Found 124 low-confidence and 65 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | SPIGRAPES_RS00855 | SPIGRAPES_RS11865 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | SPIGRAPES_RS05150 | SPIGRAPES_RS13205 |
| 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 | | |
| alanine | alsT: L-alanine symporter AlsT/DagA | SPIGRAPES_RS08750 | |
| arginine | arcA: arginine deiminase | | |
| arginine | arcC: carbamate kinase | SPIGRAPES_RS00585 | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
| arginine | rocD: ornithine aminotransferase | SPIGRAPES_RS01070 | SPIGRAPES_RS08875 |
| arginine | rocE: L-arginine permease | | |
| cellobiose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | SPIGRAPES_RS12745 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SPIGRAPES_RS00770 | SPIGRAPES_RS05230 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | SPIGRAPES_RS01045 | SPIGRAPES_RS00765 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | SPIGRAPES_RS03390 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | SPIGRAPES_RS00760 | SPIGRAPES_RS00780 |
| citrulline | arcC: carbamate kinase | SPIGRAPES_RS00585 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
| citrulline | rocD: ornithine aminotransferase | SPIGRAPES_RS01070 | SPIGRAPES_RS08875 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| D-serine | dsdX: D-serine transporter DsdX | SPIGRAPES_RS10075 | |
| deoxyinosine | deoB: phosphopentomutase | SPIGRAPES_RS14725 | |
| deoxyinosine | H281DRAFT_01112: deoxynucleoside transporter, permease component 2 | SPIGRAPES_RS00900 | SPIGRAPES_RS07580 |
| deoxyinosine | H281DRAFT_01115: deoxynucleoside transporter, permease component 1 | SPIGRAPES_RS07575 | SPIGRAPES_RS00895 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | SPIGRAPES_RS09910 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | SPIGRAPES_RS03055 | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | SPIGRAPES_RS10110 | SPIGRAPES_RS07595 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | SPIGRAPES_RS13160 | |
| fumarate | dauA: fumarate transporter DauA | SPIGRAPES_RS07310 | |
| galactose | galK: galactokinase (-1-phosphate forming) | SPIGRAPES_RS00190 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | SPIGRAPES_RS10075 | |
| glucosamine | nagK: N-acetylglucosamine kinase | SPIGRAPES_RS04720 | SPIGRAPES_RS06360 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | SPIGRAPES_RS05785 | SPIGRAPES_RS07230 |
| glucosamine | SMc02873: N-acetylglucosamine ABC transporter, substrate-binding component | SPIGRAPES_RS01545 | |
| glucose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | SPIGRAPES_RS07110 | SPIGRAPES_RS07075 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glutamate | gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) | SPIGRAPES_RS09305 | SPIGRAPES_RS03395 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| 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 | PA5503: L-histidine ABC transporter, ATPase component | SPIGRAPES_RS10500 | SPIGRAPES_RS00770 |
| histidine | PA5504: L-histidine ABC transporter, permease component | SPIGRAPES_RS10505 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | SPIGRAPES_RS06585 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | SPIGRAPES_RS06585 | SPIGRAPES_RS12910 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SPIGRAPES_RS12900 | |
| isoleucine | dddA: 3-hydroxypropionate dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | SPIGRAPES_RS01000 | |
| isoleucine | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
| isoleucine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | SPIGRAPES_RS07395 | SPIGRAPES_RS02695 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SPIGRAPES_RS13560 | SPIGRAPES_RS08615 |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | mleP: malate permease MleP | SPIGRAPES_RS11740 | |
| lactose | galK: galactokinase (-1-phosphate forming) | SPIGRAPES_RS00190 | |
| lactose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| lactose | lacK: lactose ABC transporter, ATPase component | SPIGRAPES_RS05785 | SPIGRAPES_RS09060 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | SPIGRAPES_RS06585 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | SPIGRAPES_RS06585 | SPIGRAPES_RS12910 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SPIGRAPES_RS12900 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | SPIGRAPES_RS07375 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SPIGRAPES_RS13560 | SPIGRAPES_RS08615 |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | SPIGRAPES_RS01070 | SPIGRAPES_RS08875 |
| lysine | lysN: 2-aminoadipate transaminase | SPIGRAPES_RS08875 | SPIGRAPES_RS14535 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | SPIGRAPES_RS00470 | |
| maltose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannose | mannokinase: D-mannose kinase | SPIGRAPES_RS06360 | |
| mannose | TT_C0211: mannose ABC transporter, ATPase component MalK1 | SPIGRAPES_RS05785 | SPIGRAPES_RS02390 |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | SPIGRAPES_RS07160 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | SPIGRAPES_RS10040 | |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | SPIGRAPES_RS08700 | SPIGRAPES_RS09215 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | SPIGRAPES_RS12945 | SPIGRAPES_RS09205 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagK: N-acetylglucosamine kinase | SPIGRAPES_RS04720 | SPIGRAPES_RS06360 |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | SPIGRAPES_RS05785 | SPIGRAPES_RS07230 |
| NAG | SMc02873: N-acetylglucosamine ABC transporter, substrate-binding component | SPIGRAPES_RS01545 | |
| 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 | SPIGRAPES_RS07395 | SPIGRAPES_RS07255 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| 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 | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | SPIGRAPES_RS08805 | |
| 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 | | |
| propionate | dddA: 3-hydroxypropionate dehydrogenase | | |
| propionate | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
| propionate | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| propionate | prpE: propionyl-CoA synthetase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | SPIGRAPES_RS16325 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | SPIGRAPES_RS05095 | SPIGRAPES_RS08555 |
| putrescine | gabT: gamma-aminobutyrate transaminase | SPIGRAPES_RS01070 | SPIGRAPES_RS08875 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | SPIGRAPES_RS08875 | SPIGRAPES_RS01070 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | SPIGRAPES_RS00015 | SPIGRAPES_RS04355 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | SPIGRAPES_RS00005 | SPIGRAPES_RS06730 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | SPIGRAPES_RS03055 | |
| rhamnose | rhaB: L-rhamnulokinase | SPIGRAPES_RS12930 | SPIGRAPES_RS07570 |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | SPIGRAPES_RS12875 | SPIGRAPES_RS01890 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | SPIGRAPES_RS12110 | SPIGRAPES_RS08700 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | SPIGRAPES_RS12120 | SPIGRAPES_RS11700 |
| serine | sdaB: L-serine ammonia-lyase | SPIGRAPES_RS09335 | SPIGRAPES_RS16255 |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlE: ABC transporter for polyols MtlEFGK, substrate-binding component MtlE | SPIGRAPES_RS11760 | SPIGRAPES_RS07140 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | SPIGRAPES_RS11765 | SPIGRAPES_RS07620 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | SPIGRAPES_RS05785 | SPIGRAPES_RS02390 |
| sorbitol | scrK: fructokinase | SPIGRAPES_RS15150 | SPIGRAPES_RS00150 |
| sorbitol | sdh: sorbitol dehydrogenase | SPIGRAPES_RS11790 | SPIGRAPES_RS12125 |
| succinate | dauA: succinate:H+ symporter DauA | SPIGRAPES_RS07310 | |
| sucrose | ams: sucrose hydrolase (invertase) | SPIGRAPES_RS03455 | SPIGRAPES_RS01565 |
| sucrose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | SPIGRAPES_RS13620 | SPIGRAPES_RS13615 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoB: phosphopentomutase | SPIGRAPES_RS14725 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | SPIGRAPES_RS06360 | SPIGRAPES_RS08705 |
| trehalose | treF: trehalase | SPIGRAPES_RS03455 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | SPIGRAPES_RS08805 | |
| 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 | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | SPIGRAPES_RS06585 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | SPIGRAPES_RS06585 | SPIGRAPES_RS12910 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | SPIGRAPES_RS12900 | |
| valine | dddA: 3-hydroxypropionate dehydrogenase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
| valine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SPIGRAPES_RS13560 | SPIGRAPES_RS08615 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | SPIGRAPES_RS08555 | SPIGRAPES_RS07240 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | SPIGRAPES_RS12935 | SPIGRAPES_RS08700 |
| xylitol | PS417_12060: xylitol ABC transporter, permease component | SPIGRAPES_RS08695 | SPIGRAPES_RS12120 |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | SPIGRAPES_RS01890 | SPIGRAPES_RS08690 |
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