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

Collections of regulogs classified by effector of regulator

Each effector-specific collection organizes all reconstructed regulogs for regulators that respond to a given effector, which is either a small molecule metabolite, an aminoacyl tRNA, or a protein from a multi-component regulatory system. The collected effectors are classified into major classes of biomolecules, such as amino acids, carbohydrates, nucleoides etc. The effector-specific collections may combine regulons operated by transcription factors and regulatory RNAs, such as the collection of regulons for Glycine effector.

Reconstructed Studied
Effector TF regulogs (regulons) RNA regulogs (regulons) Total regulogs (regulons) Genomes
Amino Acids
4-hydroxyproline 11 (37) 0 (0) 11 (11) 103
Arginine 29 (239) 0 (0) 29 (29) 249
Asparagine 1 (5) 0 (0) 1 (1) 11
Betaine 3 (11) 0 (0) 3 (3) 46
Branched-chain amino acids 3 (33) 0 (0) 3 (3) 33
Choline 1 (5) 0 (0) 1 (1) 11
cis-Urocanic acid 19 (117) 0 (0) 19 (19) 172
Glutamate 3 (15) 0 (0) 3 (3) 18
Glycine 3 (35) 18 (145) 21 (21) 188
Histidine 8 (55) 0 (0) 8 (8) 55
Homocysteine 17 (134) 0 (0) 17 (17) 171
L-citrulline 1 (8) 0 (0) 1 (1) 11
L-glutamine 0 (0) 1 (9) 1 (1) 14
LL-2,6-Diaminopimelate 1 (12) 0 (0) 1 (1) 12
Lysine 1 (4) 10 (102) 11 (11) 134
O-acetyl-L-serine 4 (43) 0 (0) 4 (4) 33
Ornithine 1 (8) 0 (0) 1 (1) 11
Phenylalanine 8 (67) 0 (0) 8 (8) 70
Proline 12 (42) 0 (0) 12 (12) 122
S-adenosylhomocysteine 10 (70) 9 (67) 19 (19) 151
S-adenosylmethionine 8 (74) 16 (130) 24 (24) 222
Tryptophan 10 (59) 0 (0) 10 (10) 83
Tyrosine 8 (67) 0 (0) 8 (8) 70
Aminoacyl-tRNAs
Ala-tRNA 0 (0) 5 (62) 5 (5) 68
Arg-tRNA 0 (0) 3 (26) 3 (3) 46
Asn-tRNA 0 (0) 5 (43) 5 (5) 68
Asp-tRNA 0 (0) 4 (24) 4 (4) 61
Cys-tRNA 0 (0) 4 (32) 4 (4) 53
Gly-tRNA 0 (0) 7 (64) 7 (7) 78
His-tRNA 0 (0) 3 (13) 3 (3) 50
Ile-tRNA 0 (0) 9 (92) 9 (9) 95
Leu-tRNA 0 (0) 4 (53) 4 (4) 53
Lys-tRNA 0 (0) 3 (8) 3 (3) 46
Met-tRNA 0 (0) 5 (45) 5 (5) 68
Phe-tRNA 0 (0) 6 (70) 6 (6) 73
Pro-tRNA 0 (0) 4 (31) 4 (4) 51
Ser-tRNA 0 (0) 6 (62) 6 (6) 73
Thr-tRNA 0 (0) 6 (70) 6 (6) 73
Trp-tRNA 0 (0) 6 (66) 6 (6) 73
Tyr-tRNA 0 (0) 4 (46) 4 (4) 53
Val-tRNA 0 (0) 7 (66) 7 (7) 78
Antibiotics
3,3'-neotrehalosadiamine 1 (3) 0 (0) 1 (1) 11
Bacillibactin 1 (5) 0 (0) 1 (1) 11
Chloramphenicol 1 (5) 0 (0) 1 (1) 12
Distamycin 1 (4) 0 (0) 1 (1) 7
Fe-Bacillibactin 1 (5) 0 (0) 1 (1) 11
Methicillin 1 (1) 0 (0) 1 (1) 7
Penicillin G 1 (1) 0 (0) 1 (1) 7
Ramoplanin 1 (7) 0 (0) 1 (1) 11
Tetracycline 1 (5) 0 (0) 1 (1) 12
Carbohydrates
2-deoxy-5-keto-D-gluconate 6-phosphate 2 (5) 0 (0) 2 (2) 26
2-keto-3-deoxy-6-phosphogluconate 13 (95) 0 (0) 13 (13) 110
2-keto-3-deoxygluconate 6 (33) 0 (0) 6 (6) 64
2-keto-D-gluconate 4 (19) 0 (0) 4 (4) 34
5-dehydro-D-gluconate 1 (4) 0 (0) 1 (1) 12
6-phosphogluconate 1 (13) 0 (0) 1 (1) 15
Aldotetraouronic acid 1 (4) 0 (0) 1 (1) 11
Allolactose 1 (5) 0 (0) 1 (1) 12
Allose-6-phosphate 2 (3) 0 (0) 2 (2) 19
Alpha-galactosides 2 (8) 0 (0) 2 (2) 21
Alpha-glucoside 2 (12) 0 (0) 2 (2) 30
Alpha-mannans 3 (6) 0 (0) 3 (3) 11
Arabinan 1 (6) 0 (0) 1 (1) 11
Arabinogalactan oligosaccharides 1 (1) 0 (0) 1 (1) 11
Arabinose 7 (47) 0 (0) 7 (7) 84
Ascorbate-6-phosphate 7 (26) 0 (0) 7 (7) 47
Beta-galactosides 8 (29) 0 (0) 8 (8) 67
Beta-glucoside 16 (52) 0 (0) 16 (16) 103
Beta-glucoside-6-phosphate 4 (15) 0 (0) 4 (4) 34
Cellobiose 5 (22) 0 (0) 5 (5) 39
Cellobiose-6-phosphate 7 (26) 0 (0) 7 (7) 37
Chitobiose 1 (8) 0 (0) 1 (1) 11
Chondroitin sulphate 1 (7) 0 (0) 1 (1) 11
D-allose 1 (2) 0 (0) 1 (1) 12
D-galactose-6-phosphate 2 (15) 0 (0) 2 (2) 30
D-gluconate 2 (7) 0 (0) 2 (2) 11
D-glucono-delta-lactone 1 (3) 0 (0) 1 (1) 11
D-glycerate 8 (28) 0 (0) 8 (8) 66
D-mannonate 3 (10) 0 (0) 3 (3) 39
Deoxyribose-5-phosphate 2 (10) 0 (0) 2 (2) 26
Ethanolamine 5 (21) 0 (0) 5 (5) 59
Fructose 2 (12) 0 (0) 2 (2) 25
Fructose-1,6-bisphosphate 3 (41) 0 (0) 3 (3) 30
Fructose-1,6-diphosphate 9 (66) 0 (0) 9 (9) 75
Fructose-1-phosphate 13 (55) 0 (0) 13 (13) 125
Fructose-6-phosphate 5 (44) 0 (0) 5 (5) 56
Fucose 2 (9) 0 (0) 2 (2) 21
Galactarate 1 (2) 0 (0) 1 (1) 11
Galactobiose 1 (6) 0 (0) 1 (1) 10
Galactonate 2 (7) 0 (0) 2 (2) 24
Galactosamine-6-phosphate 7 (18) 0 (0) 7 (7) 57
Galactose 11 (61) 0 (0) 11 (11) 128
Galactose-6-phosphate 1 (4) 0 (0) 1 (1) 7
Galacturonate 7 (25) 0 (0) 7 (7) 88
Galacturonate oligosaccharides 1 (8) 0 (0) 1 (1) 11
Gluconate 19 (80) 0 (0) 19 (19) 192
Glucosamine-6-phosphate 10 (54) 6 (44) 16 (16) 147
Glucose 7 (25) 0 (0) 7 (7) 22
Glucuronate 13 (38) 0 (0) 13 (13) 132
Heparin 1 (4) 0 (0) 1 (1) 11
Hyaluronan 1 (7) 0 (0) 1 (1) 11
Hyaluronate oligosaccharide phosphate 1 (6) 0 (0) 1 (1) 15
Kojibiose 3 (9) 0 (0) 3 (3) 23
L-fuculose-1-phosphate 3 (7) 0 (0) 3 (3) 42
L-galactose 1 (6) 0 (0) 1 (1) 11
L-gulonate 3 (10) 0 (0) 3 (3) 39
L-idonate 2 (11) 0 (0) 2 (2) 27
L-talarate 3 (5) 0 (0) 3 (3) 29
L-xylulose 1 (1) 0 (0) 1 (1) 10
Lactose 2 (15) 0 (0) 2 (2) 25
Maltose 23 (126) 0 (0) 23 (23) 154
Maltose-6-phosphate 3 (10) 0 (0) 3 (3) 18
Mannitol 2 (5) 0 (0) 2 (2) 31
Mannose 8 (22) 0 (0) 8 (8) 55
Mannose-6-phosphate 1 (1) 0 (0) 1 (1) 6
N-acetylgalactosamine 3 (17) 0 (0) 3 (3) 30
N-acetylgalactosamine-6-phosphate 8 (20) 0 (0) 8 (8) 59
N-acetylglucosamine 16 (71) 0 (0) 16 (16) 134
N-acetylglucosamine-6-phosphate 11 (80) 0 (0) 11 (11) 106
N-acetylmannosamine-6-phosphate 3 (8) 0 (0) 3 (3) 29
N-acetylmuramate-6-phosphate 5 (18) 0 (0) 5 (5) 60
N-acetylneuraminic acid 4 (30) 0 (0) 4 (4) 46
Nigerose-6-phosphate 2 (3) 0 (0) 2 (2) 30
O-glycans 2 (2) 0 (0) 2 (2) 11
Pectic galactan 2 (9) 0 (0) 2 (2) 11
Psicose 1 (4) 0 (0) 1 (1) 15
Raffinose 1 (4) 0 (0) 1 (1) 12
Rhamnose 15 (56) 0 (0) 15 (15) 125
Rhamnulose-1-phosphate 1 (5) 0 (0) 1 (1) 11
Rhamogalacturonate oligosaccharides 3 (13) 0 (0) 3 (3) 38
rhizopine 1 (5) 0 (0) 1 (1) 15
Ribitol 1 (1) 0 (0) 1 (1) 15
Ribose 25 (121) 0 (0) 25 (25) 222
Sialic acid 1 (3) 0 (0) 1 (1) 10
Sorbitol 3 (13) 0 (0) 3 (3) 41
Sorbitol-6-phosphate 1 (5) 0 (0) 1 (1) 12
Sorbose 1 (1) 0 (0) 1 (1) 12
Sucrose 13 (57) 0 (0) 13 (13) 127
Sucrose-6-phosphate 10 (43) 0 (0) 10 (10) 90
Tagatose-6-phosphate 2 (5) 0 (0) 2 (2) 30
Trehalose 8 (36) 0 (0) 8 (8) 85
Trehalose-6-phosphate 14 (66) 0 (0) 14 (14) 115
Xylitol 3 (5) 0 (0) 3 (3) 40
Xylose 10 (57) 0 (0) 10 (10) 86
Coenzymes
Adenosylcobalamin 4 (23) 21 (197) 25 (25) 230
Biotin 28 (222) 0 (0) 28 (28) 252
Flavin mononucleotide 8 (44) 36 (247) 44 (44) 377
Heme 3 (32) 0 (0) 3 (3) 39
NAD 1 (11) 0 (0) 1 (1) 12
NADH 18 (156) 0 (0) 18 (18) 138
Niacin 7 (57) 0 (0) 7 (7) 77
Pre-queuosine 0 (0) 2 (17) 2 (2) 30
Pre-queuosine1 0 (0) 7 (51) 7 (7) 92
Pyridoxal-5-phosphate 61 (161) 0 (0) 61 (61) 337
Tetrahydrofolate 0 (0) 3 (22) 3 (3) 50
Thiamine phosphate 4 (28) 0 (0) 4 (4) 28
Thiamine pyrophosphate 0 (0) 40 (365) 40 (40) 380
Heterocyclic Compounds
Bis-indoles 1 (4) 0 (0) 1 (1) 7
Catechin 1 (2) 0 (0) 1 (1) 11
Fisetin 2 (6) 0 (0) 2 (2) 11
Flavonoids 1 (2) 0 (0) 1 (1) 11
Paraquat 18 (85) 0 (0) 18 (18) 164
Proflavin 1 (12) 0 (0) 1 (1) 12
Quercetin 2 (6) 0 (0) 2 (2) 11
Rhodamine 6G 1 (12) 0 (0) 1 (1) 12
Inorganic Chemicals
Arsenate 5 (30) 0 (0) 5 (5) 38
Arsenite 7 (45) 0 (0) 7 (7) 53
Cadmium, ion (Cd2+) 25 (156) 0 (0) 25 (25) 215
Cobalt ion, (Co2+) 5 (36) 0 (0) 5 (5) 49
Copper ion, (Cu+) 27 (156) 0 (0) 27 (27) 228
Copper ion, (Cu2+) 6 (62) 0 (0) 6 (6) 67
Hydrogen peroxide 7 (67) 0 (0) 7 (7) 67
Inorganic phosphate 3 (32) 0 (0) 3 (3) 35
Iron ion, (Fe2+) 35 (304) 0 (0) 35 (35) 268
Lead ion, (Pb2+) 18 (96) 0 (0) 18 (18) 170
Magnesium ion, (Mg2+) 0 (0) 9 (44) 9 (9) 100
Manganese ion, (Mn2+) 24 (173) 0 (0) 24 (24) 171
Mercury ion, (Hg2+) 13 (32) 0 (0) 13 (13) 129
Molybdate 29 (126) 0 (0) 29 (29) 221
Molybdenum 1 (7) 16 (81) 17 (17) 175
Nickel ion, (Ni2+) 20 (88) 0 (0) 20 (20) 193
Nitrate 5 (46) 0 (0) 5 (5) 53
Nitric oxide 45 (240) 0 (0) 45 (45) 254
Nitrite 8 (70) 0 (0) 8 (8) 88
Oxygen 13 (115) 0 (0) 13 (13) 119
Potassium ion 2 (27) 0 (0) 2 (2) 28
Silver ion, (Ag+) 5 (37) 0 (0) 5 (5) 37
Sulfate 5 (20) 0 (0) 5 (5) 42
Sulfite 2 (10) 0 (0) 2 (2) 19
Tetrathionate 4 (14) 0 (0) 4 (4) 47
Thiosulfate 4 (37) 0 (0) 4 (4) 37
Tungsten 4 (23) 0 (0) 4 (4) 30
Zinc ion, (Zn2+) 60 (446) 0 (0) 60 (60) 362
Lipids and Fatty Acids
Gamma-linolenic acid 2 (8) 0 (0) 2 (2) 26
Linoleate 2 (8) 0 (0) 2 (2) 26
Long-chain acyl-ACP 2 (24) 0 (0) 2 (2) 30
Oleate 14 (84) 0 (0) 14 (14) 136
Oleoyl-CoA 7 (71) 0 (0) 7 (7) 73
Palmitoyl-CoA 7 (71) 0 (0) 7 (7) 73
Phytanate 2 (8) 0 (0) 2 (2) 26
Unsaturated acyl-ACP 12 (78) 0 (0) 12 (12) 90
Unsaturated acyl-CoA 12 (78) 0 (0) 12 (12) 90
Nucleotides and Nucleosides
5-phosphoribosyl 1-pyrophosphate 4 (48) 0 (0) 4 (4) 48
Adenine 0 (0) 8 (69) 8 (8) 105
Adenosine 1 (4) 0 (0) 1 (1) 15
Adenosine diphosphate ribose 26 (97) 0 (0) 26 (26) 263
Cyclic 3',5'-AMP 4 (49) 0 (0) 4 (4) 50
Cyclic diguanylate 0 (0) 9 (50) 9 (9) 104
Deoxyinosine 1 (4) 0 (0) 1 (1) 12
Deoxyribonucleotides 43 (363) 0 (0) 43 (43) 378
Guanine 3 (31) 8 (69) 11 (11) 126
Guanosine 3',5'-bis(diphosphate) 1 (10) 0 (0) 1 (1) 12
Guanosine triphosphate 2 (26) 0 (0) 2 (2) 26
Hypoxanthine 3 (31) 0 (0) 3 (3) 31
Pyrimidine nucleoside 2 (6) 0 (0) 2 (2) 6
Uracil 19 (95) 0 (0) 19 (19) 118
Xanthine 1 (3) 0 (0) 1 (1) 6
Xanthosine 1 (4) 0 (0) 1 (1) 12
Organic Chemicals
2,4-Dinitrophenol 1 (12) 0 (0) 1 (1) 12
2-Acetolactate 2 (28) 0 (0) 2 (2) 28
2-aminoethylphosphonate 6 (14) 0 (0) 6 (6) 43
2-methylcitrate 10 (60) 0 (0) 10 (10) 88
2-oxoglutarate 4 (29) 0 (0) 4 (4) 32
3-hydroxybenzoate 1 (2) 0 (0) 1 (1) 8
4,5-dihydroxypentan-2,3-dione 1 (6) 0 (0) 1 (1) 12
4-hydroxyphenylpyruvate 2 (17) 0 (0) 2 (2) 24
Acetate 1 (4) 0 (0) 1 (1) 11
Acetohydroxybutyrate 1 (16) 0 (0) 1 (1) 16
Acetoin 1 (6) 0 (0) 1 (1) 11
Allantoin 1 (2) 0 (0) 1 (1) 12
Carbonyl cyanide m-chlorophenylhydrazone 1 (12) 0 (0) 1 (1) 12
Choline 1 (7) 0 (0) 1 (1) 12
Citrate 7 (41) 0 (0) 7 (7) 41
Cumene hydroperoxide 1 (8) 0 (0) 1 (1) 11
Deoxyfructosyl glutamine 1 (3) 0 (0) 1 (1) 15
Diamide 13 (42) 0 (0) 13 (13) 119
Ethidium bromide 1 (12) 0 (0) 1 (1) 12
Ferulic acid 4 (12) 0 (0) 4 (4) 49
Formaldehyde 2 (14) 0 (0) 2 (2) 26
Formate 7 (29) 0 (0) 7 (7) 64
Fructoselysine 6-phosphate 1 (2) 0 (0) 1 (1) 11
Galangin 1 (4) 0 (0) 1 (1) 11
Gamma-aminobutyric acid 12 (39) 0 (0) 12 (12) 88
Gentisate 1 (2) 0 (0) 1 (1) 8
Glycerate 2 (20) 0 (0) 2 (2) 28
Glycerol 3-phosphate 2 (16) 0 (0) 2 (2) 22
Glycolate 8 (25) 0 (0) 8 (8) 85
Glyoxylate 1 (10) 0 (0) 1 (1) 12
Homogentisate 1 (5) 0 (0) 1 (1) 8
L-lactate 22 (100) 0 (0) 22 (22) 210
L-malate 2 (17) 0 (0) 2 (2) 30
Lactate 1 (6) 0 (0) 1 (1) 10
Malonyl-CoA 2 (18) 0 (0) 2 (2) 18
Mannopine 1 (3) 0 (0) 1 (1) 15
Methylglyoxal 1 (8) 0 (0) 1 (1) 15
p-aminobenzoyl-glutamate 1 (4) 0 (0) 1 (1) 12
p-Coumaric acid 3 (10) 0 (0) 3 (3) 41
Phenylacetyl-CoA 17 (80) 0 (0) 17 (17) 138
Protocatechuate 1 (2) 0 (0) 1 (1) 8
Putrescine 1 (9) 0 (0) 1 (1) 11
Pyruvate 7 (65) 0 (0) 7 (7) 65
Quinate 1 (2) 0 (0) 1 (1) 8
Quinone 1 (9) 0 (0) 1 (1) 11
Salicylate 2 (8) 0 (0) 2 (2) 23
Shikimate 1 (2) 0 (0) 1 (1) 8
Tamarixetin 1 (4) 0 (0) 1 (1) 11
Taurine 9 (26) 0 (0) 9 (9) 89
tert-Butyl hydroperoxide 1 (8) 0 (0) 1 (1) 11
Vanillate 10 (28) 0 (0) 10 (10) 83
Other factors
Blue light 4 (21) 0 (0) 4 (4) 45
DNA damage 41 (327) 0 (0) 41 (41) 339
Heat shock 45 (374) 0 (0) 45 (45) 339
Iron-sulfur cluster redox state 26 (216) 0 (0) 26 (26) 223
New effector 4 (11) 0 (0) 4 (4) 40
Peptides, and Proteins
BceS, sensor histidine kinase (bacitracin) 1 (7) 0 (0) 1 (1) 11
BlaR, sensor histidine kinase (beta-lactam antibiotics) 1 (4) 0 (0) 1 (1) 7
CelB, cellobiose-specific PTS component EIIB 2 (10) 0 (0) 2 (2) 30
ComP, sensor histidine kinase (ComX) 1 (4) 0 (0) 1 (1) 11
CssS, sensor histidine kinase 1 (5) 0 (0) 1 (1) 11
CysK, cysteine synthetase 2 (18) 0 (0) 2 (2) 18
Feedback-inhibited GlnA, glutamine synthetase 3 (28) 0 (0) 3 (3) 18
GlnK, sensor histidine kinase (glutamine) 1 (6) 0 (0) 1 (1) 11
GlnK-AMP, signal transduction protein 5 (16) 0 (0) 5 (5) 39
GutB, sorbitol-specific PTS EIIB component 2 (7) 0 (0) 2 (2) 30
HPr, phosphocarrier protein 19 (131) 0 (0) 19 (19) 59
HssS, sensor histidine kinase (heme) 1 (7) 0 (0) 1 (1) 7
KdpS, sensor histidine kinase 1 (2) 0 (0) 1 (1) 10
LiaS, sensor histidine kinase (bacitracin, nisin, ramoplanin, vancomycin) 1 (11) 0 (0) 1 (1) 11
LicB, lichenan-specific enzyme IIB PTS component 1 (5) 0 (0) 1 (1) 11
MalK, sensor histidine kinase (malate) 1 (5) 0 (0) 1 (1) 11
Malonyl-ACP 1 (7) 0 (0) 1 (1) 7
ManP, mannose-specific enzyme IIBCA PTS component 2 (7) 0 (0) 2 (2) 18
MtlA, mannitol-specific enzyme IICB PTS component 4 (24) 0 (0) 4 (4) 48
NreB, sensor histidine kinase (Nitrate, Nitrite) 1 (6) 0 (0) 1 (1) 7
NrgA, ammonium uptake protein 1 (10) 0 (0) 1 (1) 11
NrgB, ammonium uptake protein 1 (10) 0 (0) 1 (1) 11
Phosphorylated NtrB, signal histidine kinase 21 (193) 0 (0) 21 (21) 207
PspA regulatory protein 1 (5) 0 (0) 1 (1) 10
PyrR 0 (0) 9 (79) 9 (9) 95
RocG, glutamate dehydrogenase 2 (9) 0 (0) 2 (2) 11
SaeS, sensor histidine kinase 1 (4) 0 (0) 1 (1) 7
SdpI, signal transduction protein 1 (8) 0 (0) 1 (1) 11
SgaB, ascorbate-specific PTS system EIIB component 1 (11) 0 (0) 1 (1) 15
SgaB2, ascorbate-specific PTS system, EIIB component 1 (8) 0 (0) 1 (1) 15
SinI, antirepressor protein 1 (7) 0 (0) 1 (1) 11
Trx, thioredoxin protein 1 (12) 0 (0) 1 (1) 14
YvcQ, sensor histidine kinase 1 (4) 0 (0) 1 (1) 11
YvfT, sensor histidine kinase 1 (4) 0 (0) 1 (1) 11