Table 1.
Summary of comparative features of Helicobacter genomes
| Features of the strains | B38 | 26695 | J99 | HPAG1a | Shi470 | G27a | P12a | H. a Straina Sheeba | H. h Strain ATCC 51449 |
|---|---|---|---|---|---|---|---|---|---|
| cagPAI | NEG | POS | POS | POS | POS | POS | POS | HacGI | HHGI1 |
| Size (bp) | 1,576,758 | 1,667,867 | 1,643,831 | 1,596,366 | 1,608,547 | 1,652,982 | 1,673,813 | 1,553,927 | 1,799,146 |
| (G+C) content (%) | 39.2 | 38.9 | 39.2 | 39.1 | 38.9 | 38.9 | 38.8 | 38.2 | 35.9 |
| Total CDSs (nb)b | 1,528 | 1,637 | 1,543 | 1,539 | 1,592 | 1,611 | 1,639 | 1,696 | 1,851 |
| Complete CDSs (nb)b | 1,393 | 1,501 | 1,446 | 1,441 | 1,473 | 1,469 | 1,505 | 1,397 | 1,824 |
| Average length (bp)b | 971 | 964 | 988 | 971 | 955 | 954 | 957 | 933 | 914 |
| Coding density (%)b | 85.0 | 86.3 | 86.6 | 87.3 | 87.2 | 84.6 | 85.8 | 83.6 | 92.3 |
| Partial CDSs (nb)b | 135 | 136 | 97 | 98 | 119 | 142 | 134 | 299 | 27 |
| Truncated genes (nb)b | 2 | 9 | 10 | 7 | 4 | 7 | 7 | 11 | 11 |
| Pseudogenes (nb)b | 133(8.7%)c | 127(7.8%) | 87(5.6%) | 91(5.9%) | 115(7.2%) | 135(8.4%) | 127(7.8%) | 288(17%) | 16(0.9%) |
| Fragmented pseudogenes (nb)b |
62(4%)d | 61(3.7%) | 38(2.8%) | 43(2.8%) | 52(3.2%) | 64(3.9%) | 56(3.4%) | 81(4.8%) | 8(0.4%) |
| tRNA (nb) | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 36 | 37 |
| Ribosomal RNA genes | |||||||||
| 23S (nb) | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 |
| 16S (nb) | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 |
| 5S (nb) | 3 | 3 | 2 | 2 | 2 | 3 | 2 | 2 | 1 |
| IS-types (ORFs number) |
20ISHp609 (5) | 17 IS606 (1) IS605 (5) IS200 (1) |
6 IS606 (1 remnant) ISHp609 (1 remnant) |
7 IS606 (2 remnant) ISHp609 (1) |
5 IS606 in 3 fragments |
9 IS605 (4) |
1 | 13 ISHa1152 (2) ISHa1942 (1) ISHa1675 (1) |
2ISHp609 (1 remnant) |
aThese genomes have got a 9,369 bp (HPAG1), a 10,031 bp (G27), a 10,225 bp (P12), a 3,661 bp (Sheeba) plasmid and a 10,031 bp (G27) and a 10,225 bp (P12). Plasmids were not counted
bRevised number with the MaGe system and manual curation
cPercentage of fragments of genes/total CDSs
dPercentage of fragmented genes/total CDSs
e Number of copies