Phyletic profiles of c-di-GMP-related proteins

Table S1. Distribution of GGDEF, EAL, HD-GYP and PilZ domains in bacterial genomes^a

This is a web supplement to the paper by Ute Römling, Michael Y. Galperin, and Mark Gomelsky
"Cyclic di-GMP: the first 25 years of a universal bacterial second messenger", published in
Microbiology and Molecular Biology Reviews 77: 1-52 (2013). PubMed. Full text. Full text, PDF.
It shows the numbers of c-di-GMP-related domains in representative complete genomes from all
bacterial and archaeal species that were available in the NCBI's RefSeq database by the end of 2011.

This listing has been updated in 2016 for the review by Shan-Ho Chou and Michael Y. Galperin
"Diversity of the c-di-GMP binding proteins and mechanisms", published in J. Bacteriol. 198: 32-46 (2016).
PubMed, Full text, Full text, PDF.

The latest update includes the MshEN domain, described by Roelofs et al. in PLoS Pathogens 11: e1005232
(PubMed, Full text) and by Wang et al. in Nature Communications 7: 12481 (PubMed, Full text. Suppl., PDF).
The major changes in this update are listed at the bottom of this page^b.

The original variant of this table was prepared for the paper by Dorit Amikam and Michael Y. Galperin
"PilZ domain is part of the bacterial c-di-GMP binding protein", published in Bioinformatics 22: 3-6 (2006). PubMed. Full text, PDF.

No. Organism GenBank
entry All
proteins GGDEF
only^c GGDEF+
EAL EAL
only HD-
GYP^c PilZ MshEN Other
receptors Ribo-
switch1 Ribo-
switch2

Acidobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

1 Acidobacterium capsulatum ATCC 51196 CP001472 3,382 13 3 4 2 2 1 -

2 Candidatus Koribacter versatilis Ellin345 CP000360 4,777 11+1 - 3 9+1 22 1 -

3 Candidatus Solibacter usitatus Ellin6076 CP000473 7,826 4 - 1 1 11 1 -

4 Chloracidobacterium thermophilum B CP002514 3,054 7 - - 4 3 5 -

5 Granulicella mallensis MP5ACTX8 CP003130 4,815 2 - - - 1 - -

6 Granulicella tundricola MP5ACTX9 CP002480 4,542 13+1 6 6 2+1 3 - -

7 Terriglobus saanensis SP1PR4 CP002467 4,180 16 8 4 1 3 - -

Actinobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

8 Acidimicrobium ferrooxidans DSM 10331 CP001631 1,964 5 6 4 - 1 1 BldD

9 Acidothermus cellulolyticus 11B CP000481 2,157 6 7 3 1 2 5 BldD

10 Actinoplanes sp. SE50/110 CP003170 8,296 57 45 13 - 6 3 BldD

11 Actinosynnema mirum DSM 43827 CP001630 6,916 9 10 - - - - BldD

12 Amycolatopsis mediterranei U32 CP002000 9,228 11 7 - - - - BldD

13 Amycolicicoccus subflavus DQS3-9A1 CP002786 4,705 - - - - - - -

14 Arcanobacterium haemolyticum DSM 20595 CP002045 1,731 - - - - - - -

15 Arthrobacter arilaitensis Re117 FQ311875 3,436 - - - - - - -

16 Arthrobacter aurescens TC1 CP000474 4,587 3 3 2 - - - -

17 Arthrobacter chlorophenolicus A6 CP001341 4,590 1 3 2 - - 1 -

18 Arthrobacter phenanthrenivorans Sphe3 CP002379 4,131 1 2 1 - - - -

19 Arthrobacter sp. FB24 CP000454 4,506 1 4 4 - - - -

20 Atopobium parvulum DSM 20469 CP001721 1,353 - - - - - - -

21 Beutenbergia cavernae DSM 12333 CP001618 4,197 - - - - - - -

22 Bifidobacterium adolescentis ATCC 15703 AP009256 1,631 - - - - - - -

23 Bifidobacterium animalis subsp. lactis AD011 CP001213 1,527 - - - - - - -

24 Bifidobacterium bifidum S17 CP002220 1,783 - - - - - - -

25 Bifidobacterium breve ACS-071-V-Sch8b CP002743 1,826 - - - - - - -

26 Bifidobacterium dentium Bd1 CP001750 2,129 - - - - - - -

27 Bifidobacterium longum DJO10A CP000605 1,989 - - - - - - -

28 Brachybacterium faecium DSM 4810 CP001643 3,068 - - - - - - -

29 Catenulispora acidiphila DSM 44928 CP001700 8,914 7 7 - 2 - - BldD

30 Cellulomonas fimi ATCC 484 CP002666 3,761 3 6 2 - 1 1 - 3

31 Cellulomonas flavigena DSM 20109 CP001964 3,678 2 6 2 - - 1 - 2

32 Cellulomonas [Cellvibrio] gilvus ATCC 13127 CP002665 3,164 4 6 3 - 1 1 - 1

33 Clavibacter michiganensis subsp. michiganensis NCPPB 382 AM711867 3,079 - - - - - - -

34 Conexibacter woesei DSM 14684 CP001854 5,914 9+3 7 3 5+3 1 - -

35 Coriobacterium glomerans PW2 CP002628 1,768 - - - - - - -

36 Corynebacterium aurimucosum ATCC 700975 CP001601 2,551 - - - - - - -

37 Corynebacterium diphtheriae NCTC 13129 BX248353 2,272 - - - - - - -

38 Corynebacterium efficiens YS-314 BA000035 2,950 - - - - - - -

39 Corynebacterium glutamicum ATCC 13032 BA000036 2,993 - 1 - - - - -

40 Corynebacterium jeikeium K411 CR931997 2,137 - - - - - - -

41 Corynebacterium kroppenstedtii DSM 44385 CP001620 2,018 - - - - - - -

42 Corynebacterium pseudotuberculosis FRC41 CP002097 2,110 - - - - - - -

43 Corynebacterium resistens DSM 45100 CP002857 2,193 - - - - - - -

44 Corynebacterium ulcerans BR-AD22 CP002791 2,334 - - - - - - -

45 Corynebacterium urealyticum DSM 7109 AM942444 2,024 - - - - - - -

46 Corynebacterium variabile DSM 44702 CP002917 3,039 - - - - - - -

47 Cryptobacterium curtum DSM 15641 CP001682 1,357 - - - - - - -

48 Eggerthella lenta DSM 2243 CP001726 3,070 8+1 10 - 1+1 - 2 -

49 Eggerthella sp. YY7918 AP012211 2,680 9 11 1 2 - 1 - 1

50 Frankia alni ACN14a CT573213 6,711 8+1 7 6 0+1 - - BldD

51 Frankia sp. CcI3 CP000249 4,499 6 6 4 - - - BldD

52 Frankia sp. EAN1pec CP000820 7,191 25 11 8 - - - BldD

53 Frankia sp. EuI1c CP002299 7,083 14 13 10 - - - BldD

54 Frankia symbiont of Datisca glomerata CP002801 4,215 2 8 2 - - - BldD

55 Gardnerella vaginalis 409-05 CP001849 1,258 - - - - - - -

56 Geodermatophilus obscurus DSM 43160 CP001867 4,810 13 13 4 - 2 - BldD

57 Gordonia bronchialis DSM 43247 CP001802 4,696 1 - 2 - 1 - -

58 Intrasporangium calvum DSM 43043 CP002343 3,563 - - - 1 - - -

59 Isoptericola variabilis 225 CP002810 2,881 1 - - - - - -

60 Jonesia denitrificans DSM 20603 CP001706 2,511 - - - - - - -

61 Kineococcus radiotolerans SRS30216 CP000750 4,681 39 35 9 1 2 1 BldD

62 Kitasatospora setae KM-6054 AP010968 7,566 4 4 - 1 - - BldD

63 Kocuria rhizophila DC2201 AP009152 2,357 - - - - - - -

64 Kribbella flavida DSM 17836 CP001736 6,943 5 - - 1 - - BldD

65 Kytococcus sedentarius DSM 20547 CP001686 2,554 - - - 1 - - -

66 Leifsonia xyli subsp. xyli str. CTCB07 AE016822 2,030 - - - - - - -

67 Microbacterium testaceum StLB037 AP012052 3,676 2 - - - - - -

68 Micrococcus luteus NCTC 2665 CP001628 2,236 - - - - - - -

69 Microlunatus phosphovorus NM-1 AP012204 5,338 - - - - - - -

70 Micromonospora aurantiaca ATCC 27029 CP002162 6,222 7 9 - - - - BldD

71 Micromonospora sp. L5 CP002399 6,150 6 9 - - - - BldD

72 Mobiluncus curtisii ATCC 43063 CP001992 1,909 - - - - - - -

73 Mycobacterium abscessus ATCC 19977 CU458896 4,920 4 - - - - - -

74 Mycobacterium africanum GM041182 FR878060 3,830 - 1 1 - - - -

75 Mycobacterium avium subsp. paratuberculosis K-10 AE016958 4,350 2 3 - 1 - - -

76 Mycobacterium bovis AF2122/97 BX248333 3,920 - 1 1 - - - -

77 Mycobacterium canettii CIPT 140010059 HE572590 3,861 - 1 1 - - - -

78 Mycobacterium gilvum PYR-GCK CP000656 5,579 14 8 2 1 - - -

79 Mycobacterium leprae TN AL450380 1,605 2 1 1 - - - -

80 Mycobacterium marinum M CP000854 5,423 - - - - - - -

81 Mycobacterium rhodesiae NBB3 CP003169 6,147 - - - 1 - - -

82 Mycobacterium smegmatis str. MC2 155 CP000480 6,716 - 1 - - - - -

83 Mycobacterium sp. JDM601 CP002329 4,346 - 1 - - - - -

84 Mycobacterium sp. JLS CP000580 5,739 6 4 - 1 - - -

85 Mycobacterium sp. KMS CP000518 5,975 6 4 - 1 - - -

86 Mycobacterium sp. MCS CP000384 5,615 6 4 - 1 - - -

87 Mycobacterium tuberculosis H37Rv AL123456 3,927 - 1 1 - - - -

88 Mycobacterium ulcerans Agy99 CP000325 4,160 - - - - - - -

89 Mycobacterium vanbaalenii PYR-1 CP000511 5,979 10 4 1 1 - - -

90 Nakamurella multipartita DSM 44233 CP001737 5,240 5 6 - 1 - - BldD

91 Nocardia farcinica IFM 10152 AP006618 5,936 6 2 - - - - -

92 Nocardioides sp. JS614 CP000509 4,909 1 2 - 2 1 1 -

93 Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111 CP002040 5,497 1 2 1 1 - - BldD

94 Olsenella uli DSM 7084 CP002106 1,739 1 - - - - - - 1

95 Propionibacterium acnes KPA171202 AE017283 2,297 - - - - - - -

96 Propionibacterium freudenreichii subsp. shermanii CIP 103027 FN806773 2,375 - - - - - - -

97 Pseudonocardia dioxanivorans CB1190 CP002593 6,681 4 3 1 2 - - BldD

98 Renibacterium salmoninarum ATCC 33209 CP000910 3,507 - - - - - - -

99 Rhodococcus equi 103S FN563149 4,512 - - 2 - - - -

100 Rhodococcus erythropolis PR4 AP008957 6,437 14 4 1 - - - -

101 Rhodococcus jostii RHA1 CP000431 9,145 4 3 - 1 - - -

102 Rhodococcus opacus B4 AP011115 7,252 3 2 - 1 - - -

103 Rothia dentocariosa ATCC 17931 CP002280 2,217 - - - - - - -

104 Rothia mucilaginosa DY-18 AP011540 1,992 - - - - - - -

105 Rubrobacter xylanophilus DSM 9941 CP000386 3,140 1+1 5 1 2+1 - 1 -

106 Saccharomonospora viridis DSM 43017 CP001683 3,828 2 3 - - - - BldD

107 Saccharopolyspora erythraea NRRL 2338 AM420293 7,197 13+1 11 1 0+1 - - BldD

108 Salinispora arenicola CNS-205 CP000850 4,917 7 7 1 - - - BldD

109 Salinispora tropica CNB-440 CP000667 4,536 6 6 - - - - BldD

110 Sanguibacter keddieii DSM 10542 CP001819 3,710 1 - - - - 1 -

111 Segniliparus rotundus DSM 44985 CP001958 3,006 - - - - - - -

112 Slackia heliotrinireducens DSM 20476 CP001684 2,765 1 1 - - - - -

113 Stackebrandtia nassauensis DSM 44728 CP001778 6,379 5 3 - - - - BldD

114 Streptomyces avermitilis MA-4680 BA000030 7,671 3 5 - 1 - - BldD

115 Streptomyces bingchenggensis BCW-1 CP002047 10,022 3 4 - 1 - - BldD

116 Streptomyces cattleya NRRL 8057 FQ859185 7,475 3 3 - - - - BldD

117 Streptomyces coelicolor A3(2) AL645882 8,154 5 4 1 1 - - BldD

118 Streptomyces pratensis ATCC 33331 CP002475 6,572 2 4 - 1 - - BldD

119 Streptomyces griseus subsp. griseus NBRC 13350 AP009493 7,136 2 4 - - - - BldD

120 Streptomyces scabiei 87.22 FN554889 8,746 3 4 - - - - BldD

121 Streptomyces sp. SirexAA-E CP002993 6,357 2 4 - 1 - - BldD

122 Streptomyces violaceusniger Tu 4113 CP002994 8,985 3 4 1 1 - - BldD

123 Streptosporangium roseum DSM 43021 CP001814 8,975 1 2 1 1 - - BldD

124 Thermobifida fusca YX CP000088 3,110 1 2 1 1 - - BldD

125 Thermobispora bispora DSM 43833 CP001874 3,546 1 2 - 1 - - BldD

126 Thermomonospora curvata DSM 43183 CP001738 4,890 1 2 - 1 - - BldD

127 Tropheryma whipplei TW08/27 BX072543 783 - - - - - - -

128 Tsukamurella paurometabola DSM 20162 CP001966 4,242 7 1 - - - - -

129 Verrucosispora maris AB-18-032 CP002638 6,009 9 9 - - - - BldD

130 Xylanimonas cellulosilytica DSM 15894 CP001821 3,443 - - - - - - -

Aquificae GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

131 Aquifex aeolicus VF5 AE000657 1,560 6+1 4 4 0+1 5 - -

132 Desulfurobacterium thermolithotrophum DSM 11699 CP002543 1,509 5+1 2 2 2+1 3 1 -

133 Hydrogenobacter thermophilus TK-6 AP011112 1,893 3 1 3 - - 1 -

134 Hydrogenobaculum sp. Y04AAS1 CP001130 1,629 9 7 2 - 4 - -

135 Persephonella marina EX-H1 CP001230 2,051 12 14 2 2 4 2 -

136 Sulfurihydrogenibium azorense Az-Fu1 CP001229 1,725 4 7 1 - 3 - -

137 Sulfurihydrogenibium sp. YO3AOP1 CP001080 1,721 6 6 1 - 2 - -

138 Thermocrinis albus DSM 14484 CP001931 1,593 5 3 2 - 2 1 -

139 Thermovibrio ammonificans HB-1 CP002444 1,813 6+1 4 2 2+1 4 - -

Bacteroidetes GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

140 Bacteroides fragilis YCH46 AP006841 4,625 - - - - - - -

141 Bacteroides helcogenes P 36-108 CP002352 3,244 - - - - - - -

142 Bacteroides salanitronis DSM 18170 CP002530 3,641 - - - - - - -

143 Bacteroides thetaiotaomicron VPI-5482 AE015928 4,816 - - - - - - -

144 Bacteroides vulgatus ATCC 8482 CP000139 4,065 - - - - - - -

145 Blattabacterium sp. (Blattella germanica) str. Bge CP001487 586 - - - - - - -

146 Blattabacterium sp. (Cryptocercus punctulatus) str. Cpu CP003015 548 - - - - - - -

147 Blattabacterium sp. (Mastotermes darwiniensis) str. MADAR CP003000 541 - - - - - - -

148 Blattabacterium sp. (Periplaneta americana) str. BPLAN CP001429 581 - - - - - - -

149 Candidatus Amoebophilus asiaticus 5a2 CP001102 1,283 - - - - - - -

150 Candidatus Azobacteroides pseudotrichonymphae CFP2 AP010656 852 - - - - - - -

151 Candidatus Sulcia muelleri GWSS CP000770 227 - - - - - - -

152 Capnocytophaga canimorsus Cc5 CP002113 2,404 - - - - - - -

153 Capnocytophaga ochracea DSM 7271 CP001632 2,171 - - - - - - -

154 Cellulophaga algicola DSM 14237 CP002453 4,163 - - - - - - -

155 Cellulophaga lytica DSM 7489 CP002534 3,284 - - - - - - -

156 Chitinophaga pinensis DSM 2588 CP001699 7,192 - - - - - - -

157 Croceibacter atlanticus HTCC2559 CP002046 2,702 - - - - - - -

158 Cyclobacterium marinum DSM 745 CP002955 5,000 - - - - - - -

159 Cytophaga hutchinsonii ATCC 33406 CP000383 3,785 - - - - - - -

160 Dyadobacter fermentans DSM 18053 CP001619 5,719 - - - - - - -

161 Flavobacteriaceae bacterium 3519-10 CP001673 2,534 - - - - - - -

162 Flavobacterium branchiophilum FL-15 FQ859183 2,867 - - - - - - -

163 Flavobacterium columnare ATCC 49512 CP003222 2,646 - - - - - - -

164 Flavobacterium johnsoniae UW101 CP000685 5,017 - - - - - - -

165 Flavobacterium psychrophilum JIP02/86 AM398681 2,412 - - - - - - -

166 Fluviicola taffensis DSM 16823 CP002542 4,033 - - - - - - -

167 Gramella forsetii CU207366 3,584 - - - - - - -

168 Haliscomenobacter hydrossis DSM 1100 CP002691 6,752 - - - - - - -

169 Krokinobacter diaphorus 4H-3-7-5 CP002528 2,978 - - - - - - -

170 Lacinutrix sp. 5H-3-7-4 CP002825 2,967 - - - - - - -

171 Leadbetterella byssophila DSM 17132 CP002305 3,465 - - - - - - -

172 Maribacter sp. HTCC2170 CP002157 3,411 - - - - - - -

173 Marivirga tractuosa DSM 4126 CP002349 3,757 - - - - - - -

174 Muricauda ruestringensis DSM 13258 CP002999 3,432 - - - - - - -

175 Niastella koreensis GR20-10 CP003178 7,174 - - - - - - -

176 Odoribacter splanchnicus DSM 20712 CP002544 3,497 - - - - - - -

177 Owenweeksia hongkongensis DSM 17368 CP003156 3,485 - - - - - - -

178 Paludibacter propionicigenes WB4 CP002345 3,020 - - - - - - -

179 Parabacteroides distasonis ATCC 8503 CP000140 3,850 - - - - - - -

180 Pedobacter heparinus DSM 2366 CP001681 4,252 - - - - - - -

181 Pedobacter saltans DSM 12145 CP002545 3,792 - - - - - - -

182 Porphyromonas asaccharolytica DSM 20707 CP002689 1,699 - - - - - - -

183 Porphyromonas gingivalis W83 AE015924 1,909 - - - - - - -

184 Prevotella denticola F0289 CP002589 2,386 - - - - - - -

185 Prevotella melaninogenica ATCC 25845 CP002122 2,296 - - - - - - -

186 Prevotella ruminicola 23 CP002006 2,763 - - - - - - -

187 Rhodothermus marinus DSM 4252 CP001807 2,863 2 - - - - - -

188 Riemerella anatipestifer DSM 15868 CP002346 1,972 - - - - - - -

189 Robiginitalea biformata HTCC2501 CP001712 3,211 - - - - - - -

190 Runella slithyformis DSM 19594 CP002859 5,774 1 - - - - - -

191 Salinibacter ruber DSM 13855 CP000159 2,833 1 1 - - - - -

192 Sphingobacterium sp. 21 CP002584 5,169 - - - - - - -

193 Spirosoma linguale DSM 74 CP001769 6,938 - - - - - - -

194 Tannerella forsythia ATCC 43037 CP003191 3,001 - - - - - - -

195 Weeksella virosa DSM 16922 CP002455 2,049 - - - - - - -

196 Zobellia galactanivorans FP476056 4,733 - - - - - - -

197 Zunongwangia profunda SM-A87 CP001650 4,653 - - - - - - -

Chlamydiae GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

198 Chlamydia muridarum Nigg AE002160 904 - - - - - - -

199 Chlamydia trachomatis D/UW-3/CX AE001273 895 - - - - - - -

200 Chlamydophila abortus S26/3 CR848038 932 - - - - - - -

201 Chlamydophila caviae GPIC AE015925 1,005 - - - - - - -

202 Chlamydophila felis Fe/C-56 AP006861 1,013 - - - - - - -

203 Chlamydophila pecorum E58 CP002608 988 - - - - - - -

204 Chlamydophila pneumoniae CWL029 AE001363 1,054 - - - - - - -

205 Chlamydophila psittaci 6BC CP002549 975 - - - - - - -

206 Parachlamydia acanthamoebae UV7 FR872580 2,788 - - - - - - -

207 Protochlamydia amoebophila UWE25 BX908798 2,031 - - - - - - -

208 Simkania negevensis Z FR872582 2,518 1 - - - - - -

209 Waddlia chondrophila WSU 86-1044 CP001928 1,956 - - - - - - -

Chlorobi GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

210 Chlorobaculum parvum NCIB 8327 CP001099 2,043 1 - - - - - -

211 Chlorobium chlorochromatii CaD3 CP000108 2,002 1 - - - - - -

212 Chlorobium limicola DSM 245 CP001097 2,434 1 - - - - - -

213 Chlorobium phaeobacteroides DSM 266 CP000492 2,650 1 - - - - - -

214 Chlorobium phaeovibrioides DSM 265 CP000607 1,753 1 - - 1 - - -

215 Chlorobium tepidum TLS AE006470 2,252 1 - - - - - -

216 Chloroherpeton thalassium ATCC 35110 CP001100 2,710 8 - - 5 - 1 -

217 Chlorobium luteolum DSM 273 CP000096 2,083 1 - - 1 - - -

218 Pelodictyon phaeoclathratiforme BU-1 CP001110 2,707 1 - - - - - -

219 Prosthecochloris aestuarii DSM 271 CP001108 2,327 1 - - - - - -

Chloroflexi GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

220 Anaerolinea thermophila UNI-1 AP012029 3,177 15 3 2 10 - 1 -

221 Chloroflexus aggregans DSM 9485 CP001337 3,730 11 3 - 5 - 1 -

222 Chloroflexus aurantiacus J-10-fl CP000909 3,853 14 3 - 4 - 1 -

223 Chloroflexus sp. Y-400-fl CP001364 4,159 13 3 - 2 - 1 -

224 Dehalococcoides ethenogenes 195 CP000027 1,580 0+1 - - 2+1 - - -

225 Dehalococcoides sp. BAV1 CP000688 1,371 0+1 - - 1+1 - - -

226 Dehalococcoides sp. CBDB1 AJ965256 1,458 0+1 - - 2+1 - - - 1

227 Dehalococcoides sp. GT CP001924 1,417 0+1 - - 2+1 - - -

228 Dehalococcoides sp. VS CP001827 1,438 0+1 - - 3+1 - - - 1

229 Dehalogenimonas lykanthroporepellens BL-DC-9 CP002084 1,659 1+1 - - 1+1 - - -

230 Herpetosiphon aurantiacus ATCC 23779 CP000875 5,278 11 3 - 5 - 1 -

231 Roseiflexus castenholzii DSM 13941 CP000804 4,330 9 3 - 5 - 3 -

232 Roseiflexus sp. RS-1 CP000686 4,517 9 3 - 5 - 3 -

233 Sphaerobacter thermophilus DSM 20745 CP001823 3,485 5+2 2 1 1+2 1 - - 1 2

234 Thermobaculum terrenum ATCC BAA-798 CP001825 2,832 4 2 - 1 - - - 2 1

235 Thermomicrobium roseum DSM 5159 CP001275 2,859 2 3 2 2 1 1 - 1

Cyanobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

236 Acaryochloris marina MBIC11017 CP000828 8,383 26 27 5 - 3 13 -

237 Anabaena variabilis ATCC 29413 CP000117 5,657 8 6 1 1 - 1 -

238 cyanobacterium UCYN-A CP001842 1,199 - - - - - - -

239 Cyanothece sp. ATCC 51142 CP000806 5,304 13 18 3 2 1 4 -

240 Cyanothece sp. PCC 7424 CP001291 5,710 19 14 - 2 1 6 -

241 Cyanothece sp. PCC 7425 CP001344 5,327 7 12 2 2 1 6 -

242 Cyanothece sp. PCC 7822 CP002198 6,642 21 16 1 2 1 5 -

243 Cyanothece sp. PCC 8801 CP001287 4,367 13 10 2 2 1 3 -

244 Cyanothece sp. PCC 8802 CP001701 4,444 13 10 2 2 1 2 -

245 Gloeobacter violaceus PCC 7421 BA000045 4,430 1 - - 1 - - -

246 Microcystis aeruginosa NIES-843 AP009552 6,312 1 1 - 1 1 1 -

248 Nostoc punctiforme PCC 73102 CP001037 6,690 11 10 1 2 1 1 -

249 Nostoc sp. PCC 7120 BA000019 6,055 8 6 1 2 - 1 -

250 Prochlorococcus marinus subsp. marinus str. CCMP1375 AE017126 1,882 - - - - - - -

251 Synechococcus elongatus PCC 6301 AP008231 2,525 9 8 1 2 2 3 -

252 Synechococcus sp. CC9311 CP000435 2,892 - - - - 2 1 -

253 Synechococcus sp. CC9605 CP000110 2,645 - - - - 1 - -

254 Synechococcus sp. CC9902 CP000097 2,307 - - - - - - -

255 Synechococcus sp. JA-3-3Ab CP000239 2,760 2 - 1 2 - 4 -

256 Synechococcus sp. PCC 7002 CP000951 3,186 7 6 2 - - 3 -

257 Synechococcus sp. RCC307 CT978603 2,525 - - - - - - -

258 Synechococcus sp. WH 7803 CT971583 2,533 - - - - 1 - -

259 Synechococcus sp. WH 8102 BX548020 2,517 - - - - 1 - -

260 Synechocystis sp. PCC 6803 BA000022 3,567 13 9 4 2 - 3 -

261 Thermosynechococcus elongatus BP-1 BA000039 2,475 5 5 - 1 3 2 -

262 Trichodesmium erythraeum IMS101 CP000393 5,124 1 3 - 2 - - -

247 Trichormus ('Nostoc') azollae 0708 CP002059 3,651 2 1 2 1 - 1 -

Deferribacteres GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

248 Calditerrivibrio nitroreducens DSM 19672 CP002347 2,100 9 5 2 5 3 4 -

249 Deferribacter desulfuricans SSM1 AP011529 2,374 15 4 2 4 4 7 -

250 Denitrovibrio acetiphilus DSM 12809 CP001968 2,964 20 6 4 7 5 3 -

251 Flexistipes sinusarabici DSM 4947 CP002858 2,261 10 2 - 3 1 4 -

Deinococcus/ Thermus GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

252 Deinococcus deserti VCD115 CP001114 3,451 22+4 11 - 7+4 - 1 - 1 2

253 Deinococcus geothermalis DSM 11300 CP000359 2,857 12 - - 5 - 2 - 1

254 Deinococcus maricopensis DSM 21211 CP002454 3,264 28+3 17 1 7+3 - 1 -

255 Deinococcus proteolyticus MRP CP002536 2,656 10 7 - 3 - 2 - 1

256 Deinococcus radiodurans R1 AE000513 3,184 11+1 4 1 3+1 - 1 - 2

257 Marinithermus hydrothermalis DSM 14884 CP002630 2,205 5 4 - 2 - 3 -

258 Meiothermus ruber DSM 1279 CP001743 3,014 11+1 3 - 8+1 - 3 - 1

259 Meiothermus silvanus DSM 9946 CP002042 3,505 13 3 1 6 - 3 - 1

260 Oceanithermus profundus DSM 14977 CP002361 2,373 7 4 - 5 - 4 -

261 Thermus scotoductus SA-01 CP001962 2,458 7 2 - 3 - 1 -

262 Thermus sp. CCB_US3_UF1 CP003126 2,279 5 1 1 3 - 3 -

263 Thermus thermophilus HB27 AE017221 2,210 7 1 1 5 - 2 -

264 Truepera radiovictrix DSM 17093 CP002049 2,945 4+1 5 1 2+1 - 2 -

Firmicutes GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

265 Acetohalobium arabaticum DSM 5501 CP002105 2,262 4+1 1 - 5+1 1 1 - 2

266 Acidaminococcus fermentans DSM 20731 CP001859 2,026 4 4 1 1 - - -

267 Acidaminococcus intestini RyC-MR95 CP003058 2,401 1 1 - 2 1 - -

268 Aerococcus urinae ACS-120-V-Col10a CP002512 1,726 - - - - - - -

269 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 CP001727 3,084 4+1 3 5 5+1 1 1 - 2

270 Alkaliphilus metalliredigens QYMF CP000724 4,625 6+4 4 1 11+4 2 1 - 11 1

271 Alkaliphilus oremlandii OhILAs CP000853 2,836 9 4 1 3 2 1 - 1

272 Ammonifex degensii KC4 CP001785 2,080 7 2 1 5 1 1 -

273 Anaerococcus prevotii DSM 20548 CP001708 1,806 - - - - - - -

274 Anoxybacillus flavithermus WK1 CP000922 2,832 6+1 6 2 7+1 2 1 - 2

275 Bacillus amyloliquefaciens FZB42 CP000560 3,693 3 - 2 - - - -

276 Bacillus anthracis str. Ames AE016879 5,311 4 6 1 1 - - - 1

277 Bacillus atrophaeus 1942 CP002207 4,186 3 - 2 - 1 - -

278 Bacillus cellulosilyticus DSM 2522 CP002394 4,266 10 11 5 3 3 1 -

279 Bacillus cereus ATCC 14579 AE016877 5,255 4 4 1 - - - - 2

280 Bacillus clausii KSM-K16 AP006627 4,096 - - 1 1 - - -

281 Bacillus coagulans 2-6 CP002472 2,971 2 1 1 2 1 1 - 2

282 Bacillus cytotoxicus NVH 391-98 CP000764 4,176 2 1 - - - - - 1

283 Bacillus halodurans C-125 BA000004 4,066 3 1 1 2 2 - - 1 1

284 Bacillus licheniformis ATCC 14580 AE017333 4,196 4 - 2 - 2 - - 2

285 Bacillus megaterium DSM 319 CP001982 5,100 4 3 3 - 2 - - 1

286 Bacillus pseudofirmus OF4 CP001878 4,335 7 5 4 3 2 1 -

287 Bacillus pumilus SAFR-032 CP000813 3,681 3 1 2 - 2 - - 1

288 Bacillus selenitireducens MLS10 CP001791 3,255 22+4 19 2 8+4 2 1 - 2 2

289 Bacillus subtilis subsp. subtilis str. 168 AL009126 4,105 3 1 2 - 1 - -

290 Bacillus thuringiensis serovar konkukian str. 97-27 AE017355 5,117 4 6 1 1 - - - 1

291 Bacillus weihenstephanensis KBAB4 CP000903 5,653 3 6 1 - - - - 2

292 Brevibacillus brevis NBRC 100599 AP008955 5,949 7 5 2 9 4 - - 4

293 Butyrivibrio proteoclasticus B316 CP001810 3,811 37 17 5 13 6 1 - 2

294 Caldicellulosiruptor bescii DSM 6725 CP001393 2,666 2 4 - 6 1 1 - 3

295 Caldicellulosiruptor hydrothermalis 108 CP002219 2,546 2 5 - 8 1 1 - 2

296 Caldicellulosiruptor kristjanssonii 177R1B CP002326 2,482 2 2 - 5 1 1 - 1

297 Caldicellulosiruptor kronotskyensis 2002 CP002330 2,466 3 3 - 6 1 1 - 3

298 Caldicellulosiruptor lactoaceticus 6A CP003001 2,318 2 2 - 4 1 1 - 1

299 Caldicellulosiruptor obsidiansis OB47 CP002164 2,188 3 3 - 5 1 1 - 4

300 Caldicellulosiruptor owensensis OL CP002216 2,147 3 4 - 7 1 1 - 2

301 Caldicellulosiruptor saccharolyticus DSM 8903 CP000679 2,679 4 3 - 8 1 1 - 4

302 Candidatus Arthromitus sp. SFB-mouse-Japan AP012202 1,491 1 - - 0* - - -

303 Candidatus Arthromitus sp. SFB-mouse-Yit AP012209 1,415 1 - - 0* - - -

304 Candidatus Arthromitus sp. SFB-rat-Yit AP012210 1,343 1 - - - - - -

305 Candidatus Desulforudis audaxviator MP104C CP000860 2,157 7+5 1 - 10+5 1 3 - 3

306 Carboxydothermus hydrogenoformans Z-2901 CP000141 2,620 7+3 1 1 10+3 1 1 - 7

307 Carnobacterium sp. 17-4 CP002563 2,474 3+1 - - 0+1 - - -

308 Clostridiales genomosp. BVAB3 str. UPII9-5 CP001850 1,567 - - - - - - -

309 Clostridium acetobutylicum ATCC 824 AE001437 3,848 8 3 1 9 5 - - 2

310 Clostridium beijerinckii NCIMB 8052 CP000721 5,020 14 9 1 14 2 1 - 4 6

311 Clostridium botulinum A str. ATCC 3502 AM412317 3,590 6+2 1 1 3+2 2 - -

312 Clostridium cellulolyticum H10 CP001348 3,390 2+1 1 - 4+1 2 - -

313 Clostridium cellulovorans 743B CP002160 4,254 4 4 1 5 1 - - 4

314 Clostridium difficile 630 AM180355 3,753 18 18 1 - 1 1 - 12 4

315 Clostridium kluyveri DSM 555 CP000673 3,913 6+2 3 4 5+2 1 - - 3 1

316 Clostridium lentocellum DSM 5427 CP002582 4,182 5 2 1 7 2 1 -

317 Clostridium ljungdahlii DSM 13528 CP001666 4,184 13+3 6 3 4+3 1 - - 1

318 Clostridium novyi NT CP000382 2,325 4 3 1 4 1 1 - 1 1

319 Clostridium perfringens str. 13 BA000016 2,723 4+1 1 2 0+1 1 - - 1 1

320 Clostridium phytofermentans ISDg CP000885 3,902 8 5 - 7 2 - - 2

321 Clostridium saccharolyticum WM1 CP002109 4,154 11+5 4 1 5+5 1 - -

322 Clostridium sp. SY8519 AP012212 2,613 - - - - - - -

323 Clostridium sticklandii DSM 519 FP565809 2,573 17+5 9 2 12+5 2 1 -

324 Clostridium tetani E88 AE015927 2,432 6 - 1 1 1 - - 1 1

325 Clostridium thermocellum ATCC 27405 CP000568 3,189 6+3 1 - 5+3 11 2 - 4

326 Coprothermobacter proteolyticus DSM 5265 CP001145 1,482 2 - - 3 1 1 -

327 Desulfitobacterium hafniense Y51 AP008230 5,060 14+2 4 3 13+2 2 - - 6

328 Desulfotomaculum acetoxidans DSM 771 CP001720 4,068 10+3 4 1 5+3 2 - - 4 2

329 Desulfotomaculum carboxydivorans CO-1-SRB CP002736 2,657 6+2 - 1 6+2 2 1 - 3

330 Desulfotomaculum kuznetsovii DSM 6115 CP002770 3,398 10+5 1 - 13+5 1 2 - 8

331 Desulfotomaculum reducens MI-1 CP000612 3,276 8+5 1 1 10+5 2 - - 6

332 Desulfotomaculum ruminis DSM 2154 CP002780 3,796 14+1 4 3 11+1 4 4 - 6

333 Enterococcus faecalis V583 AE016830 3,265 - - - - - - -

334 Erysipelothrix rhusiopathiae str. Fujisawa AP012027 1,697 - - - - - - -

335 Ethanoligenens harbinense YUAN-3 CP002400 2,701 5 5 3 3 2 1 - 3

336 Eubacterium eligens ATCC 27750 CP001104 2,765 13 6 1 5 6 2 - 1

337 Eubacterium limosum KIST612 CP002273 4,509 20+2 19 2 5+2 1 - - 4

338 Eubacterium rectale ATCC 33656 CP001107 3,626 10+1 7 1 6+1 3 - - 6

339 Exiguobacterium sibiricum 255-15 CP001022 3,015 14 11 3 2 2 - -

340 Exiguobacterium sp. AT1b CP001615 3,020 15+1 9 3 3+1 2 1 - 1

341 Filifactor alocis ATCC 35896 CP002390 1,709 - - - - - - -

342 Finegoldia magna ATCC 29328 AP008971 1,813 - - - - - - -

343 Geobacillus kaustophilus HTA426 BA000043 3,540 5 3 2 3 2 1 -

344 Geobacillus sp. C56-T3 CP002050 3,315 4+1 3 1 2+1 2 1 -

345 Geobacillus sp. WCH70 CP001638 3,168 1 4 1 1 1 1 -

346 Geobacillus sp. Y4.1MC1 CP002293 3,669 3+1 5 3 3+1 2 1 -

347 Geobacillus sp. Y412MC52 CP002442 3,459 5+1 3 1 3+1 1 - - 2

348 Geobacillus sp. Y412MC61 CP001794 3,446 4+1 3 1 3+1 2 1 - 2

349 Geobacillus thermodenitrificans NG80-2 CP000557 3,445 4+1 2 2 1+1 1 1 -

350 Geobacillus thermoglucosidasius C56-YS93 CP002835 3,759 2+1 6 2 2+1 2 1 -

351 Halanaerobium hydrogeniformans CP002304 2,295 7+18 2 - 4+18 - 2 - 1

352 Halothermothrix orenii H 168 CP001098 2,342 5 - - 4 1 2 - 2 1

353 Heliobacterium modesticaldum Ice1 CP000930 3,000 3+1 3 2 10+1 1 2 - 1

354 Kyrpidia tusciae DSM 2912 CP002017 3,150 1 2 5 4 1 2 - 1

355 Lactobacillus acidophilus NCFM CP000033 1,864 1 - 2 - - - -

356 Lactobacillus amylovorus GRL 1112 CP002338 2,054 - - - - - - -

357 Lactobacillus brevis ATCC 367 CP000416 2,218 2 - 3 - - - -

358 Lactobacillus buchneri NRRL B-30929 CP002652 2,392 - - - - - - -

359 Lactobacillus casei ATCC 334 CP000423 2,771 - - - - - - -

360 Lactobacillus crispatus ST1 FN692037 2,024 - - - - - - -

361 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 CR954253 1,562 3 - - - - - -

362 Lactobacillus fermentum IFO 3956 AP008937 1,843 - - - - - - -

363 Lactobacillus gasseri ATCC 33323 CP000413 1,755 - - - - - - -

364 Lactobacillus helveticus DPC 4571 CP000517 1,610 - - - - - - -

365 Lactobacillus johnsonii NCC 533 AE017198 1,821 - - - - - - -

366 Lactobacillus kefiranofaciens ZW3 CP002764 2,162 - - - - - - -

367 Lactobacillus plantarum WCFS1 AL935263 3,108 3 - 5 - - - -

368 Lactobacillus reuteri DSM 20016 CP000705 1,900 1 - 2 - - - -

369 Lactobacillus rhamnosus GG FM179322 3,016 - - - - - - -

370 Lactobacillus ruminis ATCC 27782 CP003032 1,862 - - - - - - -

371 Lactobacillus sakei subsp. sakei 23K CR936503 1,879 - - - - - - -

372 Lactobacillus salivarius UCC118 CP000233 2,017 1 - 1 - - - -

373 Lactobacillus sanfranciscensis TMW 1.1304 CP002461 1,284 - - - - - - -

374 Lactococcus garvieae ATCC 49156 AP009332 1,947 2 - 4 - - - -

375 Lactococcus lactis subsp. lactis Il1403 AE005176 2,321 - - - - - - -

376 Leuconostoc citreum KM20 DQ489736 1,820 1 - 1 - - - -

377 Leuconostoc gasicomitatum LMG 18811 FN822744 1,912 - - - - - - -

378 Leuconostoc kimchii IMSNU 11154 CP001758 2,129 - - - - - - -

379 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 CP000414 2,005 1 - 1 - - - -

380 Leuconostoc sp. C2 CP002898 1,855 - - - - - - -

381 Listeria innocua Clip11262 AL592022 2,968 4 - 3 - - - -

382 Listeria ivanovii subsp. ivanovii PAM 55 FR687253 2,650 3 - 3 - - - -

383 Listeria monocytogenes EGD-e AL591824 2,846 4 - 3 - - - -

384 Listeria seeligeri serovar 1/2b str. SLCC3954 FN557490 2,710 4 - 3 - - - -

385 Listeria welshimeri serovar 6b str. SLCC5334 AM263198 2,774 4 - 3 - - - -

386 Lysinibacillus sphaericus C3-41 CP000817 4,771 11 8 3 3 3 - - 1

387 Macrococcus caseolyticus JCSC5402 AP009484 2,061 1 - - - - - -

388 Mahella australiensis 50-1 BON CP002360 2,870 2+1 1 3+1 1 2 - -

389 Megasphaera elsdenii DSM 20460 HE576794 2,219 3 2 1 1 - - - 1

390 Melissococcus plutonius ATCC 35311 AP012200 1,885 - - - - - - -

391 Moorella thermoacetica ATCC 39073 CP000232 2,465 8+1 - 1 9+1 1 - - 7

392 Natranaerobius thermophilus JW/NM-WN-LF CP001034 2,906 2+9 - - 5+9 1 2 - 3

393 Oceanobacillus iheyensis HTE831 BA000028 3,500 2 1 1 2 1 - - 1

394 Oenococcus oeni PSU-1 CP000411 1,691 1 - 1 - 1 - -

395 Oscillibacter valericigenes Sjm18-20 AP012044 4,721 8+2 5 4 4+2 3 - -

396 Paenibacillus mucilaginosus KNP414 CP002869 7,804 25 15 1 6 6 1 - 9

397 Paenibacillus polymyxa E681 CP000154 4,805 7+1 1 1 4+1 1 - - 2

398 Paenibacillus sp. JDR-2 CP001656 6,213 10 5 1 6 3 1 - 1

399 Paenibacillus sp. Y412MC10 CP001793 6,238 8+1 1 1 4+1 2 - -

400 Pediococcus pentosaceus ATCC 25745 CP000422 1,755 1 - 4 - 1 - -

401 Pelotomaculum thermopropionicum SI AP009389 2,920 3+5 - 1 10+5 2 1 - 8 1

402 Roseburia hominis A2-183 CP003040 3,362 14+1 7 2 11+1 3 1 -

403 Ruminococcus albus 7 CP002403 3,582 30 9 5 6 - 2 - 3

404 Selenomonas sputigena ATCC 35185 CP002637 2,255 6 4 - 7 3 - -

405 Staphylococcus aureus subsp. aureus N315 BA000018 2,624 1 - - - - - -

406 Staphylococcus carnosus subsp. carnosus TM300 AM295250 2,462 1 - - - - - -

407 Staphylococcus epidermidis ATCC 12228 AE015929 2,419 1 - - - - - -

408 Staphylococcus haemolyticus JCSC1435 AP006716 2,676 1 - - - - - -

409 Staphylococcus lugdunensis HKU09-01 CP001837 2,490 1 - - - - - -

410 Staphylococcus pseudintermedius HKU10-03 CP002439 2,450 1 - - - - - -

411 Streptococcus agalactiae 2603V/R AE009948 2,124 - - - - - - -

412 Streptococcus dysgalactiae subsp. equisimilis GGS_124 AP010935 2,100 - - - - - - -

413 Streptococcus equi subsp. zooepidemicus MGCS10565 CP001129 1,893 - - - - - - -

414 Streptococcus gallolyticus UCN34 FN597254 2,223 1 - - - 1 - -

415 Streptococcus gordonii str. Challis substr. CH1 CP000725 2,051 - - - - - - -

416 Streptococcus macedonicus ACA-DC 198 HE613569 1,977 - - - - - - -

417 Streptococcus mitis B6 FN568063 2,004 - - - - - - -

418 Streptococcus mutans UA159 AE014133 1,960 - - - - - - -

419 Streptococcus parasanguinis ATCC 15912 CP002843 2,022 - - - - - - -

420 Streptococcus parauberis KCTC 11537 CP002471 1,868 - - - - - - -

421 Streptococcus pasteurianus ATCC 43144 AP012054 1,869 - - - - - - -

422 Streptococcus pneumoniae TIGR4 AE005672 2,094 - - - - - - -

423 Streptococcus pseudopneumoniae IS7493 CP002925 2,230 - - - - - - -

424 Streptococcus pyogenes M1 GAS AE004092 1,697 - - - - - - -

425 Streptococcus sanguinis SK36 CP000387 2,270 - - - - - - -

426 Streptococcus suis 05ZYH33 CP000407 2,186 - - - - - - -

427 Streptococcus thermophilus CNRZ1066 CP000024 1,915 - - - - - - -

428 Streptococcus uberis 0140J AM946015 1,825 - - - - - - -

429 Sulfobacillus acidophilus TPY CP002901 3,754 8 2 7 4 3 2 - 1

430 Symbiobacterium thermophilum IAM 14863 AP006840 3,337 6 3 - 4 1 - - 1

431 Syntrophobotulus glycolicus DSM 8271 CP002547 3,251 6+8 5 1 7+8 3 1 - 10

432 Syntrophomonas wolfei subsp. wolfei str. Goettingen CP000448 2,504 5+3 - - 15+3 1 1 -

433 Syntrophothermus lipocalidus DSM 12680 CP002048 2,313 6+2 1 1 8+2 2 2 - 2

434 Tepidanaerobacter sp. Re1 CP002728 2,524 3 - - 3 1 1 -

435 Tetragenococcus halophilus NBRC 12172 AP012046 2,555 - - - - - - -

436 Thermaerobacter marianensis DSM 12885 CP002344 2,327 2 - - 3 1 1 - 1

437 Thermincola potens JR CP002028 2,949 9+2 5 1 13+2 3 1 - 10

438 Thermoanaerobacter brockii subsp. finnii Ako-1 CP002466 2,209 3 - 1 7 1 1 - 1

439 Thermoanaerobacter italicus Ab9 CP001936 2,270 3 1 - 5 1 1 - 1

440 Thermoanaerobacter mathranii subsp. mathranii str. A3 CP002032 2,159 1 1 - 5 1 1 - 4

441 Thermoanaerobacter pseudethanolicus ATCC 33223 CP000924 2,243 3 - 1 7 1 1 - 1 1

442 Thermoanaerobacter sp. X513 CP002210 4,895 2+1 - - 5+1 1 1 - 1

443 Thermoanaerobacter sp. X514 CP000923 2,349 2+1 - 1 7+1 1 1 - 1 1

444 Caldanaerobacter subterraneus subsp. tengcongensis MB4 AE008691 2,588 5 1 - 5 1 1 - 1

445 Thermoanaerobacter wiegelii Rt8.B1 CP002991 2,522 5+1 2 - 6+1 1 1 - 1

446 Thermoanaerobacterium thermosaccharolyticum DSM 571 CP002171 2,601 2 - - 5 1 1 -

447 Thermoanaerobacterium xylanolyticum LX-11 CP002739 2,345 6+1 1 - 4+1 1 1 - 1

448 Thermodesulfobium narugense DSM 14796 CP002690 1,807 13 7 3 4 1 1 -

449 Thermosediminibacter oceani DSM 16646 CP002131 2,197 1+1 - - 4+1 1 2 - 6

450 Veillonella parvula DSM 2008 CP001820 1,844 - - - 1 - - -

451 Weissella koreensis KACC 15510 CP002899 1,357 3 1 3 - - - -

Fusobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

452 Fusobacterium nucleatum subsp. nucleatum ATCC 25586 AE009951 2,066 - - - - - - -

453 Ilyobacter polytropus DSM 2926 CP002281 2,880 14+2 9 1 6+2 - 2 - 6

454 Leptotrichia buccalis DSM 1135 CP001685 2,220 - - - - - - -

455 Sebaldella termitidis ATCC 33386 CP001739 4,150 - - - - - - -

456 Streptobacillus moniliformis DSM 12112 CP001779 1,442 - - - - - - -

Planctomycetes GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

457 Isosphaera pallida ATCC 43644 CP002353 3,722 4 - - 1 - 2 -

458 Pirellula staleyi DSM 6068 CP001848 4,717 6+1 - 3 2+1 1 5 - 1

459 Planctomyces brasiliensis DSM 5305 CP002546 4,750 4+1 - - 5+1 2 2 -

460 Planctopirus limnophila DSM 3776 CP001744 4,258 4+1 - - 4+1 4 6 -

461 Rhodopirellula baltica SH 1 BX119912 7,325 6+2 2 1 4+2 1 5 - 1

Proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

Alpha-proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

462 Acetobacter pasteurianus IFO 3283-01 AP011121 2,987 - - - - - - -

463 Acidiphilium cryptum JF-5 CP000697 3,559 5 9 4 - 1 - -

464 Acidiphilium multivorum AIU301 AP012035 3,948 5 11 4 - 1 - -

465 Agrobacterium radiobacter K84 CP000628 6,684 7 15 1 - 5 - -

466 Agrobacterium sp. H13-3 CP002248 5,345 17 14 4 2 4 - -

467 Agrobacterium tumefaciens str. C58 AE008688 5,402 16 13 1 1 3 - -

468 Agrobacterium vitis S4 CP000633 5,389 17 15 1 2 5 - -

469 Anaplasma centrale str. Israel CP001759 923 1 - - - - - -

470 Anaplasma marginale str. St. Maries CP000030 949 1 - - - - - -

471 Anaplasma phagocytophilum HZ CP000235 1,264 1 - - - - - -

472 Asticcacaulis excentricus CB 48 CP002395 3,763 4 8 3 1 2 - -

473 Azorhizobium caulinodans ORS 571 AP009384 4,717 24 10 4 1 3 -

474 Azospirillum sp. B510 AP010946 6,309 20 19 3 6 5 1 -

475 Bartonella bacilliformis KC583 CP000524 1,283 - 1 - - - - -

476 Bartonella clarridgeiae 73 FN645454 1,330 - 1 - - - - -

477 Bartonella grahamii as4aup CP001562 1,768 - 1 - - - - -

478 Bartonella henselae str. Houston-1 BX897699 1,488 - 1 - - - - -

479 Bartonella quintana str. Toulouse BX897700 1,142 - 1 - - - - -

480 Bartonella tribocorum CIP 105476 AM260525 2,092 - 1 - - - - -

481 Beijerinckia indica subsp. indica ATCC 9039 CP001016 3,784 1 1 1 - 1 - -

482 Bradyrhizobium japonicum USDA 110 BA000040 8,317 12 23 4 3 13 - -

483 Bradyrhizobium sp. BTAi1 CP000494 7,622 15 15 3 3 12 - -

484 Bradyrhizobium sp. ORS278 CU234118 6,717 15 15 3 2 10 - -

485 Brevundimonas subvibrioides ATCC 15264 CP002102 3,327 4 3 4 - 1 - -

486 Brucella abortus biovar 1 str. 9-941 AE017223 3,085 2 2 2 - 1 - -

487 Brucella canis ATCC 23365 CP000872 3,251 6 3 2 - 1 - -

488 Brucella melitensis bv. 1 str. 16M AE008917 3,198 6 3 2 - 1 - -

489 Brucella microti CCM 4915 CP001579 3,287 6 3 2 - 1 - -

490 Brucella ovis ATCC 25840 CP000709 2,890 4 3 - - 1 - -

491 Brucella pinnipedialis B2/94 CP002078 3,324 6 3 2 - 1 - -

492 Brucella suis 1330 AE014291 3,271 5 3 2 - 1 - -

493 Candidatus Hodgkinia cicadicola Dsem CP001226 169 - - - - - - -

494 Candidatus Liberibacter asiaticus str. psy62 CP001677 1,109 1 1 - - 1 - -

495 Candidatus Liberibacter solanacearum CLso-ZC1 CP002371 1,192 1 1 - - 1 - -

496 Candidatus Midichloria mitochondrii IricVA CP002130 1,210 - - - - - - -

497 Candidatus Pelagibacter sp. IMCC9063 CP002511 1,447 - - - - - - -

498 Candidatus Pelagibacter ubique HTCC1062 CP000084 1,354 - - - - - - -

499 Candidatus Puniceispirillum marinum IMCC1322 CP001751 2,543 - - - - - - -

500 Caulobacter crescentus CB15 AE005673 3,737 4 7 3 - 2 - -

501 Caulobacter segnis ATCC 21756 CP002008 4,139 4 5 3 - 3 - -

502 Caulobacter sp. K31 CP000927 5,438 3 6 2 - 3 1 -

503 Chelativorans sp. BNC1 CP000390 4,543 4 7 1 - 1 - -

504 Dinoroseobacter shibae DFL 12 CP000830 4,187 2 1 1 - - 1 -

505 Ehrlichia canis str. Jake CP000107 925 1 - - - - - -

506 Ehrlichia chaffeensis str. Arkansas CP000236 1,105 1 - - - - - -

507 Ehrlichia ruminantium str. Welgevonden CR767821 888 2 - - - - - -

508 Erythrobacter litoralis HTCC2594 CP000157 3,011 3 7 1 - 11 - -

509 Gluconacetobacter diazotrophicus PAl 5 CP001189 3,852 8 9 1 - - 1 -

510 Gluconacetobacter xylinus NBRC 3288 AP012159 3,190 - 13 - - 4 - -

511 Gluconobacter oxydans 621H CP000009 2,664 2 4 1 1 - - -

512 Granulibacter bethesdensis CGDNIH1 CP000394 2,437 - - - - - - -

513 Hirschia baltica ATCC 49814 CP001678 3,187 4 6 4 - 2 - -

514 Hyphomicrobium denitrificans ATCC 51888 CP002083 3,512 2 5 2 - 6 - -

515 Hyphomicrobium sp. MC1 FQ859181 4,893 5 10 2 - 7 - -

516 Hyphomonas neptunium ATCC 15444 CP000158 3,505 10 9 2 - 4 - -

517 Jannaschia sp. CCS1 CP000264 4,283 2 8 2 - 1 1 -

518 Ketogulonicigenium vulgare Y25 CP002224 3,213 2 2 1 - - - -

519 Ketogulonigenium vulgarum WSH-001 CP002018 3,054 2 2 1 - - - -

919 Magnetococcus marinus MC-1 CP000471 3,716 25 17 1 16 15 2 -

520 Magnetospirillum magneticum AMB-1 AP007255 4,559 29 17 10 16 10 - -

521 Maricaulis maris MCS10 CP000449 3,063 7 5 3 - 1 - -

522 Mesorhizobium ciceri biovar biserrulae WSM1271 CP002447 6,264 13 11 2 - 2 - -

523 Mesorhizobium loti MAFF303099 BA000012 7,275 16 16 2 1 2 - -

524 Mesorhizobium opportunistum WSM2075 CP002279 6,508 12 13 3 1 1 - -

525 Methylobacterium chloromethanicum CM4 CP001298 5,516 17 19 4 7 10 - -

526 Methylobacterium extorquens PA1 CP000908 4,829 17 14 4 6 9 - -

527 Methylobacterium nodulans ORS 2060 CP001349 7,900 5 6 2 3 8 - -

528 Methylobacterium populi BJ001 CP001029 5,365 18 11 3 4 9 - -

529 Methylobacterium radiotolerans JCM 2831 CP001001 6,431 10 20 4 6 12 - -

530 Methylobacterium sp. 4-46 CP000943 6,692 12 17 1 6 14 - -

531 Methylocella silvestris BL2 CP001280 3,818 5 4 - - 1 - -

532 Micavibrio aeruginosavorus ARL-13 CP002382 2,432 7 2 5 1 1 2 -

533 Neorickettsia risticii str. Illinois CP001431 898 1 - 1 - - - -

534 Neorickettsia sennetsu str. Miyayama CP000237 932 1 - 1 - - - -

535 Nitrobacter hamburgensis X14 CP000319 4,326 6 5 3 1 6 - -

536 Nitrobacter winogradskyi Nb-255 CP000115 3,122 4 4 2 1 4 - -

537 Novosphingobium aromaticivorans DSM 12444 CP000248 3,324 1 7 1 1 8 - -

538 Novosphingobium sp. PP1Y FR856862 4,664 13 11 3 1 17 -

539 Ochrobactrum anthropi ATCC 49188 CP000758 4,799 13 6 - - 2 - -

540 Oligotropha carboxidovorans OM5 CP001196 3,722 14 7 1 1 6 - -

541 Orientia tsutsugamushi str. Boryong AM494475 1,182 1 - 1 - - - -

542 Paracoccus denitrificans PD1222 CP000489 5,077 2 - 2 - - 1 -

543 Parvibaculum lavamentivorans DS-1 CP000774 3,636 4 3 2 - 3 1 -

544 Parvularcula bermudensis HTCC2503 CP002156 2,687 4 1 2 - 3 - -

545 Pelagibacterium halotolerans B2 CP003075 3,881 10 10 2 3 3 - -

546 Phenylobacterium zucineum HLK1 CP000747 3,854 4 3 2 - - - -

547 Polymorphum gilvum SL003B-26A1 CP002568 4,393 13 12 3 0* 7 - -

548 Pseudovibrio sp. FO-BEG1 CP003147 5,468 2 9 3 - 3 - -

549 Rhizobium etli CFN 42 CP000133 5,963 14 21 - 1 7 - -

550 Rhizobium leguminosarum bv. viciae 3841 AM236086 7,150 15 22 - 3 7 - -

552 Rhodobacter capsulatus SB 1003 CP001312 3,642 2 16 2 - - 1 -

553 Rhodobacter sphaeroides 2.4.1 CP000143 4,126 9 7 - - 1 1 -

554 Rhodomicrobium vannielii ATCC 17100 CP002292 3,565 - 1 - - - - -

555 Rhodopseudomonas palustris CGA009 BX571963 4,813 22 14 4 2 8 1 -

556 Rhodospirillum centenum SW CP000613 4,002 8 6 2 2 4 - -

557 Rhodospirillum rubrum ATCC 11170 CP000230 3,841 21 15 4 2 2 2 -

558 Rickettsia africae ESF-5 CP001612 1,041 1 - 1 - - - -

559 Rickettsia akari str. Hartford CP000847 1,259 1 - 1 - - - -

560 Rickettsia bellii RML369-C CP000087 1,429 1 - 1 - - - -

561 Rickettsia canadensis str. McKiel CP000409 1,093 1 - 1 - - - -

562 Rickettsia conorii str. Malish 7 AE006914 1,374 1 - 1 - - - -

563 Rickettsia felis URRWXCal2 CP000053 1,532 1 - 1 - - - -

564 Rickettsia heilongjiangensis 054 CP002912 1,297 1 - 1 - - - -

565 Rickettsia japonica YH AP011533 971 1 - 1 - - - -

566 Rickettsia massiliae MTU5 CP000683 980 1 - 1 - - - -

567 Rickettsia peacockii str. Rustic CP001227 947 1 - 1 - - - -

568 Rickettsia prowazekii str. Madrid E AJ235269 835 1 - 1 - - - -

569 Rickettsia rickettsii str. Iowa CP000766 1,384 1 - 1 - - - -

570 Rickettsia slovaca 13-B CP002428 1,112 1 - 1 - - - -

571 Rickettsia typhi str. Wilmington AE017197 838 1 - 1 - - - -

572 Roseobacter denitrificans OCh 114 CP000362 4,129 2 6 1 - - 1 -

573 Roseobacter litoralis Och 149 CP002623 4,537 1 8 1 - - 1 -

574 Ruegeria pomeroyi DSS-3 CP000031 4,252 4 1 1 - - 1 -

575 Ruegeria sp. TM1040 CP000377 3,864 5 6 2 - - - -

551 Sinorhizobium fredii NGR234 CP001389 6,366 12 17 1 - 8 - -

576 Sinorhizobium medicae WSM419 CP000738 6,213 6 13 1 - 4 - -

577 Sinorhizobium meliloti 1021 AL591688 6,205 6 12 1 - 3 - -

578 Sphingobium chlorophenolicum L-1 CP002798 4,072 6 8 - 1 11 - - 1

579 Sphingobium japonicum UT26S AP010803 4,394 7 10 - - 12 - -

580 Sphingobium sp. SYK-6 AP012222 4,062 5 5 3 2 6 - - 1

581 Sphingomonas wittichii RW1 CP000699 5,345 12 7 1 1 9 - -

582 Sphingopyxis alaskensis RB2256 CP000356 3,195 6 6 1 - 9 - -

583 Starkeya novella DSM 506 CP002026 4,431 14 9 3 - 1 - -

584 Wolbachia endosymbiont of Culex quinquefasciatus Pel AM999887 1,275 1 - - - - - -

585 Wolbachia endosymbiont of Drosophila melanogaster AE017196 1,195 1 - - - - - -

586 Wolbachia endosymbiont strain TRS of Brugia malayi AE017321 805 1 - - - - - -

587 Wolbachia sp. wRi CP001391 1,150 1 - - - - - -

588 Xanthobacter autotrophicus Py2 CP000781 5,035 11 7 - - - 1 -

589 Zymomonas mobilis subsp. mobilis ZM4 AE008692 1,998 2 2 1 - 1 1 -

Beta-proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

590 Achromobacter xylosoxidans A8 CP002287 6,915 22 7 8 1 - 1 -

591 Acidovorax avenae subsp. avenae ATCC 19860 CP002521 4,737 27 20 5 6 3 4 -

592 Acidovorax citrulli AAC00-1 CP000512 4,709 23 17 4 3 2 2 -

593 Acidovorax ebreus TPSY CP001392 3,479 15 10 3 4 1 2 -

594 Acidovorax sp. JS42 CP000539 4,155 13 9 3 3 1 1 -

595 Alicycliphilus denitrificans BC CP002449 4,542 14 12 3 6 1 2 -

596 Aromatoleum aromaticum EbN1 CR555306 4,590 7 19 4 5 1 4 - 1

597 Azoarcus sp. BH72 AM406670 3,989 23 25 4 8 5 5 -

598 Bordetella avium 197N AM167904 3,381 9 5 5 1 2 1 -

599 Bordetella bronchiseptica RB50 BX470250 4,994 10 5 4 2 1 1 -

600 Bordetella parapertussis 12822 BX470249 4,185 8 5 4 2 1 - -

601 Bordetella pertussis Tohama I BX470248 3,436 5 2 1 1 1 - -

602 Bordetella petrii DSM 12804 AM902716 5,027 - 2 - - - - -

603 Burkholderia ambifaria AMMD CP000440 6,617 13 7 7 1 3 - BcsE

604 Burkholderia cenocepacia AU 1054 CP000458 6,477 13 5 6 2 3 - BcsE

605 Burkholderia gladioli BSR3 CP002599 7,410 12 8 8 2 3 - -

606 Burkholderia glumae BGR1 CP001503 5,773 12 5 7 2 2 - -

607 Burkholderia mallei ATCC 23344 CP000011 4,764 4 4 4 2 3 - BcsE

608 Burkholderia multivorans ATCC 17616 CP000869 6,259 9 7 6 - 2 - BcsE

609 Burkholderia phymatum STM815 CP001043 7,496 20 18 11 1 3 - -

610 Burkholderia phytofirmans PsJN CP001052 7,241 18 16 8 3 4 - - 1

611 Burkholderia pseudomallei K96243 BX571965 5,728 5 5 6 2 3 - BcsE

612 Burkholderia rhizoxinica HKI 454 FR687359 3,667 - 1 3 - - - -

613 Burkholderia sp. 383 CP000150 7,717 14 7 7 1 3 - -

614 Burkholderia sp. CCGE1001 CP002519 5,965 14 15 6 1 3 1 -

615 Burkholderia sp. CCGE1002 CP002013 5,988 18 12 7 - 3 - BcsE

616 Burkholderia sp. CCGE1003 CP002217 6,889 15 12 7 2 2 1 -

617 Burkholderia thailandensis E264 CP000086 5,634 6 4 4 2 2 - BcsE

618 Burkholderia vietnamiensis G4 CP000616 7,617 21 10 8 1 3 3 BcsE

619 Burkholderia xenovorans LB400 CP000271 8,702 15 17 12 - 5 - -

620 Candidatus Accumulibacter phosphatis clade IIA str. UW-1 CP001715 4,562 19 18 3 10 6 5 -

621 Candidatus Tremblaya princeps PCIT CP002244 121 - - - - - - -

622 Candidatus Zinderia insecticola CARI CP002161 202 - - - - - - -

623 Chromobacterium violaceum ATCC 12472 AE016825 4,407 27 16 10 11 4 1 BcsE

624 Collimonas fungivorans Ter331 CP002745 4,432 9 3 2 - 1 2 -

625 Comamonas testosteroni CNB-2 CP001220 4,803 29 14 4 5 1 2 -

626 Cupriavidus metallidurans CH34 CP000352 6,319 19 13 10 2 6 1 BcsE

627 Cupriavidus necator N-1 CP002880 7,832 12 9 3 2 6 1 -

628 Cupriavidus taiwanensis LMG19424 CU633749 5,897 11 7 1 1 6 1 -

629 Dechloromonas aromatica RCB CP000089 4,171 29 28 3 15 6 5 -

630 Delftia acidovorans SPH-1 CP000884 6,040 24 17 6 7 1 3 - 1

631 Delftia sp. Cs1-4 CP002735 5,861 26 17 7 8 1 3 -

632 Gallionella capsiferriformans ES-2 CP002159 2,894 32 25 3 18 3 5 -

633 Herbaspirillum seropedicae SmR1 CP002039 4,735 27 16 4 11 2 1 -

634 Herminiimonas arsenicoxydans CU207211 3,325 20 14 2 3 3 3 -

635 Janthinobacterium sp. Marseille CP000269 3,697 20 13 4 2 1 1 -

636 Laribacter hongkongensis HLHK9 CP001154 3,336 14 13 3 4 2 2 -

637 Leptothrix cholodnii SP-6 CP001013 4,363 20 24 - 8 5 7 -

638 Methylibium petroleiphilum PM1 CP000555 4,449 11 11 1 3 3 5 -

639 Methylobacillus flagellatus KT CP000284 2,753 9 13 5 2 3 31 - 1

640 Methylotenera mobilis JLW8 CP001672 2,338 16 24 2 6 3 4 - 1

641 Methylotenera versatilis 301 CP002056 2,764 18 28 6 6 3 5 - 1

642 Methylovorus glucosetrophus SIP3-4 CP001674 2,909 15 25 7 2 3 5 - 2

643 Methylovorus sp. MP688 CP002252 2,712 15 23 7 2 4 6 - 2

644 Neisseria gonorrhoeae FA 1090 AE004969 2,002 - - - - 1 - -

645 Neisseria lactamica 020-06 FN995097 1,972 - - - - 1 - -

646 Neisseria meningitidis MC58 AE002098 2,079 - - - - 1 - -

647 Nitrosomonas europaea ATCC 19718 AL954747 2,461 2 4 5 - 1 2 - 1

648 Nitrosomonas eutropha C91 CP000450 2,550 3 4 3 1 1 2 - 1

649 Nitrosomonas sp. AL212 CP002552 2,983 11 11 6 4 2 2 -

650 Nitrosomonas sp. Is79A3 CP002876 3,372 14 17 7 6 4 1 -

651 Nitrosospira multiformis ATCC 25196 CP000103 2,805 6 11 3 1 1 2 - 2

652 Polaromonas naphthalenivorans CJ2 CP000529 4,929 - 1 - - 1 3 -

653 Polaromonas sp. JS666 CP000316 5,453 3 3 1 - 1 2 -

654 Polynucleobacter necessarius QLW-P1DMWA-1 CP000655 2,077 3 - - 2 1 - -

655 Pseudogulbenkiania sp. NH8B AP012224 4,012 18 18 9 5 3 2 -

656 Pusillimonas sp. T7-7 CP002663 3,773 - - - - - - -

657 Ralstonia eutropha JMP134 CP000090 6,446 17 11 2 3 6 2 BcsE

658 Ralstonia pickettii 12J CP001068 4,952 12 14 4 3 3 3 - 1

659 Ralstonia solanacearum GMI1000 AL646052 5,116 12 10 4 2 2 3 -

660 Ramlibacter tataouinensis TTB310 CP000245 3,880 4 2 - - 2 3 -

661 Rhodoferax ferrireducens T118 CP000267 4,418 25 30 - 14 2 5 - 1

662 Sideroxydans lithotrophicus ES-1 CP001965 2,980 23 25 4 14 4 4 - 1

663 Taylorella equigenitalis MCE9 CP002456 1,556 - - - - - - -

664 Thauera sp. MZ1T CP001281 3,978 8 11 - 2 3 4 -

665 Thiobacillus denitrificans ATCC 25259 CP000116 2,827 15 16 4 2 3 4 - 1

666 Thiomonas intermedia K12 CP002021 3,172 14 10 4 1 2 2 -

667 Thiomonas arsenitoxydans FP475956 3,674 14 15 5 1 2 1 -

668 Variovorax paradoxus S110 CP001635 6,279 6 4 1 - 1 2 -

669 Verminephrobacter eiseniae EF01-2 CP000542 4,947 4 4 1 1 1 3 -

Gamma-proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

670 Acidithiobacillus caldus SM-1 CP002573 2,880 7 7 2 - 8 2 FleQ

671 Acidithiobacillus ferrivorans SS3 CP002985 3,093 2 14 - 1 7 1 -

672 Acidithiobacillus ferrooxidans ATCC 53993 CP001132 2,826 - 3 - - 2 - -

673 Acinetobacter baumannii ATCC 17978 CP000521 3,368 7 3 2 - 1 - -

674 Acinetobacter baylyi ADP1 CR543861 3,325 7 3 1 - 1 1 -

675 Acinetobacter pittii PHEA-2 CP002177 3,599 7 3 2 - 1 - -

676 Acinetobacter oleivorans DR1 CP002080 3,874 7 3 2 - - - -

677 Actinobacillus pleuropneumoniae L20 CP000569 2,012 - - - - - - -

678 Actinobacillus succinogenes 130Z CP000746 2,079 - - - - - - -

679 Aeromonas hydrophila subsp. hydrophila ATCC 7966 CP000462 4,122 32 13 10 14 3 2 FleQ 4

680 Aeromonas salmonicida subsp. salmonicida A449 CP000644 4,437 31 10 7 10 4 2 - 5

681 Aeromonas veronii B565 CP002607 4,028 36 11 8 10 3 2 FleQ 5

682 Aggregatibacter actinomycetemcomitans D11S-1 CP001733 2,134 - - - - - - -

683 Aggregatibacter aphrophilus NJ8700 CP001607 2,231 - - - - - - -

684 Alcanivorax borkumensis SK2 AM286690 2,755 9 3 - 1 5 1 -

685 Aliivibrio salmonicida LFI1238 FM178379 3,911 26 6 6 5 4 - BcsE, FleQ, VpsT 1

686 Alkalilimnicola ehrlichei MLHE-1 CP000453 2,865 23 18 3 1 5 1 -

687 Allochromatium vinosum DSM 180 CP001896 3,220 23 15 4 12 10 3 -

688 Alteromonas macleodii 'Deep ecotype' CP001103 4,072 26 23 4 9 7 1 FleQ

689 Alteromonas sp. SN2 CP002339 4,371 28 33 4 7 7 1 FleQ

690 Azotobacter vinelandii DJ CP001157 5,050 13 10 1 3 5 1 FleQ

691 Baumannia cicadellinicola str. Hc (Homalodisca coagulata) CP000238 595 - - - - - - -

692 Buchnera aphidicola str. APS (Acyrthosiphon pisum) BA000003 574 - - - - - - -

693 Candidatus Blochmannia floridanus BX248583 583 - - - - - - -

694 Candidatus Blochmannia pennsylvanicus str. BPEN CP000016 610 - - - - - - -

695 Candidatus Blochmannia vafer str. BVAF CP002189 587 - - - - - - -

696 Candidatus Carsonella ruddii PV AP009180 182 - - - - - - -

697 Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum) CP001277 2,155 - - - - - - -

698 Candidatus Moranella endobia PCIT CP002243 406 - - - - - - -

699 Candidatus Riesia pediculicola USDA CP001085 556 - - - - - - -

700 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) CP000488 976 - - - - - - -

701 Candidatus Vesicomyosocius okutanii HA AP009247 937 - - - - - - -

702 Cellvibrio japonicus Ueda107 CP000934 3,754 20 21 3 5 12 6 FleQ

703 Chromohalobacter salexigens DSM 3043 CP000285 3,298 11 10 2 2 3 1 -

704 Citrobacter koseri ATCC BAA-895 CP000822 5,026 10 7 12 - 4 - BcsE

705 Citrobacter rodentium ICC168 FN543502 4,913 8 7 11 1 2 - BcsE

706 Colwellia psychrerythraea 34H CP000083 4,910 35 26 5 3 9 1 FleQ 3

707 Coxiella burnetii RSA 493 AE016828 2,046 1 - - - - - -

708 Cronobacter sakazakii ATCC BAA-894 CP000783 4,434 12 9 12 - 2 - BcsE

709 Cronobacter turicensis z3032 FN543093 4,455 12 9 11 - 2 - BcsE

710 Dichelobacter nodosus VCS1703A CP000513 1,280 - - 1 - 1 - -

711 Dickeya dadantii Ech703 CP001654 3,970 15 5 7 - 2 - -

712 Dickeya zeae Ech1591 CP001655 4,163 10 3 3 - 2 - -

713 Edwardsiella ictaluri 93-146 CP001600 3,784 3 4 3 - - - -

714 Edwardsiella tarda EIB202 CP001135 3,588 8 4 5 1 2 - BcsE

715 Enterobacter aerogenes KCTC 2190 CP002824 4,912 12 8 10 1 1 - BcsE

716 Enterobacter asburiae LF7a CP003026 4,612 18 10 21 - 3 - BcsE

717 Enterobacter cloacae subsp. cloacae ATCC 13047 CP001918 5,518 15 9 15 1 2 - BcsE

718 Enterobacter sp. 638 CP000653 4,240 16 10 10 1 3 - BcsE

719 Erwinia amylovora ATCC 49946 FN666575 3,565 4 4 4 - 1 - BcsE

720 Erwinia billingiae Eb661 FP236843 4,917 12 15 10 1 3 - BcsE

721 Erwinia pyrifoliae Ep1/96 FP236842 3,691 3 4 4 - 1 - BcsE

722 Erwinia sp. Ejp617 CP002124 3,672 3 4 4 - 1 - BcsE

723 Erwinia tasmaniensis Et1/99 CU468135 3,622 6 4 6 - 4 - -

724 Escherichia coli str. K-12 substr. MG1655 U00096 4,132 12 7 10 - 2 1 BcsE

725 Escherichia coli O157:H7 str. EDL933 BA000007 5,253 12 7 9 - 2 1 BcsE

726 Escherichia fergusonii ATCC 35469 CU928158 4,266 13 8 8 - 3 1 BcsE

727 Ferrimonas balearica DSM 9799 CP002209 3,782 15 12 2 6 5 1 FleQ 3

728 Francisella novicida U112 CP000439 1,719 - 2 - - 1 - -

729 Francisella philomiragia subsp. philomiragia ATCC 25017 CP000937 1,915 - - - - 1 - -

730 Francisella sp. TX077308 CP002872 1,976 - - - - 1 - -

731 Francisella tularensis subsp. tularensis SCHU S4 AJ749949 1,804 - - - - 1 - -

732 Gallibacterium anatis UMN179 CP002667 2,500 - - - - - - -

733 gamma proteobacterium HdN1 FP929140 3,763 21 23 4 4 14 2 FleQ

734 Glaciecola nitratireducens FR1064 CP003060 3,654 40 38 6 2 4 2 FleQ

735 Glaciecola sp. 4H-3-7+YE-5 CP002526 4,547 41 24 4 5 5 1 FleQ

736 Haemophilus ducreyi 35000HP AE017143 1,717 - - - - - - -

737 Haemophilus influenzae Rd KW20 L42023 1,711 - - - - - - -

738 Haemophilus parainfluenzae T3T1 FQ312002 1,981 - - - - - - -

739 Haemophilus parasuis SH0165 CP001321 2,021 - - - - - - -

740 Hahella chejuensis KCTC 2396 CP000155 6,778 31 33 6 8 16 5 FleQ

741 Halomonas elongata DSM 2581 FN869568 3,474 3 2 - - - 1 FleQ

742 Halorhodospira halophila SL1 CP000544 2,407 10 9 3 5 4 1 -

743 Halothiobacillus neapolitanus c2 CP001801 2,537 13 10 4 2 5 - FleQ

744 Histophilus somni 129PT CP000436 1,792 - - - - - - -

745 Idiomarina loihiensis L2TR AE017340 2,640 16 17 3 1 7 1 -

746 Kangiella koreensis DSM 16069 CP001707 2,632 21 14 1 4 3 1 -

747 Klebsiella oxytoca KCTC 1686 CP003218 5,488 13 7 9 2 3 - BcsE

748 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 CP000647 5,187 13 6 14 1 3 - BcsE

749 Klebsiella variicola At-22 CP001891 5,057 14 7 10 1 3 - BcsE

750 Legionella longbeachae NSW150 FN650140 3,470 8 6 1 1 2 1 FleQ

751 Legionella pneumophila subsp. pneumophila str. Philadelphia 1 AE017354 2,942 8 11 3 - 2 - FleQ

752 Mannheimia succiniciproducens MBEL55E AE016827 2,384 - - - - - - -

753 Marinobacter adhaerens HP15 CP001978 4,411 35 28 5 9 10 2 FleQ 1

754 Marinobacter aquaeolei VT8 CP000514 4,272 30 19 5 8 11 4 FleQ

755 Marinomonas mediterranea MMB-1 CP002583 4,121 36 28 8 5 3 1 -

756 Marinomonas posidonica IVIA-Po-181 CP002771 3,491 28 17 6 6 1 - -

757 Marinomonas sp. MWYL1 CP000749 4,439 42 15 8 6 2 - -

758 Methylococcus capsulatus str. Bath AE017282 2,959 5 11 1 1 1 2 -

759 Methylomicrobium alcaliphilum FO082060 3,982 19 34 3 10 11 1 - 1

760 Methylomonas methanica MC09 CP002738 4,494 25 35 2 13 14 3 - 1

761 Moraxella catarrhalis RH4 CP002005 1,886 - - - - - - -

762 Nitrosococcus halophilus Nc4 CP001798 3,817 4 10 1 - 4 1 FleQ 1

763 Nitrosococcus oceani ATCC 19707 CP000127 2,974 2 12 - 1 4 2 FleQ

764 Nitrosococcus watsonii C-113 CP002086 2,908 2 11 - 1 4 3 FleQ

765 Pantoea ananatis LMG 20103 CP001875 4,237 13 9 8 1 2 - -

766 Pantoea sp. At-9b CP002433 5,770 17 10 11 1 3 - BcsE

767 Pantoea vagans C9-1 CP002206 4,590 15 15 10 1 3 - BcsE

768 Pasteurella multocida subsp. multocida str. Pm70 AE004439 2,015 - - - - - - -

769 Pectobacterium atrosepticum SCRI1043 BX950851 4,472 13 4 7 1 2 - BcsE

770 Pectobacterium carotovorum subsp. carotovorum PC1 CP001657 4,246 15 3 8 1 3 - BcsE

771 Pectobacterium wasabiae WPP163 CP001790 4,437 14 4 8 1 3 - BcsE

772 Photobacterium profundum SS9 CR354531 5,480 22 10 6 2 5 1 BcsE, FleQ 3

773 Photorhabdus asymbiotica FM162591 4,422 - - - - - - -

774 Photorhabdus luminescens subsp. laumondii TTO1 BX470251 4,683 - - - - - - -

775 Proteus mirabilis HI4320 AM942759 3,662 1 - - - 2 - -

776 Pseudoalteromonas atlantica T6c CP000388 4,281 33 27 3 5 5 1 FleQ

777 Pseudoalteromonas haloplanktis TAC125 CR954246 3,486 21 17 7 3 6 1 BcsE

778 Pseudoalteromonas sp. SM9913 CP001796 3,712 31 23 8 7 8 - 1

779 Pseudomonas aeruginosa PAO1 AE004091 5,567 17 16 5 3 8 2 FleQ

780 Pseudomonas brassicacearum subsp. brassicacearum NFM421 CP002585 6,095 22 20 3 5 6 1 FleQ

781 Pseudomonas entomophila L48 CT573326 5,134 19 19 2 - 9 1 FleQ

782 Pseudomonas fluorescens Pf-5 CP000076 6,137 21 19 10 4 7 - FleQ

783 Pseudomonas fulva 12-X CP002727 4,461 24 14 4 5 12 1 FleQ

784 Pseudomonas mendocina ymp CP000680 4,594 28 20 4 6 11 3 FleQ

785 Pseudomonas putida KT2440 AE015451 5,350 19 17 3 2 7 1 BcsE, FleQ

786 Pseudomonas stutzeri A1501 CP000304 4,128 19 15 3 2 8 1 BcsE, FleQ

787 Pseudomonas syringae pv. tomato str. DC3000 AE016853 5,608 16 19 2 1 8 1 FleQ

788 Pseudoxanthomonas spadix BD-a59 CP003093 3,149 11 8 1 1 3 - -

789 Pseudoxanthomonas suwonensis 11-1 CP002446 3,070 12 9 - 3 4 1 -

790 Psychrobacter arcticus 273-4 CP000082 2,120 - 1 - - 1 1 -

791 Psychrobacter cryohalolentis K5 CP000323 2,511 1 2 - - 1 1 -

792 Psychrobacter sp. PRwf-1 CP000713 2,385 - - - - - - -

793 Psychromonas ingrahamii 37 CP000510 3,541 23 32 5 5 1 1 - 4

794 Rahnella sp. Y9602 CP002505 5,111 12 8 8 1 3 - BcsE

795 Saccharophagus degradans 2-40 CP000282 4,008 25 18 2 9 12 2 FleQ 2

796 Salmonella bongori NCTC 12419 FR877557 3,863 5 7 7 - 2 - BcsE

797 Salmonella enterica serovar Paratyphi A str. ATCC 9150 CP000026 4,093 6 7 8 - 2 - BcsE

798 Salmonella enterica serovar Typhi str. CT18 AL513382 4,758 5 7 9 - 2 - BcsE

799 Salmonella enterica serovar Typhimurium LT2 AE006468 4,527 5 7 8 - 2 - BcsE

800 Serratia plymuthica AS9 CP002773 4,952 10 5 5 - 2 - BcsE

801 Serratia proteamaculans 568 CP000826 4,942 11 5 5 - 2 - BcsE

802 Serratia sp. AS12 CP002774 4,952 10 5 5 - 2 - BcsE

803 Serratia symbiotica str. 'Cinara cedri' CP002295 672 - - - - - - -

804 Shewanella amazonensis SB2B CP000507 3,645 44 24 5 8 4 2 FleQ

805 Shewanella baltica OS155 CP000563 4,489 35 25 6 11 5 2 FleQ 2

806 Shewanella denitrificans OS217 CP000302 3,754 35 22 4 8 6 3 FleQ 1

807 Shewanella frigidimarina NCIMB 400 CP000447 4,029 33 30 - 8 5 2 FleQ

808 Shewanella halifaxensis HAW-EB4 CP000931 4,278 28 18 4 5 5 2 FleQ 2

809 Shewanella loihica PV-4 CP000606 3,859 32 21 2 9 5 2 FleQ 1

810 Shewanella oneidensis MR-1 AE014299 4,467 30 23 5 9 4 2 FleQ 1

811 Shewanella pealeana ATCC 700345 CP000851 4,241 30 17 4 5 5 2 FleQ 1

812 Shewanella piezotolerans WP3 CP000472 4,933 26 17 3 6 3 2 FleQ

813 Shewanella putrefaciens CN-32 CP000681 3,972 21 21 4 6 5 1 FleQ 1

814 Shewanella sediminis HAW-EB3 CP000821 4,497 52+1 21 2 17+1 4 3 FleQ 1

815 Shewanella sp. ANA-3 CP000469 4,360 36 23 5 9 4 2 FleQ 2

816 Shewanella sp. MR-4 CP000446 3,924 37 24 4 9 4 2 FleQ 3

817 Shewanella sp. MR-7 CP000444 4,014 32 23 5 6 4 1 FleQ 3

818 Shewanella sp. W3-18-1 CP000503 4,044 21 22 5 5 5 1 FleQ 1

819 Shewanella violacea DSS12 AP011177 4,346 27 12 5 7 5 2 BcsE, FleQ 1

820 Shewanella woodyi ATCC 51908 CP000961 4,880 45 21 - 15 5 2 FleQ 2

821 Shigella boydii Sb227 CP000036 4,284 8 5 6 - 2 - BcsE

822 Shigella dysenteriae Sd197 CP000034 4,497 9 2 5 - 2 1 -

823 Shigella flexneri 2a str. 301 AE005674 4,441 6 2 6 - 2 1 BcsE

824 Shigella sonnei Ss046 CP000038 4,461 10 5 5 - 1 - BcsE

825 Sodalis glossinidius str. 'morsitans' AP008232 2,516 2 1 1 - - - -

826 Stenotrophomonas maltophilia K279a AM743169 4,386 18 10 3 2 3 1 -

827 Teredinibacter turnerae T7901 CP001614 4,255 21 15 3 6 10 2 FleQ 1

828 Thioalkalimicrobium cyclicum ALM1 CP002776 1,665 1 - - - - 1 -

829 Thioalkalivibrio sp. K90mix CP001905 2,855 22 20 4 1 6 2 -

830 Thioalkalivibrio sulfidophilus HL-EbGr7 CP001339 3,283 22 24 2 6 6 1 FleQ 4

831 Thiomicrospira crunogena XCL-2 CP000109 2,196 24 17 6 3 7 1 - 3

832 Tolumonas auensis DSM 9187 CP001616 3,130 13 8 1 2 2 - - 1

833 Vibrio anguillarum 775 CP002284 3,788 23 13 8 9 4 1 VpsT, FleQ 1

834 Vibrio cholerae O1 biovar El Tor str. N16961 AE003852 3,835 31 10 12 9 5 1 VpsT, FleQ 2

835 Vibrio fischeri ES114 CP000020 3,802 30 10 10 2 4 1 BcsE, FleQ, VpsT 1

836 Vibrio furnissii NCTC 11218 CP002377 4,462 38 15 11 8 4 1 VpsT, FleQ 1

837 Vibrio harveyi ATCC BAA-1116 CP000789 6,055 32 12 14 5 5 1 VpsT, FleQ 1

838 Vibrio parahaemolyticus RIMD 2210633 BA000031 4,832 28 16 13 5 5 1 VpsT, FleQ 2

839 Vibrio sp. EJY3 CP003241 4,786 22 13 7 5 4 1 VpsT, FleQ

840 Vibrio antiquarius sp. Ex25 CP001805 4,518 29 16 11 4 5 1 VpsT, FleQ 1

841 Vibrio splendidus LGP32 FM954972 4,431 30 18 7 9 3 1 VpsT, FleQ 1

842 Vibrio vulnificus CMCP6 AE016795 5,024 46 20 13 13 5 1 VpsT, FleQ 2

843 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis BA000021 617 - - - - - - -

844 Xanthomonas albilineans GPE PC73 FP565176 3,114 15 10 4 2 3 - -

845 Xanthomonas axonopodis pv. citri str. 306 AE008923 4,427 20 10 4 3 3 2 -

846 Xanthomonas campestris pv. campestris str. ATCC 33913 AE008922 4,181 21 10 4 3 4 1 -

847 Xanthomonas oryzae pv. oryzae KACC10331 AE013598 4,637 12 10 2 3 4 1 -

848 Xenorhabdus bovienii SS-2004 FN667741 4,260 - - - - - - -

849 Xenorhabdus nematophila ATCC 19061 FN667742 4,474 1 - 3 - - - -

850 Xylella fastidiosa 9a5c AE003849 2,832 1 2 1 1 2 - -

851 Yersinia enterocolitica subsp. enterocolitica 8081 AM286415 4,051 10 5 6 1 2 - BcsE

852 Yersinia pestis CO92 AL590842 4,067 2 3 3 - 1 - -

853 Yersinia pseudotuberculosis IP 32953 BX936398 4,038 3 3 3 1 1 - -

Delta-proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

854 Anaeromyxobacter dehalogenans 2CP-C CP000251 4,346 10 - 1 5 18 14 -

855 Anaeromyxobacter sp. Fw109-5 CP000769 4,466 10 - 1 4 14 13 -

856 Anaeromyxobacter sp. K CP001131 4,457 - - 1 4 21 15 -

857 Halobacteriovorax marinus SJ FQ312005 3,230 2 - - 12 15 1 -

858 Bdellovibrio bacteriovorus HD100 BX842601 3,587 5 - 1 6 15 3 - 1

859 Desulfarculus baarsii DSM 2075 CP002085 3,277 13 5 1 8 10 - - 1

860 Desulfatibacillum alkenivorans AK-01 CP001322 5,252 24 2 2 11 9 11 - 4

861 Desulfobacca acetoxidans DSM 11109 CP002629 2,866 4 - - 2 1 - - 3

862 Desulfobacterium autotrophicum HRM2 CP001087 4,947 25 5 2 13 10 7 -

863 Desulfobulbus propionicus DSM 2032 CP002364 3,283 15 9 1 13 14 6 - 1

864 Desulfococcus oleovorans Hxd3 CP000859 3,265 17 1 2 8 13 4 - 1

865 Desulfohalobium retbaense DSM 5692 CP001734 2,526 17+1 5 2 6 4 - - 2

866 Desulfomicrobium baculatum DSM 4028 CP001629 3,436 22 8 3 13 18 5 -

867 Desulfotalea psychrophila LSv54 CR522870 3,234 20 3 1 10 9 1 -

868 Desulfovibrio aespoeensis Aspo-2 CP002431 3,304 15 5 3 16 7 1 - 1

869 Desulfovibrio africanus str. Walvis Bay CP003221 3,725 14 6 1 10 9 4 - 1

870 Desulfovibrio alaskensis G20 CP000112 3,258 24 8 2 14 11 1 - 1

871 Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 CP003220 3,454 11 5 - 5 - - - 1

872 Desulfovibrio magneticus RS-1 AP010904 4,704 52 7 4 23 9 - -

873 Desulfovibrio salexigens DSM 2638 CP001649 3,807 29 5 5 22 10 1 -

874 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough AE017285 3,531 17 9 1 14 7 2 -

875 Desulfurivibrio alkaliphilus AHT2 CP001940 2,620 18+2 9 1 11+2 10 6 - 2

876 Geobacter bemidjiensis Bem CP001124 4,018 14 7 1 13 15 15 - 14

877 Geobacter lovleyi SZ CP001089 3,685 30 13 4 12 10 14 - 4

878 Geobacter metallireducens GS-15 CP000148 3,634 13 6 1 12 9 11 - 18

879 Geobacter sp. FRC-32 CP001390 3,798 14 5 2 16 14 - - 8

880 Geobacter sp. M18 CP002479 4,434 19 12 1 16 15 19 - 16

881 Geobacter sp. M21 CP001661 4,080 15 7 1 14 15 16 - 19

882 Geobacter sulfurreducens PCA AE017180 3,446 21 8 1 10 10 11 - 17

883 Geobacter uraniireducens Rf4 CP000698 4,357 17 1 2 15 11 10 - 28

884 Haliangium ochraceum DSM 14365 CP001804 6,719 12 - 1 2 17 13 -

885 Hippea maritima DSM 10411 CP002606 1,677 12+6 3 2 6+6 2 2 -

886 Lawsonia intracellularis PHE/MN1-00 AM180252 1,344 2 - - 1 - - -

887 Myxococcus fulvus HW-1 CP002830 7,284 18 - 2 6 24 22 -

888 Myxococcus xanthus DK 1622 CP000113 7,331 18 - 2 6 24 17 -

889 Pelobacter carbinolicus DSM 2380 CP000142 3,353 21 15 - 5 9 10 - 8

890 Pelobacter propionicus DSM 2379 CP000482 3,576 20 10 2 9 11 14 - 16

891 Sorangium cellulosum 'So ce 56' AM746676 9,384 10 1 - 2 11 11 -

892 Stigmatella aurantiaca DW4/3-1 CP002271 8,352 17 - 1 6 23 17 -

893 Syntrophobacter fumaroxidans MPOB CP000478 4,064 7 2 - 6 12 1 - 7

894 Syntrophus aciditrophicus SB CP000252 3,168 7 - - 7 5 5 -

Epsilon-proteobacteria GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

895 Arcobacter butzleri RM4018 CP000361 2,259 14 10 1 6 - - -

896 Arcobacter nitrofigilis DSM 7299 CP001999 3,126 27 11 2 5 - - -

897 Arcobacter sp. L AP012048 2,848 28 16 2 7 - - -

898 Campylobacter concisus 13826 CP000792 1,985 5 6 - - 1 - -

899 Campylobacter curvus 525.92 CP000767 1,931 5 6 - - 1 - -

900 Campylobacter fetus subsp. fetus 82-40 CP000487 1,719 6 3 1 - 1 - -

901 Campylobacter hominis ATCC BAA-381 CP000776 1,687 - 1 - - - - -

902 Campylobacter jejuni subsp. jejuni NCTC 11168 AL111168 1,623 1 - - - - - -

903 Campylobacter lari RM2100 CP000932 1,546 3 - - - - - -

904 Helicobacter acinonychis str. Sheeba AM260522 1,660 - - - - - - -

905 Helicobacter bizzozeronii CIII-1 FR871757 1,971 - - - - - - -

906 Helicobacter felis ATCC 49179 FQ670179 1,674 - - - - - - -

907 Helicobacter hepaticus ATCC 51449 AE017125 1,875 1 - - - - - -

908 Helicobacter mustelae 12198 FN555004 1,398 2 - - 1 - - -

909 Helicobacter pylori 26695 AE000511 1,576 - - - - - - -

910 Nautilia profundicola AmH CP001279 1,730 20 11 4 2 1 2 -

911 Nitratifractor salsuginis DSM 16511 CP002452 2,088 3 7 - 1 - - - 2

912 Nitratiruptor sp. SB155-2 AP009178 1,843 12 22 - - 3 1 -

913 Sulfuricurvum kujiense DSM 16994 CP002355 2,798 49+2 30 5 14+2 - 1 - 1

914 Sulfurimonas autotrophica DSM 16294 CP002205 2,158 29+2 21 2 4+2 - 3 - 1

915 Sulfurimonas denitrificans DSM 1251 CP000153 2,097 22 16 - 3 - - -

916 Sulfurospirillum deleyianum DSM 6946 CP001816 2,265 17 16 5 2 2 - -

917 Sulfurovum sp. NBC37-1 AP009179 2,438 6 12 1 - - - - 2

918 Wolinella succinogenes DSM 1740 BX571656 2,044 12 10 3 2 1 1 -

Spirochaetes GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

920 Borrelia afzelii PKo CP000395 1,215 1 - 1 1 1 - -

921 Borrelia bissettii DN127 CP002746 1,469 1 - 1 1 1 - -

922 Borrelia burgdorferi B31 AE001115 1,639 1 - 1 1 1 - -

923 Borrelia duttonii Ly CP000976 1,305 1 - 1 1 1 - -

924 Borrelia garinii PBi CP000013 932 1 - 1 1 1 - -

925 Borrelia hermsii DAH CP000048 819 1 - 1 1 1 - -

926 Borrelia recurrentis A1 CP000993 990 1 - 1 1 1 - -

927 Borrelia turicatae 91E135 CP000049 818 1 - 1 1 1 - -

928 Brachyspira hyodysenteriae WA1 CP001357 2,644 3 - - 3 1 - -

929 Brachyspira intermedia PWS/A CP002874 2,873 3 - - 3 1 - -

930 Brachyspira murdochii DSM 12563 CP001959 2,809 3 - - 4 1 - -

931 Brachyspira pilosicoli 95/1000 CP002025 2,299 3 - - 4 1 - -

932 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)' CP000777 3,600 7 5 5 5 10 1 -

933 Leptospira borgpetersenii serovar Hardjo-bovis L550 CP000348 2,945 4 - 4 4 6 1 -

934 Leptospira interrogans serovar Lai str. 56601 AE010300 4,727 13 3 5 4 5 1 -

935 Sphaerochaeta globus str. Buddy CP002541 3,017 18+5 8 1 3+5 - - -

936 Sphaerochaeta pleomorpha str. Grapes CP003155 3,159 15+4 6 2 6+4 - - -

937 Spirochaeta caldaria DSM 7334 CP002868 2,789 11 2 1 8 6 2 -

938 Spirochaeta coccoides DSM 17374 CP002659 1,822 - - - - - - -

939 Spirochaeta smaragdinae DSM 11293 CP002116 4,219 13 4 - 13 8 3 -

940 Spirochaeta thermophila DSM 6192 CP001698 2,203 6 7 - 3 8 2 -

941 Treponema azotonutricium ZAS-9 CP001841 3,474 10 - - 12 9 - -

942 Treponema brennaborense DSM 12168 CP002696 2,531 8 5 1 8 2 1 -

943 Treponema denticola ATCC 35405 AE017226 2,767 7 2 - 4 2 - -

944 Treponema pallidum subsp. pallidum str. Nichols AE000520 1,036 2 - - 3 1 - -

945 Treponema paraluiscuniculi Cuniculi A CP002103 1,010 2 - - 3 1 - -

946 Treponema primitia ZAS-2 CP001843 3,522 8 - - 8 6 - -

947 Treponema succinifaciens DSM 2489 CP002631 2,452 3 3 1 4 5 - -

Tenericutes GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

948 Acholeplasma laidlawii PG-8A CP000896 1,380 8+1 4 1 1+1 - - - 3

949 Aster yellows witches'-broom phytoplasma AYWB CP000061 693 - - - - - - -

950 Candidatus Phytoplasma australiense AM422018 696 - - - - - - -

951 Candidatus Phytoplasma mali CU469464 479 - - - - - - -

952 Mesoplasma florum L1 AE017263 682 - - - - - - -

953 Mycoplasma agalactiae PG2 CU179680 742 - - - - - - -

954 Mycoplasma arthritidis 158L3-1 CP001047 631 - - - - - - -

955 Mycoplasma bovis PG45 CP002188 765 - - - - - - -

956 Mycoplasma capricolum subsp. capricolum ATCC 27343 CP000123 812 - - - - - - -

957 Mycoplasma conjunctivae HRC/581 FM864216 691 - - - - - - -

958 Mycoplasma crocodyli MP145 CP001991 689 - - - - - - -

959 Mycoplasma fermentans PG18 AP009608 893 - - - - - - -

960 Mycoplasma gallisepticum R AE015450 726 - - - - - - -

961 Mycoplasma genitalium G37 L43967 484 - - - - - - -

962 Mycoplasma haemocanis str. Illinois CP003199 1,156 - - - - - - -

963 Mycoplasma haemofelis str. Langford 1 FR773153 1,545 - - - - - - -

964 Mycoplasma hominis strain PG21 FP236530 523 - - - - - - -

965 Mycoplasma hyopneumoniae 232 AE017332 691 - - - - - - -

966 Mycoplasma hyorhinis HUB-1 CP002170 654 - - - - - - -

967 Mycoplasma leachii PG50 CP002108 882 - - - - - - -

968 Mycoplasma mobile 163K AE017308 633 - - - - - - -

969 Mycoplasma mycoides subsp. mycoides SC str. PG1 BX293980 1,016 - - - - - - -

970 Mycoplasma penetrans HF-2 BA000026 1,037 - - - - - - -

971 Mycoplasma pneumoniae M129 U00089 689 - - - - - - -

972 Mycoplasma pulmonis UAB CTIP AL445566 782 - - - - - - -

973 Mycoplasma putrefaciens KS1 CP003021 650 - - - - - - -

974 Mycoplasma suis str. Illinois CP002525 811 - - - - - - -

975 Mycoplasma synoviae 53 AE017245 672 - - - - - - -

976 Onion yellows phytoplasma OY-M AP006628 754 - - - - - - -

977 Ureaplasma parvum serovar 3 str. ATCC 700970 AF222894 614 - - - - - - -

978 Ureaplasma urealyticum serovar 10 str. ATCC 33699 CP001184 646 - - - - - - -

Thermotogae GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

979 Fervidobacterium nodosum Rt17-B1 CP000771 1,750 16 1 - 9 2 1 -

980 Kosmotoga olearia TBF 19.5.1 CP001634 2,224 7+2 - - 14 - 1 -

981 Petrotoga mobilis SJ95 CP000879 1,898 4 1 - 2 1 - -

982 Thermosipho africanus TCF52B CP001185 1,913 16 1 - 12 2 1 -

983 Thermosipho melanesiensis BI429 CP000716 1,879 15 1 - 12 2 1 -

984 Thermotoga lettingae TMO CP000812 2,040 10 - 1 10 1 2 -

985 Thermotoga maritima MSB8 AE000512 1,858 11 - - 10 1 1 -

986 Thermotoga naphthophila RKU-10 CP001839 1,768 10 - - 5 1 1 -

987 Thermotoga neapolitana DSM 4359 CP000916 1,937 9 - - 9 1 2 -

988 Thermotoga petrophila RKU-1 CP000702 1,785 11 - - 2 1 1 -

989 Thermotoga sp. RQ2 CP000969 1,819 11 - - 7 1 1 -

990 Thermotoga thermarum DSM 5069 CP002351 1,945 8 - - 9 1 2 -

Verrucomicrobia GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

991 Akkermansia muciniphila ATCC BAA-835 CP001071 2,138 - - - - - - -

992 Coraliomargarita akajimensis DSM 45221 CP001998 3,120 - - - - - - -

993 Methylacidiphilum infernorum V4 CP000975 2,472 - - - - - - -

994 Opitutus terrae PB90-1 CP001032 4,612 1 - - 1 - 1 -

Other bacterial phyla (1 or 2 genomes) GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

995 Candidatus Methylomirabilis oxyfera FP565575 3,061 4 - - 3 - 1 - 1

996 Candidatus Cloacimonas acidaminovorans CU466930 1,815 2 - - 2 - 1 -

997 Desulfurispirillum indicum S5 CP002432 2,571 14 5 5 12 4 2 -

998 Dictyoglomus thermophilum H-6-12 CP001146 1,912 7 2 - 8 - 2 -

999 Dictyoglomus turgidum DSM 6724 CP001251 1,744 6 2 - 9 - 2 -

1000 Elusimicrobium minutum Pei191 CP001055 1,529 2 - - 1 1 1 -

1001 Uncultured Termite group 1 bacterium phylotype Rs-D17 AP009510 776 - - - - - - -

1002 Fibrobacter succinogenes subsp. succinogenes S85 CP001792 3,085 21+1 4 1 9 1 1 -

1003 Gemmatimonas aurantiaca T-27 AP009153 3,935 7+1 5 2 2 - 2 -

1004 Nitrospira defluvii FP929003 4,268 5 1 - 9 31 1 -

1005 Thermodesulfovibrio yellowstonii DSM 11347 CP001147 2,033 5 - 2 5 1 3 -

1006 Aminobacterium colombiense DSM 12261 CP001997 1,876 3 - - 4 - - -

1007 Thermanaerovibrio acidaminovorans DSM 6589 CP001818 1,738 10 3 - 12 1 1 -

1008 Thermovirga lienii DSM 17291 CP003096 1,875 11 - - 7 1 1 - 1

1009 Thermodesulfatator indicus DSM 15286 CP002683 2,195 5 1 - 2 5 1 -

1010 Thermodesulfobacterium geofontis OPF15 CP002829 1,596 9 4 - 2 6 1 -

Archaea GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other
receptors Ribo-
switch1 Ribo-
switch2

Crenarchaeota GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

1011 Acidianus hospitalis W1 CP002535 2,329 - - - - - - -

1012 Acidilobus saccharovorans 345-15 CP001742 1,499 - - - - - - -

1013 Aeropyrum pernix K1 BA000002 1,841 0* - - - - - -

1014 Caldivirga maquilingensis IC-167 CP000852 1,963 - - - - - - -

1015 Desulfurococcus kamchatkensis 1221n CP001140 1,471 - - - - - - -

1016 Desulfurococcus mucosus DSM 2162 CP002363 1,345 - - - - - - -

1017 Hyperthermus butylicus DSM 5456 CP000493 1,602 - - - - - - -

1018 Ignicoccus hospitalis KIN4/I CP000816 1,434 - - - - - - -

1019 Ignisphaera aggregans DSM 17230 CP002098 1,930 - - - - - - -

1020 Metallosphaera cuprina Ar-4 CP002656 2,029 - - - - - - -

1021 Metallosphaera sedula DSM 5348 CP000682 2,256 - - - - - - -

1022 Pyrobaculum aerophilum str. IM2 AE009441 2,605 - - - - - - -

1023 Pyrobaculum arsenaticum DSM 13514 CP000660 2,299 - - - - - - -

1024 Pyrobaculum calidifontis JCM 11548 CP000561 2,149 - - - - - - -

1025 Pyrobaculum islandicum DSM 4184 CP000504 1,978 - - - - - - -

1026 Pyrobaculum sp. 1860 CP003098 2,824 - - - - - - -

1027 Pyrolobus fumarii 1A CP002838 1,967 - - - - - - -

1028 Staphylothermus hellenicus DSM 12710 CP002051 1,599 - - - - - - -

1029 Staphylothermus marinus F1 CP000575 1,570 - - - - - - -

1030 Sulfolobus acidocaldarius DSM 639 CP000077 2,223 - - - - - - -

1031 Sulfolobus islandicus M.14.25 CP001400 2,609 - - - - - - -

1032 Sulfolobus solfataricus P2 AE006641 2,977 - - - - - - -

1033 Sulfolobus tokodaii str. 7 BA000023 2,825 - - - - - - -

1034 Thermofilum pendens Hrk 5 CP000505 1,876 - - - - - - -

1035 Thermoproteus neutrophilus V24Sta CP001014 1,966 - - - - - - -

1036 Thermoproteus tenax Kra 1 FN869859 2,049 - - - - - - -

1037 Thermoproteus uzoniensis 768-20 CP002590 2,186 - - - - - - -

1038 Thermosphaera aggregans DSM 11486 CP001939 1,387 - - - - - - -

1039 Vulcanisaeta distributa DSM 14429 CP002100 2,493 - - - - - - -

1040 Vulcanisaeta moutnovskia 768-28 CP002529 2,320 - - - - - - -

Euryarchaeaota GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

1041 Aciduliprofundum boonei T469 CP001941 1,544 - - - - - - -

1042 Archaeoglobus fulgidus DSM 4304 AE000782 2,420 - - - - - - -

1043 Archaeoglobus profundus DSM 5631 CP001857 1,823 - - - - - - -

1044 Archaeoglobus veneficus SNP6 CP002588 2,090 - - - - - - -

1045 Ferroglobus placidus DSM 10642 CP001899 2,480 - - - - - - -

1046 Halalkalicoccus jeotgali B3 CP002062 3,873 - - - - - - -

1047 Haloarcula hispanica ATCC 33960 CP002921 3,859 - - - - - - -

1048 Haloarcula marismortui ATCC 43049 AY596297 4,240 - - - - - - -

1049 Halobacterium sp. NRC-1 AE004437 2,622 - - - - - - -

1050 Haloferax volcanii DS2 CP001956 4,042 - - - - - - -

1051 Halogeometricum borinquense DSM 11551 CP001690 3,898 - - - - - - -

1052 Halomicrobium mukohataei DSM 12286 CP001688 3,349 - - - - - - -

1053 Halopiger xanaduensis SH-6 CP002839 4,221 - - - - - - -

1054 Haloquadratum walsbyi DSM 16790 AM180088 2,646 - - - - - - -

1055 Halorhabdus utahensis DSM 12940 CP001687 2,998 - - - - - - -

1056 Halorubrum lacusprofundi ATCC 49239 CP001365 3,560 - - - - - - -

1057 Haloterrigena turkmenica DSM 5511 CP001860 5,113 - - - - - - -

1058 Methanobacterium sp. AL-21 CP002551 2,493 - - - - - - -

1059 Methanobacterium sp. SWAN-1 CP002772 2,397 - - - - - - -

1060 Methanobrevibacter ruminantium M1 CP001719 2,217 - - - - - - -

1061 Methanobrevibacter smithii ATCC 35061 CP000678 1,793 - - - - - - -

1062 Methanocaldococcus fervens AG86 CP001696 1,581 - - - - - - -

1063 Methanocaldococcus infernus ME CP002009 1,442 - - - - - - -

1064 Methanocaldococcus jannaschii DSM 2661 L77117 1,786 - - - - - - -

1065 Methanocaldococcus sp. FS406-22 CP001901 1,816 - - - - - - -

1066 Methanocaldococcus vulcanius M7 CP001787 1,742 - - - - - - -

1067 Methanocella paludicola SANAE AP011532 3,004 - - - - - - -

1068 Methanococcoides burtonii DSM 6242 CP000300 2,273 - - - - - - -

1069 Methanococcus aeolicus Nankai-3 CP000743 1,490 - - - - - - -

1070 Methanococcus maripaludis S2 BX950229 1,722 - - - - - - -

1071 Methanococcus vannielii SB CP000742 1,678 - - - - - - -

1072 Methanococcus voltae A3 CP002057 1,717 - - - - - - -

1073 Methanocorpusculum labreanum Z CP000559 1,739 - - - - - - -

1074 Methanoculleus marisnigri JR1 CP000562 2,489 - - - - - - -

1075 Methanohalobium evestigatum Z-7303 CP002069 2,254 - - - - - - -

1076 Methanohalophilus mahii DSM 5219 CP001994 1,987 - - - - - - -

1077 Methanoplanus petrolearius DSM 11571 CP002117 2,785 - - - - - - -

1078 Methanopyrus kandleri AV19 AE009439 1,687 0* - - - - - -

1079 Methanoregula boonei 6A8 CP000780 2,452 - - - - - - -

1080 Methanosaeta concilii GP-6 CP002565 2,850 - - - - - - -

1081 Methanosaeta thermophila PT CP000477 1,696 - - - - - - -

1082 Methanosalsum zhilinae DSM 4017 CP002101 1,976 - - - - - - -

1083 Methanosarcina acetivorans C2A AE010299 4,540 - - - - - - -

1084 Methanosarcina barkeri str. Fusaro CP000099 3,625 - - - - - - -

1085 Methanosarcina mazei Go1 AE008384 3,371 - - - - - - -

1086 Methanosphaera stadtmanae DSM 3091 CP000102 1,534 - - - - - - -

1087 Methanosphaerula palustris E1-9c CP001338 2,655 - - - - - - -

1088 Methanospirillum hungatei JF-1 CP000254 3,139 - - - - - - -

1089 Methanothermobacter marburgensis str. Marburg CP001710 1,757 - - - - - - -

1090 Methanothermobacter thermautotrophicus str. Delta H AE000666 1,873 - - - - - - -

1091 Methanothermococcus okinawensis IH1 CP002792 1,595 - - - - - - -

1092 Methanothermus fervidus DSM 2088 CP002278 1,285 - - - - - - -

1093 Methanotorris igneus Kol 5 CP002737 1,772 - - - - - - -

1094 Natrialba magadii ATCC 43099 CP001932 4,215 - - - - - - -

1095 Natronomonas pharaonis DSM 2160 CR936257 2,822 - - - - - - -

1096 Picrophilus torridus DSM 9790 AE017261 1,535 - - - - - - -

1097 Pyrococcus abyssi GE5 AL096836 1,896 - - - - - - -

1098 Pyrococcus furiosus DSM 3638 AE009950 2,125 - - - - - - -

1099 Pyrococcus horikoshii OT3 BA000001 1,955 - - - - - - -

1100 Pyrococcus sp. NA2 CP002670 1,980 - - - - - - -

1101 Pyrococcus yayanosii CH1 CP002779 1,865 - - - - - - -

1102 Thermococcus barophilus MP CP002372 2,207 - - - - - - -

1103 Thermococcus gammatolerans EJ3 CP001398 2,157 - - - - - - -

1104 Thermococcus kodakarensis KOD1 AP006878 2,306 - - - - - - -

1105 Thermococcus onnurineus NA1 CP000855 1,976 - - - - - - -

1106 Thermococcus sibiricus MM 739 CP001463 2,036 - - - - - - -

1107 Thermococcus sp. 4557 CP002920 2,133 - - - - - - -

1108 Thermoplasma acidophilum DSM 1728 AL139299 1,481 - - - - - - -

1109 Thermoplasma volcanium GSS1 BA000011 1,499 - - - - - - -

1110 Methanocella arvoryzae MRE50 AM114193 3,103 0+1 - - 0+1 - - -

Other archaea (1 to 3 genomes) GenBank All
proteins GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other Ribo-
switch1 Ribo-
switch2

1111 Candidatus Caldiarchaeum subterraneum BA000048 1,730 - - - - - - -

1112 Halophilic archaeon DL31 CP002988 3,445 - - - - - - -

1113 Candidatus Korarchaeum cryptofilum OPF8 CP000968 1,602 - - - - - - -

1114 Nanoarchaeum equitans Kin4-M AE017199 535 - - - - - - -

1115 Cenarchaeum symbiosum DP000238 2,017 - - - - - - -

1116 Nitrosopumilus maritimus SCM1 CP000866 1,795 - - - - - - -

No. Organism GenBank All prot. GGDEF GGDEF
+EAL EAL HD-GYP PilZ MshEN Other
receptors Ribo-
switch1 Ribo-
switch2

^a The numbers in the table are linked to protein lists, which are further linked to the GenBank CDS and UniProt database entries, BLAST Link outputs, and CDD, Pfam, and InterPro domain architectures. A dash indicates the absence of the respective proteins. Numbers with asterisks indicate the presence of proteins with highly divergent or truncated sequences, not included in the total count.
The numbers of riboswitches are taken from and linked to the Rfam database; empty cells indicate absence of riboswitch entries in Rfam.
^b The major changes introduced in the 2016 update are as follows: 1) removal of the GGDEF-containing c-di-AMP-specific phosphodiesterases (GdpP/YybT family); 2) addition of the columns for MshEN and "Other receptors" (BcsE, BldD, FleQ, VspT); 3) switch of the protein entries from RefSeq to GenBank CDS entries, and 4) correction of several minor errors.
^c The numbers after the plus sign indicate GGDEF-HD-GYP domain fusions