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Table 2 PAIs in prokaryotic chromosomes (see supplementary Table 3S for the complete information) [see Additional file 3]

From: A computational approach for identifying pathogenicity islands in prokaryotic genomes

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. faecalis e
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 I CFT073 e
  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 II CFT073 e
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 LEE e
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 LEE e
Helicobacter pylori 26695 38 -3.0 82.6 Glutamate racemase (glr) cag PAI e
Helicobacter pylori J99 38.2 -3.1 83.7 Glutamate racemase (murI) cag PAI e
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 locus e
  34.9 2.1 64.1 Transposase, IS tc locus e
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-5 e
  41.6 -4.7 60.9 tRNA SPI-2 e
  15.1 0.6 100.0 Putative transposase Flagellar synthesis, siderophore receptor protein
  12.4 -5.3 100.0 - SPI-1 f
  18 -4.5 56.8 tRNA SPI-3 e
  25.5 -7.5 97.8 - SPI-4 e
Shigella flexneri 2a 2457T 50.1 -1.9 17.2 tRNA SHI-1 e
  25 -2.3 31.5 tRNA SHI-2 e
  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-1 e
  28.1 -2.5 48.2 tRNA, integrase, transposase SHI-2 e
  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 VPI e
  8.8 -3.2 100.0 - CTX locus g
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 PAI e
Yersinia pestis CO92 34.7 9.1 73.1 tRNA, integrase HPI e
  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 HPI e
  14.6 -0.6 5.6 - Iron/siderophore ABC transporters, antigen chaperone
  1. aDeviation of the G+C content of the cPAI as compared to that of the whole genome
  2. bLength percentage of horizontally transferred genes in the cPAI
  3. cGenes involved in the transfer mechanism (integrase, transposase, IS element, or tRNA gene at the boundaries)
  4. dNon-pathogenic bacterium
  5. ecPAI that entirely matches to a PAI identified from the genome sequencing paper
  6. 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.
  7. gcPAI that partly matches to a PAI identified from the genome sequencing paper
  8. 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.