Table 4 Genomic islands in the four Japanese H. pylori strains
Strain | GI number | Type | Length | Start-end | Flanking repeat (bp) | Secretion system | Left gene (annotation) | Right gene (annotation) |
|---|---|---|---|---|---|---|---|---|
F16 | GI_HP_F16_1 | prophage-like | 12245 | 471964 - 484208 (HPF16_0465 - HPF16_0478) | N/D(a) | N/D(a) | HPF16_0464 (IS605 transposase (tnpB)) | HPF16_0479 (typeIIR) |
| Â | GI_HP_F16_2 | cagPAI | 36761 | 871413 - 834651 (HPF16_0834 - HPF16_0810) | 22(b) | Type IV | HPF16_0835 (hypothetical protein) | HPF16_0809 (glutamate racemase) |
F30 | GI_HP_F30_1 (left) | type 1b TnPZ partial | 7246 | 1280406 - 1287651 (HPF30_1205 - HPF30_1211) | N/D(a) | tfs3b partial | HPF30_1204 (outer membrane protein horB) | HPF30_1212 (rpoD) |
| Â | GI_HP_F30_1 (right) | type 1b TnPZ partial | 1655 | 1237267 - 1238921 (HPF30_1166 - HPF30_1167) | N/D(a) | N/D(a) | HPF30_1165 (hypothetical protein) | HPF30_1168 (5'-methylthioadenosine/S -adenosylhomocysteine nucleosidase) |
| Â | GI_HP_F30_2 | cagPAI | 37153 | 867993 - 830839 (HPF30_0803 - HPF30_0778) | 22(c) | Type IV | HPF30_0804 (hypothetical protein) | HPF30_0777 (glutamate racemase) |
F32 | GI_HP_F32_1 | type 2 TnPZ partial | 24283 | 1058236 - 1082518 (HPF32_0988 - HPF32_1014) | N/D(a) | tfs3 partial | HPF32_0987 (hypothetical protein) | HPF32_1015 (hypothetical protein) |
| Â | GI_HP_F32_2 | cagPAI | 36609 | 534488 - 571096 (HPF32_0500 - HPF32_0524) | 44(d) | Type IV | HPF32_0499 (hypothetical protein) | HPF32_0525 (glutamate racemase) |
F57 | GI_HP_F57_1 (left) | type 1b TnPZ partial | 7246 | 103791 - 111036 (HPF57_0102 - HPF57_0109) | N/D(a) | tfs3b partial | HPF57_0101 (RNA polymerase sigma factor RpoD) | HPF57_0110 (hypothetical protein) |
| Â | GI_HP_F57_1 (right) | type 1b TnPZ partial | 1625 | 152699 - 154323 (HPF57_0147 - HPF57_0148) | N/D(a) | N/D(a) | HPF57_0146 (5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase) | HPF57_0149 (hypothetical protein) |
| Â | GI_HP_F57_2 | type 1 TnPZ | 38991 | 284353 - 323343 (HPF57_0279 - HPF57_0311) | 8(e) | tfs3b partial | HPF57_0278 (typeIIM) | HPF57_0312 (type II DNA modification enzyme ) |
| Â | GI_HP_F57_3 | cagPAI | 36797 | 562215 - 599011 (HPF57_0550 - HPF57_0575) | 22(c) | Type IV | HPF57_0549 (hypothetical protein) | HPF57_0576 (glutamate racemase) |