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

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes -- version 3.2 --

Collection of regulogs in Cyanobacteria taxonomic group

Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 3.2 --