Found 154 low-confidence and 47 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 | mhpD: 2-hydroxypentadienoate hydratase | U743_RS03565 | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | U743_RS03555 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | U743_RS03040 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | U743_RS07545 | U743_RS03570 |
| acetate | actP: cation/acetate symporter ActP | U743_RS10540 | |
| alanine | alsT: L-alanine symporter AlsT/DagA | U743_RS18170 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | BT0355: L-arabinose:Na+ symporter | U743_RS03095 | |
| arginine | gabT: gamma-aminobutyrate transaminase | U743_RS05875 | U743_RS01125 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | U743_RS05875 | U743_RS12545 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | U743_RS02990 | U743_RS16355 |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | | |
| cellobiose | bgl: cellobiase | U743_RS03545 | |
| cellobiose | glk: glucokinase | U743_RS13275 | |
| cellobiose | SSS-glucose: Sodium/glucose cotransporter | U743_RS03095 | |
| citrate | SLC13A5: citrate:Na+ symporter | U743_RS04310 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | U743_RS01940 | U743_RS15750 |
| 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 | citrullinase: putative citrullinase | U743_RS07715 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | U743_RS02990 | U743_RS16355 |
| citrulline | rocD: ornithine aminotransferase | U743_RS01125 | U743_RS05875 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | U743_RS02600 | U743_RS16750 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | U743_RS11935 | |
| deoxyinosine | deoB: phosphopentomutase | U743_RS08585 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | U743_RS07865 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | U743_RS03845 | U743_RS04305 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | U743_RS16435 | U743_RS02130 |
| 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 | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | U743_RS16355 | U743_RS01785 |
| 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 | | |
| galactose | galE: UDP-glucose 4-epimerase | U743_RS03645 | U743_RS10500 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | U743_RS16355 | U743_RS01785 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | U743_RS10725 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | U743_RS13150 | |
| glucose | glk: glucokinase | U743_RS13275 | |
| glucose | SSS-glucose: Sodium/glucose cotransporter | U743_RS03095 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | U743_RS16355 | U743_RS01785 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | U743_RS10725 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | U743_RS07800 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | U743_RS14550 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | U743_RS11515 | U743_RS12745 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | U743_RS10540 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | U743_RS10545 | |
| lactose | galE: UDP-glucose 4-epimerase | U743_RS03645 | U743_RS10500 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | U743_RS13275 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | U743_RS03545 | |
| leucine | aacS: acetoacetyl-CoA synthetase | U743_RS03845 | U743_RS04305 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | U743_RS11885 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | U743_RS04860 | U743_RS03410 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | U743_RS03005 | U743_RS10200 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | U743_RS03400 | U743_RS04850 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | U743_RS16450 | U743_RS07715 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | U743_RS16355 | U743_RS02990 |
| lysine | davT: 5-aminovalerate aminotransferase | U743_RS05875 | U743_RS01125 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | U743_RS08020 | U743_RS10200 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | U743_RS05300 | U743_RS03010 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | U743_RS13275 | |
| maltose | SSS-glucose: Sodium/glucose cotransporter | U743_RS03095 | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | U743_RS03700 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | U743_RS16355 | U743_RS02990 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | U743_RS13150 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | U743_RS03850 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | U743_RS10070 | U743_RS08005 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | U743_RS08015 | U743_RS09970 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | U743_RS08015 | U743_RS10000 |
| phenylacetate | paaK: phenylacetate-CoA ligase | U743_RS12800 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | U743_RS10070 | U743_RS08005 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | U743_RS03845 | U743_RS04305 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | U743_RS08295 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | U743_RS02990 | U743_RS16355 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | U743_RS05875 | U743_RS01125 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | U743_RS05875 | U743_RS12545 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | U743_RS02990 | U743_RS16355 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | U743_RS17665 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | U743_RS16355 | U743_RS01785 |
| 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 | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | sdaB: L-serine ammonia-lyase | U743_RS11935 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | scrK: fructokinase | U743_RS13275 | |
| sorbitol | sdh: sorbitol dehydrogenase | U743_RS16410 | U743_RS06850 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | scrK: fructokinase | U743_RS13275 | |
| sucrose | scrP: sucrose phosphorylase | U743_RS06285 | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | U743_RS12485 | U743_RS12490 |
| threonine | ltaE: L-threonine aldolase | U743_RS04625 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | U743_RS08585 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | U743_RS13275 | |
| trehalose | SSS-glucose: Sodium/glucose cotransporter | U743_RS03095 | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | U743_RS03845 | U743_RS04305 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | U743_RS11515 | U743_RS12745 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | U743_RS10200 | U743_RS02455 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | U743_RS08020 | U743_RS10200 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | U743_RS02990 | U743_RS16355 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | U743_RS16520 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| 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