Found 142 low-confidence and 58 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | dctM: 2-oxoglutarate TRAP transporter, large permease component DctM | DHAF_RS05355 | DHAF_RS23125 |
2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | DHAF_RS06240 | DHAF_RS10310 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | DHAF_RS18240 | DHAF_RS07395 |
4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | DHAF_RS07750 | |
acetate | actP: cation/acetate symporter ActP | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | DHAF_RS18790 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | gabT: gamma-aminobutyrate transaminase | DHAF_RS03890 | DHAF_RS16705 |
arginine | patA: putrescine aminotransferase (PatA/SpuC) | DHAF_RS03890 | DHAF_RS16705 |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | DHAF_RS13220 | DHAF_RS10840 |
arginine | rocE: L-arginine permease | DHAF_RS12190 | DHAF_RS06640 |
asparagine | ans: asparaginase | DHAF_RS15300 | |
asparagine | ansP: L-asparagine permease AnsP | DHAF_RS06640 | DHAF_RS12190 |
aspartate | peb1C: aspartate ABC transporter, ATPase component Peb1C | DHAF_RS05220 | DHAF_RS23680 |
aspartate | peb1D: aspartate ABC transporter, permease component 2 (Peb1D) | DHAF_RS05235 | DHAF_RS23685 |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cbpC: cellobiose ABC transporter, substrate-binding component CbpC | | |
citrate | citE: citrate lyase, citryl-ACP lyase component CitE | DHAF_RS15385 | DHAF_RS04530 |
citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | DHAF_RS09800 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | DHAF_RS22710 | DHAF_RS11405 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | DHAF_RS22715 | DHAF_RS23685 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | DHAF_RS23685 | DHAF_RS03765 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | DHAF_RS23690 | DHAF_RS18955 |
citrulline | arcC: carbamate kinase | | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | DHAF_RS13220 | |
citrulline | rocD: ornithine aminotransferase | DHAF_RS16705 | DHAF_RS03890 |
D-alanine | cycA: D-alanine:H+ symporter CycA | DHAF_RS12190 | DHAF_RS06640 |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-serine | cycA: D-serine:H+ symporter CycA | DHAF_RS06640 | DHAF_RS12190 |
deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | DHAF_RS11210 | |
deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | DHAF_RS11200 | |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | DHAF_RS18135 | DHAF_RS01655 |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DHAF_RS19070 | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | DHAF_RS02645 | DHAF_RS13285 |
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 | fucO: L-lactaldehyde reductase | DHAF_RS02645 | DHAF_RS10835 |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
fumarate | sdcL: fumarate:Na+ symporter SdcL | DHAF_RS01040 | |
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 | DHAF_RS09835 | |
galacturonate | exuT: D-galacturonate transporter ExuT | DHAF_RS05095 | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
galacturonate | uxaA: D-altronate dehydratase | DHAF_RS16340 | |
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) | | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | DHAF_RS09440 | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | DHAF_RS05095 | |
glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) | DHAF_RS23680 | DHAF_RS05220 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | DHAF_RS09525 | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | DHAF_RS00930 | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | DHAF_RS07420 | DHAF_RS03775 |
histidine | PA5504: L-histidine ABC transporter, permease component | DHAF_RS07415 | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | DHAF_RS14315 | DHAF_RS14305 |
isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | DHAF_RS11265 | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | DHAF_RS14270 | DHAF_RS18210 |
isoleucine | epi: methylmalonyl-CoA epimerase | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | DHAF_RS19070 | DHAF_RS03090 |
isoleucine | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | DHAF_RS13505 | DHAF_RS14625 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | DHAF_RS17500 | |
isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | | |
L-lactate | L-LDH: L-lactate dehydrogenase | DHAF_RS08965 | DHAF_RS22055 |
L-malate | sdlC: L-malate:Na+ symporter SdlC | DHAF_RS01040 | |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | aacS: acetoacetyl-CoA synthetase | DHAF_RS18135 | DHAF_RS01655 |
leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | DHAF_RS11265 | |
leucine | liuA: isovaleryl-CoA dehydrogenase | DHAF_RS14305 | DHAF_RS14315 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | DHAF_RS17500 | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | DHAF_RS18210 | DHAF_RS14270 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | davA: 5-aminovaleramidase | | |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | davT: 5-aminovalerate aminotransferase | DHAF_RS03890 | DHAF_RS16705 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | DHAF_RS01625 | |
lysine | gcdH: glutaryl-CoA dehydrogenase | DHAF_RS14305 | DHAF_RS14315 |
lysine | lysP: L-lysine:H+ symporter LysP | DHAF_RS06640 | DHAF_RS12190 |
maltose | MFS-glucose: glucose transporter, MFS superfamily | DHAF_RS09440 | |
maltose | susB: alpha-glucosidase (maltase) | DHAF_RS15960 | DHAF_RS02450 |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
mannose | manA: mannose-6-phosphate isomerase | DHAF_RS04205 | |
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 | DHAF_RS24105 | DHAF_RS13175 |
myoinositol | iolT: myo-inositol:H+ symporter | DHAF_RS09440 | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | DHAF_RS13220 | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
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 | DHAF_RS14270 | DHAF_RS18210 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | DHAF_RS18210 | DHAF_RS14270 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | DHAF_RS14275 | DHAF_RS03095 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | DHAF_RS14275 | DHAF_RS03095 |
phenylacetate | paaK: phenylacetate-CoA ligase | DHAF_RS17250 | DHAF_RS18135 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | DHAF_RS18210 | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
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 | DHAF_RS14270 | DHAF_RS18210 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | DHAF_RS18210 | DHAF_RS14270 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | DHAF_RS14275 | DHAF_RS03095 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | DHAF_RS14275 | DHAF_RS03095 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | DHAF_RS18210 | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | put1: proline dehydrogenase | | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | DHAF_RS13220 | |
propionate | epi: methylmalonyl-CoA epimerase | | |
propionate | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | DHAF_RS13505 | DHAF_RS14625 |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | DHAF_RS17500 | |
propionate | pccB: propionyl-CoA carboxylase, beta subunit | | |
putrescine | gabT: gamma-aminobutyrate transaminase | DHAF_RS03890 | DHAF_RS16705 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | DHAF_RS03890 | DHAF_RS16705 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | DHAF_RS13220 | DHAF_RS10840 |
putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | DHAF_RS12790 | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | fucO: L-lactaldehyde reductase | DHAF_RS02645 | DHAF_RS10835 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | DHAF_RS19070 | DHAF_RS12765 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | DHAF_RS16340 | DHAF_RS22085 |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | DHAF_RS10310 | |
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 | DHAF_RS19070 | DHAF_RS10450 |
succinate | sdc: succinate:Na+ symporter Sdc | DHAF_RS01040 | |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | MFS-glucose: glucose transporter, MFS superfamily | DHAF_RS09440 | |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | DHAF_RS20135 | DHAF_RS20130 |
threonine | ltaE: L-threonine aldolase | DHAF_RS05420 | DHAF_RS24045 |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | MFS-glucose: glucose transporter, MFS superfamily | DHAF_RS09440 | |
trehalose | treF: trehalase | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | DHAF_RS06640 | DHAF_RS12190 |
tyrosine | aacS: acetoacetyl-CoA synthetase | DHAF_RS18135 | DHAF_RS01655 |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | DHAF_RS06640 | DHAF_RS12190 |
tyrosine | fahA: fumarylacetoacetate hydrolase | DHAF_RS15245 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | DHAF_RS14315 | DHAF_RS14305 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | DHAF_RS22655 | DHAF_RS14270 |
valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | DHAF_RS11265 | |
valine | epi: methylmalonyl-CoA epimerase | | |
valine | mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit | DHAF_RS13505 | DHAF_RS14625 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | DHAF_RS13220 | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | DHAF_RS05885 | DHAF_RS09785 |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | DHAF_RS17500 | |
valine | pccB: propionyl-CoA carboxylase, beta subunit | | |
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 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