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

Collections of regulogs classified by metabolic pathways of regulated genes

Each metabolic pathway-specific collection organizes all reconstructed regulogs that control genes from a given metabolic pathway or biological process. The collected biochemical pathways are classified by major classes of biomolecules, such as amino acids, carbohydrates, nucleoides etc. The biopathway-specific collections may combine regulons operated by transcription factors and regulatory RNAs, such as the collection of regulons for Glycine metabolism.

Reconstructed Studied
Pathway TF regulogs (regulons) RNA regulogs (regulons) Total regulogs (regulons) Genomes
Amino Acids and Derivatives
Agmatine utilization 1 (3) 0 (0) 1 (1) 15
Allantoin utilization 6 (18) 0 (0) 6 (6) 42
Amino acid efflux 1 (4) 0 (0) 1 (1) 8
Amino acid metabolism 8 (49) 92 (873) 100 (100) 137
Amino acid transport 2 (8) 0 (0) 2 (2) 10
Amino acid utilization 2 (18) 0 (0) 2 (2) 21
Arginine biosynthesis 27 (230) 0 (0) 27 (27) 249
Arginine degradation 11 (109) 0 (0) 11 (11) 101
Aromatic amino acid metabolism 9 (69) 0 (0) 9 (9) 78
Asparagine degradation 7 (18) 0 (0) 7 (7) 72
Aspartate utilization 7 (19) 0 (0) 7 (7) 72
Betaine utilization 2 (4) 0 (0) 2 (2) 30
Branched-chain amino acid biosynthesis 2 (28) 4 (42) 6 (6) 47
Branched-chain amino acid degradation 19 (127) 0 (0) 19 (19) 159
Creatinine utilization 1 (4) 0 (0) 1 (1) 5
Cysteine metabolism 5 (48) 0 (0) 5 (5) 41
Ectoine utilization 6 (22) 0 (0) 6 (6) 69
Gamma-aminobutyrate utilization 15 (50) 0 (0) 15 (15) 96
Glutamate metabolism 3 (15) 0 (0) 3 (3) 18
Glutamine utilization 1 (6) 0 (0) 1 (1) 11
Glycine betaine synthesis 2 (12) 0 (0) 2 (2) 23
Glycine metabolism 3 (35) 18 (145) 21 (21) 188
Histidine biosynthesis 6 (46) 5 (46) 11 (11) 105
Histidine utilization 20 (122) 0 (0) 20 (20) 179
L-cystine transporter 1 (2) 0 (0) 1 (1) 11
Leucine biosynthesis 7 (50) 0 (0) 7 (7) 58
Lysine biosynthesis 2 (15) 10 (102) 12 (12) 136
Methionine biosynthesis 23 (191) 13 (96) 36 (36) 273
Methionine metabolism 19 (152) 11 (91) 30 (30) 246
Ornithine degradation 1 (8) 1 (12) 2 (2) 26
Proline and 4-hydrohyproline utilization 13 (46) 0 (0) 13 (13) 126
Proline utilization 1 (4) 0 (0) 1 (1) 11
Serine biosynthesis 0 (0) 3 (32) 3 (3) 34
Spermidine biosynthesis 1 (9) 0 (0) 1 (1) 11
Threonine biosynthesis 0 (0) 4 (45) 4 (4) 47
Tryptophan biosynthesis 10 (51) 6 (48) 16 (16) 117
Tyrosine degradation 6 (30) 0 (0) 6 (6) 38
Carbohydrates
1,5-Anhydro-d-Fructose utilization 2 (7) 0 (0) 2 (2) 30
2-ketogluconate utilization 4 (19) 0 (0) 4 (4) 34
Acetoin production 1 (4) 0 (0) 1 (1) 11
Acetoin utilization 1 (6) 0 (0) 1 (1) 11
Alginate utilization 1 (1) 0 (0) 1 (1) 16
Allose utilization 3 (5) 0 (0) 3 (3) 31
Alpha-galactosides utilization 3 (10) 0 (0) 3 (3) 26
Alpha-glucosides utilization 2 (12) 0 (0) 2 (2) 30
Alpha-mannans utilization 3 (6) 0 (0) 3 (3) 11
Amino sugar metabolism 0 (0) 6 (44) 6 (6) 63
Arabinan utilization 2 (12) 0 (0) 2 (2) 11
Arabinogalactan utilization 1 (1) 0 (0) 1 (1) 11
Arabinose oligosaccharide utilization 3 (15) 0 (0) 3 (3) 10
Arabinose utilization 8 (57) 0 (0) 8 (8) 94
Ascorbate utilization 8 (41) 0 (0) 8 (8) 62
Beta-glucosides utilization 26 (91) 0 (0) 26 (26) 121
C4-dicarboxylate transport 1 (4) 0 (0) 1 (1) 11
Carbohydrate metabolism 21 (62) 0 (0) 21 (21) 43
Carbon catabolism 6 (64) 0 (0) 6 (6) 64
Carbon dioxide fixation 1 (11) 0 (0) 1 (1) 14
Carbon fixation 1 (12) 0 (0) 1 (1) 14
Carbon monoxide utilization 1 (8) 0 (0) 1 (1) 10
Cellobiose utilization 13 (53) 0 (0) 13 (13) 91
Cellodextrin utilization 1 (1) 0 (0) 1 (1) 10
Central carbohydrate metabolism 17 (140) 0 (0) 17 (17) 150
Chitobiose utilization 1 (8) 0 (0) 1 (1) 11
Chondroitin sulphate utilization 1 (7) 0 (0) 1 (1) 11
Citrate metabolism 2 (10) 0 (0) 2 (2) 11
Citrate utilization 2 (10) 0 (0) 2 (2) 19
D-threitol utilization 2 (4) 0 (0) 2 (2) 9
Erythritol utilization 1 (2) 0 (0) 1 (1) 9
Ethanolamine utilization 5 (21) 0 (0) 5 (5) 59
Formate metabolism 3 (21) 0 (0) 3 (3) 46
Fructooligosaccharides utilization 4 (10) 0 (0) 4 (4) 45
Fructose utilization 20 (108) 0 (0) 20 (20) 204
Fructoselysine utilization 1 (2) 0 (0) 1 (1) 11
Fructosides utilization 1 (10) 0 (0) 1 (1) 11
Fucose utilization 5 (16) 0 (0) 5 (5) 63
Fucose-glucose oligosaccharide utilization 1 (5) 0 (0) 1 (1) 11
Galactan utilization 2 (11) 0 (0) 2 (2) 21
Galactarate utilization 13 (53) 0 (0) 13 (13) 75
Galacto-N-biose utilization 1 (4) 0 (0) 1 (1) 10
Galactonate utilization 2 (7) 0 (0) 2 (2) 24
Galactooligosaccharide utilization 3 (16) 0 (0) 3 (3) 10
Galactose utilization 12 (74) 0 (0) 12 (12) 117
Galactosides utilization 14 (55) 0 (0) 14 (14) 82
Galacturonate utilization 18 (79) 0 (0) 18 (18) 134
Global catabolite repression 1 (15) 0 (0) 1 (1) 15
Glucarate utilization 13 (55) 0 (0) 13 (13) 75
Glucomannan utilization 2 (10) 0 (0) 2 (2) 15
Gluconate utilization 21 (87) 0 (0) 21 (21) 203
Gluconeogenesis 3 (19) 0 (0) 3 (3) 41
Glucosamine utilization 1 (5) 0 (0) 1 (1) 11
Glucose utilization 2 (11) 0 (0) 2 (2) 21
Glucuronate utilization 30 (110) 0 (0) 30 (30) 177
Glycerate utilization 9 (42) 0 (0) 9 (9) 82
Glycerol utilization 2 (16) 0 (0) 2 (2) 22
Glycolate utilization 15 (45) 0 (0) 15 (15) 102
Glycolysis 3 (29) 0 (0) 3 (3) 33
Glyoxylate bypass 1 (10) 0 (0) 1 (1) 12
Heparin utilization 1 (4) 0 (0) 1 (1) 11
Hexulose metabolism 2 (4) 0 (0) 2 (2) 25
Hyaluronan utilization 1 (7) 0 (0) 1 (1) 11
Hyaluronate utilization 1 (6) 0 (0) 1 (1) 15
Idonate utilization 2 (11) 0 (0) 2 (2) 27
Inositol utilization 18 (55) 0 (0) 18 (18) 134
Kojibiose utilization 3 (9) 0 (0) 3 (3) 23
L-galactose utilization 1 (6) 0 (0) 1 (1) 11
L-gulonate utilization 3 (10) 0 (0) 3 (3) 39
L-lyxose utilization 1 (4) 0 (0) 1 (1) 12
L-talarate utilization 3 (5) 0 (0) 3 (3) 29
L-xylulose utilization 1 (1) 0 (0) 1 (1) 10
Lactate utilization 30 (126) 0 (0) 30 (30) 213
Lacto-N-biose utilization 1 (4) 0 (0) 1 (1) 10
Lactose utilization 6 (39) 0 (0) 6 (6) 59
Levan utilization 1 (2) 0 (0) 1 (1) 11
Malate utilization 3 (22) 0 (0) 3 (3) 41
Maltodextrin utilization 19 (106) 0 (0) 19 (19) 106
Maltose utilization 26 (124) 0 (0) 26 (26) 130
Mannan and beta-mannosides utilization 1 (5) 0 (0) 1 (1) 11
Mannitol utilization 7 (36) 0 (0) 7 (7) 94
Mannose utilization 10 (25) 0 (0) 10 (10) 68
Mannosides utilization 7 (17) 0 (0) 7 (7) 44
Methylcitrate utilization 10 (60) 0 (0) 10 (10) 88
N-acetylgalactosamine utilization 13 (42) 0 (0) 13 (13) 100
N-acetylglucosamine utilization 33 (174) 0 (0) 33 (33) 267
Neotrehalosadiamine biosynthesis 1 (3) 0 (0) 1 (1) 11
Nigerose utilization 2 (3) 0 (0) 2 (2) 30
O-glycans utilization 2 (2) 0 (0) 2 (2) 11
Oligoglucoside utilization 1 (1) 0 (0) 1 (1) 15
Pectic galactan utilization 1 (3) 0 (0) 1 (1) 11
Pectin and polygalacturonate utlization 3 (15) 0 (0) 3 (3) 31
Pectin utilization 1 (5) 0 (0) 1 (1) 11
Pentose utilization 1 (2) 0 (0) 1 (1) 15
Polysaccharides utilization 2 (4) 0 (0) 2 (2) 11
Possibly alpha-mannosides utilization 1 (7) 0 (0) 1 (1) 11
Psicose utilization 1 (4) 0 (0) 1 (1) 15
Pyruvate metabolism 8 (63) 0 (0) 8 (8) 75
Raffinose utilization 2 (11) 0 (0) 2 (2) 22
Rhamnogalacturonides utilization 6 (28) 0 (0) 6 (6) 49
Rhamnose oligosaccharides utilization 2 (5) 0 (0) 2 (2) 16
Rhamnose utilization 16 (61) 0 (0) 16 (16) 136
Rhizopine catabolism 1 (5) 0 (0) 1 (1) 15
Ribitol utilization 2 (3) 0 (0) 2 (2) 25
Ribose utilization 23 (113) 0 (0) 23 (23) 222
Ribulose monophosphate pathway 1 (6) 0 (0) 1 (1) 11
Santhopine utilization 2 (4) 0 (0) 2 (2) 30
Sialic acid utilization 12 (56) 0 (0) 12 (12) 88
Sorbitol utilization 5 (20) 0 (0) 5 (5) 71
Sorbitol utilization 1 (5) 0 (0) 1 (1) 12
Sorbose utilization 1 (1) 0 (0) 1 (1) 12
Starch utilization 2 (11) 0 (0) 2 (2) 11
Sucrose utilization 21 (88) 0 (0) 21 (21) 164
Sugar utilization 71 (215) 0 (0) 71 (71) 217
Tagatose utilization 2 (5) 0 (0) 2 (2) 30
Trehalose utilization 21 (94) 0 (0) 21 (21) 185
Tricarboxylic acid cycle 11 (78) 2 (14) 13 (13) 89
Xylitol utilization 4 (7) 0 (0) 4 (4) 50
Xylooligosacharides utilization 1 (4) 0 (0) 1 (1) 10
Xylose utilization 10 (57) 0 (0) 10 (10) 86
Cell Wall and Capsule
Biofilm formation 3 (18) 0 (0) 3 (3) 33
Cell wall metabolism 3 (19) 6 (37) 9 (9) 87
Intercellular adhesion 2 (12) 0 (0) 2 (2) 17
Lipopolysaccharide biosynthesis 1 (16) 0 (0) 1 (1) 16
N-acetylmuramate utilization 5 (18) 0 (0) 5 (5) 60
Cofactors, Vitamins, Prosthetic Groups, Pigments
Biotin biosynthesis 30 (235) 0 (0) 30 (30) 282
Cobalamin biosynthesis 4 (27) 21 (197) 25 (25) 252
Folate metabolism 0 (0) 3 (22) 3 (3) 50
Heme efflux 1 (7) 0 (0) 1 (1) 7
Iron-sulfur cluster biogenesis 26 (216) 0 (0) 26 (26) 223
Molybdopterin biosynthesis 12 (54) 16 (81) 28 (28) 243
NAD biosynthesis 42 (199) 0 (0) 42 (42) 315
Pyridoxine biosynthesis 18 (71) 0 (0) 18 (18) 150
Pyridoxine/pyridoxal homeostasis 79 (164) 0 (0) 79 (79) 256
Riboflavin biosynthesis 8 (44) 37 (251) 45 (45) 386
Thiamine biosynthesis 4 (28) 39 (361) 43 (43) 399
Thiamine transport 4 (28) 1 (3) 5 (5) 36
Dormancy and Sporulation
Dormancy 1 (12) 0 (0) 1 (1) 12
Sporulation 1 (7) 0 (0) 1 (1) 11
Drug resistance
Antibiotic resistance 9 (43) 0 (0) 9 (9) 98
Bacitracin resistance 2 (11) 0 (0) 2 (2) 11
Beta-lactam resistance 1 (4) 0 (0) 1 (1) 7
Drug resistance 5 (27) 0 (0) 5 (5) 65
Macrolides efflux 1 (2) 0 (0) 1 (1) 8
Multidrug efflux 44 (176) 0 (0) 44 (44) 182
Multidrug resistance 55 (297) 23 (107) 78 (78) 308
Penicillin and methicillin resistance 1 (1) 0 (0) 1 (1) 7
Penicillin resistance 1 (5) 0 (0) 1 (1) 11
Ramoplanin resistance 1 (7) 0 (0) 1 (1) 11
Salicylic acid resistance 1 (3) 0 (0) 1 (1) 11
Fatty Acids, Lipids, and Isoprenoids
Acyclic terpenes degradation 1 (1) 0 (0) 1 (1) 11
Fatty acid biosynthesis 17 (125) 0 (0) 17 (17) 146
Fatty acid degradation 22 (172) 0 (0) 22 (22) 153
Fatty acid metabolism 4 (20) 0 (0) 4 (4) 38
Lipoprotein export 1 (3) 0 (0) 1 (1) 8
Membrane Transport
Hypothetical ABC transporter 6 (39) 0 (0) 6 (6) 71
Metabolite transport 74 (219) 0 (0) 74 (74) 304
Metabolism of Aromatic Compounds
3-hydroxybenzoate degradation 1 (2) 0 (0) 1 (1) 8
Benzoate degradation 1 (2) 0 (0) 1 (1) 8
p-aminobenzoyl-glutamate utilization 1 (4) 0 (0) 1 (1) 12
Phenylacetic acid degradation 17 (80) 0 (0) 17 (17) 138
Protocatechuate degradation 2 (4) 0 (0) 2 (2) 8
Utilization of aromatic compounds 3 (24) 0 (0) 3 (3) 32
Vanillate utilization 10 (28) 0 (0) 10 (10) 83
Metal homeostasis
Copper homeostasis 4 (39) 0 (0) 4 (4) 51
Iron homeostasis 36 (303) 0 (0) 36 (36) 268
Lead resistance 18 (96) 0 (0) 18 (18) 170
Magnesium homeostasis 0 (0) 9 (44) 9 (9) 100
Manganese homeostasis 21 (155) 0 (0) 21 (21) 157
Mercury resistance 13 (32) 0 (0) 13 (13) 129
Metal homeostasis 2 (9) 0 (0) 2 (2) 25
Molybdenum homeostasis 22 (107) 13 (63) 35 (35) 251
Nickel homeostasis 16 (57) 0 (0) 16 (16) 171
Potassium homeostasis 1 (2) 0 (0) 1 (1) 10
Tungsten homeostasis 4 (23) 1 (7) 5 (5) 39
Zinc homeostasis 47 (360) 0 (0) 47 (47) 332
Miscellaneous
Anaerobic metabolism 3 (39) 0 (0) 3 (3) 39
Competence 1 (4) 0 (0) 1 (1) 11
Flavonoids response 1 (2) 0 (0) 1 (1) 11
Malonate metabolism 10 (27) 0 (0) 10 (10) 79
NULL 1 (2) 0 (0) 1 (1) 8
Phage infection protein 1 (15) 0 (0) 1 (1) 15
Polyamine homeostasis 1 (7) 0 (0) 1 (1) 11
Toxin-antitoxin system 1 (8) 0 (0) 1 (1) 11
Transport 5 (37) 0 (0) 5 (5) 30
unknown 4 (19) 0 (0) 4 (4) 41
Motility and Chemotaxis
Motility 4 (38) 0 (0) 4 (4) 10
Nitrogen Metabolism
Denitrification 7 (25) 0 (0) 7 (7) 72
Nitrate and nitrite respiration 8 (64) 0 (0) 8 (8) 81
Nitrogen assimilation 27 (254) 1 (9) 28 (28) 249
Nitrogen fixation 12 (75) 0 (0) 12 (12) 60
Nitrogen metabolism 9 (35) 0 (0) 9 (9) 64
Nucleosides and Nucleotides
Adenosine utilization 1 (4) 0 (0) 1 (1) 15
Deoxynucleoside utilization 2 (10) 0 (0) 2 (2) 26
Deoxyribonucleoside utilization 1 (11) 0 (0) 1 (1) 12
Deoxyribonucleotide biosynthesis 42 (351) 0 (0) 42 (42) 366
Nucleoside utilization 4 (19) 0 (0) 4 (4) 26
Purine metabolism 8 (95) 8 (69) 16 (16) 126
Pyrimidine metabolism 0 (0) 9 (79) 9 (9) 95
Pyrimidine utilization 20 (97) 0 (0) 20 (20) 126
Queuosine biosynthesis 0 (0) 9 (68) 9 (9) 92
Ribonucleoside utilization 2 (8) 0 (0) 2 (2) 10
Ribonucleotide reductases 1 (12) 0 (0) 1 (1) 12
Uridine utilization 1 (2) 0 (0) 1 (1) 8
Xanthine utilization 3 (12) 0 (0) 3 (3) 24
Xanthosine utilization 1 (4) 0 (0) 1 (1) 12
Phosphorus Metabolism
2-aminoethylphosphonate utilization 15 (46) 0 (0) 15 (15) 98
Phosphate metabolism 3 (32) 0 (0) 3 (3) 35
Phosphonate utilization 24 (85) 0 (0) 24 (24) 167
Phosphonoacetate utilization 1 (2) 0 (0) 1 (1) 11
Photosynthesis
Photosynthesis 2 (16) 0 (0) 2 (2) 29
Protein Metabolism
Proteolysis 1 (8) 0 (0) 1 (1) 8
Ribosome biogenesis 0 (0) 46 (451) 46 (46) 190
Regulation and Cell signaling
Quorum sensing 2 (12) 0 (0) 2 (2) 19
Second messenger response 0 (0) 9 (50) 9 (9) 104
Respiration
Energy metabolism 32 (233) 0 (0) 32 (32) 168
Formate oxydation 6 (19) 0 (0) 6 (6) 48
Tetrathionate reduction 4 (14) 0 (0) 4 (4) 47
Thiosulfate reduction 3 (29) 0 (0) 3 (3) 26
Stress Response
2-Methylhydroquinone and catechol resistance 1 (10) 0 (0) 1 (1) 11
Alkaline stress response 1 (1) 0 (0) 1 (1) 10
Carbonyl stress response 12 (33) 0 (0) 12 (12) 123
Cell wall-active antibiotics stress response 1 (11) 0 (0) 1 (1) 11
Cold shock response 1 (6) 0 (0) 1 (1) 11
DNA alkylation response 1 (6) 0 (0) 1 (1) 11
Glutathione metabolism 1 (8) 0 (0) 1 (1) 16
Heat shock response 49 (392) 0 (0) 49 (49) 355
Light-dependent DNA repair 4 (23) 0 (0) 4 (4) 40
Nitrosative stress response 39 (210) 0 (0) 39 (39) 239
Osmotic stress response 4 (38) 5 (34) 9 (9) 92
Oxidative stress response 14 (121) 0 (0) 14 (14) 109
Peroxide stress response 6 (52) 0 (0) 6 (6) 54
Phage shock response 1 (5) 0 (0) 1 (1) 10
Phenolic acid stress response 3 (10) 0 (0) 3 (3) 41
Protein secretion stress response 1 (5) 0 (0) 1 (1) 11
Salt stress response 1 (3) 0 (0) 1 (1) 14
SOS response 40 (319) 0 (0) 40 (40) 339
Superoxide stress response 18 (85) 0 (0) 18 (18) 164
Toxic fatty acid stress response 2 (8) 0 (0) 2 (2) 26
Sulfur Metabolism
Alkanesulfonates utilization 5 (10) 0 (0) 5 (5) 38
Sulfite reduction 1 (8) 0 (0) 1 (1) 11
Sulfur metabolism 4 (12) 1 (8) 5 (5) 31
Taurine utilization 9 (26) 0 (0) 9 (9) 89
Toxic metal resistance
Arsenic resistance 10 (59) 0 (0) 10 (10) 63
Cadmium resistance 26 (157) 0 (0) 26 (26) 230
Cobalt resistance 7 (42) 0 (0) 7 (7) 64
Copper resistance 29 (179) 0 (0) 29 (29) 240
Heavy metal resistance 4 (22) 0 (0) 4 (4) 40
Metal efflux 1 (6) 0 (0) 1 (1) 11
Nickel resistance 5 (36) 0 (0) 5 (5) 49
Uranium reduction 1 (3) 0 (0) 1 (1) 10
Zinc resistance 17 (107) 0 (0) 17 (17) 159
Virulence
Virulence 2 (10) 0 (0) 2 (2) 7
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