asn Phe Gln Glu Asn Ala Leu Lys
85 90 95
Glu Leu Lys Lys
S 100
(2) INFORMATION FOR SEQ ID N0:138:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH. 174 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
1S
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...174
2S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:138:
Val LysMet ArgPhePhe SerGly PheGlyPhe ValAsn GluSerVal
1 5 10 15
Leu PheGlu GluTrpLeu LeuLys GlyAlaTyr AspVal SerGlyPhe
20 25 30
Ser MetGly AlaIleLys AlaIle GluTyrAla TyrAsn GluValLeu
35 40 45
Gln GlnArg ArgIleHis SerLeu LeuLeuPhe Ser:ProCysMetLeu
SO 55 60
3S Ala HisLys SerLeuAla PheLys ArgLeuGln LeuPhe LeuPheGln
65 70 75 gp
Lys AspPro GlnSerTyr MetAsp AsnPheTyr LysGlu ValGlyLeu
85 90 95
Asp AlaGln LeuGluArg PheLys LysGluGly SerLeu GluGluLeu
loo l05 llo
Glu PheLeu LeuAspTyr LysTyr SerAspSer IleIle ArgPheLeu
115 120 125
Leu GluLys GlyValLys IleGlu ValPheIle GlyLeu LysAspArg
130 135 140
4S Ile ThrAsp IleGlnAla LeuLeu GluPhePhe MetPro LeuValGln
145 150 155 160
Val TrpGln PheLysAsp CysAsn HisLeuLeu GlnLys Ser
165 170
S0 (2) INFORMATION FOR SEQ ID N0:139:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 471 amino acids
(B) TYPE: amino acid
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(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
S (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...471
1S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:139:
Met LysAsnThr AsnThr LysGluIle LysAsnThr ArgMet LysLys
1 5 10 15
Gly TyrSerGln TyrHis ThrLeuLys LysGlyLeu LeuLys ThrAla
20 - 25 30
2O Leu LeuPheSer LeuPro LeuSerVal AlaLeuAla GluAsp AspGly
35 40 45
Phe TyrMetGly ValGly TyrGlnIle GlyGlyAla GlnGln AsnIle
50 55 60
Asn AsnLysGly SerThr LeuArgAsn AsnValIle AspAsp PheArg
2S 65 70 75 80
Gln ValGlyVal GlyMet AlaGlyGly AsnGlyLeu LeuAla LeuAla
85 90 95
Thr AsnThrThr MetAsp AlaLeuLeu GlyIleGly AsnGln IleVal
100 105 110
3O Asn ThrAsnThr ThrVal GlyAsnAsn AsnAlaGlu LeuThr GlnPhe
115 120 125
Lys LysIleLeu ProGln IleGluGln ArgPheGlu ThrAsn LysAsn
130 135 140
Ala TyrSerVal GlnAla LeuGlnVal TyrLeuSer AsnVal LeuTyr
3$ 145 150 155 160
Asn LeuValAsn AsnSer AsnAsnGly SerAsnAsn GlyVal ValPro
165 170 175
Glu TyrValGly IleIle LysValLeu TyrGlySer GInAsn GluPhe
180 185 190
4O Ser LeuLeuAla ThrGlu SerValAla LeuLeuAsn AlaLeu ThrArg
195 200 205
Val AsnLeuAsp SerAsn SerValPhe LeuLysGly LeuLeu AlaGln
2I0 215 220
Met GlnLeuPhe AsnAsp ThrSerSer AlaLysLeu GlyGln IleAla
4S 225 230 235 240
Glu AsnLeuLys AsnGly GlyAlaGly AlaMetLeu Gln.~y~AspVal
245 250 255
Lys ThrIleSer AspArg IleAlaThr TyrGlnGlu AsnLeu LysGln
260 265 270
_
SO Leu GlyGIyMet LeuLys AsnTyrAsp GluProTyr LeuPro GlnPhe
275 280 285
Gly ProGlyThr SerSer GlnHisGly ValIleAsn GlyPhe GlyIle
290 295 300
Gln ValGlyTyr LysGln PhePheGly SerLysLys AsnIle GlyLeu
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305 310 315 320
Arg TyrTyrAla PhePhe AspTyrGly PheThrGln LeuGly SerLeu
325 330 335
Asn SerAlaVal LysAla AsnIlePhe ThrTyrGly AlaGly ThrAsp
$ 340 345 350
Phe LeuTrpAsn IlePhe ArgArgVal PheSerAsp GlnSer LeuAsn
355 360 365
Val GlyValPhe GlyGly IleGlnIle AlaGlyAsn ThrTrp AspSer
370 375 380
1~ Ser LeuArgGly GlnIle GluAsnSer PheLysGlu TyrPro ThrPro
385 390 395 400
Thr AsnPheGln PheLeu PheAsnLeu GlyLeuArg AlaHis PheAla
405 410 415
Ser ThrMetHis ArgArg PheLeuSer AlaSerGln SerIle GInHis
1$ 420 425 430
Gly MetGluPhe GlyVal LysIlePro AlaIleAsn GlnArg TyrLeu
435 440 445
Lys AlaAsnGly AlaAsp ValAspTyr ArgArgLeu TyrAla PheTyr
450 455 460
2~ Ile AsnTyrThr IleGly Phe
465 470
(2) INFORMATION FOR SEQ ID N0:140:
2S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 129 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
30 (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
3$ (A) ORGANISM: Helicobacter pylori
_( i x ) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...129
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:140:
Met Lys Ser Ile Arg Arg Gly Asp Gly Leu Asn Val Val Pro Phe Ile
1 5 10 15
4$ Asp Ile Met Leu Val Leu Leu Al~ Ile Val Leu Ser Ile Ser Thr Phe
20 25 30
Ile Ala Gln Gly Lys Ile Lys Val Ser Leu Pro Asn Ala Lys Asn Ala
35 40 45
Glu Lys Ser Gln Pro Asn Asp Gln Lys Val Val Val Ile Ser Val Asp
$0 50 55 60
Glu His Asp Asn Ile Phe Val Asp Asp Lys Pro Thr Asn Leu Glu Ala
65 70 75 80
Leu Ser Ala Val Val Lys Gln Thr Asp Pro Lys Thr Leu Ile Asp Leu
85 90 95
.____.._.._ _ .. ........
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Lys Ser Asp Lys Ser Ser Arg Phe Glu Thr Phe I1~ Ser Ile Met Asp
100 105 110
Ile Leu Lys Glu His Asn His Glu Asn Phe Ser Ile Ser Thr Gln Ala
115 120 125
$ Gln
(2) INFORMATION
FOR
SEQ
ID
N0:141:
IO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 75 amir~o acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
IS (ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
{vi)ORIGINAL SOURCE:
20 (A) ORGANISM: Helicobacter
pylori
(ix;FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...75
25
(xi)SEQUENCE DESCRIPTION: SEQ
ID N0:141:
Met Leu Val Leu Leu Ala Ile Val IleSer Thr Phe Ile
Leu Ser Ala
1 5 10 15
30 Gln Gly Lys Ile Lys Val Ser Leu AlaLys Asn Ala Glu
Pro Asn Lys
20 25 30
Ser Arg Pro Asn Asp Gln Lys Val IleSer Val Asp Glu
Val Val His
35 40 45
Asp Asn Ile Phe Val Asp Asp Lys AsnLeu Glu Ala Leu
Pro Thr Ser
3S 50 55 60
Ala Val Val Lys Gln Thr Asp Pro Leu
Lys Thr
65 70 75
(2) INFORMATION FOR SEQ ID N0:142:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 223 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
'ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
SO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc feature
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(B) LOCATION 1...223
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:142:
S Met PheSerLeu SerTyrVal SerLysLys PheLeu SerValLeu Leu
1 5 10 15
Leu IleSerLeu PheLeuSer AlaCysLys SerAsn AsnLysAsp Lys
20 25 30
Leu AspGluAsn LeuLeuSer SerGlyThr Gln,SerSerLysGlu Leu
1~ 35 40 45
Asn AspLysArg AspAsnIle AspLysLys SerTyr AlaGlyLeu Glu
50 55 60
Asp ValPheLeu AspAsnLys SerIleSer ProAsn AspLysTyr Met
65 70 75 80
IS Leu LeuValPhe GlyArgAsn GlyCysSer TyrCys GluArgLeu Lys
85 90 95
Lys AspLeuLys AsnValLys GluLeuArg AsnTyr IleLysGlu His
100 105 110
Phe SerAlaTyr TyrValAsn IlgSerTyr SerLys GluHisAsn Phe
2~ 115 120 I25
Lys ValGlyAsp LysAspLys AsnAspGlu LysGlu IleLysMet Ser
130 135 140
Thr GluGluLeu AlaGlnIle TyrAlaVal GlnSer ThrProThr Ile
145 150 155 160
2S Val LeuSerAsp LysThrGly LysThrIle TyrGlu LeuProGly Tyr
165 170 175
Met ProSerVal GlnPheLeu AlaValLeu GluPhe IleGlyAsp Gly
180 185 190
Lys TyrGlnAsp ThrLysAsn AspGluAsp LeuThr LysLysLeu Lys
3~ 195 200 205
Ala TyrIleLys TyrLysThr AsnLeuSer LysSer LysSerSer
210 215 220
3S
(2) INFORMATION FOR SEQ ID N0:143:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 116 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
40 -
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/ICEY: misc_feature
S~ (B) LOCATION 1...116
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:143:
Leu Met Lys Ser Lys Ile Thr His Phe Ile Val Ile Ser Phe Val Leu
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1 5 10 15
Ser Val LeuSerAla CysLys AspGluPro LysLysSer SerGln Ser
20 25 30
His Gln AsnAsnThr LysThr ThrGlnAsn AsnGlnIle AsnGln Pro
S 35 40 45
Asn Lys AspIleLys LysIle GluHisGlu GluGluAsp GluLys Val
50 55 60
Thr Lys GluValAsn AspLeu IleAsnAsn GluAsnLys IleAsp Glu
65 70 75 80
Ile Asn AsnGluGlu AsnAla AspProSer GlnLysArg ThrAsn Asn
85 90 95
Val Leu GlnArgAla ThrAsn HisGlnAsp AsnLeuSer SerPro Leu
100 105 110
Asn Arg LysTyr
1S 115
(2) INFORMATION FOR SEQ ID N0:144:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 79 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
2S
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...79
3S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:144:
Met Phe Glu Lys Ile Arg Lys Ile Leu Ala Asp Ile Glu Asp Ser Gln
- 1 5 10 15
Asn Glu Ile Glu Met Leu Leu Lys Leu Ala Asn Leu Ser Leu Gly Asp
20 25 30
Phe Ile Glu Ile Lys Arg Gly Ser Met Asp Met Pro Lys Gly Val Asn
35 40 45
Glu Ala Phe Phe Thr Gln Leu Ser Glu Glu Val Glu Arg Leu Lys Glu
55 60
4S Leu Ile Asn Ala Leu Asn Lys Ile Lys Lys Gly Let Leu Val Phe
65 70 75
(2) INFORMATION FOR SEQ ID N0:145:
- SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 51 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
CA 02273199 1999-06-O1
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-226-
(ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
S (vi)ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix)FEATURE:
(A) NAME/KEY: misc
feature
_
(B) LOCATION 1...51
(xi)SEQUENCE DESCRIPTION: SEQ ID N0:145:
Met Ser Met Phe Ile Ser Asn Leu Ala Phe Glu His Lys
Thr Ser Asp
IS 1 5 10 15
Ala Met Glu Val Ala Lys Ile Ala Ile Leu Ser Leu Ile
Leu Gly Ser
20 25 30
Gly Ile Ile Gly Ala Leu Tyr Leu Phe Ala Lys Arg Ala
Leu Asp Ala
35 40 45
Leu Lys Lys
50
(2) INFORMATION
FOR
SEQ
ID
N0:146:
2S (i) SEQUENCE CHARACTERISTICS:
(A} LENGTH: 449 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii} MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi} ORIGINAL SOURCE:
3S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...449
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:146:
Met Gly Leu Lys Ile Lys Ile Leu Arg Leu Ser Met Asn Leu Lys Lys
1 S 10 15
4S Thr Glu Asn Ala Leu Ser Leu Thr Leu Lys Asn Phe Ile Lys Ser Glu
20 25 30
Ser Phe Gly Gly Ile Phe Leu Phe Leu Asn Ala Val Leu Ala Met Val
35 40 45
Val Ala Asn Ser Phe Leu Lys Glu Ser Tyr Phe Ala Leu Trp His Thr
S0 50 55 60
Pro Phe Gly Phe Gln Val Gly Asp Phe Phe Ile Gly Phe Ser Leu His
65 70 75 80
Asn Trp Ile Asp Asp Val Leu Met Ala Leu Phe Phe Leu Met Ile Gly
85 90 95
CA 02273199 1999-06-O1
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Leu Glu IleLysArg GluLeu LeuPheGly GluLeuSer SerPheLys
100 105 110
Lys Ala SerPhePro ValIle AlaAlaIle GlyGlyMet IleAlaPro
115 120 125
S Gly Leu IleTyrPhe PheLeu AsnAlaAsn ThrProSer GlnHisGly
130 135 140
Phe Gly IleProMet AlaThr AspIleAla PheAlaLeu GlyValIle
145 150 155 160
Met Leu LeuGlyLys ArgVal ProThrAla LeuLysVal PheLeuIle
IO 165 170 175
Thr Leu AlaValAla AspAsp LeuGlyAla IleValVal IleAlaLeu
180 185 190
Phe Tyr ThrThrAsn LeuLys PheAlaTrp LeuLeuGly AlaLeuGly
195 200 205
IS Val Val LeuValLeu AlaIle LeuAsnArg LeuAsnIle Arg_Ser_Leu
210 215 220
Ile Pro TyrLeuLeu LeuGly ValLeuLeu TrpPheCys ValHisGln
225 230 235 240
Ser Gly IleHisAla ThrIle AlaAlaVal ValLeuAla PheMetIle
2O 245 250 255
Pro Val LysIlePro LysAsp SerLysAsn ValGluLeu LeuGluLeu
260 265 270
Gly Lys ArgTyrAla GluThr SerSerGly ValLeuLeu ThrLysGlu
275 280 285
2S Gln Gln GluIleLeu HisSer IleGluGlu LysAlaSer AlaLeuGln
290 295 300
Ser Pro LeuGluArg LeuGlu HisPheLeu AlaProIle SerGlyTyr
305 310 315 320
Phe Ile MetProLeu PheAla PheAlaAsn AlaGlyVal SerValAsp
3O 325 330 335
Ser Ser IleAsnLeu GluVal AspLysVal LeuLeuGly ValIleLeu
340 345 350
Gly Leu CysLeuGly LysPro LeuGlyIle PheLeuIle ThrPheIle
355 360 365
3S Ser Glu LysLeuLys IleThr AlaArgPro LysGlyIle GlyTrpTrp
370 375 380
His Ile LeuGlyAla GlyLeu LeuAlaGly IleGlyPhe ThrMetSer
385 390 395 400
Met Phe IleSerAsn LeuAla PheThrSer GluHisLys AspAlaMet
4O 405 410 415
Glu Val AlaLysIle AlaIle LeuLeuGly SerLeuIle SexGlyIle
420_ 425 430
Ile Gly AlaLeuTyr LeuPhe AlaLeuAsp LysArgAla AlaLeuLys
435 440 445
4S Lys
(2) INFORMATION FOR SEQ ID N0:147: ..
SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 815 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 228 -
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
IO (B) LOCATION 1...815
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:147:
Met Asn Asp Lys Arg Phe Arg Lys Tyr Cys Ser Phe Ser Ile Phe Leu
IS 1 5 10 15
Ser Leu Leu Gly Thr Phe Glu Leu Glu Ala Lys Glu Glu Glu Lys Glu
20 25 30
Glu Lys Lys Thr Glu Arg Asn Lys Asp Lys Glu Lys-ASn Ala Gln His
35 40 45
2O Thr Leu Gly Lys Val Thr Thr Gln Ala Ala Lys Ile Phe Asn Tyr Asn
50 55 60
Asn Gln Thr Thr Ile Ser Ser Lys Glu Leu Glu Arg Arg Gln Ala Asn
65 70 75 80
Gln Ile Ser Asp Met Phe Arg Arg Asn Pro Asn Ile Asn Val Gly Gly
2S 85 90 95
Gly Ala Val Ile Ala Gln Lys Ile Tyr Val Arg Gly Ile Glu Asp Arg
100 105 110
Leu Ala Arg Val Thr Val Asp Gly Val Ala Gln Met Gly Ala Ser Tyr
115 120 125
3O Gly His Gln Gly Asn Thr Ile Ile Asp Pro Gly Met Leu Lys Ser Val
130 135 140
Val Val Thr Lys Gly Ala Ala Gln Ala Ser Ala Gly Pro Met Ala Leu
145 150 155 160
Ile Gly Ala Ile Lys Met Glu Thr Arg Ser Ala Ser Asp Phe Ile Pro
3S 165 170 175
Lys Gly Lys Asp Tyr Ala Ile Ser Gly Ala Ala Thr Phe Leu Thr Asn
180 185 190
Phe Gly Asp Arg Glu Thr Ile Met Gly Ala Tyr Arg Asn His His Phe
195 200 205
4O Asp Ala Leu Leu Tyr Tyr Thr His Gln Asn Ile Phe Tyr Tyr Arg Asp
210 215 220
Gly Asp Asn Ala Met Lys Asn Leu Phe Asp Pro Lys Ala Asp Asn Lys
225 230 235 240
Val Thr Ala Ser Pro Ser Glu Gln Asn Asn Val Met Ala Lys Ile Asn
4S 245 250 255
Gly Tyr Leu Ser Glu Arg Asp Thr Leu Thr Leu Ser Tyr Asn Met i.m
260 265 270
Arg Asp Asn Ala Asn Arg Pro Leu Arg Ala Asn Phe Thr Gly Thr Phe
275 280 285
SO Leu Pro Tyr Ser Cys Gly Asp Phe Asn Ala Phe Pro Asn Glu Lys Asn
290 295 300
Pro Ser Asp Cys Leu Phe Glu Asn Asp Ala Ser Leu Phe Lys Thr Tyr
305 310 315 320
Ser Val Asn Leu Val His Asn Val Ser Leu Asn Tyr Glu Arg Glu Gly
.__._.~._.~.,...- _ __~.... _ . ____._._..T....... - _
CA 02273199 1999-06-O1
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325 330 335
Gly Ser ArgPhe GlyAspPro LysLeuLys IleAsn GlyTyrThr Ser
340 345 350
Ile Arg AsnVal GlnIleAsp ProLeuPhe ArgPro SerAspIle Ala
$ 355 360 365
Thr Thr IlePro PheThrPro AsnProGln LeuSer GlnGlyGlu Glu
370 375 380
Asn Gln CysVal AlaGlnGly GlyIleTyr AspAla LeuLysGln Thr
385 390 395 400
1~ Cys Ser IleThr PheLysSer LeuGlyGly GlySer ValValAla Asn
405 410 415
Lys Asn LeuPhe IleIleAsn SerGlyPhe AsnAla AsnValIle His
420 425 430
Thr Ile AspHis LysAsnAsp AsnLeuLeu GluTyr GlyLeuAsn Tyr
1$ 435 440 445
Gln Asn LeuThr ThrPheAsp LysAlaIle ProAsp SerGluLeu Val
450 455 460
Lys Pro GlyAsp AlaProAsp AlaCysLeu ArgVal ThrGlyPro Asp
465 470 475 480
2~ Asp Pro AsnMet AsnGlyArg CysGlnArg AsnGly AlaThrAla Asn
485 490 495
Val Val GlyVal TyrAlaGln AlaAsnTyr ThrLeu HisProMet Val
500 505 510
Thr Leu GlyAla GlyThrArg TyrAspVal TyrThr LeuValAsp Lys
2$ 515 520 525
Asp Trp GlnLeu HisValThr GlnGlyPhe SerPro SerAlaAla Leu
530 535 540
Asn Val SerPro LeuGluAsn LeuAsnPhe ArgLeu SerTyrAla Tyr
545 550 555 560
Val Thr ArgGly ProMetPro GlyGlyLeu ValTrp MetArgGln Asp
565 570 575
Asn Leu ArgTyr AsnArgAsn LeuLysPro GluIle GlyGlnAsn Ala
580 585 - 590
Glu Phe AsnThr GluTyrSer SerGlnTyr PheAsp PheArgAla Ala
3$ 595 600 605
Gly Phe ValGln LeuIleSer AsnTyrIle AsnGln PheSerSer Thr
610 615 620
Leu Phe ValThr AsnLeuPro AlaGlnAsp IleIle TyrValPro Gly
625 630 635 640
Tyr Glu ValSer GlyThrAla LysTyrLys GlyPhe SerLeuGly Leu
645 650 655
Ser Val AlaArg SerTrpPro SerLeuLys GlyArg LeuIleAla Asp
660 665 670
Val Tyr GluLeu AlaAlaThr ThrGlyAsn ValPhe IleLeuThr Ala
4$ 675 680 685
Ser Tyr ThrIle ProArgThr GlyLeu~e_ IleThr TrpLeuSer Arg
690 695 700
Phe Val ThrAsn LeuSerTyr CysSerTyr SerPro TyrArgAsn Gly
705 710 715 720
$~ Pro Thr AspIle AspArgArg ProSerAsn CysPro LysThrPro Gly
725 730 735
Ile Phe HisVal Hi_sLysPro GlyTyrGly ValSer SerPhePhe Ile
740 745 750
Thr Tyr LysPro ThrTyrLys LysLeuLys GlyLeu SerLeuAsn Ala
CA 02273199 1999-06-O1
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-230-
755 760 765
Val Phe Asn Asn Val Phe Asn Gln Gln Tyr Ile Asp Gln Ala Ser Pro
770 775 780
Val Met Ser Pro Asp Glu Pro Asn Gln Asp Lys Tyr Ala Arg Gly Met
$ 785 790 795 g00
Ala Glu Pro Gly Phe Asn Ala Arg Phe Glu Ile Ser Tyr Lys Phe
805 810 815
(2) INFORMATION FOR SEQ ID N0:148:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 814 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
1$
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
ZO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
2$ (B) LOCATION 1...814
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:148:
Met ThrSer ValLeu GluLysTyr CysSerPhe SerIle PheLeuSer
30 1 5 to is
Leu LeuGly ThrPhe GluLeuGlu AlaLysGlu GluGlu LysGluGlu
20 25 30
Lys LysThr GluArg AsnLysAsp LysGluLys AsnAla GlnHisThr
35 40 45
3$ Leu GlyLys ValThr ThrGlnAla AlaLysIle PheAsn TyrAsnAsn
50 55 60
Gln ThrThr IleSer SerLysGlu LeuGluArg ArgGln AlaAsnGln
65 70 75 8p
Ile SerAsp MetPhe ArgArgAsn ProAsnIle AsnVal GlyGlyGly
40 85 90 95
Ala ValIle AlaGln LysIleTyr ValArgGly IleGlu AspArgLeu
100_ 105 110
Ala ArgVal ThrVal AspGlyVal AlaGlnMet GlyAla SerTyrGly
- 115 120 125
_4$ His GlnGly Asr~Thr IleIleAsp ProGlyMet LeuLys SerValVal
130 135 140
Val ThrLys GlyAla AlaGlnAla SerAlaGly ProMet AlaLeuIle
145 150 155 160 _
Gly AlaIle LysMet GluThrArg SerAlaSer AspPhe IleProLys
$0 165 170 175
Gly LysAsp TyrAla IleSerGly AlaAlaThr PheLeu ThrAsnPhe
180 185 190
Gly AspArg GluThr IleMetGly AlaTyrArg AsnHis HisPheAsp
195 200 205
CA 02273199 1999-06-O1
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Ala Leu Leu Tyr Tyr Thr His Gln Asn Ile Phe Tyr Tyr Arg Asp Gly
210 215 220
Asp Asn AlaMetLys AsnLeu PheAspPro LysAlaAsp AsnLysVal
225 230 235 240
Thr Ala SerProSer GluGln AsnAsnVal MetAlaLys IleAsnGly
245 250 255
Tyr Leu SerGluArg AspThr LeuThrLeu SerTyrAsn MetThrArg
260 265 270
Asp Asn AlaAsnArg ProLeu ArgAlaAsn PheThrGly ThrPheLeu
1~ 275 280 285
Pro Tyr SerCysGly AspPhe AsnAlaPhe ProAsnGlu LysAsnPro
290 295 300
Ser Asp CysLeuPhe GluAsn AspAlaSer LeuPheLys ThrTyrSer
305 310 315 320
IS Val Asn LeuValHis AsnVal SerLeuAsn TyrGluArg GluGlyGly
325 330 335
Ser Arg PheGlyAsp ProLys LeuLysIle AsnGlyTyr ThrSerIle
340 345 350
Arg Asn ValGlnIle AspPro LeuPheArg ProSerAsp IleAlaThr
2~ 355 360 365
Thr Ile ProPheThr ProAsn ProGlnLeu SerGlnGly GluGluAsn
370. - 375 380
Gln Cys ValAlaGln GlyGly IleTyrAsp AlaLeuLys GlnThrCys
385 390 395 400
2$ Ser Ile ThrPheLys SerLeu GlyGlyGly SerValVal AlaAsnLys
405 410 415
Asn Leu PheIleIle AsnSer GlyPheAsn AlaAsnVal IleHisThr
420 425 430
Ile Asp HisLysAsn AspAsn LeuLeuGlu TyrGlyLeu AsnTyrGln
3~ 435 440 445
Asn Leu ThrThrPhe AspLys AlaIlePro AspSerGlu LeuValLys
450 455 460
Pro Gly AspAlaPro AspAla CysLeuArg ValThrGly ProAspAsp
465 470 475 480
35 Pro Asn MetAsnGly ArgCys GlnArgAsn GlyAlaThr AlaAsnVal
485 490 495
Val Gly ValTyrAla GlnAla AsnTyrThr LeuHisPro MetValThr
500 505 510
Leu Gly AlaGlyThr ArgTyr AspValTyr ThrLeuVal AspLysAsp
515 520 525
Trp Gln LeuHisVal ThrGln GlyPheSer ProSerAla AlaLeuAsn
530 535 540
Val Ser ProLeuGlu AsnLeu AsnPheArg LeuSerTyr AlaTyrVal
545 550 555 560
4$ Thr Arg GlyProMet ProGly GlyLeuVal TrpMetArg GlnAspAsn
565 570 575
Leu Arg TyrAsnArg AsnLeu LysProGlu IleGlyGln AsnAlaGlu
580 585 590
Phe Asn ThrGluTyr SerSer GlnTyrPhe AspPheArg AlaAlaGly
$~ 595 600 605
Phe Val GlnLeuIle SerAsn TyrIleAsn GlnPheSer SerThrLeu
610 615 620
Phe Val ThrAsnLeu ProAla GlnAspIle IleTyrVal ProGlyTyr
625 630 635 640
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Glu ValSer GlyThr AlaLysTyr LysGlyPhe SerLeu GlyLeuSer
645 650 655
Val AlaArg SerTrp ProSerLeu LysGlyArg LeuIle AlaAspVal
660 665 670
S Tyr GluLeu AlaAla ThrThrGly AsnValPhe IleLeu ThrAlaSer
675 " 680 685
Tyr ThrIle ProArg ThrGlyLeu SerIleThr TrpLeu SerArgPhe
690 695 700
Val ThrAsn LeuSer TyrCysSer TyrSerPro TyrArg AsnGlyPro
705 710 715 720
Thr AspIle AspArg ArgProSer AsnCysPro LysThr ProGlyIle
725 730 735
Phe HisVal HisLys ProGlyTyr GlyValSer SerPhe PheIleThr
740 745 750
IS Tyr LysPro ThrTyr LysLysLeu LysGlyLeu SerLeu AsnAlaVal
755 760 765
Phe AsnAsn ValPhe AsnGlnGln TyrIleAsp GlnAla SerProVal
770 775 780
Met SerPro AspGlu ProAsnGln AspLysTyr AlaArg GlyMetAla
785 790 795 800
Glu ProGly PheAsn AlaArgPhe GluIleSer TyrLys Phe
805 810
2S
(2) INFORMATION FOR SEQ ID N0:149:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 527 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
3S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...527
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:149:
Met Lys Gln Asn Leu Lys Pro Phe Lys Met Ile Lys Glu Asn Leu Met
4S 1 5 to is
Thr Gln Ser Gln Lys Val Arg Phe Leu Ala Pro Leu Ser i..a Ala Leu
20 25 30
Ser Leu Ser Phe Asn Pro Val Gly Ala Glu Glu Asp Gly Gly Phe Met
35 40 45
S0 Thr Phe Gly Tyr Glu Leu Gly Gln Val Val Gln Gln Val Lys Asn Pro
SO 55 60
Gly Lys Ile Lys Ala Glu Glu Leu Ala Gly Leu Leu Asn Ser Thr Thr
65 70 75 80
Thr Asn Asn Thr Asn Ile Asn Ile Ala Gly Thr Gly Gly Asn Val Ala
CA 02273199 1999-06-O1
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85 90 9S
Gly ThrLeu GlyAsnLeu PheMet AsnGlnLeu GlyAsnLeu IleAsp
100 105 110
Leu TyrPro ThrLeuLys ThrAsn AsnLeuHis GlnCysGly SerThr
$ 115 120 125
Asn SerGly AsnGlyAla ThrAla AlaAlaAla ThrAsnAsn SerPro
130 135 140
Cys PheGln GlyAsnLeu AlaLeu TyrAsnGlu MetValAsp SerIle
145 150 155 160
l~ Lys ThrLeu SerGlnAsn IleSer LysAsnIle PheGlnGly AspAsn
165 170 175
Asn ThrThr SerAlaAsn LeuSer AsnGlnLeu SerGluLeu AsnThr
180 185 190
Ala SerVal TyrLeuThr TyrMet AsnSerPhe LeuAsnAla AsnAsn
1$ 195 200 205
Gln AlaGly GlyIlePhe GlnAsn AsnThrAsn GlnAlaTyr GluAsn
210 215 220
Gly ValThr AlaGlnGln IleAla TyrValLeu LysGlnAla SerIle
225 230 235 240
Thr MetGly ProSerGly AspSer GlyAlaAla GlyAlaPhe LeuAsp
245 250 255
Ala AlaLeu AlaGlnHis ValPhe AsnSerAla AsnAlaGly AsnAsp
260 265 270
Leu SerAla LysGluPhe ThrSer LeuValGln AsnIleVal AsnAsn
2$ 275 280 285
Ser GlnAsn AlaLeuThr LeuAla AsnAsnAla AsnIleSer AsnSer
290 295 300
Thr GlyTyr GlnValSer TyrGly GlyAsnIle AspGlnAla ArgSer
305 310 315 320
3~ Thr GlnLeu LeuAsnAsn ThrThr AsnThrLeu AlaLysVal ThrAla
325 330 335
Leu AsnAsn GluLeuLys AlaAsn ProTrpLeu GiyAsnPhe AlaAla
340 345 3S0
Gly AsnSer SerGlnVal AsnAla PheAsnGly PheIleThr LysIle
3$ 355 360 365
Gly TyrLys GlnPhePhe GlyGlu AsnLysAsn ValGlyLeu ArgTyr
370 375 380
Tyr GlyPhe PheSerTyr AsnGly AlaGlyVal GlyAsnGly ProThr
385 390 395 400
Tyr AsnGln ValAsnLeu LeuThr TyrGlyVal GlyThrAsp ValLeu
405 410 415
Tyr AsnVal PheSerArg SerPhe GlySerArg SerLeuAsn AlaGly
420 425 430
Phe PheGly GlyIleGln LeuAla GlyAspThr TyrIleSer ThrLeu
4$ 435 440 445
Arg AsnSer ProGlnLeu Ala:.~.ArgProThr AlaThrLys PheGln
450 455 460
Phe LeuPhe AspValGly LeuArg MetAsnPhe GlyIleLeu LysLys
465 470 475 480
$~ Asp LeuLys SerHisAsn GlnHis SerIleGlu IleGlyVal GlnIle
485 490 495
Pro ThrIle TyrAsnThr TyrTyr LysAlaGly GlyAlaGlu ValLys
500 505 510
Tyr PheArg ProTyrSer ValTyr TrpValTyr GlyTyrAla Phe
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
-234-
515 520 525
(2) INFORMATION FOR SEQ ID N0:150:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 459 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
1$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A} NAME/KEY: misc_feature
(B) LOCATION 1...459
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:150:
Val Val Leu Leu Thr Met Thr Lys Arg Leu Phe Lys Gly Leu Leu Ala
1 5 10 15
2S Ile Ser Leu Ala Val Ser Leu His Gly Gly Glu Val Lys Glu Lys Lys
20 25 30
Pro Val Lys Pro Val Lys Glu Asp Pro Gln Glu Leu Ala Ala Lys Arg
35 40 45
Val Glu Ala Phe Ser Arg Phe Ser Asn Val Val Thr Glu Ile Glu Lys
50 55 60
Lys Tyr Val Asp Lys Ile Ser Ile Ser Glu Ile Met Thr Lys Ala Ile
65 70 75 80
Glu Gly Leu Leu Ser Asn Leu Asp Ala His Ser Ala Tyr Leu Asn Glu
85 90 95
Lys Lys Phe Lys_Glu Phe Gln Ala Gln Thr Glu Gly Glu Phe Gly Gly
100 105 110
Leu Gly Ile Thr Val Gly Met Arg Asp Gly Val Leu Thr Val Ile Ala
115 120 125
Pro Leu Glu Gly Thr Pro Ala Tyr Lys Ala Gly Val Lys Ser Gly Asp
130 135 140
Ser Ile Leu Lys Ile Asn Asn Glu Ser Thr Leu Ser Met Ser Ile Asp
145 150 155 160
Asp Ala Val Asn Leu Met Arg Gly Lys Pro Lys Thr Ser Ile Gln Ile
lb5 170 175
4$ Thr Va) Val Arg Lys Asn Glu Pro Lys Pro Leu Val Phe Asn Ile Val
180 185 190
Arg Asp Ile Ile Lys Ile Pro Ser Val Tyr Val Lys Lys Ile Lys Asp
195 200 205
Thr Pro Tyr Leu Tyr Val Arg Val Asn Ser Phe Asp Lys Asn Val Thr
210 215 220
Lys Ser Val Leu Asp Gly Leu Lys Ala Asn Pro Asn Ile Lys Gly Val
225 230 235 240
Val Leu Asp Leu Arg Gly Asn Pro Gly Gly Leu Leu Asn Gln Ala Val
245 250 255
_._._ _~w~._.~,._
CA 02273199 1999-06-O1
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Gly Leu SerAsnLeu PheIleLys GluGly ValLeuVal SerGln Arg
260 265 270
Gly Lys AsnLysGlu GluAsnLeu GluTyr LysAlaAsn GlyArg Ala
275 280 285
$ Pro Tyr ThrAsnLeu ProValVal ValLeu ValAsnGly GlySer Ala
290 295 300
Ser Ala SerGluIle ValAlaGly AlaLeu GlnAspHis LysArg Ala
305 310 315 320
Ile Ile IleGlyGlu LysThrPhe GlyLys GlySerVal GlnVal Leu
1~ 325 330 335
Leu Pro ValAsnLys AspGluAla IleLys IleThrThr AlaArg Tyr
340 345 350
Tyr Leu ProSerGly ArgThrIle GlnAla LysGlyIle ThrPro Asp
355 360 365
15 Ile Val IleTyrPro GlyLysVal ProGlu AsnGluAsn LysPhe Ser
370 -- 375 380
Leu Lys GluAlaAsp LeuLysHis HisLeu GluGlnGlu LeuLys Lys
385 390 395 400
Leu Asp AspLysThr ProIleSer_LysGlu AlaAspLys AspLys Lys
2~ 405 410 415
Ser Glu GluGluLys GluValThr ProLys MetIleAsn AspAsp Ile
420 425 430
Gln Leu LysThrAla IleAspSer LeuLys ThrTrpSer IleVal Asp
435 440 445
2$ Glu Lys MetAspGlu LysValPro LysLys Lys
450 455
(2) INFORMATION FOR SEQ ID N0:151:
3O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 104 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
35 (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
40 (A) ORGANISM~.-Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...104
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:151:
Leu Leu Leu His Pro Leu His Ala His Ala Gln Val Leu Gly Phe Thr
1 5 10 15
$~. Asn His Asp His Ala Pro Trp Leu Tyr Asp Phe Ile Lys Ser Phe Cys
20 25 30
Asn Leu Ser Gly Gln Pro Phe Leu Asp Leu Gln Ala Phe Ala Ile Asn
35 40 45
Phe Asn Glu Phe Ser Asp Arg Ala Asn Ala Tyr Asn Leu Phe Leu Arg
CA 02273199 1999-06-O1 -
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50 55 60
Asp Ile Ser His Ala Asn Ile Pro Lys Lys Arg Glu Gln Met Val Leu
65 70 75 80
Ala Ser Gly Val Lys Phe Asn Val Leu Ser His Tyr His Phe Ile Ala
$ 85 90 95
Asn Ala Leu Lys Ile Arg Ala Phe
100
(2) INFORMATION FOR SEQ ID N0:152:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 165 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
1$
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
ZO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
2$ (B) LOCATION 1...165
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:152:
Met Ile GluLeu IleLeuHis AsnLys SerIleGln IleAspGlu Thr
30 1 s l0 15
Leu Leu AsnVal LysGluHis LeuGlu LysPheTyr SerAsnLys Glu
20 25 30
Gln Glu ThrIle AlaLysThr LeuGlu SerGlnThr GluLeuThr Cys
35 40 45
3$ Ser Tyr LeuLeu AspLysAsp PheSer LeuLeuGlu LysHisLeu Glu
50 55 60
Asn Ser LeuGly HisPheThr PheGlu SerGluPhe AlaLeuLeu Lys
65 70 75 80
Asp Lys GluPro LeuAsnLeu AlaGln IleLysGln IleGlyVal Leu
40 85 90 95
Lys Val IleThr TyrGluMet ThrGln AlaLeuLys AsnGlnIle-Ile
100 105 110
His Leu ThrGln IleValAsn GluGlu AsnLeuGlu PheAspGlu Glu
115 120 125
4$ Leu Val IleTyr HisLeuAsn PheLys LeuAsnGln AsnThrTyr Lys
130 135 1
_0
Val Leu AlaLys PheCysVal LeuLys LysLysGly ThrLeuHis Glu
145 150 155~ 160
Lys Phe LysAla Phe
$~ 165
(2) INFORMATION FOR SEQ ID N0:153:
(i) SEQUENCE CHARACTERISTICS:
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(A) LENGTH: 213 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
ld (A) ORGANISM: Helicobacter pylori
(ix).FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...213
IS
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:153:
Met Asp ThrGluThr GlnGlu LysPheLeu AlaTyrLeu PheGluLys
1 5 10 15
2~ Ala Leu GlnLysAsn LeuGln AlaTyrTrp IleThrThr ThrGluThr
20 25 30
Lys Asn GluLeuThr ArgGlu GluPheSer AsnLeuIle argLysThr
35 40 45
Met Ile GluLeuIle LeuHis AsnLysSer IleGlnIle AspGluThr
25 50 55 60
Leu Leu AsnValLys GluHis LeuGluLys PheTyrSer AsnLysGlu
65 70 75 80
Gln Glu ThrIleAla LysThr LeuGluSer GlnThrGlu LeuThrCys
85 90 95
30 Ser Tyr LeuLeuAsp LysAsp PheSerLeu LeuGluLys HisLeuGlu
100 105 110
Asn Ser LeuGlyHis PheThr PheGluSer GluPheAla LeuLeuLys
115 120 125
Asp Lys GluProLeu AsnLeu AlaGlnIle LysGlnIle GlyValLeu
35 130 135 140
Lys Val IleThrTyr GluMet ThrGlnAla LeuLysAsn G1nIleIle
145 150 155 160
His Leu ThrGlnIle ValAsn GluGluAsn LeuGluPhe AspGluGlu
165 170 175
Leu Val IleTyrHis LeuAsn PheLysLeu AsnGlnAsn ThrTyrLys
180 185 190
Val Leu AlaLysPhe CysVal LeuLysLys LysGlyThr LeuHisGlu
195 200 205
Lys Phe LysAlaPhe
45 210
(2) INFORMATION FOR SEQ ID N0:154:
(i) SEQUENCE CHARACTERISTICS:
w 5~ (A) LENGTH: 253 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...253
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:154:
Met AlaIle SerIle LysSerPro LysGluIle LysAla LeuArgLys
1 5 10 15
IS Ala GlyGlu LeuThr AlaGlnAla LeuAlaLeu LeuGlu ArgGluVal
20 25 30
Arg ProGly ValSer LeuLeuGlu LeuAspLys MetAla GluAspPhe
35 40 45
Ile LysSer SerHis AlaArgPro AlaPheLys GlyLeu TyrGlyPhe
50 55 60
Pro AsnSer ValCys MetSerLeu AsnGluVal ValIle HisGlyIle
65 70 75 g0
Pro ThrAsp TyrVal LeuGlnGlu GlyAspIle IleGly LeuAspLeu
85 90 95
Gly ValGlu ValAsp GlyTyrTyr GlyAspSer AlaLeu ThrLeuPro
100 105 110
Ile GlyAla IleSer ProGlnAsp GluLysLeu LeuAla CysSerLys
115 120 125
Glu SerLeu MetHis AlaIleSer SerIleArg ValGly MetHisPhe
130 135 140
Lys GluLeu SerGln IleLeuGlu GlyAlaIle ThrGlu ArgGlyPhe
145 150 155 160
Val ProLeu LysGly PheCysGly HisGlyIle GlyLys LysProHis
165 170 175
Glu GluPro GluIle ProAsnTyr LeuGluLys GlyVal LysAlaAsn
180 185 190
Ser GlyPro LysIle LysGluGly MetValPhe CysLeu GluProMet
195 200 205
Val CysGln LysGln GlyGluPro LysIleLeu AlaAsp LysTrpSer
210 215 220
Val ValSer ValAsp GlyLeuAsn ThrSerHis HisGlu HisThrIle
225 230 235 240
Ala IleVal GlyAsn LysAlaVal IleLeuThr GluArg
245 250
(2) INFORMATION FOR SEQ ID N0:155:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 247 amino acids
$0 (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
- CA 02273199 1999-06-O1
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...247
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:155:
Lys Pro Lys Arg Asn Gln Ser Pro Lys Lys Ser Arg Glu Leu Thr Ala
1 5 10 15
Gln Ala LeuAla LeuLeuGlu ArgGluVal ArgProGly ValSer Leu
I$ 20 25 30
Leu Glu LeuAsp LysMetAla GluAspPhe IleLysSer SerHis Ala
35 40 45
Arg Pro AlaPhe LysGlyLeu TyrGlyPhe ProAsnSer ValCys Met
50 55 60
2O Ser Leu AsnGlu ValValIle HisGlyIle ProThrAsp TyrVal Leu
65 70 75 80
Gln Glu GlyAsp IleIleGly LeuAspLeu GlyValGlu ValAsp Gly
85 90 95
Tyr Tyr GlyAsp SerAlaLeu ThrLeuPro IleGlyAla IleSer Pro.
25 loo los llo
Gln Asp GluLys LeuLeuAla CysSerLys GluSerLeu MetHis Ala
115 120 125
Ile Ser SerIle ArgValGly MetHisPhe LysGluLeu SerGln Ile
130 135 140
3O Leu Glu GlyAla IleThrGlu ArgGlyPhe ValProLeu LysGly Phe
145 150 155 160
Cys Gly HisGly IleGlyLys LysProHis GluGluPro GluIle Pro
165 170 175
Asn Tyr LeuGlu LysGlyVal LysAlaAsn SerGlyPro LysIle Lys
35 lso ls5 190
Glu Gly MetVal PheCysLeu GluProMet ValCysGln LysGln Gly
195 200 205
Glu Pro LysIle LeuAlaAsp LysTrpSer ValValSer ValAsp Gly
210 215 220
4O Leu Asn ThrSer HisHisGlu HisThrIle AlaIleVal GlyAsn Lys
225 230 235 240
Ala Val IleLeu ThrGluArg
245
- 4S (2) INFORMATION FOR SEQ ID N0:156:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 340 amino acids
(B) TYPE: amino acid
$O (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
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(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...340
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:156:
Met Tyr Arg Lys Asp Leu Asp Asn Tyr Leu Lys Gln Arg Leu Pro Lys
1 5 10 15
Ala Val Phe Leu Tyr Gly Glu Phe Asp Phe Phe Ile His Tyr Tyr Ile
25 30
1S Gln Thr Ile Ser Ala Leu Phe Lys Gly Asn Asn Pro Asp Thr Glu Thr
35 40 45
Ser Leu Phe Tyr Ala Ser Asp Tyr Glu Lys Ser Gln Ile Ala Thr Leu
50 55 60
Leu Glu Gln Asp Ser Leu Phe Gly Gly Ser Ser Leu Val Ile Leu Lys
20 65 70 75 80
Leu Asp Phe Ala Leu His Lys Lys Phe Lys Glu Asn Asp Ile Asn Pro
85 90 95
Phe Leu Lys Ala Leu Glu Arg Pro Ser His Asn Arg Leu Ile Ile Gly
100 105 110
Leu Tyr Asn Ala Lys Ser Asp Thr Thr Lys Tyr Lys Tyr Thr Ser Glu
115 120 125
Ile Ile Val Lys Phe Phe Gln Lys Ser Pro Leu Lys Asp Glu Ala Ile
130 135 140
Cys-Val Arg Phe Phe Thr Pro Lys Ala Trp Glu Ser Leu Lys Phe Leu
145 150 155 160
Gln Glu Arg Ala Asn Phe Leu His Leu Asp Ile Ser Gly His Leu Leu
165 170 175
Asn Ala Leu Phe Glu Ile Asn Asn Glu Asp Leu Ser Val Ser Phe Asn
180 185 190
3S Asp Leu Asp Lys Leu Ala Val Leu Asn Ala Pro Ile Thr Leu Glu Asp
195 200 205
Ile Gln Glu Leu Ser Ser Asn Ala Gly Asp Met Asp Leu Gln Lys Leu
210 215 220
Ile Leu Gly Leu Phe Leu Lys Lys Ser Val Leu Asp Ile Tyr Asp Tyr
225 230 235 240
Leu Leu Lys Glu Gly Lys Lys Asp Ala Asp Ile Leu Arg Gly Leu Glu
245 250 255
Arg Tyr Phe Tyr Gln Leu Phe Leu Phe Phe Ala His Ile Lys Thr Thr
260 265 270
4S Gly Leu Met Asp Ala Lys Glu Val Leu Gly ~~yr Ala Pro Pro Lys Glu
275 280 285
Ile Val Glu Asn Tyr Ala Lys Asn Ala Leu Arg Leu Lys Glu Ala Gly
290 295 300
Tyr Lys Arg Val Phe Glu Ile Phe Arg Leu Trp His Leu Gln Ser Met
= S0 305 310 315 320
Gln Gly Gln Lys Glu Leu Gly Phe Leu Tyr Leu Thr Pro Ile Gln Lys
325 330 335
Ile Ile Asn Pro
340
_. .____ ~_._... _ ____.... _.
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(2) INFORMATION FOR SEQ ID N0:157:
(i) SEQUENCE CHARACTERISTICS:
$ (A) LENGTH: 200 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...200
2O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:157:
Val Phe MetThrSer AlaLeu LeuC:lyLeu GlnIle ValLeuAla Val
1 5 10 15
Leu Ile ValValVal ValLeu LeuGlnLys SerSer SerIleGly Leu
20 25 30
Gly Ala TyrSerGly SerAsn AspSerLeu PheGly AlaLysGly Pro
35 40 45
Ala Ser PheMetAla LysLeu ThrMetPhe LeuGly LeuLeuPhe Val
50 55 60
Ile Asn ThrIleAla LeuGly TyrPheTyr AsnLys GluTyrGly Lys
65 70 75 80
Ser Val LeuAspGlu ThrLys ThrAsnLys GluLeu SerProLeu Val
85 90 95
Pro Ala ThrGlyThr LeuAsn ProThrLeu AsnPro ThrLeuAsn Pro
loo los llo
Th-rLeu AsnProLeu GluGln AlaProThr AsnPro LeuMetPro Thr
115 120 125
Gln Thr ProLysGlu LeuPro LysGluPro AlaLys ThrProPhe Val
130 135 140
4~ Glu Ser ProLysGln AsnGlu LysAsnGlu LysAsn AspAlaLys Glu
145 150 155 160
Asn Gly IleLysGly ValGlu LysAsnLys GluAsn AlaLys~'hrPro
165 170 175
Pro Thr ThrHisGln LysPro LysThrHis AlaThr ThrAsnAla His
l80 ls5 190
Thr Asn GlnLysLys AspGlu Lys
195 200
(2) INFORMATION FOR SEQ ID N0:158:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 159 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
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(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
IO (A) NAME/KEY: misc_feature
(B) LOCATION 1...159
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:15B:
IS Met Arg Ser Pro Asn Leu Glu Lys Glu Glu Thr Glu Ile Ile Glu Thr
1 5 10 _ 15
Leu Leu Val Arg Glu Lys Met Arg Leu Cys Pro Leu Tyr Trp Arg Ile
20 25 30
Leu Ala Phe Leu Ile Asp Ser Leu Leu Val Ala Phe Leu Leu Ser Asp
2O 35 40 45
Leu Leu Arg Ala Cys Ala Phe Leu His Ser Leu Tyr Trp Leu Thr Asn
50 55 60
Pro Ile Tyr Tyr Ser Ala Phe Val Val Met Gly Phe Ile Ile Leu Tyr
65 70 75 80
2S Gly Val Tyr Glu Ile Phe Phe Val Cys Leu Cys Lys Met Ser Leu Ala
85 90 95
Lys Leu Val Phe Arg Ile Lys Ile Ile Asp Il.e Tyr Leu Ala Asp Cys
100 105 110
Pro Ser Arg Ala Ile Leu Leu Lys Arg Leu Gly Leu Lys Ile Val Val
3O 115 120 125
Phe Leu Cys Pro Phe Leu Trp Phe Val Val Phe Lys Asn Pro Tyr His
130 135 140
Arg Ala Trp His Glu Glu Lys Ser Lys Ser Leu Leu Val Leu Phe
145 150 155
3S
(2) INFORMATION FOR SEQ ID N0:159:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 234 amino acids
40 (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
- 4S (iii} HYPOTHF'TICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori _
SO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B} LOCATION 1...234
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:159:
.._. _._ . _~...__._~
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Leu AsnThr AspPheSer HisIleThr AspIleGlu GlyMetArg Phe
1 5 10 15
Val AsnGlu GluAspAla LeuAsnLys LeuIleAsn GluIleHis Thr
S 20 25 30
Arg HisIle AspLeuLys AspSerIle MetLeuAla LeuSerPhe Asn
35 40 45
Ala LeuTyr LeuAlaAsn AlaLeuAla GlnLysPhe GlyAlaThr Tyr
50 55 60
1~Asp IleLeu PheLeuGlu ProIleLeu AlaProLeu AsnSerLys Cys
65 70 75 80
Glu IleAla LeuValSer GluSerMet AspIleVal MetAsnGlu Ser
85 90 95
Leu IleAsn SerPheAsp IleAlaLeu AspTyrVal TyrGlyGlu Ala
IS 100 105 110
Lys ArgAla TyrGluGlu AspIleLeu SerHisIle TyrGlnTyr Arg
115 120 125
Lys GlyAsn AlaIleLys SerLeuLys AspLysAsn IlePheIle Val
130 135 140
2~Asp ArgGly IleGluThr GlyPheArg AlaGlyLeu GlyValGln Thr
145 150 155 160
Cys LeuLys LysGluCys GlnAspIle TyrIleLeu ThrProIle Leu
165 I70 175
Ala GlnAsn ValAlaGln GlyLeuGlu SerLeuCys AspGlyVal Ile
2S 180 185 190
Ser ValTyr ArgProGlu CysPheVal SerValGlu HisHisTyr Lys
195 200 205
Glu LeuLys ArgLeuSer AsnGluGlu IleGluLys TyrLeuGly Ala
210 215 220
3~Asn AsnAla ProAsnLeu LysLysGlu His
225 230
(2) INFORMATION FOR SEQ ID N0:160:
3S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 287 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
4~ (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL-SOURCE:
4S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...287
S~
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:160:
Leu Lys Gln Ser Glu Met Ala Met Glu Phe Asn Asp Pro Arg Met Arg
1 5 10 15
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Phe Phe Ile Gly Asp Val Arg Asp Leu Glu Arg Leu Asn Tyr Ala Leu
20 25 30
Glu Gly ValAspIle CysIleHis AlaAla AlaLeuLys HisValPro
35 40 45
S Ile Ala GluTyrAsn ProLeuGlu CysIle LysThrAsn IleMetGly
50 '- 55 60
Ala Ser AsnValIle AsnAlaCys LeuLys AsnGluIle SerGlnVal
65 70 75 80
Ile Ala LeuSerThr AspLysAla AlaAsn ProIleAsn LeuTyrGly
IO 85 90 95
Ala Thr LysLeuCys SerAspLys LeuPhe ValSerAla AsnAsnPhe
100 105 110
Lys Gly ProSerGln ThrGlnPhe GlyVal ValArgTyr GlyAsnVal
115 120 125
IS Val Gly SerArgGly SerValVal ProPhe PheLysLys LeuValGln
130 135 140
Asn Lys AlaSerGlu IleProIle ThrAsp IleArgMet ThrArgPhe
145 150 155 160
Trp Ile ThrLeuAsp GluGlyVal SerPhe ValLeuLys SerLeuLys
2O 165 170 175
Arg Met HisGlyGly GluIlePhe ValPro LysIlePro SerMetLys
180 185 190
Met Ile AspLeuAla LysAlaLeu AlaPro AsnIlePro ThrLysIle
195 200 205
25 Ile Gly IleArgPro GlyGluLys LeuHis GluValMet IleProLys
210 215 220
Asp Glu SerHisLeu AlaLeuGlu PheGlu AspPhePhe IleIleGln
225 230 235 240
Pro Thr IleSerPhe GlnThrPro LysAsp TyrThrLeu ThrLysLeu
3O 245 250 255
His Glu LysGlyGln LysValAla ProAsp PheGluTyr SerSerHis
260 265 270
Thr Asn AsnGlnTrp LeuGluPro AspAsp LeuLeuLys LeuLeu
275 280 285
3S
(2) INFORMATION FOR SEQ ID N0:161:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 201 amino acids
4O (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
4S (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
SO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...201
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:161:
CA 02273199 1999-06-O1 -
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Met Arg LeuHisThr AlaPhePhe GlyIleAsn SerLeu LeuValAla
1 5 10 15
Thr Leu LeuIleSer GlyCysSer LeuPheLys LysArg AsnThrAsn
20 25 30
Ala Gln LeuIlePro ProSerAla AsnGlyLeu GlnAla ProIleTyr
35 40 45
Pro Pro ThrAsnPhe ThrProArg LysSerIle GlnPro LeuProSer
50 55 60
Pro Arg LeuGluAsn AsnAspGln ProIleIle SerSer AsnProThr
65 70 75 gp
Asn Ala IleProAsn ThrPro-Ile LeuThrPro AsnAsn ValIleGlu
85 90 95
Leu Asn AlaValGly MetGlyVal AlaProGlu SerThr IleSerPro
IS 100 105 110
Ser Gln AlaLeuAla LeuAlaLys ArgAlaAla IleVal AspGlyTyr
115 120 125
Arg Gln LeuGlyGlu LysMetTyr GlyIleArg ValAsn AlaGlnAsp
130 135 140
Thr Val LysAspMet ValLeuGln AsnSerVal IleLys ThrArgVal
145 150 155 160
Asn Ala LeuIleArg AsnAlaGlu IleThrGlu ThrIle TyrLysAsp
165 170 175
Gly Leu CysGlnVal SerMetGlu LeuLysLeu AspGly ArgIleTrp
180 185 190
Tyr Arg IleLeuSer GlySerArg Gly
195 - 200
(2) INFORMATION FOR SEQ ID N0:162:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 355 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...355
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:162:
Met Ser Tyr Thr Ile Asn Lys Arg Phe Ser Val Gly Val Gly Leu Arg
$0 1 5 10 15
Gly Leu Tyr Ala Thr Gly Ser Phe Asn Asn Thr Val Tyr Val Pro Leu
20 25 30
Glu Gly Ala Ser Val Leu Ser Ala Glu Gln Ile Leu Asn Leu Pro Asn
35 40 45
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Asn Val Phe Ala Asp Gln Val Pro Ser Asn Met Met Thr Leu Leu Gly
50 55 60
Asn IleGly TyrGln ProAlaLeu AsnCysGln LysAlaGly GlyAsp
65 70 75 gp
$ Met SerAsp GlnSer CysGlnGlu PheTyrAsn GlyLeuLys LysIle
85 90 95
Met GlyTyr SerGly LeuIleLys AlaSerAla AsnLeuTyr GlyThr
100 105 110
Thr GlnVal ValGln LysSerAsn GlyGlnGly ValSerGly GlyTyr
115 120 125
Arg ValGIy SerSer LeuArgVal PheAspHis GlyMetPhe SerVal
130 135 140
Val TyrAsn SerSer ValThrPhe AsnMetLys GlyGlyLeu ValAla
145 150 155 160
1$ Ile ThrGlu LeuGly ProSerLeu GlySerVal LeuThrLys GlySer
165 170 175
Leu AsnIle AsnVal SerLeuPro GlnThrLeu SerLeuAla TyrAla
180 185 190
His GlnPhe PheLys AspArgLeu ArgValGlu GlyValPhe GluArg
2~ 195 200 205
Thr PheTrp SerGln GlyAsnLys PheLeuVal ThrProAsp PheAla
210- - 215 220
Asn AlaThr TyrLys GlyLeuSer GlyThrVal AlaSerLeu AspSer
225 230 235 240
2$ Glu ThrLeu LysLys MetValGly LeuAlaAsn PheLysSer ValMet
245 250 255
Asn MetGly AlaGly TrpArgAsp ThrAsnThr PheArgLeu GlyVal
260 265 270
Thr TyrMet GlyLys SerLeuArg LeuMetGly AlaIleAsp TyrAsp
275 280 285
Gln AlaPro SerPro GlnAspAla IleGlyIle ProAspSer AsnGly
290 295 300
Tyr ThrVal AlaPhe GlyThrLys TyrAsnPhe ArgGlyPhe AspLeu
305 310 315 320
3$ Gly ValAla Gly-Ser PheThrPhe LysSerAsn ArgSerSer LeuTyr
325 330 335
Gln SerPro ThrIle GlyGlnLeu ArgIlePhe SerAlaSer LeuGly
340 345 350
Tyr Arg Trp
4~ 355
(2) INFORMATION FOR SEQ ID N0:163:
(i) SEQUENCE_CHARACTERISTICS:
4$ (A) LENGTH: 587 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
$~
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
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(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...587
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:163:
Met LysAsn PheSer ProLeuTyr CysLeu LysLysLeu LysLysArg
1 5 10 15
His LeuIle AlaLeu SerLeuPro LeuLeu SerTyrAla AsnGlyPhe
20 25 30
Lys IleGln GluGln SerLeuAsn GlyThr AlaLeuGly SerAlaTyr
35 40 45
Val AlaGly AlaArg GlyAlaAsp AlaSer PheTyrAsn ProAlaAsn
IS 50 55 60
Met GlyPhe ThrAsn AspTrpGly GluAsn ArgSerGlu PheGluMet
65 70 75 80
' Thr ThrThr ValIle AsnIlePro AlaPhe SerPheLys ValProThr
85 - 90 95
2~ Thr AsnGln GlyLeu 'TyrSerVal ThrSer LeuGluIle AspLysSer
100 105 110
Gln GynAsn IleLeu GlyIleIle AsnThr IleGlyLeu GlyAsnIle
115 120 125
Leu LysAla LeuGly AsnThrAla AlaThr AsnGlyLeu SerGlnAla
25 130 135 140
Ile AsnArg ValGln GlyLeuMet AsnLeu ThrAsnGln LysValVal
145 150 155 160
Thr LeuAla SerLys ProAspThr GlnIle ValAsnGly TrpThrGly
165 170 175
Thr ThrAsn PheVal LeuProLys PhePhe TyrLysThr ArgThrHis
180 185 190
Asn GlyPhe ThrPhe GlyGlySer PheThr AlaProSer GlyLeuGly
195 200 205
Met LysTrp AsnGly LysGlyGly GluPhe LeuHisAsp ValPheIle
3$ 210 215 220
Met MetVal GluLeu AlaProSer MetSer TyrThrIle AsnLysArg
225 230 235 240
Phe SerVal GlyVal GlyLeuArg GlyLeu TyrAlaThr GlySerPhe
245 250 255
4~ Asn AsnThr ValTyr VaIProLeu GluGly AlaSerVal LeuSerAla
260 265 270
Glu GlnIle LeuAsn LeuProAsn AsnVal PheAlaAsp GlnVal.Pro
275 280 285
Ser AsnMet MetThr LeuLeuGly AsnIle GlyTyrGln ProAlaLeu
4$ 290 295 300
Asn CysGln LysAla GlyGlyAsp MetSer AspGlnSer CysGlnGlu
305 310 315 320
Phe TyrAsn GlyLeu LysLysIle MetGly TyrSerGly LeuIleLys
325 330 335
Ala SerAla AsnLeu TyrGlyThr ThrGln ValValGln LysSerAsn
340 345 350
Gly GlnGly ValSer GlyGlyTyr ArgVal GlySerSer LeuArgVal
355 360 365
Phe AspHis GlyMet PheSerVal ValTyr AsnSerSer ValThrPhe
CA 02273199 1999-06-O1
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- 248 -
370 375 380
Asn MetLysGly GlyLeuVal AlaIle ThrGluLeu GlyPro SerLeu
385 390 395 400
Gly SerValLeu ThrLysGly SerLeu AsnIleAsn ValSer LeuPro
405 410 415
Gln ThrLeuSer LeuAlaTyr AlaHis GlnPhePhe LysAsp ArgLeu
420 425 430
Arg ValGluGly ValPheGlu ArgThr PheTrpSer GlnGly AsnLys
435 440 445
Phe LeuValThr ProAspPhe AlaAsn AlaThrTyr LysGly LeuSer
450 455 460
Gly ThrValAla SerLeuAsp SerGlu ThrLeuLys LysMet ValGly
465 470 475 480
Leu AlaAsnPhe LysSerVal MetAsn MetGlyAla GlyTrp ArgAsp
I$ 485 490 495
Thr AsnThrPhe ArgLeuGly ValThr TyrMetGly LysSer LeuArg
500 505 510
Leu MetGlyAla IleAspTyr AspGln AlaProSer ProGln AspAla
515 520 525
Ile GlyIlePro AspSerAsn GlyTyr ThrValAla PheGly ThrLys
530 535 540
Tyr AsnPheArg GlyPheAsp LeuGly ValAlaGly SerPhe ThrPhe
545 550 555 560
Lys SerAsnArg SerSerLeu TyrGln SerProThr IleGly GlnLeu
2$ 565 570 575
Arg IlePheSer AlaSerLeu GlyTyr ArgTrp
580 - 585
(2) INFORMATION FOR SEQ ID N0:164:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 205 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...205
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:164:
Leu Ile Phe Arg Phe Phe Leu Ile Leu Ser Leu Leu Lys Gly Val Leu
1 5 10 15
Leu Ala Lys Lys Asp Trp Asn Phe Phe Lys Pro Leu Glu Pro Thr Lys
20 25 30
Lys Tyr Phe Gly Ser Phe Lys Ile Gly Tyr Leu Tyr Gln His Ala Glu
35 40 45
_ .._...__._._._.~_
CA 02273199 1999-06-O1
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Thr Thr Lys Arg Phe Pro Ile Arg Pro Lys Asn Arg Pro Pro Ile Leu
50 55 60
Met AspLys IleTyr HisAspAla SerLeu GlyPheAsp AlaGly Tyr
65 70 75 80
S Vai LeuLys LysLys AlaLeuLeu GlyGly TyrLeuAsp AlaGly Met
85 90 95
Gly AspSer TyrPhe MetSerAla GlyLeu ValAlaGly ValArg Leu
100 105 110
Phe LysGly TrpVal IleProLys IleAla LeuGlyTyr GlnLeu Gln
115 120 125
Ile LeuGly AlaLys IleAspLys TyrGln PheAsnIle GlnSer Ala
130 135 140
Val GlySer ValGly LeuPhePhe AsnAla AlaLysAsn PheGly Leu
145 150 155 160
IS Ser IleGlu AlaArg GlyGlyIle ProPhe TyrPheIle GlnSer Arg
165 170 175
Phe SerLys AlaPhe GlyThrPro ArgLeu AsnIleTyr SerVal Gly
180 1B5 190
Ile ThrPhe ThrPhe TyrAspPhe ThrArg PheLeuGly
195 200 205
(2) INFORMATION FOR SEQ ID NO:165:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 253 amino acids
(B) TYPE: amino acid
. (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...253
4O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:165:
Leu Trp His Ala Ala Phe Ser Val Gly Glu Trp Gly Trp Asn Gly Asp
1 5 10 15
Glu Ile Pro Tyr Arg Asp Cys Asp Glu Trp Gly Leu Asp Asp Phe Tyr
20 25 30
Gly Val Lys Pro Thr Asr :ys Ala Gly Val Leu Ser Phe Ala Arg Ser
35 40 45
His Arg Arg Gln Asn Gln Ala Val Leu Ser Lys Pro Lys Ser Phe Arg
55 60
$0 Met Lys Lys Ile Ala Phe Ile Leu Ala Leu Trp Val Gly Leu Leu Gly
65 70 75 80
Ala Phe Glu Pro Lys Lys Ser His Ile Tyr Phe Gly Ala Met Val Gly
85 90 95
Leu Ala Pro Val Lys Ile Thr Pro Lys Pro Ala Ser Asp Ser Ser Tyr
CA 02273199 1999-06-O1
- WO 98/24475 PCT/US97/22104
- 2$0 -
100 105 110
Thr AlaPheLeu TrpGlyAla LysGly GlyTyrGln PheAla PhePhe
115 120 125
Lys AlaLeuAla LeuArgGly GluPhe SerTyrLeu MetAla IleLys
$ 130 135 140
Pro ThrAlaLeu HisThrIle AsnThr SerLeuLeu SerLeu AsnMet
145 150 155 160
Asp ValLeuSer AspPheTyr ThrTyr LysLysTyr SerPhe GlyVal
165 170 175
Tyr GlyGlyLeu GlyIleGly TyrPhe TyrGlnSer AsnHis LeuGly
180 185 190
Met LysAsnSer SerPheMet GlyTyr AsnGlyLeu PheAsn ValGly
195 200 205
Leu GlySerThr IleAspArg HisHis ArgValGlu LeuGly AlaLys
1$ 210 215 220
Ile ProPheSer LysTheArg AsnSer PheLysAsn SerTyr PheLeu
225 230 235 240
Glu SerValPhe IleHisAla AlaTyr SerTyrMet Phe
245 _ 250
(2) INFORMATION FOR SEQ ID N0:166:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 412 amino acids
2$ (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
3O (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3$ (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...412
(xi} SEQUENCE DESCRIPTION: SEQ ID N0:166:
40 -
Met Glu Ser Val Lys Thr Val Lys Thr Asn Lys Val Gly Lys Asn Thr
1 5 10 15
Glu Thr Ala Asn Thr Glu Ala Ser Lys Glu Thr His Phe Lys Gln Ala
20 25 30
4$ per Ala Ile Thr Asn Thr Leu Arg Ser Ile Gly Gly Ile Phe Thr Lys
35 40 45
Ile Ala Lys Lys Val Arg Glu Leu Val Lys Lys His Pro Lys Lys Ser
50 55 60
Ser Val Ala Leu Val VaI Leu Thr His Ile Ala Cys Lys Arg Ala Lys
$0 65 70 75 80
Glu Leu Asp Asp Lys Val Gln Asp Lys Ser Lys Gln Ala Glu Lys Glu
85 90 95
Asn Gln Ile Asn Trp Trp Lys Tyr Ser Gly Leu Thr Ile Ala Ala Ser
100 105 110
CA 02273199 1999-06-O1
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Leu LeuLeuAla AlaCysSer ThrGly AspIleAsp LysGlnIle Glu
115 120 I25
Leu GluGlnGlu LysLysGlu AlaAsn LysSerGly IleLysLeu Glu
130 135 140
$ Gln GluArgGln LysThrGlu GlnGlu ArgGlnLys ThrAsnLys Ser
145 150 155 160
Glu IleGluLeu GluGlnGlu ArgGln LysThrAsn LysSerGly Ile
165 170 175
Glu LeuAlaAsn SerGlnIle LysAla GluGlnGlu ArgGlnLys Thr
1~ 180 185 190
Glu GlnGluLys GlnLysAla AsnLys SerGluIle GluLeuGlu Gln
195 200 205
Gln LysGlnLys ThrIleAsn ThrGln ArgAspLeu IleLysGlu Gln
210 215 220
1$ Lys AspPheIle LysGluThr GluGln AsnCysGln GluLysHis Gly
225 230 235 240
Gln LeuPheIle LysLysAla ArgIle LysThrGly IleThrThr Gly
245 250 255
Ile AlaIleGlu IleGluAla GluCys LysThrPro LysProAla Lys
2~ 260 265 270
Thr AsnGlnThr ProIleGln ProLys HisLeuPro AsnSerLys Gln
275 280 285
Pro ArgSerGln ArgGlySer LysAla GlnGluLeu IleAlaTyr Leu
290 295 300
2$ Gln LysGluLeu GluSerLeu ProTyr SerGlnLys AlaIleAla Lys
305 310 315 320
Gln ValAspPhe TyrLysPro SerSer IleAlaTyr LeuGluLeu Asp
325 330 335
Pra ArgAspPhe LysValThr GluGlu TrpGlnLys GluAsnLeu Lys
340 345 350
Ile ArgSerLys AlaGlnAla LysMet LeuGluMet ArgAsnPro Gln
355 360 365
Ala HisLeuPro ThrSerGln SerLeu LeuPheVal GlnLysIle Phe
370 375 380
3$ Ala AspIleAsn LysGluIle GluAla ValAlaAsn ThrGluLys Lys
385 390 395 400
Thr GluLysAla GlyTyrGly TyrSer LysArgMet
405 410
4O {2) INFORMATION FOR SEQ ID N0:167:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 149 amino acids
(B) TYPE: amino acid
4$ {D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
$~
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
CA 02273199 1999-06-O1
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(A) NAME/KEY: misc_feature
(B) LOCATION 1...149
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:167:
Leu AsnTrp GluHisLeu MetLysLys LeuAlaPhe SerLeu LeuPhe
1 5 10 15
Thr GlyThr PheLeuGly LeuPheLeu AsnAlaSer AspPhe LysSer
20 25 30
Met AspAsn LysGlnLeu LeuGluGln AlaGlyLys ValAla ProSer
35 40 45
Glu ValPro GluPheArg ThrGluVal AsnLysArg LeuGlu AlaMet
50 55 60
Lys GluGlu GluArgGln LysTyrLys AlaAspPhe LysLys AlaMet
1$ 65 70 75 g0
Asp LysAsn LeuAlaSer LeuSerGln GluAspArg AsnLys ArgLys
85 90 95
Lys GluIle LeuGluVal IleAlaAsn LysLysLys ThrMet ThrMet
100 105 110
Lys GluTyr ArgGluGlu GlyLeuAsp LeuHisAsp CysAla CysGlu
115 120 125
Gly ProPhe HisAspHis GluLysLys GlyGlnLys GlyLys LysPro
130 135 140
Ser HisHis LysHis
25 14s
(2) INFORMATION FOR SEQ ID N0:168:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 204 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204
4S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:368:
Met Gln Ala Val Ile Leu Ala Asn Gly Glu Phe Pro Lys Ser Lys Lys
1 5 10 15
Cys Leu Asp Ile Leu Gln Asn Ala Pro Phe Leu Ile Ala Cys Asp Gly
20 25 30
Ala Val Ile Ser Leu His Ala Leu Gln Phe Lys Pro Ser Val Val Ile
35 40 45
Gly Asp Leu Asp Ser Ile Asp Ser His Leu Lys Ala Leu Tyr Asn Pro
50 55 60
CA 02273199 1999-06-O1
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Ile Arg Val Ser Glu Gln Asp Ser Asn Asp Leu Ser Lys Ala Phe Phe
65 70 75 80
Tyr AlaLeuAsn ArgGlyCys AspAsp PheIlePhe LeuGly LeuAsn
85 90 95
Gly LysArgGlu AspHisAla LeuAla AsnThrPhe LeuLeu LeuGlu
100 $~ 105 110
Tyr PheLysPhe CysLysLys IleGln SerValSer AspTyr GlyLeu
115 120 125
Phe ArgValLeu GluThrPro PheThr LeuProSer PheLys GlyGiu
130 135 140
Gln IleSerLeu PheSerLeu AspLeu LysAlaArg PheThr SerLys
145 150 155 160
Asn LeuLysTyr ProLeuLys AspLeu ArgLeuLys ThrLeu PheSer
165 170 175
15Gly SerLeuAsn GluAlaThr AsnHis CysPheSer LeuSer SerGlu
180 185 190
Pro LysSerVal ValLeuVal TyrGln LysPheSer
195 200
(2) INFORMATION FOR SEQ ID N0:169:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 280 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...280
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:169:
Val Phe AspSerLeu GlyGlyPhe LeuGlyTyr LysThrPhe LysPro
1 5 IO 15
Ile Val AspLysVal LysAsnIle AsnAlaTrp IleLysAsn TyrAsp
20 25 30
Asn Lys LysAlaGln GluIleMet GlyPheIle GluAsnPro ThrPro
35 40 45
Asp Phe GlnAs~.:.snLysPheLeu CysValLeu AsnArgGln GlyThr
50 55 60
Arg His AsnAsnTyr LeuGlyLeu ThrSerThr AsnLeuLeu IleGly
65 70 75 80
$~ Ala Ile TyrPheSer IleArgHis CysIleLys AlaThrTrp GlnAsn
85 90 95
-
Asp Arg AspGlnP_heTyrAlaPro TyrAspAsp AlaPheGln AspAsp
100 105 110
Ser Glu PheLysAsn AsnCysLeu AlaPheMet LeuPheHis ThrGln
CA 02273199 1999-06-O1
WO 98/24475 PCT/US97/22104
- 2$4 -
115 120 125
Asn Arg Ile Thr Ala Thr Gln Gly Thr Asn His Phe Ile Pro Phe Ser
130 135 140
Glu Asp GluValAsp SerLysGlu ArgTyr LeuSerHis AlaLeu Leu
$ 145 150 155 160
Asp Phe LeuLysGly GluIleLys GluPro LysLysSer AspSer Leu
165 170 175
Phe Leu AsnAlaLys LysGluAsn LysPro LeuLysPhe SerSer Ser
180 185 190
Ala Ser LysValPhe-AspAlaGly ArgGlu IleTyrArg TyrTyr His
195 200 205
Thr Gln AspPheIle HisThrPro TyrAsn AlaAsnAla SerLeu Tyr
210 215 220
Asp Ile LysGluPhe PheGlnGly ArgAsn LysGlnGly ArgLeu Asn
1$ 225 230 235 _ 240
Ser Pro ThrLysAla LysAspGlu TyrTyr LysGlnLeu TyrAla Asn
245 250 255
Leu Gln TyrAlaLeu LysAspLeu AlaLys GluIleGln ProLys Val
260 265 270
Tyr Glu TyrGlyPhe LeuArgGlu
275 280
(2) INFORMATION FOR SEQ ID N0:170:
2S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 309 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
3$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...309
(xi} SEQUENCE DESCRIPTION: SEQ ID N0:170:
Cys Asp Arg Ala Ile Pro His Trp Leu Phe Ser Leu Gly Tyr Arg Tyr
1 5 10 15
- 4$ Pro Pro Pro Leu Lys Pro Thr Asn Ala Phe Asn Leu Glu Val Phe Asp
20 25 30
Ser Leu Gly Gly Phe Leu Gly Tyr Lys Thr Phe Lys Pro Ile Val Asp
35 40 45
Lys Val Lys Asn Ile Asn Ala Trp Ile Lys Asn Tyr Asp Asn Lys Lys
$0 50 55 60
Ala Gln Glu Ile Met Gly Phe Ile Glu Asn Pro Thr Pro Asp Phe Gln
65 70 75 80
Asn Asn Lys Phe Leu Cys Val Leu Asn Arg Gln Gly Thr Arg His Asn
85 90 95
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Asn TyrLeuGly LeuThrSer ThrAsn LeuLeuIle GlyAla IleTyr
100 105 110
Phe SerIleArg HisCysIle LysAla ThrTrpGln AsnAsp ArgAsp
115 120 125
$ Gln PheTyrAla ProTyrAsp AspAla PheGlnAsp AspSer GluPhe
130 135 140
Lys AsnAsnCys LeuAlaPhe MetLeu PheHisThr GlnAsn ArgIle
145 150 155 160
Thr AlaThrGln GlyThrAsn HisPhe IleProPhe SerGlu AspGlu
165 170 175
Val AspSerLys GluArgTyr LeuSer HisAlaLeu LeuAsp PheLeu
180 185 190
Lys GlyGluIle LysGluPro LysLys SerAspSer LeuPhe LeuAsn
195 200 205
I$Ala LysLysGlu AsnLysPro LeuLys PheSerSer SerAla SerLys
210 215 220
Val PheAspAla GlyArgGlu IleTyr ArgTyrTyr HisThr GlnAsp
225 230 235 240
Phe IleHisThr ProTyrAsn AlaAsn AlaSerLeu TyrAsp IleLys
245 250 255
Glu PhePheGln GlyArgAsn LysGln GlyArgLeu AsnSer ProThr
260 - 265 270
Lys AlaLysAsp GluTyrTyr LysGln LeuTyrAla AsnLeu GlnTyr
275 280 285
2$Ala LeuLysAsp LeuAlaLys GluIle GlnProLys ValTyr GluTyr
290 295 300
Gly PheLeuArg Glu
305
3O (2) INFORMATION FOR SEQ ID N0:171:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 187 amino acids
(B) TYPE: amino acid
35 (D) TOPOLOGY: linear
{ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
{ix) FEATURE.
(A) NAME/KEY: misc_feature
(B) LOCATION 1...187
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:171:
Leu Glu Thr Tyr Ile Ile Asp Ala Asp Asn Ile Asp Gly Asp Leu Phe
1 5 10 15
Phe Tyr Asn Leu Thr Arg Asn Ser Asn Asp Phe Ser Met Leu Pro Val
20 25 30
Phe Glu Leu Asp Arg Ile Ala Gln Lys Ile Arg Asn Ile Leu Lys Lys
CA 02273199 1999-06-O1
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-256-
35 40 45
His Gly Ser Arg Lys Asp Ile Ile Leu Lys His Asn Glu Ile Lys Glu
50 55 60
Ala Phe PheSerPro PheLysPro GlnLeu LysThrVal GlnValPhe
$ 65 70 75 80
Leu Ser HisSerHis Al~'~AspLys AsnLys AlaLeuGly ValLysAsp
85 90 95
Tyr Leu GluSerLys ThrLysArg LysVal PheIleAsp SerLeuPhe
100 105 110
Trp Asp TyrLysAsp AspValLeu AsnLys LeuAlaLys HisAspAsp
115 120 125
Ile Ser LysIleGlu AspAlaPhe ThrLeu IleLeuArg LysSerLeu
130 135 140
Gln Asp MetIleGlu LysCysPro TyrPhe ValPheLeu GlnSerLys
IS 145 150 155 160
Asn Ser ValSerAsn GlnGlyLeu SerArg IleThrTyr SerAlaTrp
165 170 175
Ile Tyr GluGluLeu LysIleAla SerPhe Tyr
180 185
(2) INFORMATION FOR SEQ ID N0:172:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 198 amino acids
2$ (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
3O (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3$ (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...198
(xi)SEQUENCE SEQID
DESCRIPTION: N0:172:
40
Leu Glu ThrTyrIleIle AspAla AspAsnIle AspGlyAsp LeuPhe
1 5 10 15
Phe Tyr AsnLeuThrArg AsnSer AsnAspPhe SerMetLeu ProVal
20 25 30
45 Phe Glu LeuAspArgIle AlaGln LyrcIleArg AsnIleLeu LysLys
35 40 45
His Gly SerArgLysAsp IleIle LeuLysHis AsnGluIle LysGlu
50 55 60
Ala Phe PheSerProPhe LysPro GlnLeuLys ThrValGln ValPhe
$0 65 70 75 BO
Leu Ser HisSerHisAla AspLys AsnLysAla LeuGlyVal LysAsp
85 90 95
Tyr Leu GluSerLysThr LysArg LysValPhe IleAspSer LeuPhe
100 105 110
CA 02273199 1999-06-O1
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-2S7-
Trp Asp Tyr Lys Asp Asp Val Leu Asn Lys Leu Ala Lys His Asp Asp
115 120 125
Ile Ser Lys Ile Glu Asp Ala Phe Thr Leu Ile Leu Arg Lys Ser Leu
130 135 140
S Gln Asp Met Ile Glu Lys Cys Pro Tyr Phe Val Phe Leu GIn Ser Lys
145 150 155 160
Asn Ser Val Ser Asn Gln Gly Leu Ser Arg Ile Thr Tyr Ser Ala Trp
165 170 175
Ile Tyr Glu Glu Leu Lys Ile Ala Ser Phe Leu Leu Ala Leu Leu Thr
180 185 190
Arg Val Ala Gln Phe Gln
195
1S
(2) INFORMATION FOR SEQ ID N0:173:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 189 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
2S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...189
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:173:
Met Met ThrLys AsnAla TyrAlaPhe ValValIle GluLysSer Ile
3S 1 5 to is
Met Val PheLys CysAla LysAspLys GlyLeuIle ProIleThr Glu
- 20 25 30
Gly Phe ValPro LeuLys GluGlyPhe LeuArgSer PheLysGlu Arg
35 40 45
Cys Asn LeuAsp PheLeu GluAsnLeu AspLeuLeu PheLeuTyr Asp
50 55 60
Tyr Gln PhePro SerGlu ValPheSer LeuCysLys AspLeuLys Asn
65 7D 75 gp
Ser Ile TrpAsp ArgLys LeuValVal ValLeuVal GluAlaLeu Glu
4S 85 90 95
Gly Phi.ItsGly LeuAsn LeuSerLeu LysIleGlu AspArgHis Ser
100 105 110
Asn Ser LeuGly AsnGly ValGlnLys LeuLeuThr AsnAlaAsp Leu
115 120 125
S0 Gly Ser AsnHis LysPro IleValIIe AspSerMet LysThrTyr His
130 135 140
Gln Ser GlnGln GluLys TyrLysArg GluArgGly GluThrLeu Glu
145 150 155 160
Val Arg ProThr ThrPro ProSerTyr GlyGlyGly SerIIeArg Ile
CA 02273199 1999-06-O1
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-2S8-
165 170 175
Ser Gly Asp Lys Lys Pro Asp Ser Asn Glu Glu Asn Phe
180 185
S (2) INFORMATION FOR SEQ ID N0:174:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 590 amino acids
(B) TYPE: amino acid
1~ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
1S
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...590
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:I74:
ZS Met Lys Ala Ile Lys Ile Leu Leu Ile Met Thr Leu Ser Leu Asn Ala
1 5 10 15
Ile Ser ValAsnArg AlaLeuPhe AspLeuLys AspSer GlnLeuLys
20 25 30
Gly Glu LeuThrPro LysIleVal AspPheGly GlyTyr LysSerAsn
35 40 45
Thr Thr GluTrpGly AlaThrAla LeuAsnTyr IleAsn AlaAlaAsn
50 55 60
Gly Asp AlaLysLys PheSerAla LeuValGlu LysMet ArgPheAsn
65 70 75 80
3S Ser Gly IleLeu-Gly AsnPheArg AlaHisAla HisLeu ArgGlnAla
85 90 95
Leu Lys LeuGlnLys AsnLeuLys TyrCysLeu LysIle IleAlaArg
100 105 110
Asp Ser PheTyrSer TyrArgThr GlyIleTyr IlePro LeuGlyIle
115 120 125
Ser Leu LysAspGln LysThrAla GlnLysMet LeuAla AspLeuSer
130 135 140
Val Val GlyAlaTyr LeuLysLys GlnGlnGlu AsnGlu LysAlaGln
145 - 150 155 160
4S Ser Pro TyrTyrArg SerAsnAsn TyrTyrAsn SerTyr TyrSerPro
165 170 175
Tyr Tyr GlyMetTyr GlyMetTyr GlyMetGly MetTyr GlyMetTyr
180 185 190
Gly Met GlyMetTyr AspPheTyr AspPheTyr AspGly MetTyrGly
SD 195 200 205
Phe Tyr ProAsnMet PhePheMet MetGlnVal GlnAsp TyrLeuMet
210 215 220
Leu Glu AsnTyrMet TyrAlaLeu AspGlnGlu GluIle LeuAspHis
225 230 235 240
CA 02273199 1999-06-O1
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-2$9-
Asp Ala Ser Ile Asn Gln Leu Asp Thr Pro Thr Asp Asp Asp Arg Asp
245 250 255
Asp Lys AspAsp LysSerSer GlnProAla AsnLeuMet SerPhe Tyr
260 265 270
$ Arg Asp ProLys PheSerLys AspIleGln ThrAsnArg LeuAsn Ser
275 280 285
Ala Leu ValAsn LeuAspAsn SerHisMet LeuLysAsp AsnSer Leu
290 295 300
Phe His ThrLys AlaMetPro ThrLysSer ValAspAla IleThr Ser
1~ 305 310 315 320
Gln Ala LysGlu LeuAsnHis LeuValGly GlnIleLys GluMet Lys
325 330 335
Gln Asp GlyAla SerProAsn LysIleAsp SerValVal AsnLys Ala
340 345 350
1$ Met Glu ValArg AspLysLeu AspAsnAsn LeuAsnGln LeuAsp Asn
355 - 360 365
Asp Leu LysAsp GlnLysGly LeuSerSer GluGlnGln AlaGln Val
370 375 380
Asp Lys AlaLeu AspSerVal Gln-GlnLeu SerHisSer SerAsp Val
385 390 395 400
Val Gly AsnTyr LeuAspGly SerLeuLys IleAspGly AspAsp Arg
405 410 415
Asp Asp LeuAsn AspAlaIle AsnAsnPro MetGlnGln ProAla Gln
420 425 430
2$ Gln Thr ProIle AsnAsnMet AspAsnThr HisAlaAsn AspSer Lys
435 440 445
Asp Gln GlyGly AsnAlaLeu IleAsnPro AsnAsnAla ThrAsn Asp
450 455 460
Asp His AsnAsp AspHisMet AspThrAsn ThrThrAsp ThrSer Asn
3~ 465 470 475 480
Ala Asn AspThr ProThrAsp AspLysAsp AlaSerGly AsnAsn Thr
485 490 495
Gly Asp MetAsn AsnThrAsp ThrGlyAsn ThrAspThr GlyAsn Thr
500 505 510
3$ Asp Thr GlyAsn ThrAspAsp MetSerAsn MetAsnAsn GlyAsn Asp
515 520 525
Asp Thr GlyAsn ThrAsnAsp AspMetGly AsnSerAsn AspMet Gly
530 535 540
Asp Asp MetAsn AsnAlaAsn AspMetAsn AspAspMet GlyAsn Ser
40 545 550 555 560
Asn Asp AspMet GlyAspMet GlyAspMet AsnAspAsp MetGly Gly
565 570 575
Asp Met GlyAsp MetGlyAsp MetGlyGly AspMetGly Asn
580 585 590
4$
(2) INFORMATION FOR SEQ ID N0:175:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 195 amino acids
$~ (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...195
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:175:
Leu Asn LeuArgLeu AlaGly AlaSerVal LeuThrAla CysValPhe
1 5 10 15
Ser Gly CysPhePhe LeuLys MetPheAsp LysLysLeu SerSerAsn
IS 20 25 30
Asp Trp HisIleGln LysVal GluMetAsn HisGInVal TyrAspIle
35 40 45
Glu Thr MetLeuAla AspSer AlaPheArg GluHisGlu GluGluGln
50 55 60
2O Asp Ser SerLeuAsn ThrAla LeuProGlu AspLysThr AlaIIeGlu
65 70 75 80
Ala Lys GluGlnGlu GlnLys GluLysArg LysHisTrp TyrGluLeu
85 90 95
Phe Lys LysLysPro LysPro LysSerSer MetGlyGlu PheValPhe
25 loo l05 to
Asp Gln LysGluAsn ArgIle TyrGlyLys GlyTyrCys AsnArgTyr
115 _ 120 125
Phe Ala SerTyrThr TrpGln GlyAspArg HisIleAla IleGluAsp
130 135 140
30 Ser Gly IleSerArg LysVal CysArgAsp GluHisLeu MetAlaPhe
145 150 155 160
Glu Leu GluPheMet GluAsn PheLysGly AsnPheAla ValThrLys
165 170 175
Gly Lys AspThrLeu IleLeu AspAsnGln LysMetLys IleTyrLeu
35 180 185 190
Lys Thr Pro
_. 195
(2) INFORMATION FOR SEQ ID N0:176:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 744 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: p~otein
(iii) HYPOTHETICAL: YES
SO (vi} ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc feature
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(B) LOCATION 1...744
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:176:
$ Met LeuLys LeuAlaSer LysThr IleCysLeu SerLeu IleSerSer
1 5 10 15
Phe ThrAla ValGluAla PheGln LysHisGln LysAsp GlyPhePhe
20 25 30
Ile GluAla GlyPheGlu ThrGly LeuLeuGln GlyThr GlnThrGln
1~ 35 40 45
Glu GlnThr IleAlaThr Thr_GinGluLysPro LysPro LysProLys
50 55 60
Pro LysPro IleThrPro GlnSer ThrTyrGly LysTyr TyrIleSer
65 70 75 80
1$ Gln SerThr IleLeuLys AsnAla ThrGluLeu PheAla GluAspAsn
85 90 95
Ile ThrAsn LeuThrPhe TyrSer GlnAsnPro ValTyr ValThrAla
100 105 110
Tyr AsnGln GluSerAla GluGlu AlaGlyTyr GlyAsn AsnSerLeu
2~ 115 120 125
Ile MetIle GlnAsnPhe LeuPro TyrAsnLeu AsnAsn IleGluLeu
130 135 140
Ser TyrThr AspAspGln GlyAsn ValValSer LeuGly ValIleGlu
145 150 155 160
2$ Thr IlePro LysGlnSer GlnIle IleLeuPro AlaSer LeuPheAsn
165 170 175
Asp ProGln LeuAsnAla AspGly PheGlnGln LeuGln ThrAsnThr
180 185 190
Thr ArgPhe SerAspAla SerThr GlnAsnLeu PheAsn LysLeuSer
195 200 205
Lys ValThr ThrAsnLeu GlnMet ThrTyrIle AsnTyr AsnGlnPhe
210 215 220
Ser SerGly AsnGlySer GlySer LysProPro CysPro ProTyrGlu
225 230 235 240
3$ Asn GlnAla AsnCysVal AlaLys ValProPro PheThr SerGlnAsp
245 250 255
Ala LysAsn LeuThrAsn LeuMet LeuAsnMet MetAla ValPheAsp
260 265 270
Ser LysSer TrpGluAsp AlaVal LeuAsnAla ProPhe GlnPheSer
275 280 285
Asp AsnAsn LeuSerAla ProCys TyrSerAsp TyrLeu ThrCysVal
290 295 300
Asn ProTyr AsnAspGly LeuVal AspProLys LeuIle AlaLysAsn
305 310 315 320
4$ L~s GlyAsp GluTyrAsn IleGlu AsnGlyGln ThrGly SerValIle
325 330 335
Leu ThrPro GlnAspVal IleTyr SerTyrArg ValAla AsnAsnIle
340 345 350
Tyr ValAsn LeuLeuPro ThrArg GlyGlyAsp LeuGly LeuGlySer
$0 355 360 365
Gln TyrGly GlyProAsn GIyPro GlyAspAsp GlyThr AsnPheGly
370 375 380
Ala LeuGly IleLeuSer ProPhe LeuAspPro GluIle LeuPheGly
385 390 395 400
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Lys Glu Leu Asn Lys Val Ala Ile Met Gln Leu Arg Asp Ile Ile His
405 410 415
Glu TyrGlyHis ThrLeuGly TyrThrHis AsnGly AsnMetThr Tyr
420 425 430
$ Gln ArgValArg MetCysGlu GluAsnAsn GlyPro GluGluArg Cys
435 440 445
Gln GlyGlyArg IleGluGln ValAspGly LysGIu ValGlnVal Phe
450 455 460
Asp AsnGlyHis GluValArg AspThrAsp Gly.SerThrTyrAsp Val
1~ 465 470 475 480
Cys SerArgPhe LysAspLys ProTyrThr AlaGly SerTyrPro Asn
485 490 495
Ser IleTyrThr AspCysSer GlnValPro AlaGly LeuIleGly Val
500 505 510
IS Thr SerAlaVal TrpGlnGln LeuIleAsp GlnAsn AlaLeuPro Val
515 - 520 525
Asp PheThrAsn LeuSerSer GlnThrAsn TyrLeu AsnAlaSer Leu
530 535 540
Asn ThrGlnAsp PheAlaThr Thr-MetLeu SerAla IleSerGln Ser
2~ 545 550 555 560
Leu SerSerSer LysSerSer AlaThrThr TyrArg ThrSerLys Thr
565 570 575
Ser ArgProPhe GlyAlaPro LeuLeuGly ValAsn LeuLysMet Gly
580 585 590
25 Tyr GlnLysTyr PheAsnAsp TyrLeuGly LeuSer SerTyrGly Ile
595 600 605
Ile LysTyrAsn TyrAlaGln AlaAsnAsn GluLys IleGlnGln Leu
610 615 620
Ser TyrGlyVal GlyMetAsp ValLeuPhe AspPhe IleThrAsn Tyr
625 630 635 640
Thr AsnGluLys AsnProLys SerAsnLeu ThrLys LysValPhe Thr
645 650 655
Ser SerLeuGly ValPheGly GlyLeuArg GlyLeu TyrAsnSer Tyr
660 665 670
35 Tyr LeuLeuAsn GlnTyrLys GlySerGly AsnLeu AsnValThr Gly
675 680 685
Gly LeuAsnTyr ArgTyrLys HisSerLys TyrSer IleGlyIle Ser
690 695 700
Val ProLeuVal GlnLeuLys SerArgIle ValSer SerAspGly Ala
4~ 705 71~ 715 720
Tyr ThrAsnSer IleThrLeu AsnGluGly GlySer HisPheLys Val
725 730 735
Phe PheAsnTyr GlyTrpIle Phe
74
0
45
(2) INFORMATION FOR SEQ ID N0:177:
(i} SEQUENCE CHARACTERISTICS:
(A) LENGTH: 529 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
( ix ) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...529
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:177:
Met Thr TyrIleAsn TyrAsn GlnPheSer SerGlyAsn GlySer Gly
1 5 10 15
Ser Lys ProProCys ProPro TyrGluAsn GlnAlaAsn CysVal AIa
IS 20 25 30
Lys Val ProProPhe ThrSer GlnAspAla LysAsnLeu ThrAsn Leu
35 40 45
Met Leu AsnMetMet AlaVal PheAspSer LysSerTrp GluAsp Ala
50 55 60
2O Val Leu AsnAlaPro PheGln PheSerAsp AsnAsnLeu SerAla Pro
65 70 75 80
Cys Tyr SerAspTyr LeuThr CysValAsn ProTyrAsn AspGly Leu
85 90 95
Val Asp ProLysLeu IleAla LysAsnLys GlyAspGlu TyrAsn Ile
25 loo l05 llo
Glu Asn GlyGlnThr GlySer ValIleLeu ThrProGln AspVal Ile
115 120 125
Tyr Ser TyrArgVal AlaAsn AsnIleTyr ValAsnLeu LeuPro Thr
130 135 140
3O Arg Gly GlyAspLeu GlyLeu GlySerGln TyrGlyGly ProAsn Gly
145 150 155 160
Pro Gly AspAspGly ThrAsn PheGlyAla LeuGlyIle LeuSer Pro
165 170 175
Phe Leu AspProGlu IleLeu PheGlyLys GluLeuAsn LysVal Ala
35 180 185 190
Ile Met GlnLeuArg AspIle IleHisGlu TyrGlyHis ThrLeu Gly
195 200 205
Tyr Thr HisAsnGly AsnMet ThrTyrGln ArgValArg MetCys Glu
210 215 220
4O Glu Asn AsnGlyPro GluGlu ArgCysGln GlyGlyArg IleGlu Gln
225 230 235 240
Val Asp GlyLysGlu ValGln ValPheAsp AsnGlyHis GluVal Arg
245 250 255
Asp Thr AspGlySer ThrTyr AspValCys SerArgPhe LysAsp Lys
45 260 265 270
Pro Tyr ThrAlaGly SerTyr ProAsnSer ~:.fTyrThr AspCys Ser
275 280 285
Gln Val ProAlaGly LeuIle GlyValThr SerAlaVal TrpGln Gln
290 295 300
SO Leu Ile AspGlnAsn AlaLeu ProValAsp PheThrAsn LeuSer Ser
305 310 315 320
Gln Thr AsnTyrLeu AsnAla SerLeuAsn ThrGlnAsp PheAla Thr
325 330 335
Thr Met LeuSerAla IleSer GlnSerLeu SerSerSer LysSer Ser
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340 345 _ 350
Ala ThrThr TyrArgThr SerLys ThrSerArg ProPhe GlyAlaPro
355 360 365
Leu LeuGly ValAsnLeu LysMet GlyTyrGln LysTyr PheAsnAsp
S 370 375 380
Tyr LeuGly LeuSerSer TyrGly IleIleLys TyrAsn TyrAlaGln
385 390 395 400
Ala AsnAsn GluLysIle GlnGln LeuSerTyr GlyVal GlyMetAsp
405 410 415
1~ Val LeuPhe AspPheIle ThrAsn TyrThrAsn GluLys AsnProLys
420 _ 425 430
Ser AsnLeu ThrLysLys ValPhe ThrSerSer LeuGly ValPheGly
435 440 445
Gly LeuArg GlyLeuTyr AsnSer TyrTyrLeu LeuAsn GlnTyrLys
IS 450 455 460
Gly SerGly AsnLeuAsn ValThr GlyGlyLeu AsnTyr ArgTyrLys
465 470 475 4g0
His SerLys TyrSerIle GlyIle SerValPro LeuVal GlnLeuLys
485 490 495
2~ Ser ArgIle ValSerSer AspGly AlaTyrThr AsnSer IleThrLeu
500 505 510
Asn GluGly GlySerHis PheLys ValPhePhe AsnTyr GlyTrpIle
515 520 525
Phe
2S
(2) INFORMATION FOR SEQ ID N0:178:
(i) SEQUENCE CHARACTERISTICS:
3~ (A) LENGTH: 187 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
3S
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...187
4S (xi) SEQUENCE r~ESCRIPTION: SEQ ID N0:178:
Leu Gly Cys Val Ser Met Thr Leu Gly Ile Asp Glu Ala Gly Arg Gly
1 5 10 15
Cys Leu Ala Gly Ser Leu Phe Val Ala Gly Val Val Cys Asn Glu Lys
S~ 20 25 30
Ile Ala Leu Glu Phe Leu Lys Met Gly Leu Lys Asp Ser Lys Lys Leu
35 40 45
Ser Pro Lys Lys Arg Phe Phe Leu Glu Asp Lys Ile Lys Thr His Gly
55 60
_._.__. . _.......__r..._. ~._._..._.
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Glu Val GlyPhe PheValVal LysLysSer AlaAsnGlu IleAspHis
65 70 75 g0
Leu Gly LeuGly AlaCysLeu LysLeuAla IleGluGlu IleValGlu
85 90 95
$ Asn Gly CysSer LeuAlaAsn GluIleLys IleAspGly AsnThrAla
100 105 110
Phe Gly LeuAsn LysArgTyr ProAsnIle GlnThrIle IleLysGly
115 120 125
Asp Glu ThrIle AlaGlnIle AlaMetAla SerValLeu AlaLysAla
130 135 140
Ser Lys AspArg GluMetLeu GluLeuHis AlaLeuPhe LysGluTyr
145 150 155 160
Gly Trp AspLys AsnCysGly TyrGlyThr LysGlnHis IleGluAla
165 170 175
1$ Ile Asn LysLeu GlyAlaThr LeuSerSer Ala
180 185
(2) INFORMATION FOR SEQ ID N0:179:
2O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 204 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
2$ (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
30 (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204
3$
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:179:
Met Thr LeuGly IleAspGlu AlaGly ArgGlyCys LeuAlaGly Ser
1 5 10 15
40 I~euPhe ValAla GlyValVal CysAsn GluLysIle AlaLeuGlu Phe
20 25 30
Leu Lys MetGly _LeuLysAsp SerLys LysLeuSer ProLysLys Arg
35 40 45
Phe Phe LeuGlu AspLysIle LysThr HisGlyGlu ValGlyPhe Phe
4$ 50 55 60
Val Val LysLys SerAlaAsn GluIle AspHisLeu GlyLeuGly Ala
65 70 75 80
Cys Leu LysLeu AlaIleGlu GluIle ValGluAsn GlyCysSer Leu
85 90 95
$0 Ala Asn GluIle LysIleAsp GlyAsn ThrAlaPhe GlyLeuAsn Lys
100 105 110
Arg Tyr ProAsn IleGlnThr IleIle LysGlyAsp GluThrIle Ala
115 120 125
Gln Ile AlaMet AlaSerVal LeuAla LysAlaSer LysAspArg Glu
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130 135 140
Met Leu Glu Leu His Ala Leu Phe Lys Glu Tyr Gly Trp Asp Lys Asn
145 150 155 160
Cys Gly Tyr Gly Thr Lys Gln His Ile Glu Ala Ile Asn Lys Leu Gly
S 165 170 175
Ala Thr Pro Phe His Arg His Ser Phe Thr Leu Lys Asn Arg Ile Leu
180 185 190
Asn Pro Lys Leu Leu Glu Val Glu Gln Arg Leu Val
195 200
(2) INFORMATION FOR SEQ ID N0:180:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 192 amino acids
IS (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
ZO (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
ZS ( i.x ) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...192
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:180:
Met Asn Ala Leu Lys Lys Leu Ser Phe Cys Ala Leu Leu Ser Leu Gly
1 5 10 15
Leu Phe AlaGln ThrValHis AlaGlnHis LeuLys AspThrIle Asn
20 25 30
3S Tyr Pro AspTrp LeuLysIle AsnLeuPhe AspLys LysAsnPro Pro
35 40 45
Asn Gln TyrVal GlySerAla SerIleSer GlyLys ArgAsnAsp Phe
50 55 60
Tyr Ser AsnTyr IleProTyr AspAspLys LeuPro ProGluLys Asn
65 70 75 g0
Ala Glu GluIle AlaLeuLeu ArgAlaArg MetAsn~AlaTyrSer Thr
85 90 95
Leu Glu SerAla LeuLeuThr LysMetCys AsnArg IleValLys Ala
100 105 110
4S Leu Gln ValLys AsnAsnVal IleSerHis LeuPhe GlyPheVal 'asp
115 120 125
Phe Leu ThrSer LysSerIle LeuAlaLys ArgPhe ValAspThr Thr
130 135 140
Asn His ArgVal TyrValMet ValGlnPhe ProPhe IleGlnPro Glu
SO 145 150 155 160
Asp Leu IleAla TyrPheLys AlaLysArg IleAsp LeuSerLeu Ala
165 170 175
Ser Ala ThrAsn LeuSerAla IleLeuAsn LysAla LeuPheHis Leu
180 185 190
. _. . _ _____.._....r __ . ... _
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(2) INFORMATION FOR SEQ ID N0:181:
(i) SEQUENCE CHARACTERISTICS:
S (A) LENGTH: 86 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
l~
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...86
ZO (xi)SEQUENCE SEQ ID
DESCRIPTION: N0:18:1:
Met AsnAlaLeu LysLys LeuSerPhe CysAlaLeu LeuSer LeuGly
1 5 10 15
Leu PheAlaGln ThrVal HisAlaGln HisLeuLys AspThr IleAsn
20 25 30
Tyr ProAspTrp LeuLys IleAsnLeu PheAspLys LysAsn ProPro
35 40 45
Asn GlnTyrVal GlySer AlaSerIle SerGlyLys ArgAsn AspPhe
50 55 60
Tyr SerAsnTyr IlePro TyrAspAsp LysLeuPro ProGlu ArgThr
65 70 75 80
Leu LysLysSer LeuPhe
85
3S (2) INFORMATION FOR SEQ ID N0:182:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 75 amino acids
(B) TYPE: amino acid
4~ (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
S~ (A) NAME/KEY: misc_feature
(B) LOCATION 1...75
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:182:
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Leu Lys Ile Leu Thr Leu Phe Leu IIe Gly Leu Asn Ala Leu Phe Ala
1 5 10 15
Leu Asp Leu Asn Ala Leu Lys Thr Glu Ile Lys Glu Thr Tyr Leu Lys
20 25 30
Glu Tyr Lys Asp Leu Lys Leu Glu Ile Glu Thr Ile Asn Leu Glu Ile
35 40 45
Pro Glu Arg Phe Ser His Ala Ser Ile Leu Ser Tyr Glu Leu Asn Ala
50 55 60
Ser Asn Lys Leu Lys Lys Asp Gly Ser Cys Phe
65 70 75
(2) INFORMATION FOR SEQ ID N0:183:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 211 amino acids _ _
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...211
3O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:183:
Met Phe SerIleIle LeuGly GlyGlyGly GlyAsn ThrProCys Gly
1 5 10 15
Leu Thr TrpGlnHis PheLys LeuGlyAsp LeuPhe GluIleGlu Lys
20 25 30
Thr Leu SerPheAsn LysAsp AlaLeuThr GlnGly GlnAspTyr Asp
35 40 45
Tyr Ile ThrArgThr SerGln AsnGlnGly ValLeu GlnThrThr Gly
50 55 60
40 Phe Val AsnAlaGlu AsnLeu AsnProPro PheThr TrpSerLeu Gly
65 70 75 80
Leu Leu GlnMet-Asp PhePhe TyrArgLys LysSer TrpTyrAla Gly
85 90 95
Gln Phe MetArgLys IleThr ProLysThr GluIle LysAsnLys Ile
- 45 loo los llo
Asn Ser ..r,,IleAla HisTyr PheThrThr LeuLeu AsnAlaLeu Lys
115 120 125
Arg Pro LeuLeuSer ValLeu ValArgAsp IleAsp LysThrPhe Arg
130 135 140
$0 Glu Gln LysIleGln LeuPro LeuLysPro ThrAla LysThrGln Ser
145 150 155 160
Leu Asp GlyIleAsp PheAsp PheMetHis ThrLeu IleAsnAla Leu
165 170 175
Met Lys GlnThrIle GlnGly ValValGln TyrCys AspAlaLys Ile
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180 185 190
Gln Ala Thr Lys Glu Val Ile Ser Gln Glu Thr Pro Ile Gln Lys Asp
195 200 205
Ser Leu Phe
210
(2) INFORMATION FOR SEQ ID N0:184:
(i) SEQUENCE CHARACTERISTICS:
l~ (A) LENGTH: 406 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
1$
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...406
2S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:184:
Val IleGly ProLeuSer SerGln LeuAsnAla IleLysTrp GlyGlu
1 5 10 15
Phe LysLeu GlyAspLeu PheGlu AlaSerAsn GlyAspPhe AspIle
20 25 30
Gln LysArg HisIleAsn HisLys GlyGluPhe ValIleThr AlaGly
35 40 45
Leu SerAsn AsnGlyVal LeuGly GlnSerAsp IleLysAla LysVal
50 55 60
Phe GluSer HisThrIle ThrIle AspMetPhe GlyCysAla PheTyr
65 70 75 g0
Arg --SerPhe AlaTyrLys MetVal ThrHisAla ArgValPhe SerLeu
85 90 95
Lys ProLys PheGluIle AsnHis LysIleGly LeuPheLeu SerThr
loo l05 llo
Leu PhePhe GlyTyrHis LysLys PheGlyTyr GluAsnMet CysSer
115 120 125
Trp AlaLys IleLysAsn AspLys ValIleLeu ProLeuLys ProThr
130 135 140
4$ Ala AsnThr GlnThrLeu GluGly IleAspPhe AspPheMet GluLys
145 150 155 160
Phe IleAla GluLeuGlu GlnCys ArgLeuAla GluLeuGln AlaTyr
165 170 175
Leu LysAla ThrGlyLeu GluAsn ThrThrLeu SerAsnAsp GluGlu
180 185 190
Asn AlaLeu AsnValPhe AsnAsn SerGlyGly GlyGlyGly AsnThr
195 200 205
Pro CysGly LeuThrTrp GlnHis PheLysLeu GlyAspLeu PheGlu
210 215 220
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Ile Glu Lys Thr Leu Ser Phe Asn Lys Asp Ala Leu Thr Gln Gly Gln
225 230 235 240
Asp Tyr Asp Tyr Ile Thr Arg Thr Ser Gln Asn Gln Gly Val Leu Gln
245 250 255
$ Thr ThrGly PheValAsn AlaGlu AsnLeu AsnProPro PheThrTrp
260 265 270
Ser LeuGly LeuLeuGln MetAsp PhePhe TyrArgLys LysSerTrp
275 280 285
Tyr AlaGly GlnPheMet ArgLys IleThr ProLysThr GluIleLys
1~ 290 295 300
Asn LysIle AsnSerArg IleAla HisTyr PheThrThr LeuLeuAsn
305 310 315 320
Ala LeuLys ArgProLeu LeuSer ValLeu ValArgAsp IleAspLys
325 330 335
1$ Thr PheArg GluGlnLys IleGln LeuPro LeuLysPro ThrAlaLys
340 345 350
Thr GlnSer LeuAspGly IleAsp PheAsp PheMetHis ThrLeuIle
355 360 365
Asn AlaLeu MetLysGln ThrIle GlnGly ValVa1Gln TyrCysAsp
20 370 375 380
Ala LysIle GlnAlaThr LysGlu ValIle SerGlnGlu ThrProIle
385 390 395 400
Gln LysAsp SerLeuPhe
405
2$
(2) INFORMATION FOR SEQ ID N0:185:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 275 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
3S (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...275
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:185:
4$
Met Ser Lys Ser Leu Tyr Gln Thr Leu Asn Val Ser G_a Asn Ala Ser
1 5 10 15
Gln Asp Glu Ile Lys Lys Ser Tyr Arg Arg Leu Ala Arg Gln Tyr His
20 25 30
Pro Asp Leu Asn Lys Thr Lys Glu Ala Glu Glu Lys Phe Lys Glu Ile
35 40 45
Asn Ala Ala Tyr Glu Ile Leu Ser Asp Glu Glu Lys Arg Arg Gln Tyr
50 55 60
Asp Gln Phe Gly Asp Asn Met Phe Gly Gly Gln Asn Phe 5er Asp Phe
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65 70 75 80
Ala ArgSerArg GlyProSer GluAsp LeuAspAsp IleLeuSer Ser
85 90 95
Ile PheGlyLys GlyGlyPhe SerGln ArgPheSer GlnAsnSer Gln
S 100 105 110
Gly PheSerGly PheAsnPhe SerAsn PheAlaPro GluAsnLeu Asp
115 120 125
Val ThrAlaIle LeuAsnVal SerVal LeuAspThr LeuLeuGly Asn
130 135 140
Lys LysGlnVal SerValAsn AsnGlu ThrPheSer LeuLysIle Pro
145 150 155 160
Ile GlyValGlu GluGlyGlu LysIle ArgValArg AsnLysGly Lys
165 170 175
Met GlyArgThr GlyArgGly AspLeu LeuLeuGln IleHisIle Glu
IS 180 185 190
Glu AspGluMet TyrArgArg GluLys AspAspIle IleGlnIle Phe
195 200 205
Asp LeuProLeu LysThrAla LeuPhe GlyGlyLys IleGluIle Ala
210 215 - 220
Zd Thr TrpHisLys ThrLeuThr LeuThr IleProPro AsnThrLys Ala
225 230 235 240
Met GlnLysPhe ArgIleLys AspLys GlyIlELys SerArgLys Thr
245 250 255
Ser HisValGly AspCysIle AlaSer SerPheAsp LeuLeuLys Leu
2S 260 265 270
Lys Arg Phe
275
(2) INFORMATION FOR SEQ ID N0:186:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 278 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
3S
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
4S (B) LOCATION 1...:'78
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:186:
Met Ser Lys Ser Leu Tyr Gln Thr Leu Asn Val Ser Glu Asn Ala Ser _
SD 1 5 10 15
Gln Asp Glu Ile Lys Lys Ser Tyr Arg Arg Leu Ala Arg Gln Tyr His
20 25 30
Pro Asp Leu Asn Lys Thr Lys Glu Ala Glu Glu Lys Phe Lys Glu Ile
40 45
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Asn Ala Ala Tyr Glu Ile Leu Ser Asp Glu Glu Lys Arg Arg Gln Tyr
50 55 60
Asp GlnPheGly AspAsnMet PheGly GlyGlnAsn PheSerAsp Phe
65 70 75 80
Ala ArgSerArg GlyProSer GluAsp LeuAspAsp IleLeuSer Ser
85 90 95
Ile PheGlyLys GlyGlyPhe SerGln ArgPheSer GlnAsnSer Gln
100 105 110
Gly PheSerGly PheAsnPhe SerAsn PheAlaPro GluAsnLeu Asp
115 120 125
Val ThrAlaIle LeuAsnVal SerVal LeuAspThr LeuLeuGly Asn
130 135 140
Lys LysGlnVal SerVal.AsnAsnGlu ThrPheSer LeuLysIle Pro
145 150 155 160
Ile GlyValGlu GluGlyGlu LysIle ArgValArg AsnLysGly Lys
165 170 175
Met GlyArgThr GlyArgGly AspLeu LeuLeuGln IleHisIle Glu
180 185 190
Glu AspGluMet TyrArgArg GluLys AspAspIle IleGlnIle Phe
ZO 195 200 205
Asp LeuProLeu LysThrAla LeuPhe GlyGlyLys IleGluIle Ala
210 215 220
Thr TrpHisLys ThrLeuThr LeuThr IleProPro AsnThrLys Ala
225 230 235 240
Met GlnLysPhe ArgIleLys AspLys GlyIleLys SerArgLys Thr
245 250 255
Ser HisValGly AspCysIle AlaSer SerPheAsp LeuProLys Ile
260 265 270
Glu ThrLeuLeu MetSer
275
(2) INFORMATION FOR SEQ ID N0:187:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 232 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B} LOCATION 1...232
SO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:187:
Val Val Gln Lys Phe Asn Phe Tyr Lys Thr Gly Gly Met Arg Leu Lys
1 5 10 15
His Phe Lys Thr Phe Leu Phe Ile Thr Met Ala Val Ile Val Ile Gly
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20 25 , 30
Thr GlyCys 'AlaAsnLys LysLysLys LysAsp GluTyrAsn LysPro
35 40 45
Ala IlePhe TrpTyrGln GlyIleLeu ArgGlu IleLeuPhe AlaAsn
50 55 60
Leu GluThr AlaAspAsn TyrTyrSer SerLeu GlnSerGlu HisIle
65 70 75 80
Asn SerPro LeuValPro GluAlaMet LeuAla LeuGlyGln AlaHis
85 90 95
Met LysLys LysGluTyr ValLeuAla SerPhe TyrPheAsp GluTyr
100 105 110
Ile LysArg PheGlyThr LysAspAsn ValAsp TyrLeuThr PheLeu
115 120 125
Lys LeuGln SerHisTyr TyrAlaPhe LysAsn HisSerLys AspGln
IS 130 135 140
Glu PheIle SerAsnSer IleValSer LeuGly GluPheIle GluLys
145 150 155 160
Tyr ProAsn SerArgTyr ArgProTyr ValGlu TyrMetGln IleLys
165 170 175
Phe IleLeu GlyGlnAsn GluLeuAsn ArgAla IleAlaAsn ValTyr
180 185 190
Lys LysArg HisLysPro GluGlyVal LysArg TyrLeuGlu ArgIle
195 200 205
Asp GluThr LeuGluLys GluThrLys ProLys ProSerHis MetPro
210 215 220
Trp TyrVal LeuIlePhe AspTrp
225 230
(2) INFORMATION FOR SEQ ID N0:188:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 114 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...114
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:188:
Met Arg Phe Leu Asn Asn Lys His Arg Glu Lys Gly Leu Lys Ala Glu
1 5 to is
Glu Glu Ala Cys Gly Phe Leu Lys Thr Leu Gly Phe Glu Met Ile Glu
20 25 30
Arg Asn Phe Phe Ser Gln Phe Gly Glu Ile Asp Ile Ile Ala Leu Lys
35 40 45
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Lys Gly Val Leu His Phe Ile Glu Val Lys Ser Gly Glu Asn Phe Asp
50 55 60
Pro Ile Tyr Ala Ile Thr Pro Ser Lys Lys Met Ile Lys Thr
Lys Leu
65 70 75 g0
$ Ile Arg Cys Tyr Leu Ser Gln Lys Asn Ser Asp Phe Cys Ile
Asp Pro
85 90 95
Asp Ala Leu Ile Val Lys Asn Gly Glu Leu Leu Glu Asn Ile
Lys Phe
100 105 110
Thr Phe
(2) INFORMATION
FOR
SEQ
ID
N0:189:
(i) SEQUENCE CHARACTERISTICS:
1$ (A) LENGTH: 101 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY. linear
(ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter
pylori
(ix)FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...101
3O (xi)SEQUENCE DESCRIPTION: SEQ
ID N0:189:
Met Gly Ser Ile Gly Ala Met Thr Ser Ser Asp Arg Tyr Phe
Lys Gly
1 5 10 15
Gln Glu Gly Val Ala Ser Glu Lys Pro Glu Gly Ile Glu Gly
Leu Val
20 25 30
Arg Val Pro Tyr Arg Gly Lys Val Met Ile Phe Gln Leu Val
Ser Asp
35 40 45
Gly Gly Val Arg Ser Ser Met Gly Gly Ala Lys Asn Ile Leu
Tyr Gln
50 55 60
Glu Leu Tyr Gln Asn AIa Glu Phe Ile Thr Ser Ala Gly Leu
Val Glu
65 70 75 gp
Lys Lys Ser His VaI His Gly Val Thr Lys Glu Ala Pro Asn
Asp Ile
85 90 95
- Ile Met Gly Glu Phe
loo
(2) INFORMATION FOR SEQ ID N0:190:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 481 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii)MOLECULE TYPE: protein
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(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...481
1~
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:190:
Met Arg Ile Leu Gln Arg Ala Leu Thr Phe Glu Asp Val Leu Met Val
1 5 10 15
IS Pro ArgLys SerSer ValLeuPro LysAsp ValSerLeu LysSerArg
20 25 30
Leu ThrLys AsnIle GlyLeuAsn IlePro PheIleSer AlaAlaMet
35 40 45
Asp ThrVal ThrGlu HisLysThr AlaIle AlaMetAla ArgLeuGly
50 55 60
Gly IleGly IleVal HisLysAsn MetAsp IleGlnThr GlnValLys
65 70 75 BO
Glu IleThr LysVal LysLysSer GluSer GlyValIle AsnAspPro
85 90 95
2$ Ile PheIle HisAla HisArgThr LeuAla AspAlaLys ValIleThr
100 105 110
Asp AsnTyr LysIle SerGlyVal ProVal ValAspAsp LysGlyLeu
115 120 125
Leu IleGly IleLeu ThrAsnArg AspVal ArgPheGlu ThrAspLeu
130 135 140
Ser LysLys ValGly AspValMet ThrLys MetProLeu ValThrAla
145 150 155 160
His ValGly IleSer LeuAspGlu AlaSer AspLeuMet HisLysHis
165 170 175
35 Lys IleGlu LysLeu ProIleVal AspLys AspAsnVal LeuLysGly
180 185 190
Leu IleThr IleLys AspIleGln LysArg IleGluTyr ProGluAla
195 200 205
Asn LysAsp AspPhe GlyArgLeu ArgVal GlyAlaAla IleGlyVal
210 215 220
Gly GlnLeu AspArg AlaGluMet LeuVal LysAlaGly ValAspAla
225 230 235 240
Leu ValLeu AspSer AlaHisGly HisSer AlaAsnIle LeuHisThr
245 250 255
4$ Leu GluGlu IleLys LysSerLeu ValVal AspValIle ValGlyAsn
260 265 270
Val ValThr LysGlu AlaThrSer AspLeu IleSerAla GlyAlaAsp
275 280 285
Ala ValLys ValGly IleGlyPro GlySer IleCysThr ThrArgIle
5~. 290 295 300
Val AlaGly ValGly MetProGln ValSer AlaIleAsp AsnCysVal
305 310 315 320
Glu ValAla SerLys PheAspIle ProVal IleAlaAsp GlyGlyIle
325 330 335
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Arg TyrSer GlyAsp ValAlaLys AlaLeuAla L_euGlyAla SerSer
340 345 350
Val MetIle GlySer LeuLeuAla GlyThrGlu GluSerPro GlyAsp
355 360 365
Phe MetIle TyrGln GlyArgGln TyrLysSer TyrArgGly MetGly
370 375 380
Ser IleGly AlaMet ThrLysGly SerSerAsp ArgTyrPhe GlnGlu
385 390 395 400
Gly ValAla SerGlu LysLeuVal ProGluGly IleGluGly ArgVal
405 410 415
Pro TyrArg GlyLys VaISerAsp MetIlePhe GlnLeuVal GlyGly
420 425 430
Val ArgSer SerMet GlyTyrGln GlyAlaLys AsnIleLeu GluLeu
435 440 445
Tyr GlnAsn AlaGlu PheValGlu IleThrSer AlaGlyLeu LysGlu
450 455 460
Ser HisVal HisGly ValAspIle ThrLysGlu AlaProAsn TyrTyr
465 470 475 480
Gly
(2) INFORMATIOIG FOR SEQ ID N0:191:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 204 amino acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
35
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204
4O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:191:
Met Gln Gly Phe Leu Leu Gln Thr Gln Ser Ile Arg Asp Glu Asp Leu
1 5 10 15
Ile Val His Val Leu Thr Lys Asn Gln Leu Lys Thr Leu Tyr Arg Phe
~'S 20 25 30
Tyr Gly Lys Arg His Ser Val Leu Asn Val Gly Arg Lys Ile Asp Phe
40 45
Glu Glu Glu Asn Asp Asp Lys Phe Leu Pro Lys Leu Arg Asn Ile Leu
50 55 60
50 His Leu Gly Tyr Ile Trp Glu Arg Glu Met Glu Arg Leu Phe Phe Trp
65 70 75 . BO
Gln Arg Phe Cys Ala Leu Leu Phe Lys His Leu Glu Gly Val His Ser
85 90 95
Leu Asp Ser Ile Tyr Phe Asp Thr Leu Asp Asp Gly Ala Ser Lys Leu
......._...~..~..~.__~..-~....__......
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loo los llo
Ser Lys Gln His Pro Leu Arg LeuGlu Met Tyr Ala Val Leu
Val Ile
115 120 125
Leu Asn Phe Glu Gly Arg Leu TyrAsn Ser Cys Phe Leu Cys
Gln Ser
S 130 135 140
Asp Ala Lys Leu Glu Arg Ser LeuAla Gln Gly Phe Ile Leu
Val Ala
145 150 155 160
Ala His Pro Ser Cys Leu Lys SerLeu Asp Leu Glu Lys Ile
Ala Lys
165 170 175
Gln Ala Phe Phe Arg Thr Gln IleAsp Leu Glu Thr Glu Glu
Ser Thr
180 185 190
VaI Glu Glu Leu Trp Arg Thr LeuGly Phe
Leu Asn
195 200
IS (2) INFORMATION
FOR
SEQ
ID
N0:192:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 82 amino
acids
(B) TYPE: amino acid
2~ (D) TOPOLOGY: linear
(ii)MOLECULE TYPE: protein
(iii)HYPOTHETICAL: YES
2S
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter
pylori
(ix)FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...82
(xi)SEQUENCE DESCRIPTION:
SEQ ID N0:192:
3S Met Gly Val Gly Arg Val Gly AlaLeu Leu Ala Cys Ala Gly
Asn Met
1 5 10 15
Pro Met Gly Ile Gly Ala Ile AlaIle Asn Gly Gly Arg Gln
Ala Ile
20 25 30
Arg Ser Arg Met Leu Val Val AspAsp Lys Arg Leu Glu Gln
Asp Ile
35 40 45
Val Gln Lys Met Leu Pro Gly ArgPro Val Thr Ala Leu Ser
Asn Trp
50 _ 55 50
Trp Cys Leu Cys Ile Pro Lys AlaIle Arg Ala Arg Cys Cys
Arg Gly
65 70 75 80
4S Glu Arg
(2) INFORMATION
FOR
SEQ
ID
N0:193:
SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 67 amino
acids
(B) TYPE: amino acid
(D) TOPOLOGY: linear
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(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
IO (B) LOCATION 1...67
(xi~ SEQUENCE DESCRIPTION: SEQ ID N0:193:
Leu Ser Gly Thr Ala Val Ser Cys Arg Cys Thr Cys Arg Ile Gln Leu
1S 1 5 10 15
Val Leu Val Arg Thr Ser Ile Pro Val Val Ile Gly Cys Ser Cys Pro
20 25 30
Phe Leu Ser Ser Ile Gly Phe Thr Thr Gly Thr His Gln Ser Pro Val
35 40 45
20 Lys Arg Cys Gly VaI Asn Ala Gly Lys Thr Pro Ser Lys Lys His Leu
50 55 60
His Leu Asn
ZS (2) INFORMATION FOR SEQ ID N0:194:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 114 amino acids
(B) TYPE: amino acid
30 (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
3S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4O (A) NAME/KEY: misc_feature
(B) LOCATION 1...114
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:194:
--- 4S Val Trp Leu Ala Ala Leu Gly Phe Leu Ile Thr Ala Val Gly Leu Pro
1 5 .0 15
Val Ile Thr Val Ile Ala Leu Ala Lys Val Gly Gly Ser Ser Thr Pro
20 25 30
Ser Ala Ile Arg Ser Ala Gly Met Pro Ala Ala Cys Trp Arg Arg Ser
SO 35 40 45
Ala Thr Trp Arg Ser Ala Arg Cys Ser Pro Phe Arg Ala Pro Pro Arg
50 55 60
Cys Pro Ser Lys Val Ser Val Val Pro Leu Leu Gly Glu Glu Ala Ala
65 70 75 80
.. .~.__ _ .. .__ ..~.._ _ _...._.__.__ _.
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Arg Arg Cys Ser Ser Thr Ala Trp Arg Thr Ser Ser Ser Pro Trp Pro
g5 ~ 90 95
Ser Pro Ser Thr Pro Val Ala Cys Trp Thr Pro Ser Asp Ala Ser Ser
100 105 110
S Pro Arg
(2) INFORMATION
FOR
SEQ
ID N0:195:
IO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
1S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
ZO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
ZS (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:195:
30
TATACCATGG
TGGGCGCTAA
20
(2) INFORMATION
FOR
SEQ
ID N0:196:
3S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
40
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
4S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
SO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:196:
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ATGAATTCGA GTAAGGATTT TTG 23
(2) INFORMATION FOR SEQ ID N0:197:
S
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
1S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
2S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:197:
TTAACCATGG TGAAAAGCGA TA 22
(2) INFORMATION FOR SEQ ID N0:198:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
3S (D) TOPOLOGY: circular
iii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
_ 4S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
SO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:198:
TAGAATTCGC ATAACGATCA ATC 23
(2) INFORMATION FOR SEQ ID N0:199:
_._. .... _._ _.____-_.._~._.._ _._ ...
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(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
1$ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:199:
ATATCCATGG
TGAGTTTGAT
GA 22
2S (2) INFORMATION
FOR
SEQ
ID N0:200:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
3S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LQCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:200:
ATGAATTCAA
TTTTTTATTT
TGCCA
25
SO (2) INFORMATION
FOR
SEQ
ID N0:201:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
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(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL:' NO
(iv) ANTI-SENSE: NO
IO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc
feature
IS _
(B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:201:
AATTCCATGG
TGGGGGCTAT
G 21
20
(2) INFORMATION
FOR SEQ
ID N0:202:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
2S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
30
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
3S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc
feature
40 _
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:202:
ATGAATTCTC
GATAGCCAAA
ATC 23
4S
(2) INFORMATION
FOR SEQ
IL N~:203:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
SO (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
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(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:203:
IS AATTCCATGG
TGCATAACTT
CCATT
25
(2) INFORMATION
FOR
SEQ
ID N0:204:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
2S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NQ
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
3S (A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:204:
AAGAATTCTC
TAGCATCCAA
ATGGA
25
(2) INFORMATION
FOR
SEQ
ID N0:205:
(i) SEQUENCE CHARACTERISTICS:
4S (A) LENGTH: 24 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
S0 (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
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(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S ( ix) FEATURE
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:205:
ATTTCCATGG
TCATGTCTCA
TATT
24
(2) INFORMATION FOR SEQ ID N0:206:
IS (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
2S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:206:
3S
ATGAATTCCA
TCTTTTATTC
CAC
23
(2) INFORMATION
FOR
SEQ
ID N0:207:
4O (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 27 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
4S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
SO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
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(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...27
S (xi) SEQUENCE DESCRIPTION: SEQ ID N0:207:
AACCATGGTG ATTTTAAGCA TTGAAAG 27
(2) INFORMATION FOR SEQ ID N0:208:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 28 base pairs
{B) TYPE: nucleic acid
(C) STRANDEDNESS: double
1S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...28
3O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:208:
AAGAATTCCA
CTCAAAATTT
TTTAACAG
28
(2) INFORMATION
FOR
SEQ
ID N0:209:
3S
{i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
40 (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
45
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
S0
(ix) FEATURE:
(A) NAME/KEY: misc
feature
_
(B) LOCATION 1...25
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(xi) SEQUENCE DESCRIPTION: SEQ ID N0:209:
GATCATCCAT
ATGTTATCTT
CTAAT
25
S (2) INFORMATION
FOR
SEQ
ID N0:210:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
1~ (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
IS (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
2~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
2S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:210:
TGAATTCAAC
CATTTTAACC
CTG
23
(2) INFORMATION
FOR
SEQ
ID N0:211:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 27 base pairs
(B) TYPE: nucleic acid
3S (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4O (iii) HYPOTHETICAL:-NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
4S ('~) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...27
S~ _ .
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:211:
TATACCATGG
TGAAATTTTT
TCTTTTA
27
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(2) INFORMATION FOR SEQ ID N0:212:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
1~
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
IS (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
2~ (B) LOCATION 1...25
(xi) SEQG'ENCE DESCRIPTION: SEQ ID N0:212:
AGAATTCAAT TGCGTCTTGT AAAAG 25
(2) INFORMATION FOR SEQ ID N0:213:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 24 base pairs
3~ (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
4O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:213:
TATACCATGG TGATGGACAA ACTC 24
(2) INFORMATION FOR SEQ ID N0:214:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
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(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
$ (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
1~
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
IS (A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:214:
2O ATGAATTCCC
ACTTGGGGCG
ATA
23
(2) INFORMATION
FOR
SEQ
ID N0:215:
(i) SEQUENCE CHARACTERISTICS:
2S (A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
3S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
4fl (A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:215:
4S TTATGGATCC
AAACCAATTA
AAACT
25
(2) INFORMATION
FOR
SEQ
ID N0:216:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
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(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IO (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:216:
1S
TATCTCGAGT TATAGAGAAG GGC 23
{2) INFORMATION FOR SEQ ID N0:217:
ZO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
2S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3O (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3S (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:217:
TTAACCATGG TGAAAAGCGA TA 22
(2) INFORMATION FOR SEQ ID N0:218:
4S (i) SEQUENCE CHARACTERTSTICS:
(A) LENGTH: 24 ...a ~e pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
SO
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPbTHETICAL: NO
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(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24
IO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:218:
TAGAATTCGC
CTCTAAAACT
TTAG
24
(2) INFORMATION
FOR
SEQ
ID N0:219:
1$
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
20 (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
2$
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
30
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
3$ (xi) SEQUENCE DESCRIPTION: SEQ ID N0:219:
TTAACCATGG
TGAAAAGCGA
TA 22
(2) INFORMATION
FOR
SEQ
ID N0:220:
40
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
~O
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
_.... _..W .. .. _..._....-_-~ ~,.~. .
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(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:220:
TAGAATTC GC ATAACGATCA ATC 23
(2) INFORMATION
FOR SEQ
ID N0:221:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
IS (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2O (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
2S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
30
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:221:
ATATCCATGG
TGAGTTTGAT
GA ,
22
3S (2) INFORMATION
FOR SEQ
ID N0:222:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
S~ (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25
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(xi) SEQUENCE DESCRIPTION: SEQ ID N0:222:
ATGAATTCAA TTTTTTATTT TGCCA 25
$
(2) INFORMATION FOR SEQ ID N0:223:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
{B) TYPE: nucleic acid
{C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
1$
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
2O (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
2$ (B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:223:
AATTCCATGG CTATCCAAAT CCG 23
(2) INFORMATION FOR SEQ ID N0:224:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
3$ (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
.__ 4$ (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylox~
(ix) FEATURE: _
(A) NAME/KEY: misc_feature
$0 (B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:224:
ATGAATTCGC CAAAATCGTA GTATT 25
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(2) INFORMATION
FOR
SEQ
ID N0:225:
(i) SEQUENCE CHARACTERISTICS:
S (A) LENGTH: 24 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
1S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:225:
2S GATACCATGG
AATTTATGAA
AAAG
24
(2) INFORMATION
FOR
SEQ
ID N0:226:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3S (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
( ix FEATURE
)
4S (A) NAME/KT;Y: misc_feature
(B) LOCa_~.' JN 1. . .25
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:226:
SO TGAATTCGAA
AAAGTGTAGT
TATAC
25
(2) INFORMATION
FOR
SEQ
ID N0:227:
(i) SEQUENCE CHARACTERISTICS:
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(A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid
(C} STRANDEDNESS: double
(D) TOPOLOGY: circular
S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
IO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
IS (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:227:
20
CCCTTCATTT
TAGAAATCG
lg
(2) INFORMATION
FOR SEQ
ID N0:228:
2S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
30
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4O (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:228:
45
ATTTCAACCA
ATTCAATGCG
20
(2) INFORMATION
FOR SEQ
ID N0:229:
SO (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
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(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
{ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20
IS (xi) SEQUENCE DESCRIPTION: SEQ ID N0:229:
GCCCCTTTTG ATTTGAAGCT 20
(2) INFORMATION FOR SEQ ID N0:230:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
2S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
3S
(ix) FEATURE:
- (A) NAME/KEY: misc_feature
{B) LOCATION 1...22
4O (xi) SEQUENCE DESCRIPTION: SEQ ID N0:230:
TCGCTCCAAG ATACCAAGAA GT 22
(2) INFORMATION FOR SEQ ID N0:231:
4S
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
S0 (D} TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
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(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
S (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
lO
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:231:
CTTGAATTAG
GGGCAAAGAT
CG 22
IS (2) INFORMATION
FOR
SEQ
ID N0:232:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
20 (C) STR.ANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2S (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
3O (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
3S
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:232:
ATGCGTTTTT
ACCCAAAGAA
GT 22
4O (2) INFORMATION
FOR
SEQ
ID N0:233:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
4S (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
SO (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
. ~. ~.~..... ~ ..._.. _ _._ __ _ __..__r...._. . _ _.. _ _ _._
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(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc
feature
_
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:233:
ATAACGCCAC
TTCCTTATTG
GT 22
lO
(2) INFORMATION
FOR
SEQ
ID N0:234:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 19 base pairs
1S (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
2O
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
2S (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc
feature
3O _
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:234:
CTTTGGGTAA
AAACGCATC
19
3S
(2) INFORMATION
FOR
SEQ
ID N0:235:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
4O (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
4S
(iii) F__F~THETICAL: NO
(iv) ANTI-SENSE: NO
SO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc feature
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(B) LOCATION 1...20
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:235:
S CGATCTTTGA
TCCTAATTCA
20
(2) INFORMATION
FOR
SEQ
ID N0:236:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
IS (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
2S (A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:236:
3O ATCAAGTTGC
CTATGCTGA
19
(2) INFORMATION
FOR
SEQ
ID N0:237:
(i) SEQUENCE CHARACTERISTICS:
3S (A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
40 (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
4S
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
S0 (A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:237:
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TTGAACACTT TTGATTATGC GG _ 22
(2) INFORMATION FOR SEQ ID N0:238:
S (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA_(genomic)
{iii) HYPOTHETICAL: NO
IS (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
2O (ix) FEATURE:
{A) NAME/KEY: misc_feature
(B) LOCATION 1..,23
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:238:
2S
GGATTATGCG ATTGTTTTAC AAG 23
(2) INFORMATION FOR SEQ ID N0:239:
30 (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
3S
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
4U (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
4S (ix) FEATURE:
(A) NAME/KEY: misc_feature
{B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:239:
S0
GTCTTTAGCA AAAATGGCGT C 21
{2) INFORMATION FOR SEQ ID N0:24.0:
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(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
S (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
1S
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...21
ZO (xi) SEQUENCE DESCRIPTION: SEQ ID N0:240:
AATGAGCGTA
AGAGAGCCTT
C 21
(2) INFORMATION
FOR
SEQ
ID N0:241:
2S
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C} STRANDEDNESS: double
3~ (D} TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
3S
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A} ORGANISM: Helicobacter pylori
40
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...18
4S (xi) SEQUENCE DESCRIPTION SEQ ID N0:241:
CTTATGGGGG
TATTGTCA
18
(2) INFORMATION
FOR
SEQ
ID N0:242:
SO _.
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
_..___.~-..~.____..... .~__...__ _.~._.r..
CA 02273199 1999-06-O1
DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTS PARTiE DE CETTE DEMANDS OU CE BREVET
COMPREND PLUS D'UN TOME_
CECI EST LE TOME _ ~ DE,~
NOTE. Pour les tomes additionels, veuillez contacter le Bureau canadien des
brevets
3'?a~3i~9
JUMBO APPLlCATIONSIPATENTS
THIS SECTION OF THE APPLfCATION/PATENT CONTAINS MORE
THAN ONE VOLUME
THIS IS VOLUME ,. L_ OF ~ -
NOTE: For additional ~oiumes ~piease contact-the Canadian Patent Ofifice
