Strain | Disease | Population | Length | % GC | CDS | Core |
cagA
(c)
|
vacA
(d)
|
homAB
| Reference |
---|
 |  | subpopulation | (bp)(a,b) | content |  | genes |  |  |  |  |
---|
F57 | Gastric cancer | hpEastAsia hspEAsia | 1609006 | 38.7 | 1521 | 1402 | ABD | s1a-m1-i1 | -/B | This work |
F32 | Gastric cancer | hpEastAsia hspEAsia | 1578824, 2637 | 38.9 | 1492 | 1385 | ABD | s1a-m1-i1 | -/E(e) | This work |
F30 | Duodenal ulcer | hpEastAsia hspEAsia | 1570564, 9129 | 38.8 | 1485 | 1385 | ABD | s1a-m1-i1 | -/B | This work |
F16 | Gastritis | hpEastAsia hspEAsia | 1575399 | 38.9 | 1500 | 1402 | ABD | s1a-m1-i1 | -/B | This work |
51 | Duodenal ulcer | hpEastAsia hspEAsia | 1589954 | 38.8 | 1509 | 1424 | ABD | s1a-m1-i1 | -/B | Â |
52 | ? | hpEastAsia hspEAsia | 1568826 | 38.9 | 1496 | 1383 | (A/B)(D/B)D | (s1a)-m1-i1 (f) | -/B | Â |
Shi470 | Gastritis | hpEastAsia hspAmerind | 1608548 | 38.9 | 1517 | 1401 | AB(D/C),CC(g) | s1b-m1-i1 | -/B | [21] |
v225d | Gastritis | hpEastAsia hspAmerind | 1588278, 7326 | 39.0 | 1506 | 1377 | AB(C/D)(C/D), (tr) (g,h) | s1a-m1-i1 | -/B | [22] |
Cuz20 | ? | hpEastAsia hspAmerind | 1635449 | 38.9 | 1527 | 1364 | AB(D/C)×5(tr) (h) | s1a-m2-i2 | -/A |  |
Sat464 | ? | hpEastAsia hspAmerind | 1629557, 8712 | 38.9 | 1465 | 1376 | AB(D/C) | s1b-m1-i1 | -/B | Â |
PeCan4 | Gastric cancer | hpEastAsia hspAmerind? | 1560342, 7228 | 39.1 | 1525 | 1388 | A(B/A)BC | s1a-m1-i1 | -/B | Â |
26695 | Gastritis | hpEurope | 1667867 | 38.9 | 1575 | 1411 | ABC | s1a-m1-i1 | A/- | [28] |
HPAG1 | Gastritis | hpEurope | 1596366, 9370 | 39.1 | 1492 | 1394 | A(B/A)C | s1b-m1-i1 | B/- | [30] |
G27 | ? | hpEurope | 1652982, 10031 | 38.9 | 1560 | 1400 | ABCC | s1b-m1-i1 | B/- | [56] |
P12 | Duodenal ulcer | hpEurope | 1673813, 10225 | 38.8 | 1593 | 1396 | ABCC | s1a-m1-i1 | A/- | [49] |
B38 | MALT lymphoma | hpEurope | 1576758 | 39.2 | 1493 | 1388 | - | s2-m1-i2 | A/- | [51] |
B8(i) | Gastric ulcer(i) | hpEurope | 1673997, 6032 | 38.8 | 1578 | 1385 | ABC | s1a-m2-i2 (j) | A/A | [57] |
SJM180 | Gastritis | hpEurope? | 1658051 | 38.9 | 1515 | 1381 | ABC | s1b-m1-i1 | B/B | Â |
J99 | Duodenal ulcer | hpAfrica1 hspWAfrica | 1643831 | 39.2 | 1502 | 1383 | (A/B)C | s1b-m1-i1 | A/B | [2] |
908(k) | Duodenal ulcer | hpAfrica1 hspWAfrica | 1549666 | 39.3 | 1503 | 1393 | ABC | -s1b-(-)-i1 (j,k,l) | -/-(k) | [139] |
- a) The first number is the length of the chromosome and the second number (when present) is that of the plasmid.
- b) Accession numbers are as follows: F57 [DDBJ:AP011945.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011945.1], F32 [DDBJ:AP011943.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011943.1, DDBJ:AP011944.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011944.1], F30 [DDBJ:AP011941.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011941.1, DDBJ: AP011942.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011942.1], F16 [DDBJ:AP011940.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011940.1], 51 [GenBank:CP000012.1], 52 [GenBank:CP001680.1], Shi470 [GenBank:NC_010698.2], v225d [GenBank:CP001582.1, GenBank:CP001583.1], Cuz20 [GenBank:CP002076.1], Sat464 [GenBank:CP002071.1, GenBank:CP002072.1], PeCan4 [GenBank:NC_014555.1, GenBank:NC_014556.1], 26695 [GenBank:NC_000915.1], HPAG1 [GenBank:NC_008086.1, GenBank:NC_008087.1], G27 [GenBank:NC_011333.1, GenBank:NC_011334.1], P12 [GenBank:NC_011498.1, GenBank:NC_011499.1], B38 [GenBank:NC_012973.1], B8 [GenBank:NC_014256.1, GenBank:NC_014257.1], SJM180 [GenBank:NC_014560.1], J99 [GenBank:NC_000921.1], 908 [GenBank:CP002184.1]. Draft sequence of the East Asian strain 98-10 [140]. 98-10, [GenBank:NZ_ABSX01000001.1] - [GenBank:NZ_ABSX01000051.1].
- c) Letters in parentheses are the hybrid EPIYA segment. For example, (A/B) is a hybrid of EPIYA-A and EPIYA-B segments [21, 22, 141].
- d) Reference [142, 143].
- e) Designated as homE as it was very different from homA or homB.
- f) "s" region locates outside of the ORF.
- g) A second cagA gene between cagM and cagP.
- h) (tr), truncation.
- i) Mongolian gerbil-adapted, originally from gastric ulcer.
- j) vacA gene is split.
- k) According to a reference [139], the sequence might not represent a complete genome, although it is deposited as a complete circular genome in GenBank.
- l) "m" region was not available because of a deletion in the center of the ORF.