Found 157 low-confidence and 47 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 | ARNIT_RS06050 | ARNIT_RS06360 |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | ARNIT_RS00085 | |
4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | ARNIT_RS13950 | ARNIT_RS06115 |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | ARNIT_RS04745 | |
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 | ARNIT_RS03795 | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | gabT: gamma-aminobutyrate transaminase | ARNIT_RS06120 | ARNIT_RS11930 |
arginine | patA: putrescine aminotransferase (PatA/SpuC) | ARNIT_RS11930 | ARNIT_RS06120 |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | ARNIT_RS13950 | ARNIT_RS05955 |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | ARNIT_RS15665 | ARNIT_RS12720 |
cellobiose | bgl: cellobiase | | |
cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
citrate | citT: citrate:succinate antiporter CitT | ARNIT_RS02215 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ARNIT_RS01655 | ARNIT_RS05320 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | ARNIT_RS13580 | ARNIT_RS01645 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | ARNIT_RS13580 | ARNIT_RS16500 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | ARNIT_RS14270 | |
citrulline | arcC: carbamate kinase | | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | ARNIT_RS08940 | ARNIT_RS05955 |
citrulline | rocD: ornithine aminotransferase | ARNIT_RS13880 | ARNIT_RS11930 |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | ARNIT_RS02910 | |
D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | ARNIT_RS02895 | ARNIT_RS13590 |
D-serine | dsdA: D-serine ammonia-lyase | ARNIT_RS02585 | |
D-serine | dsdX: D-serine transporter DsdX | ARNIT_RS11970 | |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | ARNIT_RS13950 | ARNIT_RS06115 |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | ARNIT_RS05260 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | ARNIT_RS06730 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | ARNIT_RS13950 | ARNIT_RS06115 |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | ARNIT_RS13950 | ARNIT_RS06115 |
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 | | |
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 | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
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) | ARNIT_RS03495 | |
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 | ARNIT_RS00065 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | ARNIT_RS07020 | |
histidine | hutH: histidine ammonia-lyase | ARNIT_RS11570 | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | ARNIT_RS05320 | ARNIT_RS13775 |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ARNIT_RS06725 | |
isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | ARNIT_RS06730 | ARNIT_RS06725 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ARNIT_RS02495 | ARNIT_RS11565 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ARNIT_RS06920 | ARNIT_RS08965 |
isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | ARNIT_RS08955 | ARNIT_RS06930 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | ARNIT_RS07760 | |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | aacS: acetoacetyl-CoA synthetase | | |
leucine | atoB: acetyl-CoA C-acetyltransferase | ARNIT_RS06730 | |
leucine | liuA: isovaleryl-CoA dehydrogenase | | |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ARNIT_RS13965 | ARNIT_RS00660 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | ARNIT_RS06725 | |
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) | ARNIT_RS06920 | ARNIT_RS08965 |
leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | ARNIT_RS08955 | ARNIT_RS06930 |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | ARNIT_RS05955 | ARNIT_RS00055 |
lysine | hglS: D-2-hydroxyglutarate synthase | | |
lysine | lat: L-lysine 6-aminotransferase | ARNIT_RS13880 | |
lysine | lysN: 2-aminoadipate transaminase | ARNIT_RS10285 | ARNIT_RS13880 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | ARNIT_RS11485 | |
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 | manA: mannose-6-phosphate isomerase | ARNIT_RS01490 | |
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 | ARNIT_RS04410 | ARNIT_RS05955 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ARNIT_RS03495 | |
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 | ARNIT_RS06725 | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | ARNIT_RS06725 | ARNIT_RS11565 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ARNIT_RS06730 | |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ARNIT_RS06730 | |
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 | atoB: acetyl-CoA C-acetyltransferase | ARNIT_RS06730 | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | ARNIT_RS08945 | ARNIT_RS06940 |
phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | ARNIT_RS06935 | ARNIT_RS08950 |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | ARNIT_RS08960 | ARNIT_RS06925 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | ARNIT_RS08965 | |
phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | ARNIT_RS08955 | ARNIT_RS06930 |
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 | ARNIT_RS08940 | ARNIT_RS05955 |
propionate | prpE: propionyl-CoA synthetase | | |
putrescine | gabT: gamma-aminobutyrate transaminase | ARNIT_RS06120 | ARNIT_RS11930 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ARNIT_RS11930 | ARNIT_RS06120 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ARNIT_RS13950 | ARNIT_RS05955 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | ARNIT_RS00985 | ARNIT_RS00610 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ARNIT_RS02495 | |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | snatA: L-serine transporter | ARNIT_RS09940 | ARNIT_RS09155 |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | ARNIT_RS02495 | ARNIT_RS11565 |
succinate | sdc: succinate:Na+ symporter Sdc | ARNIT_RS07760 | |
sucrose | scrK: fructokinase | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | snatA: L-threonine transporter snatA | ARNIT_RS09940 | ARNIT_RS09155 |
threonine | tdcB: L-threonine dehydratase | ARNIT_RS02585 | |
threonine | tdcE: 2-ketobutyrate formate-lyase | | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | ARNIT_RS13950 | ARNIT_RS06115 |
thymidine | deoA: thymidine phosphorylase DeoA | ARNIT_RS07045 | ARNIT_RS05260 |
thymidine | deoB: phosphopentomutase | | |
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 | aacS: acetoacetyl-CoA synthetase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | atoB: acetyl-CoA C-acetyltransferase | ARNIT_RS06730 | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
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 | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ARNIT_RS06725 | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ARNIT_RS06920 | ARNIT_RS08965 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | ARNIT_RS06930 | ARNIT_RS08955 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ARNIT_RS04410 | ARNIT_RS05955 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ARNIT_RS05135 | |
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 | ARNIT_RS06590 | |
xylose | xylT: D-xylose transporter | | |
This GapMind analysis is from Apr 09 2024. 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