Found 147 low-confidence and 70 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) | HL45_RS11740 | HL45_RS15220 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | HL45_RS15970 | HL45_RS11980 |
| 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 | actP: cation/acetate symporter ActP | HL45_RS17065 | |
| alanine | cycA: L-alanine symporter CycA | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | HL45_RS11900 | HL45_RS13385 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arabinose | xacF: alpha-ketoglutarate semialdehyde dehydrogenase | HL45_RS05005 | HL45_RS15220 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | HL45_RS17980 | HL45_RS05005 |
| arginine | rocD: ornithine aminotransferase | HL45_RS16550 | HL45_RS12380 |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | HL45_RS16330 | HL45_RS03700 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| cellobiose | glk: glucokinase | HL45_RS14305 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | HL45_RS04820 | HL45_RS17210 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | HL45_RS04815 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | HL45_RS17980 | HL45_RS05005 |
| citrulline | rocD: ornithine aminotransferase | HL45_RS16550 | HL45_RS12380 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | HL45_RS10525 | HL45_RS02045 |
| 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 | HL45_RS00165 | HL45_RS16525 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | HL45_RS11740 | HL45_RS15220 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | HL45_RS09440 | |
| deoxyinosine | deoB: phosphopentomutase | HL45_RS09445 | HL45_RS00870 |
| deoxyinosine | deoD: deoxyinosine phosphorylase | HL45_RS13620 | HL45_RS02875 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | HL45_RS09430 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | HL45_RS09425 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | HL45_RS10600 | HL45_RS10860 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | HL45_RS10575 | HL45_RS18395 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | HL45_RS09765 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | HL45_RS11740 | HL45_RS15220 |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | HL45_RS11740 | HL45_RS15220 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | HL45_RS08640 | HL45_RS15220 |
| 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 | HL45_RS11905 | |
| 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 | HL45_RS13215 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | HL45_RS03805 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HL45_RS19250 | HL45_RS19720 |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | HL45_RS13405 | HL45_RS15970 |
| glucuronate | garR: tartronate semialdehyde reductase | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | HL45_RS16375 | |
| glucuronate | udh: D-glucuronate dehydrogenase | HL45_RS12725 | HL45_RS16385 |
| glycerol | dhaD: glycerol dehydrogenase | HL45_RS18395 | HL45_RS10575 |
| glycerol | dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M | HL45_RS16070 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | HL45_RS05450 | HL45_RS06255 |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | HL45_RS00545 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HL45_RS00550 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | HL45_RS08150 | HL45_RS13265 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | HL45_RS18395 | HL45_RS10575 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | HL45_RS15725 | HL45_RS16295 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | HL45_RS16300 | HL45_RS06110 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | HL45_RS07575 | |
| 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 | glk: glucokinase | HL45_RS14305 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | HL45_RS10600 | HL45_RS10860 |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | HL45_RS00545 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HL45_RS00550 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | HL45_RS06255 | HL45_RS04990 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | HL45_RS07575 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | HL45_RS13265 | HL45_RS08150 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | HL45_RS07065 | HL45_RS06770 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | HL45_RS15725 | HL45_RS16295 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | HL45_RS16300 | HL45_RS06110 |
| lysine | davA: 5-aminovaleramidase | HL45_RS08240 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | HL45_RS15220 | HL45_RS07605 |
| lysine | davT: 5-aminovalerate aminotransferase | HL45_RS16550 | HL45_RS02005 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | HL45_RS08150 | HL45_RS13265 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | HL45_RS17115 | HL45_RS06175 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | HL45_RS17895 | HL45_RS09035 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | HL45_RS00870 | HL45_RS01150 |
| 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 | HL45_RS05005 | HL45_RS15220 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HL45_RS19250 | HL45_RS19720 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | HL45_RS08425 | |
| 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 | HL45_RS08150 | HL45_RS13265 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | HL45_RS02485 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | HL45_RS02485 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | HL45_RS08380 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | HL45_RS06120 | HL45_RS15715 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | HL45_RS15725 | HL45_RS16295 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | HL45_RS16300 | HL45_RS06110 |
| phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | HL45_RS08425 | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | HL45_RS08150 | HL45_RS13265 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | HL45_RS02485 | |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | HL45_RS02485 | |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | HL45_RS08380 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pfor: phenylacetaldeyde:ferredoxin oxidoreductase | HL45_RS04015 | HL45_RS02480 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | HL45_RS00540 | HL45_RS10065 |
| phenylalanine | PPDCbeta: phenylpyruvate decarboxylase, beta subunit | HL45_RS00545 | |
| proline | put1: proline dehydrogenase | HL45_RS17965 | HL45_RS16315 |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | HL45_RS17980 | HL45_RS05005 |
| proline | putP: proline:Na+ symporter | HL45_RS03330 | HL45_RS17975 |
| propionate | mctC: propionate:H+ symporter | HL45_RS17065 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | HL45_RS07575 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | HL45_RS16550 | HL45_RS12380 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | HL45_RS02005 | HL45_RS16550 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | HL45_RS15220 | HL45_RS07605 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | mctC: pyruvate symporter MctC | HL45_RS17065 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | HL45_RS18395 | HL45_RS10575 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | HL45_RS16375 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | HL45_RS10575 | |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | HL45_RS09625 | HL45_RS16370 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | scrK: fructokinase | HL45_RS08680 | HL45_RS03770 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | scrK: fructokinase | HL45_RS08680 | HL45_RS03770 |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | HL45_RS11740 | HL45_RS15220 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | HL45_RS04955 | HL45_RS18095 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | HL45_RS11740 | HL45_RS15220 |
| thymidine | deoB: phosphopentomutase | HL45_RS09445 | HL45_RS00870 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | HL45_RS14305 | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | | |
| trehalose | thuF: trehalose ABC transporter, permease component 1 (ThuF) | HL45_RS05590 | HL45_RS01445 |
| trehalose | thuG: trehalose ABC transporter, permease component 2 (ThuG) | HL45_RS01440 | HL45_RS05585 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | HL45_RS10600 | HL45_RS10860 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | HL45_RS09625 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | HL45_RS05450 | HL45_RS06255 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | HL45_RS08150 | HL45_RS08380 |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | HL45_RS00545 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HL45_RS00550 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | HL45_RS08150 | HL45_RS13265 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | HL45_RS15725 | HL45_RS16295 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | HL45_RS16300 | HL45_RS06110 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | HL45_RS15220 | HL45_RS11740 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | HL45_RS07575 | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xylB: xylulokinase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
| xylose | xyrA: xylitol reductase | HL45_RS05600 | HL45_RS07565 |
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