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. Request reprint.

The current version covers genomes of 330 bacterial and archaeal species sequenced by the end of 2006.
The original 200-genome version described in the above paper can be found here.

Organism GenBank
entry		 No.
genes		 Stand-
alone
REC		 DNA-binding RNA Enzymatic CheV Other
RRs		 All
RRs
Actinobacteria OmpR NarL NtrC LytR ActR AraC AmiR GGDEF/
EAL		 RpfG HisK PP2C CheB
Acidothermus cellulolyticus CP000481 2157 5 7 6 - 1 - - 1 2 - - 1 2 - 2 27
Arthrobacter aurescens CP000474 4587 - 9 6 - 1 - - 1 1 - - 1 - - 3 22
Arthrobacter sp. FB24 CP000454 4506 1 15 9 - 1 - - 1 - - - 1 - - 2 30
Bifidobacterium adolescentis AP009256 1631 - 3 8 - 2 - - 1 - - - - - - - 14
Bifidobacterium longum AE014295 1727 - 5 4 - - - - 1 - - - - - - - 10
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
Frankia alni ACN14a CT573213 6711 8 13 22 - - - - 1 - - - 2 - - 3 49
Frankia sp. CcI3 CP000249 4499 7 14 8 - - - - 1 - - - 1 - - 1 32
Leifsonia xyli AE016822 2030 1 7 11 - - - - 1 - - - - - - 1 21
Mycobacterium avium subsp. paratuberculosis AE016958 4350 2 10 4 - - - - 1 - - - - - - 1 18
Mycobacterium bovis BX248333 3920 - 9 2 - - - - 1 - - - - - - - 12
Mycobacterium leprae AL450380 1605 - 4 - - - - - 1 - - - - - - - 5
Mycobacterium smegmatis CP000480 6716 3 12 16 - 1 - - 1 - - - 1 - - 1 35
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
Rhodococcus sp. RHA1 CP000431 9145 2 11 25 - 1 - - 1 - - - - - - 1 41
Rubrobacter xylanophilus CP000386 3140 2 9 8 - - - - - - - - 1 - - - 20
Streptomyces avermitilis BA000030 7671 3 26 35 - 1 - - 1 - - - 3 - - 1 70
Streptomyces coelicolor AL645882 8154 3 21 53 - 1 - - 1 - - - 2 - - 3 84
Thermobifida fusca CP000088 3110 2 8 13 - 1 - - 1 - - - 1 - - 2 28
Tropheryma whipplei BX072543 783 - 1 1 - - - - - - - - - - - - 2
Cyanobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF/
EAL		 RpfG HisK PP2C CheB CheV Other All
Anabaena variabilis CP000117 5657 21 14 16 - - - 1 - 5 1 14 3 - - 13 88
Gloeobacter violaceus BA000045 4430 7 10 15 - - - - - - - 1 - - - 6 39
Nostoc sp. PCC 7120 BA000019 6055 24 15 17 - - - 2 - 6 1 15 4 - - 12 96
Prochlorococcus marinus CCMP1375 AE017126 1882 - 4 2 - - - - - - - - - - - - 6
Synechococcus elongatus PCC 6301 AP008231 2525 5 8 1 - - - - - 2 - - - - - 3 19
Synechococcus sp. CC9605 CP000110 2756 2 6 1 - - - - - - - - - - - - 9
Synechococcus sp. CC9902 CP000097 2358 1 5 1 - - - - - - - - - - - - 7
Synechococcus sp. JA-3-3Ab CP000239 2897 7 8 6 - - - - - 2 1 1 1 - - 5 31
Synechococcus sp. WH 8102 BX548020 2517 - 6 3 - - - - - - - - - - - - 9
Synechocystis sp. PCC 6803 BA000022 3567 7 10 7 - - - 1 - 5 2 5 1 - - 9 47
Thermosynechococcus elongatus BA000039 2475 4 7 4 - - - - - 2 - - 1 - - 6 24
Trichodesmium erythraeum CP000393 5124 8 6 3 - - - - - 2 - 3 2 - - 7 31
Alpha-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF/
EAL		 RpfG HisK PP2C CheB CheV Other All
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
Bartonella henselae BX897699 1488 2 6 - 2 - - - - - - - - - - 1 11
Bartonella quintana BX897700 1142 2 6 - 2 - - - - - - - - - - 1 11
Bradyrhizobium japonicum BA000040 8317 30 22 23 5 - 2 - 1 2 2 2 - 2 - 5 96
Brucella abortus AE017223 3085 3 10 3 3 - 1 - - 1 - - - - - 1 22
Brucella melitensis 16M AE008917 3198 3 10 3 3 - 1 - - 1 - - - - - 1 22
Brucella suis 1330 AE014291 3271 3 10 3 3 - 1 - - 1 - - - - - 1 22
Caulobacter crescentus AE005673 3737 14 12 2 4 - 2 - 1 2 - - - 2 - 6 45
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
Gluconobacter oxydans CP000009 2664 6 9 1 1 - - - - - - 2 - 1 - 1 21
Granulibacter bethesdensis CP000394 2437 2 10 3 2 - 1 - 1 - - - - - - 1 19
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 - - - - 8 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
Neorickettsia sennetsu CP000237 932 - 1 - - - - - - 1 - - - - - - 2
Nitrobacter hamburgensis CP000319 4326 11 13 4 4 - 1 - - 3 1 1 - 1 - 2 41
Nitrobacter winogradskyi CP000115 3122 8 8 3 3 - 1 - - 2 - 1 - 1 - 2 29
Novosphingobium aromaticivorans CP000248 3324 7 12 5 5 2 - - 1 - - - - - - 1 33
Paracoccus denitrificans CP000489 5077 4 14 7 8 - 1 - 1 1 - 1 1 - - 2 40
Pelagibacter ubique CP000084 1354 - 3 - 1 - 1 - - - - - - - - - 5
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 2 2 2 - 2 - 3 54
Rhodospirillum rubrum CP000230 3841 15 5 3 9 6 - 1 - 6 1 2 - 3 - 6 57
Rickettsia bellii CP000087 1429 - 2 - 1 - - - - 1 - - - - - - 4
Rickettsia conorii AE006914 1374 - 2 - 1 - - - - 1 - - - - - - 4
Rickettsia felis CP000053 1532 - 2 - 1 - - - - 1 - - - - - - 4
Rickettsia prowazekii AJ235269 835 - 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 meliloti AL591688 6205 15 16 12 5 1 1 - 1 1 - - - 2 - 3 57
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 Drosophila AE017196 1195 - 1 - - - - - - 1 - - - - - - 2
Zymomonas mobilis AE008692 1998 2 6 - 1 1 - - - - - - - 2 - 1 13
Beta-proteobacteria GenBank Genes REC OmpR NarL NtrC LytR ActR AraC AmiR GGDEF/
EAL		 RpfG HisK PP2C CheB CheV Other All
Azoarcus sp. BH72 AM406670 3989 14 16 9 13 1 - - - 9 3 - - 2 2 3 72
Azoarcus sp. EbN1 CR555306 4609 6 11 13 10 1 - - - 5 - - - - - 1 47
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