Found 170 low-confidence and 29 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) | AL1_RS07810 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | AL1_RS13280 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | pta: phosphate acetyltransferase | AL1_RS06580 | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | | |
| acetate | pta: phosphate acetyltransferase | AL1_RS06580 | |
| alanine | alsT: L-alanine symporter AlsT/DagA | AL1_RS04860 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | AL1_RS06795 | AL1_RS04690 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | AL1_RS07810 | |
| arginine | rocD: ornithine aminotransferase | AL1_RS05070 | AL1_RS08245 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| asparagine | glt: aspartate:proton symporter Glt | | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | AL1_RS08135 | AL1_RS06795 |
| citrate | acn: aconitase | | |
| citrate | icd: isocitrate dehydrogenase | AL1_RS13260 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AL1_RS01105 | AL1_RS02295 |
| 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 | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | AL1_RS07810 | |
| citrulline | rocD: ornithine aminotransferase | AL1_RS05070 | AL1_RS08245 |
| 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 | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | AL1_RS07810 | |
| deoxyinosine | deoB: phosphopentomutase | AL1_RS13095 | |
| deoxyinosine | pta: phosphate acetyltransferase | AL1_RS06580 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AL1_RS02400 | |
| 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) | AL1_RS07810 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| deoxyribose | pta: phosphate acetyltransferase | AL1_RS06580 | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | AL1_RS07810 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | AL1_RS14100 | AL1_RS02400 |
| ethanol | pta: phosphate acetyltransferase | AL1_RS06580 | |
| fructose | BT1758: fructose transporter | AL1_RS05720 | |
| fructose | scrK: fructokinase | AL1_RS12130 | AL1_RS04765 |
| fucose | aldA: lactaldehyde dehydrogenase | AL1_RS07810 | |
| 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 | galP: galactose:H+ symporter GalP | AL1_RS06795 | AL1_RS04690 |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | uxaB: tagaturonate reductase | AL1_RS01310 | |
| gluconate | edd: phosphogluconate dehydratase | AL1_RS03905 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| glucosamine | nagP: N-acetylglucosamine transporter NagP | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | AL1_RS08135 | AL1_RS06795 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | AL1_RS03770 | AL1_RS09320 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AL1_RS09315 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | AL1_RS01395 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | AL1_RS02400 | AL1_RS00395 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| isoleucine | vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA | AL1_RS03325 with AL1_RS03320 | |
| isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| L-lactate | L-LDH: L-lactate dehydrogenase | AL1_RS10870 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | AL1_RS10745 | AL1_RS11465 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | AL1_RS10400 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | AL1_RS01395 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AL1_RS01765 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA | AL1_RS03325 with AL1_RS03320 | |
| leucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | AL1_RS08245 | AL1_RS05070 |
| lysine | lysN: 2-aminoadipate transaminase | AL1_RS05070 | AL1_RS08245 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | malI: maltose transporter | AL1_RS00220 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | AL1_RS03880 | AL1_RS02455 |
| mannose | STP6: mannose:H+ symporter | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | AL1_RS07555 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | AL1_RS04690 | AL1_RS06795 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagP: N-acetylglucosamine transporter NagP | | |
| 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 | AL1_RS02400 | AL1_RS08600 |
| 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 | atoB: acetyl-CoA C-acetyltransferase | | |
| 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 | proY: proline:H+ symporter | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | AL1_RS07810 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| propionate | prpE: propionyl-CoA synthetase | AL1_RS15215 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | AL1_RS07810 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | AL1_RS05070 | AL1_RS08245 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AL1_RS05070 | AL1_RS08245 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AL1_RS07810 | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | AL1_RS07810 | |
| 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 | AL1_RS12690 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | AL1_RS02400 | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | AL1_RS08135 | AL1_RS06795 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | AL1_RS10525 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | AL1_RS07810 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | AL1_RS13095 | |
| thymidine | pta: phosphate acetyltransferase | AL1_RS06580 | |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | AL1_RS08135 | AL1_RS06795 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | AL1_RS01395 | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| valine | vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA | AL1_RS03325 with AL1_RS03320 | |
| valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| 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 | AL1_RS04690 | AL1_RS06795 |
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