Response regulators encoded in bacterial and archaeal genomesa

This is an updated versionb of the web supplement to the paper "Structural classification of bacterial
response regulators: Diversity of output domains and domain combinations" by Michael Y. Galperin,
published in the Journal of Bacteriology (2006) 188: 4169-4182. Abstract in PubMed
Free full text (HTML). Free full text (PDF). PDF from PubMed Central.

This updated version was prepared as a supplement to the review by Urs Jenal and Michael Y. Galperin
"Single-domain response regulators: molecular switches with emerging roles in cell organization and dynamics",
published in Current Opinion in Microbiology (2009) 12: 152-160. Abstract in PubMed, Article Outline
and another paper that is still in preparation.

This version includes 555 genomes, representing all bacterial and archaeal species that were sequenced by the end of 2008.
The original 200-genome version described in the 2006 paper can be found here.

Organism GenBank
entry		 No.
genes		 Stand-
alone
RECb		 DNA-binding RNA Enzymatic CheV Other
RRsb		 All
RRs
Acidobacteria OmpR NarL NtrC LytR ActR AraC AmiR WspR/
PleD		 GGDEF/
EALb		 PvrR RpfG HisK PP2C CheB
Acidobacteria bacterium Ellin345 CP000360 4777 36 11 16 15 6 - - - 1 - - 4 1 2 2 - 13 107
Solibacter usitatus CP000473 7826 38 14 16 14 9 - - - 1 - - - 1 2 1 - 10 106
Actinobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Acidothermus cellulolyticus CP000481 2157 5 7 6 - 1 - - 1 1 - 1 - - 1 2 - 1 26
Arthrobacter aurescens CP000474 4587 - 9 6 - 1 - - 1 1 - - - - 1 - - 3 22
Arthrobacter sp. FB24 CP000454 4506 1 15 9 - 1 - - 1 - - - - - 1 - - 1 29
Bifidobacterium adolescentis AP009256 1631 - 3 8 - 2 - - 1 - - - - - - - - - 14
Bifidobacterium longum AE014295 1727 - 5 4 - - - - 1 - - - - - - - - - 10
Clavibacter michiganensis AM711867 3079 - 9 17 - - - - 1 - - - - - - - - 1 28
Corynebacterium diphtheriae BX248353 2272 - 6 5 - - - - - - - - - - - - - - 11
Corynebacterium efficiens BA000035 2950 - 6 7 - - - - - - - - - - - - - - 13
Corynebacterium glutamicum BA000036 2993 - 8 6 - - - - - - - - - - - - - - 14
Corynebacterium jeikeium CR931997 2137 - 6 3 - - - - - - - - - - - - - - 9
Corynebacterium urealyticum AM942444 2024 - 5 3 - - - - - - - - - - - - - 1 9
Frankia alni CT573213 6711 8 13 22 - - - - 1 - - - - - 2 - - 3 49
Frankia sp. CcI3 CP000249 4499 7 14 8 - - - - 1 - - - - - 1 - - 1 32
Frankia sp. EAN1pec CP000820 7191 6 15 34 - - - - 1 - - - - - 1 - - 10 67
Kineococcus radiotolerans CP000750 4681 5 9 18 - - - - 1 - - - - - - 2 - 6 41
Kocuria rhizophila AP009152 2357 1 3 8 - - - - 1 - - - - - - - - 1 14
Leifsonia xyli AE016822 2030 1 7 11 - - - - 1 - - - - - - - - 1 21
Mycobacterium abscessus CU458896 4920 1 11 6 - - - - 1 - - - - - - - - - 19
Mycobacterium avium AE016958 4350 2 10 4 - - - - 1 - - - - - - - - 1 18
Mycobacterium bovis BX248333 3920 - 9 2 - - - - 1 - - - - - - - - - 12
Mycobacterium gilvum CP000656 5579 4 13 8 - 1 - - 1 - 1 - - - 1 - - 1 30
Mycobacterium leprae AL450380 1605 - 4 - - - - - 1 - - - - - - - - - 5
Mycobacterium marinum CP000854 5423 2 9 5 - - - - 1 - - - - - 1 - - 1 19
Mycobacterium smegmatis CP000480 6716 3 12 16 - 1 - - 1 - - - - - 1 - - 1 35
Mycobacterium sp. JLS CP000580 5739 2 14 11 - 1 - 1 1 - - - - - 1 - - 1 32
Mycobacterium sp. KMS CP000518 5975 3 14 9 - 1 - - 1 - - - - - 1 - - 3 32
Mycobacterium sp. MCS CP000384 5615 2 13 10 - 1 - - 1 - - - - - 1 - - 1 29
Mycobacterium tuberculosis H37Rv AL123456 3927 1 9 2 - - - - 1 - - - - - - - - - 13
Mycobacterium ulcerans CP000325 4160 2 8 3 - - - - 1 - - - - - 1 - - 1 16
Mycobacterium vanbaalenii CP000511 5979 3 15 13 - 1 - - 1 - - - - - 1 - - 3 37
Nocardia farcinica AP006618 5936 2 10 17 - 1 - - 1 - - - - - 1 - - 1 33
Nocardioides sp. JS614 CP000509 4909 3 22 16 - 1 - - 1 - - - - - - 1 - 2 46
Propionibacterium acnes AE017283 2297 1 5 6 - - - - 1 - - - - - - - - - 13
Renibacterium salmoninarum CP000910 3507 2 7 4 - 1 - - 1 - - - - - - - - 2 17
Rhodococcus jostii CP000431 9145 2 11 25 - 1 - - 1 - - - - - - - - 1 41
Rubrobacter xylanophilus CP000386 3140 2 9 8 - - - - - - - - - - 1 - - - 20
Saccharopolyspora erythraea AM420293 7197 1 17 27 - 2 - - 1 - - - - - - - - 1 49
Salinispora arenicola CP000850 4917 1 18 10 - 1 - - 1 1 - - - - - - - 1 33
Salinispora tropica CP000667 4536 1 16 11 - 1 - - 1 1 - - - - - - - 1 32
Streptomyces avermitilis BA000030 7671 3 26 35 - 1 - - 1 - - - - - 3 - - 1 70
Streptomyces coelicolor AL645882 8154 3 21 53 - 1 - - 1 - - - - - 2 - - 3 84
Streptomyces griseus AP009493 7136 4 24 39 - 1 - - 1 - - - - - 3 - - 6 78
Thermobifida fusca CP000088 3110 2 8 13 - 1 - - 1 - - - - - 1 - - 2 28
Tropheryma whipplei BX072543 783 - 1 1 - - - - - - - - - - - - - - 2
Aquificae GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Aquifex aeolicus AE000657 1560 1 1 - 3 - - - - - - - - - - - - - 5
Hydrogenobaculum sp. Y04AAS1 CP001130 1629 1 4 - 1 - - - - - - - - - - 1 1 - 8
Sulfurihydrogenibium sp. YO3AOP1 CP001080 1721 1 6 - 4 1 - - - - - - - - - - 1 - 13
Bacteroidetes GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Bacteroides fragilis AP006841 4625 2 8 2 8 6 - 1 - - - - - 1 1 - - - 29
Bacteroides thetaiotaomicron AE015928 4816 2 6 - 8 10 - - - - - - - 1 - - - - 27
Bacteroides vulgatus CP000139 4065 2 5 - 9 4 - - - - - - - 1 - - - 2 23
Candidatus Amoebophilus asiaticus CP001102 1283 - - - - - - - - - - - - - - - - - 0
Candidatus Azobacteroides pseudotrichonymphae AP010656 852 - - - - - - - - - - - - - - - - - 0
Candidatus Sulcia muelleri CP000770 227 - - - - - - - - - - - - - - - - - 0
Cytophaga hutchinsonii CP000383 3785 14 3 5 4 3 - - - - - - - 1 - - - 5 35
Flavobacterium johnsoniae CP000685 5017 18 11 10 5 20 - - - - - - - 1 - - - 5 70
Flavobacterium psychrophilum AM398681 2412 - 4 2 2 5 - - - - - - - - - - - 4 17
Gramella forsetii CU207366 3584 9 4 3 4 9 - - - - - - - - - - - 5 34
Parabacteroides distasonis CP000140 3850 2 7 1 7 8 - - - - - - - 1 1 - - 3 30
Porphyromonas gingivalis AE015924 1909 - 2 1 2 - - - - - - - - - - - - 1 6
Salinibacter ruber CP000159 2833 4 7 3 4 6 - - - - - - - - - 1 - 1 26
Chlamydiae GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Chlamydia muridarum AE002160 904 - 1 - 1 - - - - - - - - - - - - - 2
Chlamydia trachomatis AE001273 895 - 1 - 1 - - - - - - - - - - - - - 2
Chlamydophila abortus CR848038 932 - 1 - 1 - - - - - - - - - - - - - 2
Chlamydophila caviae AE015925 1005 - 1 - 1 - - - - - - - - - - - - - 2
Chlamydophila felis AP006861 1013 - 1 - 1 - - - - - - - - - - - - - 2
Chlamydophila pneumoniae AE001363 1054 - 1 - 1 - - - - - - - - - - - - - 2
Protochlamydia amoebophila BX908798 2031 - 1 - 1 - - - - - - - - - - - - - 2
Chlorobi/ green sulfur bacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Chlorobaculum parvum CP001099 2043 3 4 - - - - - - - - - - - - - - - 7
Chlorobium chlorochromatii CP000108 2002 - 3 - - - - - - - - - - - - - - - 3
Chlorobium limicola CP001097 2434 1 2 - 3 - - - - - - - - - 1 - - 1 8
Chlorobium phaeobacteroides CP000492 2650 1 2 1 - - - - - - - - - - 1 - - - 5
Chlorobium phaeovibrioides CP000607 1753 1 3 - 2 - - - - - - - - - - - - - 6
Chlorobium tepidum AE006470 2252 2 2 - - - - - - - - - - - - - - - 4
Chloroherpeton thalassium CP001100 2710 12 2 - 2 - - - - - - - 1 1 - - - 9 27
Pelodictyon luteolum CP000096 2083 3 7 1 3 - - - - - - - - - 1 - - - 15
Pelodictyon phaeoclathratiforme CP001110 2707 2 2 - 2 - - - - - - - - - 1 - - - 7
Prosthecochloris aestuarii CP001108 2327 2 2 - 2 - - - - - - - - - - - - - 6
Chloroflexi GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Chloroflexus aurantiacus CP000909 3853 16 15 12 - - - - 3 4 1 - 2 1 - 2 - 8 64
Dehalococcoides ethenogenes CP000027 1580 2 14 8 - - - - - - - - 1 - - - - 1 26
Dehalococcoides sp. BAV1 CP000688 1371 2 8 7 - - - - - - - - 1 - - - - 1 19
Dehalococcoides sp. CBDB1 AJ965256 1458 2 18 7 - - - - - - - - 2 - - - - 1 30
Herpetosiphon aurantiacus CP000875 5278 34 20 17 2 - - 1 2 3 2 - 2 2 - 1 - 9 95
Roseiflexus castenholzii CP000804 4330 18 19 10 - - - - 2 2 - - 1 3 1 2 - 10 68
Roseiflexus sp. RS-1 CP000686 4517 18 19 12 - - - - 2 - - - 1 2 1 2 - 9 66
Cyanobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Acaryochloris marina CP000828 8383 28 21 11 - - - 1 - 9 7 - - 7 1 - 1 19 105
Anabaena variabilis CP000117 5657 21 14 16 - - - 1 - 4 1 2 1 14 3 - - 13 90
Cyanothece sp. ATCC 51142 CP000806 5304 13 13 7 - - - - - 2 2 - 1 4 1 - - 12 55
Cyanothece sp. PCC 7424 CP001291 5710 21 18 10 - - - 2 - 5 3 - 1 7 2 1 - 12 82
Cyanothece sp. PCC 8801 CP001287 4367 11 13 6 - - - - - 5 4 - 1 3 2 2 - 10 57
Gloeobacter violaceus BA000045 4430 7 10 15 - - - - - - - - - 1 - - - 6 39
Microcystis aeruginosa AP009552 6312 4 8 5 - - - - - 1 - - - 3 1 - - 3 25
Nostoc punctiforme CP001037 6690 31 19 16 - - - 5 - 3 3 1 1 15 3 1 - 12 110
Nostoc sp. PCC 7120 BA000019 6055 24 15 17 - - - 2 - 5 - 1 1 15 4 - - 12 96
Prochlorococcus marinus AE017126 1882 - 4 2 - - - - - - - - - - - - - - 6
Synechococcus elongatus AP008231 2525 5 8 1 - - - - - 2 - - - - - - - 3 19
Synechococcus sp. CC9311 CP000435 2892 2 10 4 - - - - - - - - - - - - - - 16
Synechococcus sp. CC9605 CP000110 2645 2 6 1 - - - - - - - - - - - - - - 9
Synechococcus sp. CC9902 CP000097 2307 1 5 1 - - - - - - - - - - - - - - 7
Synechococcus sp. JA-3-3Ab CP000239 2760 7 8 6 - - - - - 2 - - 1 1 1 - - 5 31
Synechococcus sp. PCC 7002 CP000951 3186 6 10 5 - - - 1 - 1 3 - - 4 2 - - 7 39
Synechococcus sp. RCC307 CT978603 2525 1 8 1 - - - - - - - - - - - - - - 10
Synechococcus sp. WH 7803 CT971583 2533 2 8 2 - - - - - - - - - - - - - 1 13
Synechococcus sp. WH 8102 BX548020 2517 - 6 3 - - - - - - - - - - - - - - 9
Synechocystis sp. PCC 6803 BA000022 3567 7 10 7 - - - 1 - 4 - 1 2 5 1 - - 9 47
Thermosynechococcus elongatus BA000039 2475 4 7 4 - - - - - 2 1 1 - - 1 - - 6 26
Trichodesmium erythraeum CP000393 5124 8 6 3 - - - - - 1 1 - - 3 2 - - 7 31
Deinococcus-Thermus GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Deinococcus geothermalis CP000359 2857 9 11 7 - - - - - - - - - 1 - - - 3 31
Deinococcus radiodurans AE000513 3184 8 8 6 - - - - - - - - - 2 - - - 2 26
Thermus thermophilus AE017221 2210 3 7 3 - - - - - - - - 1 - - - - - 14
Firmicutes GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Alkaliphilus metalliredigens CP000724 4625 3 27 8 2 5 - 5 2 - - - - - 1 1 1 7 62
Alkaliphilus oremlandii CP000853 2836 1 19 1 4 4 - 3 - - - - - - 1 1 1 2 37
Anoxybacillus flavithermus CP000922 2832 4 5 7 - - - 1 - 2 - - - - 1 1 1 1 23
Bacillus amyloliquefaciens CP000560 3693 3 16 12 - 1 - - - - - - - - - 1 1 2 36
Bacillus anthracis AE016879 5311 2 30 8 - 3 - - - - - - - - 1 - - 3 47
Bacillus cereus AE016877 5255 2 28 9 - 2 - - - - - - - - 1 - 1 3 46
Bacillus clausii AP006627 4096 2 15 13 1 1 - 6 - - - - - - - - 1 2 41
Bacillus halodurans BA000004 4066 4 16 10 2 - - 7 - 2 - - - - - 1 2 4 48
Bacillus licheniformis AE017333 4196 4 11 14 - 1 - 2 - - - - - - - 1 1 3 37
Bacillus pumilus CP000813 3681 2 11 8 - 2 - 1 - - - - - - - 1 1 3 29
Bacillus subtilis AL009126 4105 3 13 12 - 2 - 1 - - - - - - - 1 1 2 35
Bacillus thuringiensis AE017355 5117 2 30 10 - 3 - 1 - - - - - - 1 - 1 3 51
Bacillus weihenstephanensis CP000903 5653 2 38 9 - 2 - - - - - - - - 1 - 1 2 55
Caldicellulosiruptor saccharolyticus CP000679 2679 4 6 2 - - - 10 - - - - 1 1 - 3 - 4 31
Candidatus Desulforudis audaxviator CP000860 2157 2 2 1 - 2 - - 2 4 - - 1 - - 1 - 1 16
Carboxydothermus hydrogenoformans Z-2901 CP000141 2620 5 5 2 1 2 - - 1 1 - - - - - 2 - 1 20
Clostridium acetobutylicum ATCC 824 AE001437 3848 4 21 7 - 3 - - 1 - - - - - - 1 1 5 43
Clostridium beijerinckii NCIMB 8052 CP000721 5020 9 35 4 1 5 - 11 1 - - - 2 3 - 3 1 5 80
Clostridium botulinum AM412317 3590 3 26 2 - 4 - - - 1 - - - - - 1 1 5 43
Clostridium difficile AM180355 3753 1 39 1 1 7 - 1 1 1 - - - - - - - 1 53
Clostridium kluyveri CP000673 3913 2 30 - - 2 - 1 - 1 - - - - - 2 - 3 41
Clostridium novyi CP000382 2325 1 9 1 - 2 - 3 - - - - - - - 1 - 2 19
Clostridium perfringens BA000016 2723 1 13 1 - 2 - 3 1 - - - - - - - - - 21
Clostridium phytofermentans CP000885 3902 3 26 5 - 4 - 21 - - - - 1 - - 1 1 1 63
Clostridium tetani AE015927 2432 2 20 1 1 2 - 2 1 - - - - - - - - 1 30
Clostridium thermocellum CP000568 3189 7 13 1 - - - 3 - 1 - - 2 2 1 4 - 2 36
Coprothermobacter proteolyticus CP001145 1482 2 2 - 1 - - - - - - - 1 - - 1 - - 7
Desulfitobacterium hafniens AP008230 5060 8 35 10 4 4 - 1 1 1 - - - - - 1 - 7 72
Desulfotomaculum reducens CP000612 3276 6 8 2 5 1 - 1 4 1 - - - - - 1 - 2 31
Enterococcus faecalis AE016830 3265 - 11 2 - 3 - 1 1 - - - - - - - - - 18
Exiguobacterium sibiricum CP001022 3015 3 14 2 - 1 - 1 - - - - - - 1 - 1 2 25
Finegoldia magna AP008971 1813 - 11 1 - 1 - - - - - - - - - - - - 13
Geobacillus kaustophilus BA000043 3540 3 10 5 1 1 - 5 - 1 - - - - - 1 - 2 29
Geobacillus thermodenitrificans CP000557 3445 4 12 5 - 1 - 4 - 1 - - - - - 1 - 1 29
Heliobacterium modesticaldum CP000930 3000 6 7 1 2 2 - - 2 1 1 - - - 1 2 - 3 28
Lactobacillus acidophilus CP000033 1864 - 6 - - 2 - - - - - - - - - - - - 8
Lactobacillus brevis CP000416 2218 - 7 1 - 1 - - - - - - - - - - - 1 10
Lactobacillus casei CP000423 2771 - 12 3 - 2 - - - - - - - - - - - - 17
Lactobacillus delbrueckii CR954253 1562 - 5 - - 1 - - - - - - - - - - - - 6
Lactobacillus fermentum AP008937 1843 - 4 1 - - - - - - - - - - - - - 1 6
Lactobacillus gasseri CP000413 1755 - 5 - - - - - - - - - - - - - - - 5
Lactobacillus helveticus CP000517 1610 - 4 - - - - - - - - - - - - - - - 4
Lactobacillus johnsonii AE017198 1821 - 6 1 - 2 - - - - - - - - - - - - 9
Lactobacillus plantarum AL935263 3059 - 6 2 - 6 - 1 - - - - - - - - - - 15
Lactobacillus reuteri CP000705 3720 - 6 1 - 1 - - - - - - - - - - - 1 9
Lactobacillus sakei CR936503 1879 - 6 2 - 2 - - - - - - - - - - - - 10
Lactobacillus salivarius CP000233 2017 1 5 2 - 1 - - - - - - - - - - - - 9
Lactococcus lactis AE005176 2321 - 6 1 - - - - - - - - - - - - - - 7
Leuconostoc citreum DQ489736 1820 - 6 - - 1 - - - - - - - - - - - - 7
Leuconostoc mesenteroides CP000414 2005 - 7 1 - 2 - - - - - - - - - - - - 10
Listeria innocua AL592022 2968 1 10 2 - 2 - 1 1 - - - - - - - 1 - 18
Listeria monocytogenes AL591824 2846 1 9 1 - 1 - 1 1 - - - - - - - 1 - 15
Listeria welshimeri AM263198 2774 1 10 2 - 3 - 1 1 - - - - - - - 1 - 19
Lysinibacillus sphaericus CP000817 4771 3 29 12 - 2 - 2 1 - - - - - 1 1 1 2 54
Moorella thermoacetica CP000232 2465 2 4 2 - 3 - 1 1 2 - - - - - 1 - 1 17
Natranaerobius thermophilus CP001034 2906 5 4 5 - 3 - 1 1 1 - - - - - 1 - 3 24
Oceanobacillus iheyensis BA000028 3500 2 8 7 - 1 - 1 - - - - - - - 1 - 1 21
Oenococcus oeni CP000411 1691 - 5 - - 1 - - - - - - - - - - - - 6
Pediococcus pentosaceus CP000422 1755 - 5 1 - 2 - - - - - - - - - - - 1 9
Pelotomaculum thermopropionicum AP009389 2920 3 9 3 4 1 - - 2 - - - - - - 1 - 2 25
Staphylococcus aureus BA000018 2624 1 9 4 - 2 - 1 - - - - - - - - - - 17
Staphylococcus epidermidis AE015929 2419 - 9 4 - 2 - 1 - - - - - - - - - - 16
Staphylococcus haemolyticus AP006716 2676 - 9 4 - 2 - - - - - - - - - - - - 15
Staphylococcus saprophyticus AP008934 2514 - 6 3 - 2 - - - - - - - - - - - - 11
Streptococcus agalactiae AE009948 2124 - 13 2 - 3 - 1 - - - - - - - - - 1 20
Streptococcus equi CP001129 1893 - 6 3 - 3 - 3 - - - - - - - - - - 15
Streptococcus gordonii CP000725 2051 - 9 2 - 2 - 3 - - - - - - - - - - 16
Streptococcus mutans AE014133 1960 - 9 3 - 2 - - - - - - - - - - - - 14
Streptococcus pneumoniae AE005672 2094 - 8 2 - 2 - 2 - - - - - - - - - - 14
Streptococcus pyogenes AE004092 1697 - 5 3 - 1 - 3 - - - - - - - - - - 12
Streptococcus sanguinis CP000387 2270 - 9 3 - 1 - 1 1 - - - - - - - - - 15
Streptococcus suis CP000407 2186 1 5 2 - 1 - 1 - - - - - - - - - 2 12
Streptococcus thermophilus CP000024 1915 1 5 2 - 2 - - - - - - - - - - - - 10
Symbiobacterium thermophilum AP006840 3337 5 10 11 2 1 - - 1 1 - - - - - 1 - 2 34
Syntrophomonas wolfei CP000448 2504 9 3 1 - 2 - 1 - 1 - - 3 - - 3 - 1 24
Thermoanaerobacter pseudethanolicus CP000924 2243 2 5 1 - 1 - - 1 1 - - - - - - - 1 12
Thermoanaerobacter sp. X514 CP000923 2349 2 6 1 - 1 - 3 1 1 - - - - - - - 1 16
Thermoanaerobacter tengcongensis AE008691 2588 3 7 1 - 2 - 2 - 3 - - - - - 1 - 2 21
Alpha-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Acidiphilium cryptum CP000697 3559 2 13 1 4 - - - - - - - - - - 1 - - 21
Agrobacterium tumefaciens AE008688 5402 14 22 8 5 - 1 - 1 2 - - - 1 - 1 - 3 58
Anaplasma marginale CP000030 949 - 1 - 1 - - - - 1 - - - - - - - - 3
Anaplasma phagocytophilum CP000235 1264 - 1 - 1 - - - - 1 - - - - - - - - 3
Azorhizobium caulinodans AP009384 4717 16 15 7 6 1 3 - 1 2 - 1 - 1 - 1 - 5 59
Bartonella bacilliformis CP000524 1283 2 7 - 2 - - - - - - - - - - - - 1 12
Bartonella henselae BX897699 1488 2 6 - 2 - - - - - - - - - - - - 1 11
Bartonella quintana BX897700 1142 2 6 - 2 - - - - - - - - - - - - 1 11
Bartonella tribocorum AM260525 2092 2 6 - 2 - - - - - - - - - - - - 1 11
Beijerinckia indica CP001016 3784 9 14 2 6 - 1 - 1 1 - - - 1 - 1 - 3 39
Bradyrhizobium japonicum BA000040 8317 30 22 23 5 - 2 - 1 1 - 1 2 2 - 2 - 5 96
Bradyrhizobium sp. BTAi1 CP000494 7622 29 18 13 5 - 2 - 1 - - - 1 1 1 4 - 3 78
Bradyrhizobium sp. ORS278 CU234118 6717 26 16 8 6 - 2 - 1 - - - 2 1 1 3 - 5 71
Brucella abortus AE017223 3085 3 10 3 3 - 1 - - 1 - - - - - - - 1 22
Brucella canis CP000872 3251 3 9 3 2 - 1 - - - - - - - - - - 1 19
Brucella melitensis AE008917 3198 3 10 3 3 - 1 - - 1 - - - - - - - 1 22
Brucella ovis CP000709 2890 3 10 3 2 - 1 - - 1 - - - - - - - 1 21
Brucella suis AE014291 3271 3 10 3 3 - 1 - - 1 - - - - - - - 1 22
Caulobacter crescentus AE005673 3737 14 12 2 4 - 2 - 1 2 - - - - - 2 - 6 45
Caulobacter sp. K31 CP000927 5438 24 14 5 3 - 1 - 1 - - - - - - 3 - 7 58
Dinoroseobacter shibae CP000830 4187 2 11 6 5 - 1 - 1 1 - - - - 1 - - 2 30
Ehrlichia canis CP000107 925 - 1 - 1 - - - - 1 - - - - - - - - 3
Ehrlichia chaffeensis CP000236 1105 - 1 - 1 - - - - 1 - - - - - - - - 3
Ehrlichia ruminantium CR767821 888 - 1 - 1 - - - - 1 - - - - - - - - 3
Erythrobacter litoralis CP000157 3011 6 6 2 4 2 - - - - - - - - - 1 - 2 23
Gluconacetobacter diazotrophicus AM889285 3852 6 12 2 3 - - - - - 1 - - - - 2 - 3 29
Gluconobacter oxydans CP000009 2664 6 9 1 1 - - - - - - - - 2 - 1 - 1 21
Granulibacter bethesdensis CP000394 2437 2 10 3 2 - 1 - 1 - - - - - - - - 1 20
Hyphomonas neptunium CP000158 3505 5 10 2 3 - 1 - 2 2 - - - - - - - 2 27
Jannaschia sp. CCS1 CP000264 4283 5 8 1 4 - 1 - 1 1 - - - - 1 - - 4 26
Magnetospirillum magneticum AP007255 4559 30 15 11 6 - - - - 4 2 2 9 2 4 3 - 12 100
Maricaulis maris CP000449 3063 18 7 3 3 - 1 - - 3 - - - - 1 1 - 3 40
Mesorhizobium loti BA000012 7275 12 23 10 5 - 2 - 1 2 - - - 2 - 1 - 1 59
Mesorhizobium sp. BNC1 CP000390 4543 10 9 6 3 - 1 - 1 1 - - - - - 1 - 3 35
Methylobacterium chloromethanicum CP001298 5516 27 16 11 7 - 1 - 1 2 - - 3 1 - 2 - 6 77
Methylobacterium extorquens CP000908 4829 29 15 12 5 - 1 - 1 2 - - 2 1 - 2 - 6 76
Methylobacterium populi CP001029 5365 30 19 12 6 - 1 - 1 2 - - 1 1 - 2 - 3 78
Methylobacterium radiotolerans CP001001 6431 32 21 15 6 - 1 - 1 2 - - 2 3 - 3 - 9 95
Methylobacterium sp. 4-46 CP000943 6692 37 16 11 6 - 1 - 1 2 - - 2 1 - 3 - 7 87
Methylocella silvestris CP001280 3818 15 11 9 4 - 1 - 1 1 - - - - - 1 - 2 45
Neorickettsia sennetsu CP000237 932 - 1 - - - - - - 1 - - - - - - - - 2
Nitrobacter hamburgensis CP000319 4326 11 13 4 4 - 1 - - 1 - 2 1 1 - 1 - 2 41
Nitrobacter winogradskyi CP000115 3122 8 8 3 3 - 1 - - 1 - 1 - 1 - 1 - 2 29
Novosphingobium aromaticivorans CP000248 3324 7 12 5 5 2 - - 1 - - - - - - - - 1 33
Ochrobactrum anthropi CP000758 4799 5 12 6 5 - 1 - - 1 - - - 1 - - - 1 32
Oligotropha carboxidovorans CP001196 3722 8 11 5 3 - 1 - 1 1 - 1 1 2 - 1 - 2 37
Orientia tsutsugamushi Boryong AM494475 1182 - 1 - 1 - - - - 1 - - - - - - - - 3
Orientia tsutsugamushi str. Ikeda AP008981 1967 - 1 - 1 - - - - 1 - - - - - - - - 3
Paracoccus denitrificans CP000489 5077 4 14 7 8 - 1 - 1 1 - - - 1 1 - - 2 40
Parvibaculum lavamentivorans CP000774 3636 12 9 8 3 - 1 - - 1 - - - - - - - 5 39
Pelagibacter ubique CP000084 1354 - 3 - 1 - 1 - - - - - - - - - - - 5
Phenylobacterium zucineum CP000747 3854 18 10 4 3 - 1 - 1 1 - - - - - 3 - 7 48
Rhizobium etli CP000133 5963 23 17 12 5 - 1 - 1 2 - - - 2 - 2 - 3 68
Rhizobium leguminosarum AM236086 7150 17 23 9 6 - 1 - 3 1 - - 1 3 - 2 - 4 70
Rhodobacter sphaeroides CP000143 4126 15 14 8 6 - 1 - - 1 - - - 1 1 2 - 3 52
Rhodopseudomonas palustris BX571963 4813 18 11 8 4 - 1 - 1 1 - 1 2 2 - 2 - 3 54
Rhodospirillum centenum CP000613 4002 17 13 7 5 - 1 - - 1 - - 1 1 - 3 - 5 54
Rhodospirillum rubrum CP000230 3841 15 5 3 9 6 - 1 - 4 1 1 1 2 - 3 - 6 57
Rickettsia akari CP000847 1259 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia bellii CP000087 1429 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia canadensis CP000409 1093 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia conorii AE006914 1374 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia felis CP000053 1532 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia massiliae CP000683 980 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia prowazekii AJ235269 835 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia rickettsii CP000766 1384 - 2 - 1 - - - - 1 - - - - - - - - 4
Rickettsia typhi AE017197 838 - 2 - 1 - - - - 1 - - - - - - - - 4
Roseobacter denitrificans CP000362 4129 5 9 6 3 - 1 - 1 1 - - - - 1 1 - 3 31
Silicibacter pomeroyi CP000031 4252 2 9 5 5 - 1 - - 1 - - - - 1 - - 2 26
Silicibacter sp. TM1040 CP000377 3864 11 10 3 5 - 1 - - 1 - - - 1 1 - - 2 35
Sinorhizobium medicae CP000738 6213 19 15 12 6 - 1 - 1 - - - - 1 - 1 - 7 63
Sinorhizobium meliloti AL591688 6205 15 16 12 5 1 1 - 1 1 - - - - - 2 - 3 57
Sphingomonas wittichii CP000699 5345 16 15 6 4 2 - - 1 - - - - 1 - 2 - 4 51
Sphingopyxis alaskensis CP000356 3195 6 5 1 6 2 1 - 1 - - - - - - 1 - 2 25
Wolbachia endosymbiont of Brugia malayi AE017321 805 - 1 - - - - - - 1 - - - - - - - - 2
Wolbachia endosymbiont of Culex quinquefasciatus AM999887 1275 - 1 - - - - - - 1 - - - - - - - - 2
Wolbachia endosymbiont of Drosophila AE017196 1195 - 1 - - - - - - 1 - - - - - - - - 2
Xanthobacter autotrophicus CP000781 5035 10 21 5 9 - 2 - 2 - - - - 1 - - - 2 52
Zymomonas mobilis AE008692 1998 2 6 - 1 1 - - - - - - - - - 2 - 1 13
Beta-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Acidovorax avenae CP000512 4709 9 18 10 6 2 2 - 1 - - - 1 2 - 2 - 3 56
Acidovorax sp. JS42 CP000539 4155 6 13 8 2 2 2 - 1 1 - - 1 2 - 1 - - 39
Aromatoleum aromaticum CR555306 4590 6 11 13 10 1 - - - - 4 1 - - - - - 1 47
Azoarcus sp. BH72 AM406670 3989 13 16 9 13 1 - - - 4 5 - 3 - - 2 2 1 69
Bordetella avium AM167904 3381 2 13 6 2 - 2 - - 1 - 1 - - - 2 - - 29
Bordetella bronchiseptica BX470250 4994 2 18 7 2 - 2 - - - - 1 - - - 1 - - 33
Bordetella parapertussis BX470249 4185 2 16 5 2 - 2 - - - - 1 - - - 1 - - 29
Bordetella pertussis BX470248 3436 1 13 4 1 - 2 - - - - - - - - 1 - - 22
Bordetella petrii AM902716 5027 3 17 6 2 1 2 - - - - - - - - 1 - 2 34
Burkholderia ambifaria CP000440 6617 6 26 9 5 - 2 2 1 1 1 - 1 1 - 3 - 4 62
Burkholderia cenocepacia CP000458 6477 7 27 8 6 - 2 2 1 1 - - 1 1 - 3 - 8 67
Burkholderia mallei CP000011 4764 6 14 5 5 - 2 - 1 - - - 2 1 - 1 - 1 38
Burkholderia multivorans CP000869 6259 6 26 13 5 - 2 - 1 1 - - - 1 - 3 - 5 63
Burkholderia phymatum CP001043 7496 19 27 25 6 - 2 - 1 1 - - - 2 - 2 1 5 91
Burkholderia phytofirmans CP001052 7241 20 27 21 5 - 2 1 2 1 - - 1 2 - 2 1 6 91
Burkholderia pseudomallei BX571965 5728 3 15 11 1 - 2 - - - - - 1 1 - 1 - 3 38
Burkholderia sp. 383 CP000150 7717 6 34 12 5 1 2 2 1 1 - - 1 1 - 3 - 7 76
Burkholderia thailandensis CP000086 5634 7 20 14 2 1 2 - 1 - - - 2 1 - 4 - 5 59
Burkholderia vietnamiensis CP000616 7617 9 24 16 7 - 2 2 1 1 - - 1 2 - 2 - 5 72
Burkholderia xenovorans CP000271 8702 7 26 18 4 - 2 - 1 - - - - 2 - 1 1 5 67
Chromobacterium violaceum AE016825 4407 6 10 7 5 4 1 - 1 2 3 4 5 - 2 3 3 9 65
Cupriavidus taiwanensi CU633749 5897 5 21 18 6 2 2 - 1 1 - 1 - 1 - 2 1 4 65
Dechloromonas aromatica CP000089 4171 16 17 12 14 2 1 - 1 7 5 - 7 2 1 2 2 9 98
Delftia acidovorans CP000884 6040 8 32 16 5 2 2 - - 3 1 1 1 2 - 1 1 2 77
Herminiimonas arsenicoxydans CU207211 3325 6 15 7 4 1 2 - 1 1 1 - - - - 1 1 3 43
Janthinobacterium sp CP000269 3697 8 21 12 3 1 2 - 1 2 - - - - - 2 - 4 56
Leptothrix cholodnii CP001013 4363 12 17 17 7 1 2 - - 1 4 - 3 3 - 4 - 6 77
Methylibium petroleiphilum CP000555 4449 4 10 19 5 1 2 - 2 - 1 - 1 1 - 1 - 3 50
Methylobacillus flagellatus CP000284 2753 9 8 10 7 1 1 - - - 1 - 1 1 - 1 - - 40
Neisseria gonorrhoeae AE004969 2002 - 1 - 1 - - - - - - - - - - - - - 2
Neisseria meningitidis AE002098 2079 - 1 1 1 - 1 - - - - - - - - - - 1 5
Nitrosomonas europaea AL954747 2461 3 7 - 4 - 1 - - - 2 1 - - - 1 - - 19
Nitrosomonas eutropha CP000450 2550 3 4 2 4 - 1 - - - 1 1 - - - 1 - 1 18
Nitrosospira multiformis CP000103 2805 10 2 3 3 - 1 - - 2 3 1 - - - 1 - 2 28
Polaromonas naphthalenivorans CP000529 4929 8 17 15 4 1 1 - 1 - - - - 4 - - - 3 54
Polaromonas sp. JS666 CP000316 5453 17 13 14 3 1 1 - 2 - - 1 - 2 1 1 - 6 62
Polynucleobacter necessarius CP000655 2077 - 2 4 1 - 1 - - - - - - - - - - - 8
Ralstonia eutropha CP000090 6446 7 22 17 5 1 2 - 1 1 - - 1 2 - 2 1 7 69
Ralstonia metallidurans CP000352 6319 8 34 26 4 1 2 - 1 1 - 1 - 1 - 2 1 5 87
Ralstonia pickettii CP001068 4952 7 23 16 4 - 2 - 1 - - 1 - 1 - 1 1 3 60
Ralstonia solanacearum AL646052 5116 7 27 14 5 1 2 - 1 - - 1 - 1 - 1 1 3 64
Rhodoferax ferrireducens CP000267 4418 13 15 15 11 2 1 - 1 1 5 - 1 2 - 2 1 8 78
Thiobacillus denitrificans CP000116 2827 5 7 8 7 1 1 - 1 2 3 - 1 - - 1 1 - 38
Verminephrobacter eiseniae CP000542 4947 5 5 6 2 2 1 - - - - - - 1 - 1 1 - 24
Delta-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Anaeromyxobacter dehalogenans CP000251 4346 32 5 3 28 - 1 - - 4 - - 2 3 - 6 - 12 96
Anaeromyxobacter sp. Fw109-5 CP000769 4466 31 4 4 24 2 1 - - 4 - - 2 2 - 6 - 15 95
Anaeromyxobacter sp. K CP001131 4457 28 5 3 29 1 1 - - 4 - - 2 2 - 6 - 15 96
Bdellovibrio bacteriovorus BX842601 3587 13 9 2 6 - 1 - - 1 - - - 1 - 2 - 6 41
Desulfatibacillum alkenivorans CP001322 5252 32 7 2 15 - 1 - - 6 1 - 7 4 2 4 - 22 103
Desulfococcus oleovorans CP000859 3265 26 3 1 10 - - - - - - - 3 1 1 2 - 14 61
Desulfotalea psychrophila CR522870 3234 5 3 1 11 - - - - 2 - - 3 - - 2 - 4 31
Desulfovibrio desulfuricans CP000112 3865 24 1 2 15 1 - - - 2 1 - 4 2 1 2 4 6 65
Desulfovibrio vulgaris AE017285 3531 21 2 3 22 2 - - - 1 1 - 5 4 1 2 3 9 76
Geobacter bemidjiensis CP001124 4018 26 11 2 26 - 1 - - 5 2 - 4 6 3 6 1 19 112
Geobacter lovleyi CP001089 3685 30 8 4 24 1 - - - 8 2 - 4 7 1 3 2 10 104
Geobacter metallireducens CP000148 3634 21 7 1 17 1 - 1 1 5 - - 3 8 1 5 1 8 81
Geobacter sulfurreducens AE017180 3446 23 7 4 26 - - - 1 8 2 - 4 2 1 3 1 9 91
Geobacter uraniireducens CP000698 4357 26 7 6 32 2 - 1 1 6 1 - 3 3 2 6 1 15 112
Lawsonia intracellularis AM180252 1344 2 - - 4 - - - - - - - - - - 1 2 - 9
Myxococcus xanthus CP000113 7331 42 11 3 29 2 4 - - 8 - - 2 6 - 5 1 23 136
Pelobacter carbinolicus CP000142 3353 10 8 3 11 - - - 1 6 4 - - 1 - 1 1 5 51
Pelobacter propionicus CP000482 3576 15 6 4 13 - - - 1 3 5 - 3 3 - 2 2 9 66
Sorangium cellulosum AM746676 9384 39 11 3 22 - 2 - - 1 - - 1 4 - 2 - 34 119
Syntrophobacter fumaroxidans CP000478 4064 23 6 4 18 - - - - 1 2 - 3 1 - 2 - 6 66
Syntrophus aciditrophicus CP000252 3168 10 1 5 10 - - - - - - - 3 - 1 2 - 1 33
Epsilon-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF GGDEF/
EAL		 PvrR RpfG HisK PP2C CheB CheV Other All
Arcobacter butzleri CP000361 2259 5 30 - - 1 - - - - 1 - 1 1 - 1 1 2 43
Campylobacter concisus CP000792