Found 145 low-confidence and 62 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 | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | H589_RS0110555 | H589_RS0111930 |
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 | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | H589_RS0106750 | |
arabinose | araE: L-arabinose:H+ symporter | H589_RS0105145 | |
arginine | rocE: L-arginine permease | | |
arginine | rocF: arginase | H589_RS0117030 | |
asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | H589_RS0105870 | H589_RS0100760 |
asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | H589_RS0105875 | H589_RS0112205 |
asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | H589_RS0105865 | |
asparagine | ans: asparaginase | H589_RS0118680 | |
aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | H589_RS0105870 | H589_RS0100760 |
aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | H589_RS0105875 | H589_RS0112205 |
aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | H589_RS0105865 | |
cellobiose | bgl: cellobiase | | |
cellobiose | glk: glucokinase | H589_RS0113290 | |
citrate | cit1: citrate:H+ symporter Cit1 | H589_RS0108870 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | H589_RS0110275 | H589_RS0118135 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | H589_RS0118130 | H589_RS0115925 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | H589_RS0105870 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | H589_RS0100435 | H589_RS0115910 |
citrulline | arcC: carbamate kinase | | |
D-alanine | AZOBR_RS08235: D-alanine ABC transporter, permease component 1 | H589_RS0112345 | H589_RS0101630 |
D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | H589_RS0112350 | H589_RS0101625 |
D-alanine | AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 | H589_RS0112355 | H589_RS0101640 |
D-alanine | AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 | H589_RS0112360 | H589_RS0101620 |
D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | H589_RS0101635 | H589_RS0112340 |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | H589_RS0110950 | H589_RS0105840 |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | | |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | H589_RS0118000 | |
deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | H589_RS19655 | |
deoxyribonate | garK: glycerate 2-kinase | H589_RS0102230 | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoK: deoxyribokinase | H589_RS0116170 | |
deoxyribose | deoP: deoxyribose transporter | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | H589_RS0106750 | |
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 | galE: UDP-glucose 4-epimerase | H589_RS0103695 | H589_RS0111125 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | H589_RS0105145 | |
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 | gntA: gluconate TRAP transporter, small permease component | H589_RS0109225 | |
gluconate | gntB: gluconate TRAP transporter, large permease component | H589_RS0109230 | H589_RS0110060 |
gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | H589_RS0113685 | H589_RS0109220 |
gluconate | gntK: D-gluconate kinase | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | H589_RS0103925 | |
glucose | glk: glucokinase | H589_RS0113290 | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | garK: glycerate 2-kinase | H589_RS0102230 | |
glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | H589_RS0110555 | |
glucuronate | garR: tartronate semialdehyde reductase | H589_RS0102830 | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | H589_RS0105870 | H589_RS0100760 |
glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | H589_RS0105875 | H589_RS0112205 |
glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | H589_RS0105865 | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | H589_RS0117805 | |
histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | H589_RS0105870 | H589_RS0100760 |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | H589_RS0105875 | H589_RS0112205 |
histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | H589_RS0105865 | H589_RS0115925 |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
isoleucine | dddA: 3-hydroxypropionate dehydrogenase | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
isoleucine | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
isoleucine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | H589_RS0107295 | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | H589_RS0117160 | H589_RS0116820 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | H589_RS0112340 | H589_RS0101635 |
isoleucine | pco: propanyl-CoA oxidase | H589_RS0100550 | |
isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
lactose | galE: UDP-glucose 4-epimerase | H589_RS0103695 | H589_RS0111125 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | glk: glucokinase | H589_RS0113290 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | atoB: acetyl-CoA C-acetyltransferase | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | | |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | H589_RS0114155 | H589_RS0104280 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
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) | H589_RS0112340 | H589_RS0101635 |
leucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
lysine | davD: glutarate semialdehyde dehydrogenase | H589_RS0109990 | H589_RS0118155 |
lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
lysine | lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) | H589_RS0100555 | |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | H589_RS0100395 | H589_RS0118050 |
lysine | patD: 5-aminopentanal dehydrogenase | H589_RS0109990 | H589_RS0102680 |
maltose | glk: glucokinase | H589_RS0113290 | |
maltose | susB: alpha-glucosidase (maltase) | H589_RS0102155 | H589_RS0112520 |
mannitol | mt2d: mannitol 2-dehydrogenase | H589_RS0110660 | H589_RS0108180 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannitol | scrK: fructokinase | H589_RS0116170 | |
mannose | manA: mannose-6-phosphate isomerase | H589_RS0116375 | |
mannose | manP: mannose PTS system, EII-CBA components | H589_RS0115575 | |
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 | H589_RS0115820 | |
myoinositol | iolT: myo-inositol:H+ symporter | H589_RS0105145 | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | H589_RS0107295 | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | H589_RS0103925 | |
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 | | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | H589_RS0116710 | |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | H589_RS0107120 | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | H589_RS0112345 | H589_RS0101630 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | H589_RS0112340 | H589_RS0101635 |
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 | H589_RS0114955 | H589_RS0107295 |
propionate | dddA: 3-hydroxypropionate dehydrogenase | | |
propionate | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
propionate | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | H589_RS0107295 | |
propionate | pco: propanyl-CoA oxidase | H589_RS0100550 | |
propionate | putP: propionate transporter; proline:Na+ symporter | H589_RS0113975 | |
putrescine | gabT: gamma-aminobutyrate transaminase | H589_RS0118185 | H589_RS0104130 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | H589_RS0100395 | H589_RS0118050 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | H589_RS0109990 | H589_RS0118155 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | H589_RS0116820 | H589_RS0116710 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | H589_RS0116170 | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | H589_RS0116710 | |
sucrose | ams: sucrose hydrolase (invertase) | | |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | H589_RS0105190 | H589_RS0105195 |
threonine | lpd: dihydrolipoyl dehydrogenase | H589_RS0105200 | H589_RS0113295 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | | |
thymidine | nupC: thymidine permease NupC | H589_RS0118000 | |
trehalose | glk: glucokinase | H589_RS0113290 | |
trehalose | treF: trehalase | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | H589_RS0101620 | H589_RS0112360 |
tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | H589_RS0112350 | H589_RS0101625 |
tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | H589_RS0101630 | H589_RS0112345 |
tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | H589_RS0101635 | |
tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | H589_RS0107120 | |
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 | dddA: 3-hydroxypropionate dehydrogenase | | |
valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
valine | hpcD: 3-hydroxypropionyl-CoA dehydratase | | |
valine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | H589_RS0107295 | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | H589_RS0112340 | H589_RS0101635 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | H589_RS0107295 | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | H589_RS0102830 | |
valine | pco: propanyl-CoA oxidase | H589_RS0100550 | |
valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | H589_RS0115575 | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | H589_RS0109350 | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
xylose | xylT: D-xylose transporter | H589_RS0105145 | |
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