Found 165 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | B506_RS00085 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | ybhL: acetate uptake transporter YbhL | B506_RS02605 | |
| alanine | cycA: L-alanine symporter CycA | B506_RS00110 | B506_RS08465 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabT: gamma-aminobutyrate transaminase | | |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | | |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | B506_RS08415 | B506_RS05540 |
| arginine | rocE: L-arginine permease | B506_RS00615 | B506_RS00110 |
| asparagine | acaP: aspartate permease AcaP | B506_RS07450 | B506_RS02425 |
| aspartate | acaP: aspartate permease AcaP | B506_RS07450 | B506_RS02425 |
| cellobiose | bgl: cellobiase | B506_RS07860 | B506_RS01420 |
| citrate | acn: aconitase | | |
| citrate | cit1: citrate:H+ symporter Cit1 | B506_RS04560 | |
| citrate | icd: isocitrate dehydrogenase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B506_RS03185 | B506_RS07080 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | B506_RS01945 | B506_RS00635 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | B506_RS05670 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | gabT: gamma-aminobutyrate transaminase | | |
| citrulline | patA: putrescine aminotransferase (PatA/SpuC) | | |
| citrulline | patD: gamma-aminobutyraldehyde dehydrogenase | B506_RS08415 | B506_RS05540 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | B506_RS00110 | B506_RS08465 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | B506_RS00110 | B506_RS08465 |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | B506_RS00085 | |
| deoxyinosine | deoB: phosphopentomutase | B506_RS04420 | B506_RS07815 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B506_RS01475 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | B506_RS00085 | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | B506_RS00085 | |
| fucose | aldA: lactaldehyde dehydrogenase | B506_RS05540 | B506_RS08415 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | B506_RS01010 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | B506_RS08290 | |
| glucuronate | garR: tartronate semialdehyde reductase | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | acaP: L-glutamate permease AcaP | B506_RS07450 | B506_RS02425 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | LAT2: L-histidine transporter | B506_RS02475 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | epi: methylmalonyl-CoA epimerase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | B506_RS01475 | B506_RS05090 |
| isoleucine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | B506_RS01455 | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | B506_RS07860 | B506_RS01420 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | B506_RS01455 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | B506_RS08415 | |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | B506_RS07085 | B506_RS03190 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | B506_RS07080 | B506_RS02570 |
| lysine | lat: L-lysine 6-aminotransferase | | |
| lysine | lysN: 2-aminoadipate transaminase | B506_RS07945 | B506_RS05025 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | malK_Sm: maltose ABC transporter, ATPase component | B506_RS02080 | B506_RS06405 |
| maltose | malX_Sm: maltose ABC transporter, substrate-binding component | B506_RS02085 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | B506_RS01475 | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | B506_RS06860 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | B506_RS08415 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | B506_RS01010 | |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | B506_RS01475 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | B506_RS01555 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | B506_RS01555 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | B506_RS07720 | B506_RS00110 |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | B506_RS08415 | |
| propionate | epi: methylmalonyl-CoA epimerase | | |
| propionate | lctP: propionate permease | B506_RS06080 | |
| propionate | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | B506_RS01455 | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | | |
| propionate | prpE: propionyl-CoA synthetase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B506_RS08415 | B506_RS05540 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | B506_RS05540 | B506_RS08415 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | sdaB: L-serine ammonia-lyase | | |
| sorbitol | sdh: sorbitol dehydrogenase | B506_RS01475 | B506_RS05090 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| threonine | aldA: lactaldehyde dehydrogenase | B506_RS05540 | B506_RS08415 |
| threonine | tdh: L-threonine 3-dehydrogenase | | |
| threonine | tynA: aminoacetone oxidase | | |
| threonine | yvgN: methylglyoxal reductase (NADPH-dependent) | B506_RS06460 | B506_RS05595 |
| thymidine | ald-dh-CoA: acetaldehyde dehydrogenase, acylating | B506_RS00085 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | B506_RS04420 | B506_RS07815 |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treB: trehalose PTS system, EII-BC components TreB | B506_RS04430 | B506_RS07030 |
| trehalose | treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) | B506_RS01025 | B506_RS07030 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | B506_RS00615 | B506_RS00110 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | epi: methylmalonyl-CoA epimerase | | |
| valine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B506_RS08415 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | B506_RS01455 | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know