Found 174 low-confidence and 36 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | G415_RS0109135 | G415_RS0105430 |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | G415_RS0109130 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | G415_RS0101870 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | G415_RS0101090 | |
| 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 | satP: acetate/proton symporter satP | G415_RS0107715 | |
| alanine | cycA: L-alanine symporter CycA | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | put1: proline dehydrogenase | G415_RS0108290 | |
| arginine | rocD: ornithine aminotransferase | G415_RS0106790 | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | G415_RS0101040 | |
| asparagine | ans: asparaginase | | |
| asparagine | glt: aspartate:proton symporter Glt | | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | G415_RS0100540 | G415_RS0105700 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | G415_RS0100535 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | G415_RS0100535 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | put1: proline dehydrogenase | G415_RS0108290 | |
| citrulline | rocD: ornithine aminotransferase | G415_RS0106790 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | G415_RS0105505 | G415_RS0103885 |
| 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 | G415_RS0100810 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | G415_RS0101870 | |
| deoxyinosine | deoB: phosphopentomutase | G415_RS0108560 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | G415_RS0100670 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | G415_RS0106195 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | G415_RS0101870 | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | G415_RS0101870 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | G415_RS0103575 | G415_RS0100670 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | G415_RS0104220 | |
| 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 | dctQ: fumarate TRAP transporter, small permease component DctQ | G415_RS0107630 | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | G415_RS0104650 | |
| 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 | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | G415_RS0102720 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | G415_RS0101870 | |
| 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 | G415_RS0106925 | |
| glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | G415_RS0100700 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | G415_RS0105565 | G415_RS0104835 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | G415_RS0100670 | G415_RS0108445 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | G415_RS0107485 | G415_RS0108720 |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | G415_RS0102415 | G415_RS0108255 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | G415_RS0103410 | G415_RS0104870 |
| L-lactate | L-LDH: L-lactate dehydrogenase | G415_RS0107380 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | G415_RS0107630 | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | G415_RS0104650 | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | G415_RS0100700 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | G415_RS0103410 | G415_RS0107480 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | G415_RS0105565 | G415_RS0104835 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | G415_RS0103405 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | G415_RS0107485 | G415_RS0108720 |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | G415_RS0102415 | G415_RS0108255 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | G415_RS0101870 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | | |
| lysine | lysN: 2-aminoadipate transaminase | G415_RS0104595 | G415_RS0106790 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| 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 | G415_RS0103975 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | G415_RS0101870 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | G415_RS0102720 | |
| 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 | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | G415_RS0105565 | G415_RS0104835 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | G415_RS0105565 | G415_RS0104835 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | G415_RS0100670 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | G415_RS0109095 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | G415_RS0109095 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | G415_RS0105565 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | G415_RS0108245 | G415_RS0107505 |
| phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | G415_RS0107500 | G415_RS0108250 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | G415_RS0108260 | G415_RS0107490 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | G415_RS0108720 | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | G415_RS0108255 | G415_RS0108700 |
| 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 | G415_RS0108290 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | G415_RS0103410 | G415_RS0104870 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | G415_RS0101870 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | G415_RS0101830 | G415_RS0106790 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | G415_RS0106790 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | G415_RS0101870 | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| 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 | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | G415_RS0108445 | G415_RS0100670 |
| succinate | satP: succinate:H+ symporter SatP | G415_RS0107715 | |
| sucrose | scrK: fructokinase | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | pccA: propionyl-CoA carboxylase, alpha subunit | G415_RS0103410 | G415_RS0104870 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | G415_RS09480 | |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | G415_RS0101870 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | G415_RS0108560 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | G415_RS0100700 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | G415_RS0105565 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | G415_RS0105565 | G415_RS0104835 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | G415_RS0107485 | G415_RS0108720 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | G415_RS0102415 | G415_RS0107495 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | G415_RS0101870 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | G415_RS0103410 | G415_RS0104870 |
| 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