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

Collection of regulogs in Cyanobacteria taxonomic group

General statistics
Genomes 14
TF regulogs 19
TF regulons 182
TF binding sites 1035
RNA regulogs 11
RNA regulons 64
RNA sites 86

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
Cyanothece sp. ATCC 51142 15 143 4 6 19 149
Cyanothece sp. PCC 7425 16 85 7 16 23 101
Cyanothece sp. PCC 8801 14 113 5 5 19 118
Gloeobacter violaceus PCC 7421 9 25 7 8 16 33
Microcystis aeruginosa NIES-843 14 78 4 4 18 82
Nostoc sp. PCC 7120 13 135 5 9 18 144
Prochlorococcus marinus str. MIT 9313 10 23 3 3 13 26
Synechococcus elongatus PCC 7942 15 49 4 5 19 54
Synechococcus sp. JA-3-3Ab 12 34 7 10 19 44
Synechococcus sp. PCC 7002 16 89 4 4 20 93
Synechococcus sp. WH 8102 9 20 3 3 12 23
Synechocystis sp. PCC 6803 16 110 4 4 20 114
Thermosynechococcus elongatus BP-1 13 49 5 7 18 56
Trichodesmium erythraeum IMS101 10 82 2 2 12 84
Genomic distribution of regulons
Family Type Regulator Function
ArsR TF ArsR
2 ArsR

Synechococcus sp. PCC 7002
2 ArsR

Synechocystis sp. PCC 6803
2 ArsR

Cyanothece sp. ATCC 51142
2 ArsR

Cyanothece sp. PCC 8801
1 ArsR

Cyanothece sp. PCC 7425
2 ArsR

Microcystis aeruginosa NIES-843
1 ArsR

Synechococcus elongatus PCC 7942
1 ArsR

Prochlorococcus marinus str. MIT 9313
1 ArsR

Synechococcus sp. JA-3-3Ab
1 ArsR

Synechococcus sp. WH 8102
Arsenic resistance
TF SmtB
2 SmtB

Synechococcus sp. PCC 7002
2 SmtB

Synechocystis sp. PCC 6803
1 SmtB

Cyanothece sp. PCC 8801
1 SmtB

Cyanothece sp. PCC 7425
1 SmtB

Microcystis aeruginosa NIES-843
2 SmtB

Nostoc sp. PCC 7120
2 SmtB

Synechococcus elongatus PCC 7942
1 SmtB

Thermosynechococcus elongatus BP-1
Zinc resistance
CRP TF Crp
5 Crp

Synechococcus sp. PCC 7002
12 Crp

Synechocystis sp. PCC 6803
16 Crp

Cyanothece sp. ATCC 51142
16 Crp

Cyanothece sp. PCC 8801
10 Crp

Cyanothece sp. PCC 7425
6 Crp

Microcystis aeruginosa NIES-843
10 Crp

Nostoc sp. PCC 7120
12 Crp

Trichodesmium erythraeum IMS101
2 Crp

Synechococcus elongatus PCC 7942
3 Crp

Prochlorococcus marinus str. MIT 9313
3 Crp

Synechococcus sp. JA-3-3Ab
1 Crp

Synechococcus sp. WH 8102
5 Crp

Thermosynechococcus elongatus BP-1
TF NtcA
16 NtcA

Synechococcus sp. PCC 7002
18 NtcA

Synechocystis sp. PCC 6803
21 NtcA

Cyanothece sp. ATCC 51142
22 NtcA

Cyanothece sp. PCC 8801
15 NtcA

Cyanothece sp. PCC 7425
20 NtcA

Microcystis aeruginosa NIES-843
28 NtcA

Nostoc sp. PCC 7120
18 NtcA

Trichodesmium erythraeum IMS101
10 NtcA

Synechococcus elongatus PCC 7942
3 NtcA

Prochlorococcus marinus str. MIT 9313
9 NtcA

Synechococcus sp. JA-3-3Ab
4 NtcA

Synechococcus sp. WH 8102
6 NtcA

Gloeobacter violaceus PCC 7421
14 NtcA

Thermosynechococcus elongatus BP-1
Nitrogen assimilation
FUR TF Fur
17 Fur

Synechococcus sp. PCC 7002
18 Fur

Synechocystis sp. PCC 6803
17 Fur

Cyanothece sp. ATCC 51142
14 Fur

Cyanothece sp. PCC 8801
14 Fur

Cyanothece sp. PCC 7425
10 Fur

Microcystis aeruginosa NIES-843
30 Fur

Nostoc sp. PCC 7120
15 Fur

Trichodesmium erythraeum IMS101
5 Fur

Synechococcus elongatus PCC 7942
1 Fur

Prochlorococcus marinus str. MIT 9313
3 Fur

Synechococcus sp. JA-3-3Ab
3 Fur

Gloeobacter violaceus PCC 7421
6 Fur

Thermosynechococcus elongatus BP-1
Iron homeostasis
TF PerR
2 PerR

Synechococcus sp. PCC 7002
2 PerR

Synechocystis sp. PCC 6803
3 PerR

Cyanothece sp. ATCC 51142
3 PerR

Cyanothece sp. PCC 7425
3 PerR

Synechococcus elongatus PCC 7942
2 PerR

Gloeobacter violaceus PCC 7421
Peroxide stress response
TF Zur
3 Zur

Synechococcus sp. PCC 7002
3 Zur

Synechocystis sp. PCC 6803
17 Zur

Cyanothece sp. ATCC 51142
9 Zur

Cyanothece sp. PCC 8801
5 Zur

Cyanothece sp. PCC 7425
5 Zur

Microcystis aeruginosa NIES-843
8 Zur

Nostoc sp. PCC 7120
6 Zur

Trichodesmium erythraeum IMS101
3 Zur

Synechococcus elongatus PCC 7942
2 Zur

Prochlorococcus marinus str. MIT 9313
1 Zur

Synechococcus sp. JA-3-3Ab
3 Zur

Synechococcus sp. WH 8102
3 Zur

Gloeobacter violaceus PCC 7421
3 Zur

Thermosynechococcus elongatus BP-1
Zinc homeostasis
GntR/MocR TF sll5086
1 sll5086

Synechocystis sp. PCC 6803
1 sll5086

Synechococcus elongatus PCC 7942
HrcA TF HrcA
3 HrcA

Synechococcus sp. PCC 7002
2 HrcA

Synechocystis sp. PCC 6803
3 HrcA

Cyanothece sp. ATCC 51142
2 HrcA

Cyanothece sp. PCC 8801
2 HrcA

Cyanothece sp. PCC 7425
2 HrcA

Microcystis aeruginosa NIES-843
3 HrcA

Nostoc sp. PCC 7120
3 HrcA

Trichodesmium erythraeum IMS101
1 HrcA

Synechococcus elongatus PCC 7942
1 HrcA

Prochlorococcus marinus str. MIT 9313
2 HrcA

Synechococcus sp. JA-3-3Ab
2 HrcA

Synechococcus sp. WH 8102
2 HrcA

Gloeobacter violaceus PCC 7421
1 HrcA

Thermosynechococcus elongatus BP-1
Heat shock response
LexA TF LexA
2 LexA

Synechococcus sp. PCC 7002
3 LexA

Cyanothece sp. ATCC 51142
2 LexA

Cyanothece sp. PCC 8801
4 LexA

Cyanothece sp. PCC 7425
2 LexA

Microcystis aeruginosa NIES-843
5 LexA

Nostoc sp. PCC 7120
4 LexA

Prochlorococcus marinus str. MIT 9313
1 LexA

Synechococcus sp. JA-3-3Ab
2 LexA

Synechococcus sp. WH 8102
1 LexA

Gloeobacter violaceus PCC 7421
SOS response
LuxR TF PedR
5 PedR

Synechococcus sp. PCC 7002
8 PedR

Synechocystis sp. PCC 6803
5 PedR

Cyanothece sp. ATCC 51142
5 PedR

Cyanothece sp. PCC 8801
4 PedR

Cyanothece sp. PCC 7425
4 PedR

Microcystis aeruginosa NIES-843
7 PedR

Nostoc sp. PCC 7120
3 PedR

Trichodesmium erythraeum IMS101
2 PedR

Synechococcus elongatus PCC 7942
2 PedR

Prochlorococcus marinus str. MIT 9313
2 PedR

Synechococcus sp. JA-3-3Ab
2 PedR

Thermosynechococcus elongatus BP-1
Photosynthesis; Carbon fixation
LysR TF CcmR
5 CcmR

Synechococcus sp. PCC 7002
8 CcmR

Synechocystis sp. PCC 6803
8 CcmR

Cyanothece sp. ATCC 51142
7 CcmR

Cyanothece sp. PCC 8801
4 CcmR

Cyanothece sp. PCC 7425
5 CcmR

Microcystis aeruginosa NIES-843
4 CcmR

Nostoc sp. PCC 7120
3 CcmR

Synechococcus elongatus PCC 7942
2 CcmR

Synechococcus sp. JA-3-3Ab
3 CcmR

Gloeobacter violaceus PCC 7421
3 CcmR

Thermosynechococcus elongatus BP-1
Carbon dioxide fixation
TF NtcB
5 NtcB

Synechococcus sp. PCC 7002
4 NtcB

Synechocystis sp. PCC 6803
5 NtcB

Cyanothece sp. ATCC 51142
4 NtcB

Cyanothece sp. PCC 8801
3 NtcB

Cyanothece sp. PCC 7425
4 NtcB

Microcystis aeruginosa NIES-843
5 NtcB

Nostoc sp. PCC 7120
3 NtcB

Trichodesmium erythraeum IMS101
3 NtcB

Synechococcus elongatus PCC 7942
2 NtcB

Synechococcus sp. JA-3-3Ab
1 NtcB

Gloeobacter violaceus PCC 7421
3 NtcB

Thermosynechococcus elongatus BP-1
Nitrogen assimilation
TF PirR
2 PirR

Synechococcus sp. PCC 7002
2 PirR

Synechocystis sp. PCC 6803
1 PirR

Cyanothece sp. ATCC 51142
Salt stress response
NrdR TF NrdR
1 NrdR

Synechococcus elongatus PCC 7942
1 NrdR

Prochlorococcus marinus str. MIT 9313
1 NrdR

Synechococcus sp. WH 8102
1 NrdR

Gloeobacter violaceus PCC 7421
1 NrdR

Thermosynechococcus elongatus BP-1
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
3 NrtR

Synechocystis sp. PCC 6803
2 NrtR

Cyanothece sp. ATCC 51142
2 NrtR

Cyanothece sp. PCC 8801
2 NrtR

Cyanothece sp. PCC 7425
2 NrtR

Microcystis aeruginosa NIES-843
2 NrtR

Nostoc sp. PCC 7120
2 NrtR

Trichodesmium erythraeum IMS101
2 NrtR

Thermosynechococcus elongatus BP-1
NAD biosynthesis
TF NrtR2
3 NrtR2

Synechococcus sp. PCC 7002
1 NrtR2

Cyanothece sp. PCC 7425
NAD biosynthesis
OmpR TF SphR
4 SphR

Synechococcus sp. PCC 7002
4 SphR

Synechocystis sp. PCC 6803
11 SphR

Cyanothece sp. ATCC 51142
12 SphR

Cyanothece sp. PCC 8801
5 SphR

Cyanothece sp. PCC 7425
5 SphR

Microcystis aeruginosa NIES-843
12 SphR

Nostoc sp. PCC 7120
11 SphR

Trichodesmium erythraeum IMS101
2 SphR

Synechococcus elongatus PCC 7942
4 SphR

Synechococcus sp. JA-3-3Ab
1 SphR

Synechococcus sp. WH 8102
3 SphR

Thermosynechococcus elongatus BP-1
Phosphate metabolism
[Other] TF SufR
3 SufR

Synechococcus sp. PCC 7002
3 SufR

Synechocystis sp. PCC 6803
4 SufR

Cyanothece sp. ATCC 51142
3 SufR

Cyanothece sp. PCC 8801
2 SufR

Cyanothece sp. PCC 7425
2 SufR

Microcystis aeruginosa NIES-843
2 SufR

Nostoc sp. PCC 7120
2 SufR

Trichodesmium erythraeum IMS101
2 SufR

Synechococcus elongatus PCC 7942
2 SufR

Prochlorococcus marinus str. MIT 9313
2 SufR

Synechococcus sp. JA-3-3Ab
2 SufR

Synechococcus sp. WH 8102
2 SufR

Thermosynechococcus elongatus BP-1
Iron-sulfur cluster biogenesis
RF00059 RNA TPP
1 TPP

Synechococcus sp. PCC 7002
1 TPP

Synechocystis sp. PCC 6803
1 TPP

Cyanothece sp. ATCC 51142
1 TPP

Cyanothece sp. PCC 8801
1 TPP

Cyanothece sp. PCC 7425
1 TPP

Microcystis aeruginosa NIES-843
1 TPP

Nostoc sp. PCC 7120
1 TPP

Trichodesmium erythraeum IMS101
1 TPP

Synechococcus elongatus PCC 7942
1 TPP

Prochlorococcus marinus str. MIT 9313
1 TPP

Synechococcus sp. JA-3-3Ab
1 TPP

Synechococcus sp. WH 8102
1 TPP

Gloeobacter violaceus PCC 7421
1 TPP

Thermosynechococcus elongatus BP-1
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
1 yybP-ykoY

Nostoc sp. PCC 7120
2 yybP-ykoY

Synechococcus sp. JA-3-3Ab
1 yybP-ykoY

Gloeobacter violaceus PCC 7421
RF00162 RNA SAM
1 SAM

Synechococcus sp. JA-3-3Ab
1 SAM

Gloeobacter violaceus PCC 7421
Methionine biosynthesis
RF00174 RNA Cobalamin
1 Cobalamin

Synechococcus sp. PCC 7002
2 Cobalamin

Cyanothece sp. ATCC 51142
1 Cobalamin

Cyanothece sp. PCC 8801
2 Cobalamin

Cyanothece sp. PCC 7425
3 Cobalamin

Nostoc sp. PCC 7120
2 Cobalamin

Synechococcus elongatus PCC 7942
1 Cobalamin

Prochlorococcus marinus str. MIT 9313
3 Cobalamin

Synechococcus sp. JA-3-3Ab
1 Cobalamin

Synechococcus sp. WH 8102
2 Cobalamin

Gloeobacter violaceus PCC 7421
2 Cobalamin

Thermosynechococcus elongatus BP-1
Cobalamin biosynthesis
RF00379 RNA ydaO-yuaA
1 ydaO-yuaA

Synechococcus sp. PCC 7002
1 ydaO-yuaA

Cyanothece sp. PCC 8801
2 ydaO-yuaA

Cyanothece sp. PCC 7425
1 ydaO-yuaA

Microcystis aeruginosa NIES-843
3 ydaO-yuaA

Nostoc sp. PCC 7120
Cell wall metabolism; Osmotic stress response
RF00442 RNA ykkC-yxkD
1 ykkC-yxkD

Synechocystis sp. PCC 6803
2 ykkC-yxkD

Cyanothece sp. PCC 7425
1 ykkC-yxkD

Microcystis aeruginosa NIES-843
1 ykkC-yxkD

Synechococcus sp. WH 8102
1 ykkC-yxkD

Gloeobacter violaceus PCC 7421
Multidrug resistance
RF00557 RNA L10_leader
1 L10_leader

Synechococcus sp. PCC 7002
1 L10_leader

Synechocystis sp. PCC 6803
1 L10_leader

Cyanothece sp. ATCC 51142
1 L10_leader

Cyanothece sp. PCC 8801
1 L10_leader

Cyanothece sp. PCC 7425
1 L10_leader

Microcystis aeruginosa NIES-843
1 L10_leader

Nostoc sp. PCC 7120
1 L10_leader

Synechococcus elongatus PCC 7942
1 L10_leader

Synechococcus sp. JA-3-3Ab
1 L10_leader

Gloeobacter violaceus PCC 7421
1 L10_leader

Thermosynechococcus elongatus BP-1
Ribosome biogenesis
RF00559 RNA L21_leader
1 L21_leader

Synechococcus sp. JA-3-3Ab
Ribosome biogenesis
RF01051 RNA GEMM_RNA_motif
5 GEMM_RNA_motif

Cyanothece sp. PCC 7425
1 GEMM_RNA_motif

Thermosynechococcus elongatus BP-1
Second messenger response
RF01068 RNA mini-ykkC
1 mini-ykkC

Gloeobacter violaceus PCC 7421
Multidrug resistance
RF01739 RNA glnA
1 glnA

Synechocystis sp. PCC 6803
2 glnA

Cyanothece sp. ATCC 51142
1 glnA

Cyanothece sp. PCC 8801
3 glnA

Cyanothece sp. PCC 7425
1 glnA

Trichodesmium erythraeum IMS101
1 glnA

Synechococcus elongatus PCC 7942
1 glnA

Prochlorococcus marinus str. MIT 9313
1 glnA

Synechococcus sp. JA-3-3Ab
2 glnA

Thermosynechococcus elongatus BP-1
Nitrogen assimilation