Table 2.
PAIs in prokaryotic chromosomes (see supplementary Table 3S for the complete information) [see Additional file 3]
| Strain | Size (kb) | Δ G+C (%)a | HGT (%)b | Evidence of GIc | Characteristics |
| Bacillus halodurans C-125d | 8.1 | -2.7 | 100.0 | Transposase | ABC transporters |
| Bacillus subtilis 168d | 4.9 | -2.3 | 13.6 | - | Flagellar protein |
| Bordetella bronchiseptica RB50 | 15.3 | -1.6 | 36.7 | tRNA | TTSS |
| 8 | 4.3 | 93.2 | - | Hemin transport system | |
| Bordetella pertussis Tohama I | 7.9 | 4.6 | 93.1 | - | Heme uptake |
| 15.3 | -1.2 | 39.8 | tRNA | TTSS | |
| Bradyrhizobium japonicum USDA 110d | 6.4 | -4.3 | 100.0 | - | Nodulation |
| Chromobacterium violaceum ATCC 12472 | 11.8 | -9.3 | 100.0 | - | TTSS |
| 15.5 | -6.5 | 86.4 | - | TTSS | |
| Enterococcus faecalis V583 | 137.5 | -4.7 | 83.8 | tRNA | NN in E. faecalise |
| Escherichia coli CFT073 | 7.1 | -6.3 | 85.8 | tRNA, integrase, IS | Hypotheticals |
| 60.1 | -1.8 | 33.0 | tRNA, transposase, phage genes | F1C and S fimbrial protein, iron uptake | |
| 48.5 | -3.5 | 46.1 | tRNA, integrase, transposase | PAI ICFT073e | |
| 29.1 | 2.7 | 57.8 | IS | ISEc8, antigen 43 precursor, fimbrial protein | |
| 6 | -9.8 | 87.1 | - | Fimbrial protein | |
| 43.3 | -2.7 | 19.7 | Transposase | PAI IICFT073e | |
| Escherichia coli K12d | 9.8 | -3.8 | 100.0 | Integrase, putative transposase | Fimbrial protein |
| 8.5 | 6.1 | 43.3 | - | Citrate-dependent iron transport | |
| Escherichia coli O157:H7 EDL933 | 7 | -4.9 | 42.2 | Putative transposase | Glucosyltransferase |
| 13.5 | -4.4 | 100.0 | - | Pilin subunit, transporter and member of exoprotein | |
| 7 | -4.9 | 42.1 | Putative transposase, IS proteins | Glycosyl transferase, IS1 proteins | |
| 14.9 | -13.3 | 100.0 | tRNA | TTSS | |
| 44.7 | -9.2 | 87.3 | tRNA, integrase, phage genes | LEEe | |
| Escherichia coli O157:H7 Sakai | 7 | -4.6 | 45.6 | Transposase | Ferric enterochelin esterase |
| 17 | -14.0 | 100.0 | tRNA | TTSS | |
| 44.7 | -9.4 | 89.7 | tRNA | LEEe | |
| Helicobacter pylori 26695 | 38 | -3.0 | 82.6 | Glutamate racemase (glr) | cagPAIe |
| Helicobacter pylori J99 | 38.2 | -3.1 | 83.7 | Glutamate racemase (murI) | cagPAIe |
| Mesorhizobium loti MAFF303099d | 12.7 | -5.5 | 100.0 | - | TTSS, nodulation protein |
| Nitrosomonas europaea ATCC 19718d | 16.9 | 2.5 | 34.9 | Recombinase | Transmembrane sensors, outer membrane efflux |
| Photorhabdus luminescens subsp. laumondii TTO1 | 23.2 | 8.3 | 68.2 | - | Putative fimbrial proteins |
| 36.3 | 7.7 | 87.4 | tRNA, IS, transposase | Lipoprotein, pilus | |
| 50.6 | -1.5 | 17.0 | - | TTSS locuse | |
| 34.9 | 2.1 | 64.1 | Transposase, IS | tc locuse | |
| Salmonella enterica Typhi Ty2 | 6.7 | 0.6 | 26.4 | - | Fimbrial protein |
| 41.3 | -4.7 | 61.2 | tRNA | SPI-2e | |
| 10.3 | -6.5 | 57.7 | tRNA, transposase | SPI-5e | |
| 6.7 | -2.4 | 95.5 | tRNA | Fimbrial protein | |
| 12.4 | -5.2 | 100.0 | - | SPI-1f | |
| 25.5 | -7.3 | 91.6 | - | SPI-4e | |
| Salmonella enterica Typhi CT18 (Salmonella enterica Typhi Typhi) | 6.7 | 0.6 | 26.4 | - | Fimbrial protein |
| 6.7 | -2.5 | 95.5 | tRNA | Fimbrial protein | |
| 10.3 | -6.6 | 57.7 | tRNA, transposase | SPI-5e | |
| 41.3 | -4.7 | 61.2 | tRNA | SPI-2e | |
| 12.4 | -5.2 | 100.0 | IS, transposase | SPI-1f | |
| 25.5 | -7.3 | 91.6 | - | SPI-4e | |
| Salmonella typhimurium LT2 (S. enterica serovar Typhimurium LT2) | 6.7 | 0.6 | 26.4 | - | Fimbrial protein |
| 8.3 | -3.5 | 77.4 | - | Fimbrial protein | |
| 9.5 | -6.6 | 52.2 | tRNA | SPI-5e | |
| 41.6 | -4.7 | 60.9 | tRNA | SPI-2e | |
| 15.1 | 0.6 | 100.0 | Putative transposase | Flagellar synthesis, siderophore receptor protein | |
| 12.4 | -5.3 | 100.0 | - | SPI-1f | |
| 18 | -4.5 | 56.8 | tRNA | SPI-3e | |
| 25.5 | -7.5 | 97.8 | - | SPI-4e | |
| Shigella flexneri 2a 2457T | 50.1 | -1.9 | 17.2 | tRNA | SHI-1e |
| 25 | -2.3 | 31.5 | tRNA | SHI-2e | |
| 22.6 | -4.1 | 48.0 | tRNA, recombinase | Fimbrial protein | |
| Shigella flexneri 2a 301 | 13.7 | 1.8 | 83.6 | Putative transposase | Enterochelin esterase, oxidoreductase (Fe-S subunit) |
| 7.5 | -3.1 | 54.8 | tRNA | Oxidoreductases (Fe-S subunit) | |
| 53.5 | -2.1 | 8.1 | tRNA, integrase, transposase | SHI-1e | |
| 28.1 | -2.5 | 48.2 | tRNA, integrase, transposase | SHI-2e | |
| 28.9 | -3.4 | 50.1 | tRNA, transposase, integrase | Fimbrial protein | |
| Staphylococcus aureus Mu50 | 5.3 | -7.0 | 100.0 | tRNA | SaPIm3f |
| Staphylococcus aureus MW2 | 6.3 | 0.4 | 43.8 | - | ν Saβg |
| Staphylococcus aureus N315 | 5.3 | -6.9 | 100.0 | tRNA | SaPIn3f |
| Vibrio cholerae N16961 | 4.3 | -11.5 | 87.9 | Transposase | VPIe |
| 8.8 | -3.2 | 100.0 | - | CTX locusg | |
| Vibrio parahaemolyticus RIMD 2210633 chromosome I | 16.7 | 2.9 | 39.6 | - | TTSS |
| 11.3 | 0.0 | 11.1 | - | TTSS, iron transport | |
| Vibrio parahaemolyticus RIMD 2210633 chromosome II | 9 | 0.5 | 26.1 | - | Flagellar biosynthesis |
| 3.7 | 4.9 | 79.2 | - | Iron transport | |
| Xanthomonas campestris pv. campestris ATCC 33913 | 23.1 | -1.8 | 10.0 | Transposase | Hrp PAIe |
| Yersinia pestis CO92 | 34.7 | 9.1 | 73.1 | tRNA, integrase | HPIe |
| 8 | -1.7 | 48.7 | Transposase | Iron transport system | |
| 6.1 | -0.9 | 100.0 | Transposase | Fimbrial protein, secreted protein | |
| Yersinia pestis KIM | 34.7 | 9.1 | 76.8 | tRNA, integrase | HPIe |
| 14.6 | -0.6 | 5.6 | - | Iron/siderophore ABC transporters, antigen chaperone | |
aDeviation of the G+C content of the cPAI as compared to that of the whole genome
bLength percentage of horizontally transferred genes in the cPAI
cGenes involved in the transfer mechanism (integrase, transposase, IS element, or tRNA gene at the boundaries)
dNon-pathogenic bacterium
ecPAI that entirely matches to a PAI identified from the genome sequencing paper
fcPAI that matches to one end of a PAI identified from the genome sequencing paper. The other end of the PAI is present in a PAI-like region not overlapping GIs.
gcPAI that partly matches to a PAI identified from the genome sequencing paper
Bold characters denote that a sequenced strain containing the cPAI is the same as or closely related to the host strain of the queried PAI loci.