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Table 1 Summary of the 48 bacterial genomes used in this study and the PAS/PDC domains identified

From: Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus

Speciesa Subspecies/strain Accession number Phylum Pathogenicityb Motilityc Total proteinsd PDC/PAS proteinse PAS domainsf PDC domainsg
[Gram positive]          
Bifidobacterium animalis lactis AD011 NC_011835.1 Actinobacteria 0 0 1527 5 4 2
Corynebacterium diphtheriae (Ci) NCTC 13129 NC_002935.2 Actinobacteria 1 0 2272 4 2 2
Corynebacterium glutamicum (Cg) ATCC 13032 NC_006958.1 Actinobacteria 0 0 3057 7 5 4
Micrococcus luteus (Ml) NCTC 2665 NC_012803.1 Actinobacteria 0 0 2236 5 4 3
Mycobacterium leprae TN NC_002677.1 Actinobacteria 1 0 1605 6 7 1
Mycobacterium smegmatis (Ms) MC2 155 NC_008596.1 Actinobacteria 0 0 6717 20 17 10
Mycobacterium tuberculosis (Mt) CDC1551 NC_002755.2 Actinobacteria 1 0 4189 10 6 7
Streptomyces coelicolor (Stc) A3(2) NC_003888.3 Actinobacteria 0 0 8154 51 48 18
Bacillus anthracis (Ba) CDC 684 NC_012581.1 Firmicutes 1 0 5902 43 30 30
Bacillus cereus (Bc) ATCC 10987 NC_003909.8 Firmicutes 1 1 5843 41 30 25
Bacillus megaterium (Bm) QM B1551 NC_010010.2 Firmicutes 0 1 5612 53 57 21
Bacillus subtilis (Bs) subtilis 168 NC_000964.3 Firmicutes 0 1 4176 32 21 30
Clostridium acetobutylicum (Ca) ATCC 824 NC_003030.1 Firmicutes 0 1 3847 36 16 34
Clostridium botulinum A str. ATCC 3502 NC_009496.1 Firmicutes 1 1 3590 48 31 40
Clostridium difficile (Cd) 630 NC_009089.1 Firmicutes 1 1 3749 49 49 26
Enterococcus faecalis (Efs) V583 NC_004668.1 Firmicutes 1 0 3264 9 7 7
Enterococcus faecium (Efm) DO NZ_AAAK00000000 Firmicutes 1 0 3114 9 3 10
Lactobacillus casei (Lc) ATCC 334 NC_008526.1 Firmicutes 0 0 2768 8 6 4
Lactococcus lactis (Ll) cremoris MG1363 NC_009004.1 Firmicutes 0 0 2434 5 5 0
Listeria monocytogenes (Lm) EGD-e NP_463535.1 Firmicutes 1 1 2846 12 9 7
Macrococcus caseolyticus (Mc) JCSC5402 NC_011999.1 Firmicutes 0 0 2052 7 6 4
Staphylococcus aureus (SaU) aureus USA300_TCH1516 NC_010079.1 Firmicutes 1 0 2693 8 5 7
Staphylococcus aureus (SaC) aureus COL NC_002951.2 Firmicutes 1 0 2612 8 5 7
Staphylococcus carnosus (Sc) carnosus TM300 NC_012121.1 Firmicutes 0 0 2461 9 8 5
Staphylococcus epidermidis (Se) ATCC 12228 NC_004461.1 Firmicutes 1 0 2416 8 5 7
Staphylococcus haemolyticus (Sh) JCSC1435 NC_007168.1 Firmicutes 1 0 2676 7 5 4h
Staphylococcus lugdunensis (Sl) HKU09-01 CP_001837.1 Firmicutes 1 0 2490 7 5 5
Staphylococcus pseudintermedius (Sp) HKU10-03 NC_014925.1 Firmicutes 1 0 2450 8 5 7
Staphylococcus saprophyticus (Ss) saprophyticus ATCC15305 NC_007350.1 Firmicutes 1 0 2446 6 4 5
Streptococcus agalactiae 2603 V/R NC_004116.1 Firmicutes 1 0 2124 11 6 7
Streptococcus pneumoniae (Spn) D39 NC_008533.1 Firmicutes 1 0 1914 8 5 4
Streptococcus pyogenes (Spy) MGAS10270 NC_008022.1 Firmicutes 1 0 1986 11 4 10
[Gram negative]          
Nostoc punctiforme PCC 73102 NC_010628.1 Cyanobacteria 0 1 6689 97 131 38
Synechococcus sp CC9311 NC_008319.1 Cyanobacteria 0 1 2892 12 8 6
Agrobacterium tumefaciens C58 NC_003062.2 Proteobacteria 0 1 5355 63 61 27
Bartonella henselae Houston-1 NC_005956.1 Proteobacteria 1 0 1488 8 10 2
Bradyrhizobium sp BTAi1 NC_009485.1 Proteobacteria 0 1 7621 98 103 51
Escherichia coli (Ec) K-12 substr. MG1655 NC_000913.2 Proteobacteria 0 1 4146 32 24 18
Helicobacter pylori 83 CP002605.1 Proteobacteria 1 1 1609 5 1 7
Klebsiella pneumoniae (Kp) 342 NC_011283.1 Proteobacteria 1 0 5768 33 24 18
Neisseria meningitidis MC58 NC_003112.1 Proteobacteria 1 0 2063 3 2 1
Pseudomonas aeruginosa PAO1 NC_002516.1 Proteobacteria 1 1 5571 70 71 35
Salmonella enterica arizonae serovar NC_010067.1 Proteobacteria 1 1 4500 21 12 13
Shigella flexneri 2a str. 2457 T NC_004741.1 Proteobacteria 1 0 4060 18 11 9
Vibrio cholerae MJ-1236 NC_012668.1 Proteobacteria 1 1 3772 71 42 59
Yersinia pestis CO92 NC_003143.1 Proteobacteria 1 1 4066 20 10 13
Leptospira biflexa serovar Patoc CP000788.1 Spirochaetes 0 1 3726 67 76 30
Treponema pallidum pallidum SS14 CP000805.1 Spirochaetes 1 1 1028 5 1 6
  1. aFor those included in our phylogenetic analysis, abbreviations for species names are shown in parentheses.
  2. b1: pathogenic, 0: non-pathogenic.
  3. c1: motile, 0: non-motile.
  4. dTotal number of proteins in the genome.
  5. eTotal number of PAS/PDC-containing proteins identified in the genome.
  6. fTotal number of PAS domains identified.
  7. gTotal number of PDC domains identified.
  8. hOne of the PDC/PAS-containing proteins in Staphylococcus haemolyticus (Sh.3, YP_253148.1, PhoR) does not have the PDC domain identified by HHblits nor HHsearch, although all other Staphylococcus PhoR homologs have clearly identified PDC domains. However, as noted in Supplementary Table S1, a very weakly conserved PDC-like region was identified in this protein based on the predicted secondary structure. This potential PDC domain is not included in this table nor in our analysis.