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

Collection of regulogs in Mycobacteriaceae taxonomic group

General statistics
Genomes 9
TF regulogs 30
TF regulons 154
TF binding sites 512
RNA regulogs 12
RNA regulons 80
RNA sites 131

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
Mycobacterium abscessus ATCC 19977 21 65 11 14 32 79
Mycobacterium avium 104 12 46 9 15 21 61
Mycobacterium flavescens PYR-GCK 17 55 10 17 27 72
Mycobacterium leprae TN 9 20 4 6 13 26
Mycobacterium marinum M 13 44 10 17 23 61
Mycobacterium smegmatis str. MC2 155 25 88 10 19 35 107
Mycobacterium sp. JLS 24 77 8 13 32 90
Mycobacterium tuberculosis H37Rv 13 47 9 15 22 62
Mycobacterium vanbaalenii PYR-1 20 70 9 15 29 85
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
1 ArgR

Mycobacterium smegmatis str. MC2 155
1 ArgR

Mycobacterium tuberculosis H37Rv
1 ArgR

Mycobacterium abscessus ATCC 19977
1 ArgR

Mycobacterium avium 104
1 ArgR

Mycobacterium marinum M
1 ArgR

Mycobacterium leprae TN
1 ArgR

Mycobacterium vanbaalenii PYR-1
1 ArgR

Mycobacterium flavescens PYR-GCK
1 ArgR

Mycobacterium sp. JLS
Arginine biosynthesis
ArsR TF ArsR
2 ArsR

Mycobacterium smegmatis str. MC2 155
2 ArsR

Mycobacterium tuberculosis H37Rv
2 ArsR

Mycobacterium abscessus ATCC 19977
1 ArsR

Mycobacterium marinum M
1 ArsR

Mycobacterium vanbaalenii PYR-1
3 ArsR

Mycobacterium flavescens PYR-GCK
2 ArsR

Mycobacterium sp. JLS
Arsenic resistance
TF SutR
1 SutR

Mycobacterium smegmatis str. MC2 155
1 SutR

Mycobacterium vanbaalenii PYR-1
1 SutR

Mycobacterium flavescens PYR-GCK
1 SutR

Mycobacterium sp. JLS
Sulfur metabolism
TF Znr
1 Znr

Mycobacterium smegmatis str. MC2 155
1 Znr

Mycobacterium tuberculosis H37Rv
1 Znr

Mycobacterium avium 104
1 Znr

Mycobacterium marinum M
1 Znr

Mycobacterium leprae TN
2 Znr

Mycobacterium vanbaalenii PYR-1
2 Znr

Mycobacterium flavescens PYR-GCK
1 Znr

Mycobacterium sp. JLS
Zinc homeostasis
DeoR TF MSMEG_3264
2 MSMEG_3264

Mycobacterium smegmatis str. MC2 155
2 MSMEG_3264

Mycobacterium sp. JLS
Erythritol utilization; D-threitol utilization
TF MSMEG_3606
2 MSMEG_3606

Mycobacterium smegmatis str. MC2 155
2 MSMEG_3606

Mycobacterium sp. JLS
D-threitol utilization
DtxR TF MntR
2 MntR

Mycobacterium smegmatis str. MC2 155
1 MntR

Mycobacterium tuberculosis H37Rv
1 MntR

Mycobacterium abscessus ATCC 19977
1 MntR

Mycobacterium avium 104
2 MntR

Mycobacterium marinum M
2 MntR

Mycobacterium vanbaalenii PYR-1
2 MntR

Mycobacterium flavescens PYR-GCK
2 MntR

Mycobacterium sp. JLS
Manganese homeostasis
FUR TF Zur
6 Zur

Mycobacterium smegmatis str. MC2 155
6 Zur

Mycobacterium tuberculosis H37Rv
4 Zur

Mycobacterium abscessus ATCC 19977
6 Zur

Mycobacterium avium 104
5 Zur

Mycobacterium marinum M
1 Zur

Mycobacterium leprae TN
9 Zur

Mycobacterium vanbaalenii PYR-1
4 Zur

Mycobacterium flavescens PYR-GCK
6 Zur

Mycobacterium sp. JLS
Zinc homeostasis
GntR/MocR TF MSMEG_4140
4 MSMEG_4140

Mycobacterium smegmatis str. MC2 155
1 MSMEG_4140

Mycobacterium abscessus ATCC 19977
1 MSMEG_4140

Mycobacterium vanbaalenii PYR-1
1 MSMEG_4140

Mycobacterium flavescens PYR-GCK
2 MSMEG_4140

Mycobacterium sp. JLS
Metabolite transport
TF PdxQ
2 PdxQ

Mycobacterium smegmatis str. MC2 155
2 PdxQ

Mycobacterium abscessus ATCC 19977
Pyridoxine/pyridoxal homeostasis; Metabolite transport
TF PdxQ3
1 PdxQ3

Mycobacterium abscessus ATCC 19977
Pyridoxine/pyridoxal homeostasis
TF PdxR2
1 PdxR2

Mycobacterium abscessus ATCC 19977
Pyridoxine/pyridoxal homeostasis
TF PdxR3
2 PdxR3

Mycobacterium smegmatis str. MC2 155
1 PdxR3

Mycobacterium abscessus ATCC 19977
1 PdxR3

Mycobacterium vanbaalenii PYR-1
1 PdxR3

Mycobacterium flavescens PYR-GCK
1 PdxR3

Mycobacterium sp. JLS
Pyridoxine/pyridoxal homeostasis
TF PdxW
2 PdxW

Mycobacterium avium 104
2 PdxW

Mycobacterium marinum M
Pyridoxine/pyridoxal homeostasis
GntR/Others TF IolR
3 IolR

Mycobacterium smegmatis str. MC2 155
3 IolR

Mycobacterium vanbaalenii PYR-1
3 IolR

Mycobacterium flavescens PYR-GCK
Inositol utilization
TF LldR
2 LldR

Mycobacterium smegmatis str. MC2 155
2 LldR

Mycobacterium sp. JLS
Lactate utilization
TF Mce2R
1 Mce2R

Mycobacterium smegmatis str. MC2 155
1 Mce2R

Mycobacterium tuberculosis H37Rv
1 Mce2R

Mycobacterium abscessus ATCC 19977
1 Mce2R

Mycobacterium vanbaalenii PYR-1
1 Mce2R

Mycobacterium sp. JLS
Fatty acid metabolism
TF PhnF
5 PhnF

Mycobacterium smegmatis str. MC2 155
2 PhnF

Mycobacterium abscessus ATCC 19977
4 PhnF

Mycobacterium vanbaalenii PYR-1
3 PhnF

Mycobacterium sp. JLS
Phosphonate utilization; 2-aminoethylphosphonate utilization
HrcA TF HrcA
4 HrcA

Mycobacterium smegmatis str. MC2 155
3 HrcA

Mycobacterium tuberculosis H37Rv
3 HrcA

Mycobacterium abscessus ATCC 19977
3 HrcA

Mycobacterium avium 104
3 HrcA

Mycobacterium marinum M
3 HrcA

Mycobacterium leprae TN
4 HrcA

Mycobacterium vanbaalenii PYR-1
4 HrcA

Mycobacterium flavescens PYR-GCK
4 HrcA

Mycobacterium sp. JLS
Heat shock response
IclR TF LtbR
2 LtbR

Mycobacterium smegmatis str. MC2 155
2 LtbR

Mycobacterium tuberculosis H37Rv
2 LtbR

Mycobacterium abscessus ATCC 19977
2 LtbR

Mycobacterium avium 104
2 LtbR

Mycobacterium marinum M
2 LtbR

Mycobacterium vanbaalenii PYR-1
2 LtbR

Mycobacterium flavescens PYR-GCK
2 LtbR

Mycobacterium sp. JLS
Leucine biosynthesis
LacI TF RhaR
1 RhaR

Mycobacterium smegmatis str. MC2 155
1 RhaR

Mycobacterium sp. JLS
Rhamnose utilization
LexA TF LexA
8 LexA

Mycobacterium smegmatis str. MC2 155
11 LexA

Mycobacterium tuberculosis H37Rv
8 LexA

Mycobacterium abscessus ATCC 19977
9 LexA

Mycobacterium avium 104
9 LexA

Mycobacterium marinum M
3 LexA

Mycobacterium leprae TN
7 LexA

Mycobacterium vanbaalenii PYR-1
8 LexA

Mycobacterium flavescens PYR-GCK
7 LexA

Mycobacterium sp. JLS
SOS response
MerR TF HspR
4 HspR

Mycobacterium smegmatis str. MC2 155
3 HspR

Mycobacterium tuberculosis H37Rv
3 HspR

Mycobacterium abscessus ATCC 19977
3 HspR

Mycobacterium avium 104
3 HspR

Mycobacterium marinum M
2 HspR

Mycobacterium leprae TN
4 HspR

Mycobacterium vanbaalenii PYR-1
4 HspR

Mycobacterium flavescens PYR-GCK
4 HspR

Mycobacterium sp. JLS
Heat shock response
NrdR TF NrdR
4 NrdR

Mycobacterium smegmatis str. MC2 155
2 NrdR

Mycobacterium tuberculosis H37Rv
2 NrdR

Mycobacterium abscessus ATCC 19977
2 NrdR

Mycobacterium avium 104
2 NrdR

Mycobacterium marinum M
2 NrdR

Mycobacterium leprae TN
2 NrdR

Mycobacterium vanbaalenii PYR-1
2 NrdR

Mycobacterium flavescens PYR-GCK
2 NrdR

Mycobacterium sp. JLS
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
2 NrtR

Mycobacterium smegmatis str. MC2 155
2 NrtR

Mycobacterium tuberculosis H37Rv
2 NrtR

Mycobacterium abscessus ATCC 19977
2 NrtR

Mycobacterium avium 104
2 NrtR

Mycobacterium marinum M
2 NrtR

Mycobacterium leprae TN
2 NrtR

Mycobacterium vanbaalenii PYR-1
2 NrtR

Mycobacterium flavescens PYR-GCK
2 NrtR

Mycobacterium sp. JLS
NAD biosynthesis
RpiR TF EutR
2 EutR

Mycobacterium vanbaalenii PYR-1
2 EutR

Mycobacterium sp. JLS
Ethanolamine utilization
TetR TF AcnR
2 AcnR

Mycobacterium smegmatis str. MC2 155
1 AcnR

Mycobacterium tuberculosis H37Rv
2 AcnR

Mycobacterium abscessus ATCC 19977
2 AcnR

Mycobacterium avium 104
1 AcnR

Mycobacterium marinum M
1 AcnR

Mycobacterium leprae TN
2 AcnR

Mycobacterium vanbaalenii PYR-1
2 AcnR

Mycobacterium flavescens PYR-GCK
2 AcnR

Mycobacterium sp. JLS
Tricarboxylic acid cycle
TF AmtR
1 AmtR

Mycobacterium smegmatis str. MC2 155
2 AmtR

Mycobacterium abscessus ATCC 19977
2 AmtR

Mycobacterium sp. JLS
Nitrogen metabolism
TF BioQ
3 BioQ

Mycobacterium smegmatis str. MC2 155
3 BioQ

Mycobacterium abscessus ATCC 19977
3 BioQ

Mycobacterium vanbaalenii PYR-1
3 BioQ

Mycobacterium flavescens PYR-GCK
3 BioQ

Mycobacterium sp. JLS
Biotin biosynthesis
TF PaaR
4 PaaR

Mycobacterium abscessus ATCC 19977
Phenylacetic acid degradation
RF00059 RNA TPP
3 TPP

Mycobacterium smegmatis str. MC2 155
2 TPP

Mycobacterium tuberculosis H37Rv
2 TPP

Mycobacterium abscessus ATCC 19977
2 TPP

Mycobacterium avium 104
2 TPP

Mycobacterium marinum M
2 TPP

Mycobacterium leprae TN
2 TPP

Mycobacterium vanbaalenii PYR-1
4 TPP

Mycobacterium flavescens PYR-GCK
3 TPP

Mycobacterium sp. JLS
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
2 yybP-ykoY

Mycobacterium smegmatis str. MC2 155
1 yybP-ykoY

Mycobacterium tuberculosis H37Rv
1 yybP-ykoY

Mycobacterium abscessus ATCC 19977
1 yybP-ykoY

Mycobacterium marinum M
4 yybP-ykoY

Mycobacterium vanbaalenii PYR-1
2 yybP-ykoY

Mycobacterium flavescens PYR-GCK
2 yybP-ykoY

Mycobacterium sp. JLS
RF00174 RNA Cobalamin
5 Cobalamin

Mycobacterium smegmatis str. MC2 155
2 Cobalamin

Mycobacterium tuberculosis H37Rv
2 Cobalamin

Mycobacterium abscessus ATCC 19977
3 Cobalamin

Mycobacterium avium 104
3 Cobalamin

Mycobacterium marinum M
2 Cobalamin

Mycobacterium leprae TN
1 Cobalamin

Mycobacterium vanbaalenii PYR-1
2 Cobalamin

Mycobacterium flavescens PYR-GCK
1 Cobalamin

Mycobacterium sp. JLS
Cobalamin biosynthesis
RF00230 RNA T-box(Ile)
1 T-box(Ile)

Mycobacterium smegmatis str. MC2 155
1 T-box(Ile)

Mycobacterium tuberculosis H37Rv
1 T-box(Ile)

Mycobacterium abscessus ATCC 19977
1 T-box(Ile)

Mycobacterium marinum M
1 T-box(Ile)

Mycobacterium leprae TN
1 T-box(Ile)

Mycobacterium vanbaalenii PYR-1
1 T-box(Ile)

Mycobacterium flavescens PYR-GCK
Amino acid metabolism
RF00379 RNA ydaO-yuaA
1 ydaO-yuaA

Mycobacterium smegmatis str. MC2 155
1 ydaO-yuaA

Mycobacterium tuberculosis H37Rv
1 ydaO-yuaA

Mycobacterium abscessus ATCC 19977
1 ydaO-yuaA

Mycobacterium avium 104
1 ydaO-yuaA

Mycobacterium marinum M
1 ydaO-yuaA

Mycobacterium leprae TN
1 ydaO-yuaA

Mycobacterium vanbaalenii PYR-1
1 ydaO-yuaA

Mycobacterium flavescens PYR-GCK
1 ydaO-yuaA

Mycobacterium sp. JLS
Osmotic stress response; Cell wall metabolism
RF00380 RNA ykoK
1 ykoK

Mycobacterium smegmatis str. MC2 155
2 ykoK

Mycobacterium tuberculosis H37Rv
1 ykoK

Mycobacterium abscessus ATCC 19977
3 ykoK

Mycobacterium avium 104
2 ykoK

Mycobacterium marinum M
Magnesium homeostasis
RF00442 RNA ykkC-yxkD
1 ykkC-yxkD

Mycobacterium avium 104
1 ykkC-yxkD

Mycobacterium vanbaalenii PYR-1
1 ykkC-yxkD

Mycobacterium flavescens PYR-GCK
Multidrug resistance
RF00504 RNA Glycine
1 Glycine

Mycobacterium smegmatis str. MC2 155
2 Glycine

Mycobacterium tuberculosis H37Rv
1 Glycine

Mycobacterium abscessus ATCC 19977
1 Glycine

Mycobacterium avium 104
2 Glycine

Mycobacterium marinum M
1 Glycine

Mycobacterium vanbaalenii PYR-1
1 Glycine

Mycobacterium flavescens PYR-GCK
1 Glycine

Mycobacterium sp. JLS
Glycine metabolism
RF00515 RNA PyrR
1 PyrR

Mycobacterium smegmatis str. MC2 155
1 PyrR

Mycobacterium tuberculosis H37Rv
1 PyrR

Mycobacterium abscessus ATCC 19977
1 PyrR

Mycobacterium avium 104
1 PyrR

Mycobacterium marinum M
1 PyrR

Mycobacterium vanbaalenii PYR-1
1 PyrR

Mycobacterium flavescens PYR-GCK
1 PyrR

Mycobacterium sp. JLS
Pyrimidine metabolism
RF00557 RNA L10_leader
1 L10_leader

Mycobacterium abscessus ATCC 19977
Ribosome biogenesis
RF00634 RNA SAM-IV
2 SAM-IV

Mycobacterium smegmatis str. MC2 155
1 SAM-IV

Mycobacterium tuberculosis H37Rv
2 SAM-IV

Mycobacterium abscessus ATCC 19977
1 SAM-IV

Mycobacterium avium 104
1 SAM-IV

Mycobacterium marinum M
2 SAM-IV

Mycobacterium vanbaalenii PYR-1
2 SAM-IV

Mycobacterium flavescens PYR-GCK
2 SAM-IV

Mycobacterium sp. JLS
Sulfur metabolism
RF01057 RNA SAH_riboswitch
1 SAH_riboswitch

Mycobacterium smegmatis str. MC2 155
1 SAH_riboswitch

Mycobacterium abscessus ATCC 19977
1 SAH_riboswitch

Mycobacterium avium 104
1 SAH_riboswitch

Mycobacterium marinum M
1 SAH_riboswitch

Mycobacterium flavescens PYR-GCK
1 SAH_riboswitch

Mycobacterium sp. JLS
Methionine metabolism