Found 174 low-confidence and 26 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 | adh: acetaldehyde dehydrogenase (not acylating) | C683_RS01225 | |
| 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 | C683_RS05740 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | C683_RS01225 | |
| arginine | rocD: ornithine aminotransferase | | |
| arginine | rocE: L-arginine permease | C683_RS03460 | C683_RS03825 |
| asparagine | ans: asparaginase | | |
| cellobiose | bgl: cellobiase | | |
| citrate | acn: aconitase | | |
| citrate | icd: isocitrate dehydrogenase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | C683_RS05310 | C683_RS02270 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | C683_RS01225 | |
| citrulline | rocD: ornithine aminotransferase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | C683_RS03050 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | C683_RS01225 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | C683_RS00525 | C683_RS02490 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | C683_RS01225 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | C683_RS01225 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | C683_RS06290 | C683_RS02490 |
| fucose | aldA: lactaldehyde dehydrogenase | C683_RS01225 | |
| 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 | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | C683_RS04740 | |
| glucosamine | manX: glucosamine PTS system, EII-AB component ManX | C683_RS04685 | |
| glucosamine | manY: glucosamine PTS system, EII-C component ManY | C683_RS04680 | |
| glucosamine | manZ: glucosamine PTS system, EII-D component ManZ | C683_RS04675 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | C683_RS01225 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | | |
| 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 | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | acn: (2R,3S)-2-methylcitrate dehydratase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | C683_RS03460 | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | C683_RS04120 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | C683_RS04115 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C683_RS04110 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | C683_RS01375 | C683_RS02490 |
| isoleucine | prpB: 2-methylisocitrate lyase | | |
| isoleucine | prpC: 2-methylcitrate synthase | | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| 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) | | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | C683_RS04120 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | C683_RS04115 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C683_RS04110 | |
| leucine | ilvE: L-leucine transaminase | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | | |
| lysine | lysN: 2-aminoadipate transaminase | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | mapP: maltose 6'-phosphate phosphatase | C683_RS02540 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| 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 | C683_RS05390 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | C683_RS01225 | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | C683_RS02545 | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | C683_RS03825 | C683_RS03460 |
| 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 | C683_RS01375 | C683_RS02490 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | C683_RS01265 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | C683_RS01265 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| 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 | C683_RS03825 | C683_RS03460 |
| 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 | opuBA: proline ABC transporter, ATPase component OpuBA/BusAA | C683_RS05310 | C683_RS02320 |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | C683_RS01225 | |
| propionate | acn: (2R,3S)-2-methylcitrate dehydratase | | |
| propionate | prpB: 2-methylisocitrate lyase | | |
| propionate | prpC: 2-methylcitrate synthase | | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | prpE: propionyl-CoA synthetase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | C683_RS01225 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | C683_RS01225 | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | C683_RS01225 | |
| 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 | serP: L-serine permease SerP | C683_RS03825 | C683_RS03460 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | C683_RS02490 | C683_RS01375 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | C683_RS03360 | C683_RS06005 |
| threonine | acn: (2R,3S)-2-methylcitrate dehydratase | | |
| threonine | prpB: 2-methylisocitrate lyase | | |
| threonine | prpC: 2-methylcitrate synthase | | |
| threonine | prpD: 2-methylcitrate dehydratase | | |
| threonine | serP1: L-threonine uptake transporter SerP1 | C683_RS03825 | C683_RS03460 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | C683_RS01225 | |
| thymidine | nupC: thymidine permease NupC | C683_RS01070 | |
| trehalose | treF: trehalase | C683_RS03360 | C683_RS06005 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | C683_RS03825 | C683_RS03460 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | C683_RS03825 | C683_RS03460 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | acn: (2R,3S)-2-methylcitrate dehydratase | | |
| valine | Bap2: L-valine permease Bap2 | C683_RS03460 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | C683_RS04120 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | C683_RS04115 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C683_RS04110 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C683_RS01225 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | prpB: 2-methylisocitrate lyase | | |
| valine | prpC: 2-methylcitrate synthase | | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| 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