Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 4.0 --

Collection of regulogs in Rhizobiales taxonomic group

General statistics
Genomes 15
TF regulogs 97
TF regulons 539
TF binding sites 2353
RNA regulogs 12
RNA regulons 124
RNA sites 221

This collection involves all regulons that were tentatively predicted by applying integrative comparative genomic approach to a single taxonomic group of closely-related genomes. To infer the regulons operated by transcription factors (TFs), we combined the identification of TF binding sites and cross-genome comparison of regulons with the analysis of the genomic and functional context of candidate target genes. To infer the regulons operated by regulatory RNAs such as riboswitches, we identified candidate RNA regulatory elements using HMM profiles and further analyzed their genomic and functional context.

Studied genomes and reconstructed regulon statistics
TF RNA Total
Genomes Regulons Sites Regulons Sites Regulons Sites
Agrobacterium tumefaciens str. C58 (Cereon) 54 262 9 18 63 280
Azorhizobium caulinodans ORS 571 26 91 8 13 34 104
Bartonella quintana str. Toulouse 8 13 2 3 10 16
Bradyrhizobium japonicum USDA 110 34 166 6 12 40 178
Bradyrhizobium sp. BTAi1 35 147 8 12 43 159
Brucella melitensis 16M 27 111 9 14 36 125
Mesorhizobium loti MAFF303099 42 168 10 21 52 189
Mesorhizobium sp. BNC1 28 115 10 17 38 132
Nitrobacter winogradskyi Nb-255 13 34 7 11 20 45
Rhizobium etli CFN 42 57 252 9 16 66 268
Rhizobium leguminosarum bv. viciae 3841 55 258 10 19 65 277
Rhizobium sp. NGR234 57 253 10 17 67 270
Rhodopseudomonas palustris CGA009 22 124 9 20 31 144
Sinorhizobium meliloti 1021 56 252 8 15 64 267
Xanthobacter autotrophicus Py2 25 107 9 13 34 120
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF SahR
5 SahR

Sinorhizobium meliloti 1021
5 SahR

Rhizobium sp. NGR234
4 SahR

Rhizobium leguminosarum bv. viciae 3841
4 SahR

Rhizobium etli CFN 42
4 SahR

Agrobacterium tumefaciens str. C58 (Cereon)
3 SahR

Mesorhizobium sp. BNC1
4 SahR

Mesorhizobium loti MAFF303099
3 SahR

Brucella melitensis 16M
2 SahR

Azorhizobium caulinodans ORS 571
2 SahR

Xanthobacter autotrophicus Py2
Methionine metabolism
CRP TF FnrN/FixK/AadR
10 FnrN/FixK/AadR

Sinorhizobium meliloti 1021
11 FnrN/FixK/AadR

Rhizobium sp. NGR234
14 FnrN/FixK/AadR

Rhizobium leguminosarum bv. viciae 3841
13 FnrN/FixK/AadR

Rhizobium etli CFN 42
16 FnrN/FixK/AadR

Agrobacterium tumefaciens str. C58 (Cereon)
7 FnrN/FixK/AadR

Mesorhizobium sp. BNC1
6 FnrN/FixK/AadR

Mesorhizobium loti MAFF303099
6 FnrN/FixK/AadR

Brucella melitensis 16M
28 FnrN/FixK/AadR

Rhodopseudomonas palustris CGA009
21 FnrN/FixK/AadR

Bradyrhizobium japonicum USDA 110
20 FnrN/FixK/AadR

Bradyrhizobium sp. BTAi1
3 FnrN/FixK/AadR

Nitrobacter winogradskyi Nb-255
5 FnrN/FixK/AadR

Azorhizobium caulinodans ORS 571
5 FnrN/FixK/AadR

Xanthobacter autotrophicus Py2
Oxidative stress response; Nitrogen fixation
TF NnrR
12 NnrR

Sinorhizobium meliloti 1021
9 NnrR

Rhizobium sp. NGR234
5 NnrR

Rhizobium etli CFN 42
8 NnrR

Agrobacterium tumefaciens str. C58 (Cereon)
12 NnrR

Mesorhizobium sp. BNC1
5 NnrR

Brucella melitensis 16M
11 NnrR

Rhodopseudomonas palustris CGA009
13 NnrR

Bradyrhizobium japonicum USDA 110
10 NnrR

Bradyrhizobium sp. BTAi1
Denitrification
DeoR TF RhaR
2 RhaR

Sinorhizobium meliloti 1021
2 RhaR

Rhizobium sp. NGR234
2 RhaR

Rhizobium leguminosarum bv. viciae 3841
2 RhaR

Rhizobium etli CFN 42
2 RhaR

Agrobacterium tumefaciens str. C58 (Cereon)
2 RhaR

Mesorhizobium loti MAFF303099
Rhamnose utilization
DtxR TF MntR
2 MntR

Rhizobium sp. NGR234
2 MntR

Mesorhizobium sp. BNC1
2 MntR

Mesorhizobium loti MAFF303099
2 MntR

Bradyrhizobium sp. BTAi1
Manganese homeostasis
FUR TF Irr
10 Irr

Sinorhizobium meliloti 1021
11 Irr

Rhizobium sp. NGR234
9 Irr

Rhizobium leguminosarum bv. viciae 3841
7 Irr

Rhizobium etli CFN 42
12 Irr

Agrobacterium tumefaciens str. C58 (Cereon)
4 Irr

Mesorhizobium sp. BNC1
8 Irr

Mesorhizobium loti MAFF303099
4 Irr

Brucella melitensis 16M
3 Irr

Bartonella quintana str. Toulouse
9 Irr

Rhodopseudomonas palustris CGA009
11 Irr

Bradyrhizobium japonicum USDA 110
5 Irr

Bradyrhizobium sp. BTAi1
3 Irr

Nitrobacter winogradskyi Nb-255
9 Irr

Azorhizobium caulinodans ORS 571
9 Irr

Xanthobacter autotrophicus Py2
Iron homeostasis
TF Mur
1 Mur

Sinorhizobium meliloti 1021
1 Mur

Rhizobium sp. NGR234
2 Mur

Rhizobium leguminosarum bv. viciae 3841
1 Mur

Rhizobium etli CFN 42
2 Mur

Agrobacterium tumefaciens str. C58 (Cereon)
2 Mur

Mesorhizobium sp. BNC1
2 Mur

Brucella melitensis 16M
1 Mur

Bartonella quintana str. Toulouse
2 Mur

Rhodopseudomonas palustris CGA009
3 Mur

Bradyrhizobium japonicum USDA 110
3 Mur

Bradyrhizobium sp. BTAi1
3 Mur

Nitrobacter winogradskyi Nb-255
1 Mur

Azorhizobium caulinodans ORS 571
1 Mur

Xanthobacter autotrophicus Py2
Manganese homeostasis
TF Zur
3 Zur

Sinorhizobium meliloti 1021
2 Zur

Rhizobium sp. NGR234
5 Zur

Rhizobium leguminosarum bv. viciae 3841
6 Zur

Rhizobium etli CFN 42
6 Zur

Agrobacterium tumefaciens str. C58 (Cereon)
2 Zur

Mesorhizobium sp. BNC1
1 Zur

Mesorhizobium loti MAFF303099
2 Zur

Brucella melitensis 16M
1 Zur

Bartonella quintana str. Toulouse
3 Zur

Rhodopseudomonas palustris CGA009
2 Zur

Bradyrhizobium japonicum USDA 110
4 Zur

Bradyrhizobium sp. BTAi1
2 Zur

Nitrobacter winogradskyi Nb-255
Zinc homeostasis
Fis TF NifA
4 NifA

Sinorhizobium meliloti 1021
10 NifA

Rhizobium sp. NGR234
2 NifA

Rhizobium leguminosarum bv. viciae 3841
8 NifA

Rhizobium etli CFN 42
10 NifA

Mesorhizobium loti MAFF303099
9 NifA

Rhodopseudomonas palustris CGA009
13 NifA

Bradyrhizobium japonicum USDA 110
15 NifA

Bradyrhizobium sp. BTAi1
1 NifA

Nitrobacter winogradskyi Nb-255
12 NifA

Azorhizobium caulinodans ORS 571
11 NifA

Xanthobacter autotrophicus Py2
Nitrogen fixation
TF NtrC
4 NtrC

Sinorhizobium meliloti 1021
7 NtrC

Rhizobium sp. NGR234
5 NtrC

Rhizobium leguminosarum bv. viciae 3841
6 NtrC

Rhizobium etli CFN 42
3 NtrC

Agrobacterium tumefaciens str. C58 (Cereon)
2 NtrC

Mesorhizobium sp. BNC1
2 NtrC

Mesorhizobium loti MAFF303099
3 NtrC

Brucella melitensis 16M
6 NtrC

Rhodopseudomonas palustris CGA009
6 NtrC

Bradyrhizobium japonicum USDA 110
8 NtrC

Bradyrhizobium sp. BTAi1
2 NtrC

Nitrobacter winogradskyi Nb-255
6 NtrC

Azorhizobium caulinodans ORS 571
8 NtrC

Xanthobacter autotrophicus Py2
Nitrogen assimilation
GntR/MocR TF BBta_7471
1 BBta_7471

Bradyrhizobium sp. BTAi1
TF Blr6977
1 Blr6977

Bradyrhizobium japonicum USDA 110
TF EutR
3 EutR

Sinorhizobium meliloti 1021
4 EutR

Rhizobium sp. NGR234
3 EutR

Rhizobium leguminosarum bv. viciae 3841
3 EutR

Rhizobium etli CFN 42
2 EutR

Agrobacterium tumefaciens str. C58 (Cereon)
3 EutR

Mesorhizobium loti MAFF303099
Ectoine utilization
TF Mll0059
3 Mll0059

Sinorhizobium meliloti 1021
2 Mll0059

Rhizobium sp. NGR234
2 Mll0059

Rhizobium leguminosarum bv. viciae 3841
3 Mll0059

Rhizobium etli CFN 42
2 Mll0059

Agrobacterium tumefaciens str. C58 (Cereon)
2 Mll0059

Mesorhizobium loti MAFF303099
TF Mll2434
1 Mll2434

Mesorhizobium loti MAFF303099
1 Mll2434

Bradyrhizobium japonicum USDA 110
TF OapR
1 OapR

Azorhizobium caulinodans ORS 571
Amino acid metabolism
TF PdxQ
2 PdxQ

Mesorhizobium loti MAFF303099
Pyridoxine/pyridoxal homeostasis
TF PdxQ2
2 PdxQ2

Agrobacterium tumefaciens str. C58 (Cereon)
Metabolite transport; Pyridoxine/pyridoxal homeostasis
TF PdxQ3
1 PdxQ3

Bradyrhizobium japonicum USDA 110
1 PdxQ3

Bradyrhizobium sp. BTAi1
1 PdxQ3

Azorhizobium caulinodans ORS 571
Pyridoxine/pyridoxal homeostasis
TF PdxR
1 PdxR

Mesorhizobium sp. BNC1
2 PdxR

Rhodopseudomonas palustris CGA009
Pyridoxine/pyridoxal homeostasis
TF PdxR2
1 PdxR2

Nitrobacter winogradskyi Nb-255
Pyridoxine/pyridoxal homeostasis
TF PdxW
1 PdxW

Mesorhizobium loti MAFF303099
1 PdxW

Bradyrhizobium japonicum USDA 110
1 PdxW

Bradyrhizobium sp. BTAi1
1 PdxW

Azorhizobium caulinodans ORS 571
Pyridoxine/pyridoxal homeostasis
TF SMb20039
1 SMb20039

Sinorhizobium meliloti 1021
1 SMb20039

Rhizobium sp. NGR234
1 SMb20039

Rhizobium leguminosarum bv. viciae 3841
1 SMb20039

Rhizobium etli CFN 42
1 SMb20039

Agrobacterium tumefaciens str. C58 (Cereon)
1 SMb20039

Mesorhizobium sp. BNC1
1 SMb20039

Mesorhizobium loti MAFF303099
1 SMb20039

Brucella melitensis 16M
1 SMb20039

Bradyrhizobium japonicum USDA 110
1 SMb20039

Bradyrhizobium sp. BTAi1
1 SMb20039

Azorhizobium caulinodans ORS 571
TF TauR
1 TauR

Sinorhizobium meliloti 1021
Taurine utilization
TF TauR2
3 TauR2

Rhodopseudomonas palustris CGA009
TF YrdX
2 YrdX

Rhizobium leguminosarum bv. viciae 3841
1 YrdX

Rhizobium etli CFN 42
1 YrdX

Azorhizobium caulinodans ORS 571
TF YrdX2
1 YrdX2

Sinorhizobium meliloti 1021
1 YrdX2

Rhizobium sp. NGR234
3 YrdX2

Xanthobacter autotrophicus Py2
GntR/Others TF AnsR
2 AnsR

Rhizobium etli CFN 42
2 AnsR

Agrobacterium tumefaciens str. C58 (Cereon)
Aspartate utilization; Asparagine degradation
TF Atu2740
3 Atu2740

Sinorhizobium meliloti 1021
3 Atu2740

Agrobacterium tumefaciens str. C58 (Cereon)
Sugar utilization
TF Atu3908
2 Atu3908

Agrobacterium tumefaciens str. C58 (Cereon)
TF BioR
1 BioR

Rhizobium sp. NGR234
1 BioR

Agrobacterium tumefaciens str. C58 (Cereon)
1 BioR

Mesorhizobium loti MAFF303099
3 BioR

Brucella melitensis 16M
2 BioR

Bradyrhizobium japonicum USDA 110
2 BioR

Bradyrhizobium sp. BTAi1
2 BioR

Azorhizobium caulinodans ORS 571
Biotin biosynthesis
TF Bll4368
5 Bll4368

Bradyrhizobium japonicum USDA 110
3 Bll4368

Bradyrhizobium sp. BTAi1
Glycolate utilization; Lactate utilization
TF GlcC
5 GlcC

Sinorhizobium meliloti 1021
3 GlcC

Rhizobium sp. NGR234
3 GlcC

Agrobacterium tumefaciens str. C58 (Cereon)
3 GlcC

Mesorhizobium sp. BNC1
3 GlcC

Mesorhizobium loti MAFF303099
4 GlcC

Brucella melitensis 16M
Glycolate utilization
TF HutC
5 HutC

Sinorhizobium meliloti 1021
3 HutC

Rhizobium sp. NGR234
4 HutC

Rhizobium leguminosarum bv. viciae 3841
2 HutC

Rhizobium etli CFN 42
5 HutC

Agrobacterium tumefaciens str. C58 (Cereon)
3 HutC

Mesorhizobium sp. BNC1
5 HutC

Mesorhizobium loti MAFF303099
2 HutC

Brucella melitensis 16M
2 HutC

Bradyrhizobium japonicum USDA 110
2 HutC

Bradyrhizobium sp. BTAi1
Histidine utilization
TF HypR
5 HypR

Sinorhizobium meliloti 1021
2 HypR

Rhizobium leguminosarum bv. viciae 3841
2 HypR

Rhizobium etli CFN 42
4 HypR

Agrobacterium tumefaciens str. C58 (Cereon)
2 HypR

Mesorhizobium sp. BNC1
1 HypR

Brucella melitensis 16M
Proline and 4-hydrohyproline utilization
TF LldR
2 LldR

Xanthobacter autotrophicus Py2
Lactate utilization
TF MdcY
2 MdcY

Sinorhizobium meliloti 1021
2 MdcY

Rhizobium sp. NGR234
2 MdcY

Rhizobium leguminosarum bv. viciae 3841
2 MdcY

Rhizobium etli CFN 42
3 MdcY

Bradyrhizobium japonicum USDA 110
2 MdcY

Azorhizobium caulinodans ORS 571
2 MdcY

Xanthobacter autotrophicus Py2
Malonate metabolism
TF NagQ
2 NagQ

Sinorhizobium meliloti 1021
2 NagQ

Rhizobium sp. NGR234
1 NagQ

Rhizobium leguminosarum bv. viciae 3841
1 NagQ

Rhizobium etli CFN 42
2 NagQ

Agrobacterium tumefaciens str. C58 (Cereon)
2 NagQ

Mesorhizobium loti MAFF303099
2 NagQ

Brucella melitensis 16M
N-acetylglucosamine utilization
TF PhnF
2 PhnF

Sinorhizobium meliloti 1021
2 PhnF

Rhizobium sp. NGR234
2 PhnF

Rhizobium leguminosarum bv. viciae 3841
2 PhnF

Rhizobium etli CFN 42
2 PhnF

Agrobacterium tumefaciens str. C58 (Cereon)
2 PhnF

Mesorhizobium loti MAFF303099
2 PhnF

Brucella melitensis 16M
2 PhnF

Rhodopseudomonas palustris CGA009
2 PhnF

Bradyrhizobium japonicum USDA 110
2 PhnF

Bradyrhizobium sp. BTAi1
1 PhnF

Azorhizobium caulinodans ORS 571
2 PhnF

Xanthobacter autotrophicus Py2
Phosphonate utilization
TF RPA0105
2 RPA0105

Rhodopseudomonas palustris CGA009
TF UxuR2
1 UxuR2

Sinorhizobium meliloti 1021
1 UxuR2

Rhizobium sp. NGR234
1 UxuR2

Rhizobium leguminosarum bv. viciae 3841
1 UxuR2

Rhizobium etli CFN 42
3 UxuR2

Agrobacterium tumefaciens str. C58 (Cereon)
4 UxuR2

Bradyrhizobium japonicum USDA 110
Galacturonate utilization
TF VanR
2 VanR

Rhizobium leguminosarum bv. viciae 3841
3 VanR

Agrobacterium tumefaciens str. C58 (Cereon)
1 VanR

Rhodopseudomonas palustris CGA009
1 VanR

Bradyrhizobium japonicum USDA 110
1 VanR

Bradyrhizobium sp. BTAi1
Vanillate utilization
HrcA TF HrcA
2 HrcA

Sinorhizobium meliloti 1021
3 HrcA

Rhizobium sp. NGR234
3 HrcA

Rhizobium leguminosarum bv. viciae 3841
4 HrcA

Rhizobium etli CFN 42
1 HrcA

Agrobacterium tumefaciens str. C58 (Cereon)
2 HrcA

Mesorhizobium sp. BNC1
5 HrcA

Mesorhizobium loti MAFF303099
1 HrcA

Brucella melitensis 16M
1 HrcA

Bartonella quintana str. Toulouse
2 HrcA

Rhodopseudomonas palustris CGA009
4 HrcA

Bradyrhizobium japonicum USDA 110
3 HrcA

Bradyrhizobium sp. BTAi1
3 HrcA

Nitrobacter winogradskyi Nb-255
2 HrcA

Azorhizobium caulinodans ORS 571
2 HrcA

Xanthobacter autotrophicus Py2
Heat shock response
LacI TF AduR
1 AduR

Sinorhizobium meliloti 1021
1 AduR

Rhizobium leguminosarum bv. viciae 3841
1 AduR

Rhizobium etli CFN 42
1 AduR

Agrobacterium tumefaciens str. C58 (Cereon)
Adenosine utilization
TF AfrR
2 AfrR

Sinorhizobium meliloti 1021
2 AfrR

Rhizobium sp. NGR234
1 AfrR

Rhizobium leguminosarum bv. viciae 3841
1 AfrR

Rhizobium etli CFN 42
2 AfrR

Mesorhizobium loti MAFF303099
2 AfrR

Brucella melitensis 16M
1,5-Anhydro-d-Fructose utilization
TF AglR
2 AglR

Sinorhizobium meliloti 1021
2 AglR

Rhizobium sp. NGR234
3 AglR

Rhizobium leguminosarum bv. viciae 3841
2 AglR

Rhizobium etli CFN 42
2 AglR

Agrobacterium tumefaciens str. C58 (Cereon)
2 AglR

Mesorhizobium sp. BNC1
2 AglR

Mesorhizobium loti MAFF303099
Alpha-glucosides utilization
TF Atu5239
2 Atu5239

Agrobacterium tumefaciens str. C58 (Cereon)
1 Atu5239

Bradyrhizobium japonicum USDA 110
TF GntR
3 GntR

Xanthobacter autotrophicus Py2
Gluconate utilization
TF IdnR
5 IdnR

Rhizobium sp. NGR234
5 IdnR

Rhizobium leguminosarum bv. viciae 3841
5 IdnR

Rhizobium etli CFN 42
4 IdnR

Agrobacterium tumefaciens str. C58 (Cereon)
2 IdnR

Bradyrhizobium sp. BTAi1
2 IdnR

Azorhizobium caulinodans ORS 571
2 IdnR

Xanthobacter autotrophicus Py2
Idonate utilization
TF IolR
2 IolR

Rhizobium etli CFN 42
2 IolR

Mesorhizobium loti MAFF303099
Inositol utilization
TF KglR
1 KglR

Sinorhizobium meliloti 1021
1 KglR

Azorhizobium caulinodans ORS 571
Sugar utilization
TF Mll1683
1 Mll1683

Rhizobium sp. NGR234
2 Mll1683

Rhizobium leguminosarum bv. viciae 3841
2 Mll1683

Rhizobium etli CFN 42
1 Mll1683

Mesorhizobium loti MAFF303099
3 Mll1683

Bradyrhizobium japonicum USDA 110
3 Mll1683

Bradyrhizobium sp. BTAi1
Sugar utilization
TF MocR
2 MocR

Sinorhizobium meliloti 1021
2 MocR

Rhizobium sp. NGR234
2 MocR

Rhizobium leguminosarum bv. viciae 3841
2 MocR

Rhizobium etli CFN 42
2 MocR

Mesorhizobium loti MAFF303099
Rhizopine catabolism
TF NGR_b22600
2 NGR_b22600

Rhizobium sp. NGR234
Sugar utilization
TF PckR
11 PckR

Sinorhizobium meliloti 1021
10 PckR

Rhizobium sp. NGR234
10 PckR

Rhizobium leguminosarum bv. viciae 3841
11 PckR

Rhizobium etli CFN 42
11 PckR

Agrobacterium tumefaciens str. C58 (Cereon)
7 PckR

Mesorhizobium sp. BNC1
10 PckR

Mesorhizobium loti MAFF303099
9 PckR

Brucella melitensis 16M
2 PckR

Azorhizobium caulinodans ORS 571
5 PckR

Xanthobacter autotrophicus Py2
Central carbohydrate metabolism
TF PsiR
2 PsiR

Sinorhizobium meliloti 1021
2 PsiR

Rhizobium sp. NGR234
2 PsiR

Rhizobium leguminosarum bv. viciae 3841
2 PsiR

Agrobacterium tumefaciens str. C58 (Cereon)
Psicose utilization
TF RL3595
2 RL3595

Rhizobium leguminosarum bv. viciae 3841
2 RL3595

Rhizobium etli CFN 42
2 RL3595

Agrobacterium tumefaciens str. C58 (Cereon)
2 RL3595

Azorhizobium caulinodans ORS 571
Sugar utilization
TF RL4253
2 RL4253

Rhizobium sp. NGR234
2 RL4253

Rhizobium leguminosarum bv. viciae 3841
2 RL4253

Rhizobium etli CFN 42
Sugar utilization
TF RbsR2
1 RbsR2

Rhizobium leguminosarum bv. viciae 3841
1 RbsR2

Agrobacterium tumefaciens str. C58 (Cereon)
Ribose utilization
TF RhiR
2 RhiR

Rhizobium sp. NGR234
2 RhiR

Rhizobium leguminosarum bv. viciae 3841
2 RhiR

Rhizobium etli CFN 42
2 RhiR

Agrobacterium tumefaciens str. C58 (Cereon)
Rhamnogalacturonides utilization
TF SMb20014
1 SMb20014

Sinorhizobium meliloti 1021
1 SMb20014

Rhizobium sp. NGR234
1 SMb20014

Agrobacterium tumefaciens str. C58 (Cereon)
1 SMb20014

Mesorhizobium sp. BNC1
Sugar utilization
TF SMb20537
2 SMb20537

Sinorhizobium meliloti 1021
2 SMb20537

Rhizobium sp. NGR234
2 SMb20537

Rhizobium leguminosarum bv. viciae 3841
2 SMb20537

Rhizobium etli CFN 42
2 SMb20537

Agrobacterium tumefaciens str. C58 (Cereon)
Sugar utilization
TF SMb20667
2 SMb20667

Sinorhizobium meliloti 1021
2 SMb20667

Rhizobium sp. NGR234
2 SMb20667

Rhizobium leguminosarum bv. viciae 3841
2 SMb20667

Rhizobium etli CFN 42
2 SMb20667

Azorhizobium caulinodans ORS 571
2 SMb20667

Xanthobacter autotrophicus Py2
Sugar utilization
TF SMb20717
2 SMb20717

Sinorhizobium meliloti 1021
2 SMb20717

Rhizobium sp. NGR234
2 SMb20717

Rhizobium leguminosarum bv. viciae 3841
2 SMb20717

Rhizobium etli CFN 42
Sugar utilization
TF SMb21598
2 SMb21598

Sinorhizobium meliloti 1021
2 SMb21598

Rhizobium sp. NGR234
2 SMb21598

Rhizobium leguminosarum bv. viciae 3841
2 SMb21598

Rhizobium etli CFN 42
2 SMb21598

Agrobacterium tumefaciens str. C58 (Cereon)
2 SMb21598

Mesorhizobium loti MAFF303099
Sugar utilization
TF SMb21706
1 SMb21706

Sinorhizobium meliloti 1021
1 SMb21706

Rhizobium sp. NGR234
3 SMb21706

Rhizobium leguminosarum bv. viciae 3841
1 SMb21706

Rhizobium etli CFN 42
1 SMb21706

Agrobacterium tumefaciens str. C58 (Cereon)
1 SMb21706

Mesorhizobium loti MAFF303099
Sugar utilization
TF SMc04260
2 SMc04260

Sinorhizobium meliloti 1021
2 SMc04260

Rhizobium sp. NGR234
3 SMc04260

Rhizobium leguminosarum bv. viciae 3841
2 SMc04260

Rhizobium etli CFN 42
4 SMc04260

Agrobacterium tumefaciens str. C58 (Cereon)
2 SMc04260

Mesorhizobium loti MAFF303099
Sugar utilization
TF SmoR
1 SmoR

Sinorhizobium meliloti 1021
1 SmoR

Rhizobium etli CFN 42
2 SmoR

Agrobacterium tumefaciens str. C58 (Cereon)
2 SmoR

Mesorhizobium loti MAFF303099
Sorbitol utilization; Mannitol utilization
TF SocR
2 SocR

Rhizobium leguminosarum bv. viciae 3841
2 SocR

Rhizobium etli CFN 42
2 SocR

Agrobacterium tumefaciens str. C58 (Cereon)
Santhopine utilization
TF ThuR
2 ThuR

Sinorhizobium meliloti 1021
2 ThuR

Rhizobium sp. NGR234
3 ThuR

Rhizobium etli CFN 42
2 ThuR

Agrobacterium tumefaciens str. C58 (Cereon)
2 ThuR

Brucella melitensis 16M
Trehalose utilization
TF XylR
1 XylR

Sinorhizobium meliloti 1021
1 XylR

Rhizobium sp. NGR234
4 XylR

Rhizobium leguminosarum bv. viciae 3841
3 XylR

Rhizobium etli CFN 42
3 XylR

Agrobacterium tumefaciens str. C58 (Cereon)
3 XylR

Brucella melitensis 16M
1 XylR

Bradyrhizobium japonicum USDA 110
1 XylR

Bradyrhizobium sp. BTAi1
Xylose utilization
TF blr3394
1 blr3394

Bradyrhizobium japonicum USDA 110
1 blr3394

Bradyrhizobium sp. BTAi1
Sugar utilization
TF pRL90265
3 pRL90265

Sinorhizobium meliloti 1021
1 pRL90265

Rhizobium leguminosarum bv. viciae 3841
1 pRL90265

Rhizobium etli CFN 42
Sugar utilization
LexA TF LexA
17 LexA

Sinorhizobium meliloti 1021
16 LexA

Rhizobium sp. NGR234
18 LexA

Rhizobium leguminosarum bv. viciae 3841
18 LexA

Rhizobium etli CFN 42
19 LexA

Agrobacterium tumefaciens str. C58 (Cereon)
15 LexA

Mesorhizobium sp. BNC1
14 LexA

Mesorhizobium loti MAFF303099
12 LexA

Brucella melitensis 16M
1 LexA

Bartonella quintana str. Toulouse
12 LexA

Rhodopseudomonas palustris CGA009
11 LexA

Bradyrhizobium japonicum USDA 110
10 LexA

Bradyrhizobium sp. BTAi1
8 LexA

Nitrobacter winogradskyi Nb-255
9 LexA

Azorhizobium caulinodans ORS 571
10 LexA

Xanthobacter autotrophicus Py2
SOS response
LuxR TF FixJ
2 FixJ

Sinorhizobium meliloti 1021
6 FixJ

Rhizobium leguminosarum bv. viciae 3841
2 FixJ

Rhizobium etli CFN 42
Oxidative stress response; Nitrogen fixation
TF FixJ
4 FixJ

Sinorhizobium meliloti 1021
2 FixJ

Rhizobium sp. NGR234
1 FixJ

Rhizobium leguminosarum bv. viciae 3841
1 FixJ

Mesorhizobium sp. BNC1
2 FixJ

Mesorhizobium loti MAFF303099
1 FixJ

Rhodopseudomonas palustris CGA009
1 FixJ

Bradyrhizobium japonicum USDA 110
1 FixJ

Bradyrhizobium sp. BTAi1
1 FixJ

Nitrobacter winogradskyi Nb-255
2 FixJ

Azorhizobium caulinodans ORS 571
1 FixJ

Xanthobacter autotrophicus Py2
Oxidative stress response
LysR TF Bll2166
2 Bll2166

Rhizobium sp. NGR234
2 Bll2166

Bradyrhizobium japonicum USDA 110
2 Bll2166

Bradyrhizobium sp. BTAi1
2 Bll2166

Xanthobacter autotrophicus Py2
TF GulR
5 GulR

Bradyrhizobium japonicum USDA 110
5 GulR

Bradyrhizobium sp. BTAi1
2 GulR

Azorhizobium caulinodans ORS 571
Glucarate utilization; Galactarate utilization
MerR TF CadR-PbrR
1 CadR-PbrR

Sinorhizobium meliloti 1021
1 CadR-PbrR

Rhizobium sp. NGR234
1 CadR-PbrR

Rhizobium leguminosarum bv. viciae 3841
1 CadR-PbrR

Rhizobium etli CFN 42
2 CadR-PbrR

Agrobacterium tumefaciens str. C58 (Cereon)
4 CadR-PbrR

Mesorhizobium sp. BNC1
1 CadR-PbrR

Mesorhizobium loti MAFF303099
1 CadR-PbrR

Brucella melitensis 16M
1 CadR-PbrR

Rhodopseudomonas palustris CGA009
1 CadR-PbrR

Bradyrhizobium sp. BTAi1
1 CadR-PbrR

Nitrobacter winogradskyi Nb-255
1 CadR-PbrR

Azorhizobium caulinodans ORS 571
2 CadR-PbrR

Xanthobacter autotrophicus Py2
Lead resistance; Cadmium resistance
TF CueR
5 CueR

Sinorhizobium meliloti 1021
5 CueR

Rhizobium sp. NGR234
2 CueR

Rhizobium leguminosarum bv. viciae 3841
1 CueR

Rhizobium etli CFN 42
2 CueR

Agrobacterium tumefaciens str. C58 (Cereon)
3 CueR

Mesorhizobium sp. BNC1
1 CueR

Mesorhizobium loti MAFF303099
2 CueR

Brucella melitensis 16M
Copper resistance
TF LiuR
10 LiuR

Sinorhizobium meliloti 1021
10 LiuR

Rhizobium sp. NGR234
10 LiuR

Rhizobium leguminosarum bv. viciae 3841
9 LiuR

Rhizobium etli CFN 42
9 LiuR

Agrobacterium tumefaciens str. C58 (Cereon)
4 LiuR

Mesorhizobium sp. BNC1
6 LiuR

Mesorhizobium loti MAFF303099
10 LiuR

Brucella melitensis 16M
1 LiuR

Bartonella quintana str. Toulouse
Branched-chain amino acid degradation
TF MerR
1 MerR

Sinorhizobium meliloti 1021
1 MerR

Rhizobium sp. NGR234
Mercury resistance
TF NmlR
1 NmlR

Bradyrhizobium japonicum USDA 110
1 NmlR

Bradyrhizobium sp. BTAi1
Carbonyl stress response
TF SoxR
4 SoxR

Sinorhizobium meliloti 1021
3 SoxR

Rhizobium sp. NGR234
4 SoxR

Rhizobium leguminosarum bv. viciae 3841
2 SoxR

Rhizobium etli CFN 42
4 SoxR

Agrobacterium tumefaciens str. C58 (Cereon)
3 SoxR

Mesorhizobium loti MAFF303099
2 SoxR

Xanthobacter autotrophicus Py2
Superoxide stress response
ModE TF ModE
1 ModE

Sinorhizobium meliloti 1021
1 ModE

Rhizobium sp. NGR234
1 ModE

Rhizobium leguminosarum bv. viciae 3841
1 ModE

Rhizobium etli CFN 42
1 ModE

Agrobacterium tumefaciens str. C58 (Cereon)
1 ModE

Mesorhizobium loti MAFF303099
1 ModE

Bradyrhizobium sp. BTAi1
1 ModE

Azorhizobium caulinodans ORS 571
1 ModE

Xanthobacter autotrophicus Py2
Molybdenum homeostasis
TF ModE
2 ModE

Rhodopseudomonas palustris CGA009
Molybdopterin biosynthesis
NadQ TF NadQ
1 NadQ

Sinorhizobium meliloti 1021
1 NadQ

Rhizobium sp. NGR234
1 NadQ

Rhizobium leguminosarum bv. viciae 3841
1 NadQ

Rhizobium etli CFN 42
1 NadQ

Agrobacterium tumefaciens str. C58 (Cereon)
1 NadQ

Mesorhizobium sp. BNC1
2 NadQ

Mesorhizobium loti MAFF303099
1 NadQ

Rhodopseudomonas palustris CGA009
1 NadQ

Bradyrhizobium japonicum USDA 110
1 NadQ

Bradyrhizobium sp. BTAi1
1 NadQ

Nitrobacter winogradskyi Nb-255
1 NadQ

Xanthobacter autotrophicus Py2
NAD biosynthesis
NikR TF NikR
2 NikR

Brucella melitensis 16M
2 NikR

Rhodopseudomonas palustris CGA009
2 NikR

Bradyrhizobium japonicum USDA 110
5 NikR

Bradyrhizobium sp. BTAi1
Nickel homeostasis
NrdR TF NrdR
1 NrdR

Sinorhizobium meliloti 1021
1 NrdR

Rhizobium sp. NGR234
2 NrdR

Rhizobium leguminosarum bv. viciae 3841
2 NrdR

Rhizobium etli CFN 42
2 NrdR

Agrobacterium tumefaciens str. C58 (Cereon)
2 NrdR

Mesorhizobium sp. BNC1
1 NrdR

Mesorhizobium loti MAFF303099
2 NrdR

Brucella melitensis 16M
1 NrdR

Bartonella quintana str. Toulouse
1 NrdR

Rhodopseudomonas palustris CGA009
2 NrdR

Bradyrhizobium japonicum USDA 110
1 NrdR

Bradyrhizobium sp. BTAi1
2 NrdR

Nitrobacter winogradskyi Nb-255
1 NrdR

Azorhizobium caulinodans ORS 571
1 NrdR

Xanthobacter autotrophicus Py2
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
2 NrtR

Rhizobium etli CFN 42
2 NrtR

Bradyrhizobium sp. BTAi1
NAD biosynthesis
ROK TF XylR
2 XylR

Sinorhizobium meliloti 1021
1 XylR

Rhizobium sp. NGR234
2 XylR

Rhizobium leguminosarum bv. viciae 3841
2 XylR

Rhizobium etli CFN 42
2 XylR

Agrobacterium tumefaciens str. C58 (Cereon)
3 XylR

Mesorhizobium sp. BNC1
3 XylR

Mesorhizobium loti MAFF303099
2 XylR

Bradyrhizobium japonicum USDA 110
Xylose utilization
RpiR TF EutR
2 EutR

Sinorhizobium meliloti 1021
2 EutR

Rhizobium sp. NGR234
2 EutR

Rhizobium leguminosarum bv. viciae 3841
2 EutR

Rhizobium etli CFN 42
2 EutR

Agrobacterium tumefaciens str. C58 (Cereon)
2 EutR

Mesorhizobium sp. BNC1
Ethanolamine utilization
Rrf2 TF NsrR
2 NsrR

Xanthobacter autotrophicus Py2
Nitrosative stress response
TF RirA
23 RirA

Sinorhizobium meliloti 1021
12 RirA

Rhizobium sp. NGR234
19 RirA

Rhizobium leguminosarum bv. viciae 3841
16 RirA

Rhizobium etli CFN 42
13 RirA

Agrobacterium tumefaciens str. C58 (Cereon)
5 RirA

Mesorhizobium sp. BNC1
6 RirA

Mesorhizobium loti MAFF303099
8 RirA

Brucella melitensis 16M
4 RirA

Bartonella quintana str. Toulouse
Iron homeostasis
TetR TF PaaR
3 PaaR

Rhizobium sp. NGR234
5 PaaR

Rhodopseudomonas palustris CGA009
4 PaaR

Xanthobacter autotrophicus Py2
Phenylacetic acid degradation
TF PsrA
2 PsrA

Rhodopseudomonas palustris CGA009
2 PsrA

Bradyrhizobium japonicum USDA 110
2 PsrA

Bradyrhizobium sp. BTAi1
Fatty acid degradation
TF RutR
6 RutR

Sinorhizobium meliloti 1021
6 RutR

Rhizobium sp. NGR234
5 RutR

Rhizobium leguminosarum bv. viciae 3841
5 RutR

Rhizobium etli CFN 42
5 RutR

Agrobacterium tumefaciens str. C58 (Cereon)
4 RutR

Mesorhizobium sp. BNC1
6 RutR

Mesorhizobium loti MAFF303099
3 RutR

Brucella melitensis 16M
3 RutR

Bradyrhizobium sp. BTAi1
Pyrimidine utilization
RF00050 RNA FMN
1 FMN

Sinorhizobium meliloti 1021
1 FMN

Rhizobium sp. NGR234
3 FMN

Rhizobium leguminosarum bv. viciae 3841
2 FMN

Rhizobium etli CFN 42
1 FMN

Agrobacterium tumefaciens str. C58 (Cereon)
1 FMN

Mesorhizobium loti MAFF303099
1 FMN

Brucella melitensis 16M
1 FMN

Bradyrhizobium japonicum USDA 110
1 FMN

Bradyrhizobium sp. BTAi1
Riboflavin biosynthesis
RF00059 RNA TPP
3 TPP

Sinorhizobium meliloti 1021
3 TPP

Rhizobium sp. NGR234
3 TPP

Rhizobium leguminosarum bv. viciae 3841
3 TPP

Rhizobium etli CFN 42
3 TPP

Agrobacterium tumefaciens str. C58 (Cereon)
2 TPP

Mesorhizobium sp. BNC1
3 TPP

Mesorhizobium loti MAFF303099
2 TPP

Brucella melitensis 16M
1 TPP

Rhodopseudomonas palustris CGA009
1 TPP

Bradyrhizobium japonicum USDA 110
1 TPP

Bradyrhizobium sp. BTAi1
1 TPP

Nitrobacter winogradskyi Nb-255
2 TPP

Azorhizobium caulinodans ORS 571
2 TPP

Xanthobacter autotrophicus Py2
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Mesorhizobium sp. BNC1
1 yybP-ykoY

Bradyrhizobium sp. BTAi1
1 yybP-ykoY

Xanthobacter autotrophicus Py2
RF00174 RNA Cobalamin
4 Cobalamin

Sinorhizobium meliloti 1021
4 Cobalamin

Rhizobium sp. NGR234
3 Cobalamin

Rhizobium leguminosarum bv. viciae 3841
2 Cobalamin

Rhizobium etli CFN 42
6 Cobalamin

Agrobacterium tumefaciens str. C58 (Cereon)
3 Cobalamin

Mesorhizobium sp. BNC1
6 Cobalamin

Mesorhizobium loti MAFF303099
4 Cobalamin

Brucella melitensis 16M
9 Cobalamin

Rhodopseudomonas palustris CGA009
5 Cobalamin

Bradyrhizobium japonicum USDA 110
3 Cobalamin

Bradyrhizobium sp. BTAi1
3 Cobalamin

Nitrobacter winogradskyi Nb-255
2 Cobalamin

Azorhizobium caulinodans ORS 571
3 Cobalamin

Xanthobacter autotrophicus Py2
Cobalamin biosynthesis
RF00442 RNA ykkC-yxkD
1 ykkC-yxkD

Rhizobium sp. NGR234
1 ykkC-yxkD

Rhizobium leguminosarum bv. viciae 3841
1 ykkC-yxkD

Rhizobium etli CFN 42
1 ykkC-yxkD

Rhodopseudomonas palustris CGA009
1 ykkC-yxkD

Bradyrhizobium sp. BTAi1
1 ykkC-yxkD

Azorhizobium caulinodans ORS 571
1 ykkC-yxkD

Xanthobacter autotrophicus Py2
Multidrug resistance
RF00504 RNA Glycine
1 Glycine

Sinorhizobium meliloti 1021
1 Glycine

Rhizobium sp. NGR234
1 Glycine

Rhizobium leguminosarum bv. viciae 3841
1 Glycine

Rhizobium etli CFN 42
1 Glycine

Agrobacterium tumefaciens str. C58 (Cereon)
2 Glycine

Mesorhizobium sp. BNC1
2 Glycine

Mesorhizobium loti MAFF303099
1 Glycine

Brucella melitensis 16M
1 Glycine

Bartonella quintana str. Toulouse
1 Glycine

Rhodopseudomonas palustris CGA009
1 Glycine

Bradyrhizobium japonicum USDA 110
1 Glycine

Bradyrhizobium sp. BTAi1
1 Glycine

Nitrobacter winogradskyi Nb-255
2 Glycine

Azorhizobium caulinodans ORS 571
1 Glycine

Xanthobacter autotrophicus Py2
Glycine metabolism
RF00513 RNA Trp_leader
1 Trp_leader

Agrobacterium tumefaciens str. C58 (Cereon)
1 Trp_leader

Mesorhizobium sp. BNC1
1 Trp_leader

Mesorhizobium loti MAFF303099
1 Trp_leader

Brucella melitensis 16M
1 Trp_leader

Rhodopseudomonas palustris CGA009
Tryptophan biosynthesis
RF00517 RNA serC
1 serC

Sinorhizobium meliloti 1021
1 serC

Rhizobium sp. NGR234
1 serC

Rhizobium leguminosarum bv. viciae 3841
1 serC

Rhizobium etli CFN 42
1 serC

Agrobacterium tumefaciens str. C58 (Cereon)
1 serC

Mesorhizobium sp. BNC1
1 serC

Mesorhizobium loti MAFF303099
1 serC

Brucella melitensis 16M
1 serC

Rhodopseudomonas palustris CGA009
1 serC

Bradyrhizobium japonicum USDA 110
1 serC

Bradyrhizobium sp. BTAi1
1 serC

Nitrobacter winogradskyi Nb-255
1 serC

Azorhizobium caulinodans ORS 571
1 serC

Xanthobacter autotrophicus Py2
Serine biosynthesis
RF00518 RNA speF
1 speF

Sinorhizobium meliloti 1021
1 speF

Rhizobium sp. NGR234
1 speF

Rhizobium leguminosarum bv. viciae 3841
1 speF

Agrobacterium tumefaciens str. C58 (Cereon)
1 speF

Mesorhizobium sp. BNC1
1 speF

Mesorhizobium loti MAFF303099
1 speF

Brucella melitensis 16M
1 speF

Bartonella quintana str. Toulouse
1 speF

Rhodopseudomonas palustris CGA009
1 speF

Nitrobacter winogradskyi Nb-255
1 speF

Azorhizobium caulinodans ORS 571
1 speF

Xanthobacter autotrophicus Py2
Ornithine degradation
RF00520 RNA ybhL
1 ybhL

Sinorhizobium meliloti 1021
1 ybhL

Rhizobium sp. NGR234
1 ybhL

Rhizobium leguminosarum bv. viciae 3841
1 ybhL

Rhizobium etli CFN 42
1 ybhL

Agrobacterium tumefaciens str. C58 (Cereon)
1 ybhL

Mesorhizobium sp. BNC1
1 ybhL

Mesorhizobium loti MAFF303099
1 ybhL

Brucella melitensis 16M
RF00521 RNA SAM_alpha
2 SAM_alpha

Sinorhizobium meliloti 1021
2 SAM_alpha

Rhizobium sp. NGR234
2 SAM_alpha

Rhizobium leguminosarum bv. viciae 3841
2 SAM_alpha

Rhizobium etli CFN 42
2 SAM_alpha

Agrobacterium tumefaciens str. C58 (Cereon)
2 SAM_alpha

Mesorhizobium sp. BNC1
2 SAM_alpha

Mesorhizobium loti MAFF303099
1 SAM_alpha

Brucella melitensis 16M
2 SAM_alpha

Rhodopseudomonas palustris CGA009
2 SAM_alpha

Bradyrhizobium japonicum USDA 110
2 SAM_alpha

Bradyrhizobium sp. BTAi1
2 SAM_alpha

Nitrobacter winogradskyi Nb-255
1 SAM_alpha

Azorhizobium caulinodans ORS 571
1 SAM_alpha

Xanthobacter autotrophicus Py2
Methionine biosynthesis
RF01068 RNA mini-ykkC
1 mini-ykkC

Rhizobium sp. NGR234
2 mini-ykkC

Rhizobium leguminosarum bv. viciae 3841
2 mini-ykkC

Rhizobium etli CFN 42
1 mini-ykkC

Mesorhizobium sp. BNC1
1 mini-ykkC

Mesorhizobium loti MAFF303099
2 mini-ykkC

Rhodopseudomonas palustris CGA009
1 mini-ykkC

Nitrobacter winogradskyi Nb-255
1 mini-ykkC

Azorhizobium caulinodans ORS 571
1 mini-ykkC

Xanthobacter autotrophicus Py2
Multidrug resistance