Found 104 low-confidence and 83 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 | | |
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 | SE16_RS07345 | SE16_RS13645 |
acetate | actP: cation/acetate symporter ActP | SE16_RS01385 | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SE16_RS12950 | SE16_RS15150 |
alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | SE16_RS12935 | SE16_RS14790 |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | SE16_RS12945 | SE16_RS14780 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | arcA: arginine deiminase | | |
arginine | arcC: carbamate kinase | SE16_RS11340 | |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | SE16_RS01260 | SE16_RS12730 |
asparagine | bgtA: aspartate ABC transporter, ATPase component BgtA | SE16_RS15010 | SE16_RS11275 |
asparagine | bgtB': aspartate ABC transporter, permease component 1 (BgtB) | SE16_RS15000 | |
aspartate | bgtA: aspartate ABC transporter, ATPase component BgtA | SE16_RS15010 | SE16_RS11275 |
aspartate | bgtB': aspartate ABC transporter, permease component 1 (BgtB) | SE16_RS15000 | |
cellobiose | aglE': glucose ABC transporter, substrate-binding component (AglE) | SE16_RS03550 | |
cellobiose | aglF': glucose ABC transporter, permease component 1 (AglF) | SE16_RS03545 | |
cellobiose | aglG': glucose ABC transporter, permease component 2 (AglG) | SE16_RS03540 | SE16_RS12350 |
cellobiose | aglK': glucose ABC transporter, ATPase component (AglK) | SE16_RS08755 | SE16_RS02415 |
cellobiose | bgl: cellobiase | SE16_RS08470 | SE16_RS08495 |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SE16_RS15010 | SE16_RS11275 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | SE16_RS09375 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | SE16_RS09375 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | SE16_RS09565 | |
citrulline | arcC: carbamate kinase | SE16_RS11340 | |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | larD: D,L-lactic acid transporter | SE16_RS13535 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | SE16_RS15125 | |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | SE16_RS01120 | SE16_RS04000 |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | SE16_RS13660 | SE16_RS11575 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | SE16_RS11160 | SE16_RS02095 |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | SE16_RS08700 | SE16_RS04050 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | SE16_RS06160 | |
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 | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | pgmA: alpha-phosphoglucomutase | SE16_RS06805 | SE16_RS14175 |
galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | SE16_RS09225 | |
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 | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | SE16_RS13090 | |
glucose | aglE': glucose ABC transporter, substrate-binding component (AglE) | SE16_RS03550 | |
glucose | aglF': glucose ABC transporter, permease component 1 (AglF) | SE16_RS03545 | |
glucose | aglG': glucose ABC transporter, permease component 2 (AglG) | SE16_RS03540 | SE16_RS12350 |
glucose | aglK': glucose ABC transporter, ATPase component (AglK) | SE16_RS08755 | SE16_RS02415 |
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 | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | dmeA: L-glutamate transporter DmeA | SE16_RS09185 | |
glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | SE16_RS13830 | SE16_RS00355 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | SE16_RS13555 | |
histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | SE16_RS14995 | |
histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | SE16_RS15005 | SE16_RS09375 |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | SE16_RS15010 | SE16_RS11275 |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | SE16_RS08930 | SE16_RS05905 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SE16_RS12950 | SE16_RS15150 |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | SE16_RS08915 | SE16_RS03415 |
L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | SE16_RS01390 | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
lactose | lacP: lactose permease LacP | | |
lactose | pgmA: alpha-phosphoglucomutase | SE16_RS06805 | SE16_RS14175 |
leucine | aacS: acetoacetyl-CoA synthetase | SE16_RS01120 | SE16_RS04000 |
leucine | liuA: isovaleryl-CoA dehydrogenase | SE16_RS05905 | SE16_RS08930 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | SE16_RS03415 | SE16_RS08915 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | SE16_RS08740 | SE16_RS14460 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | SE16_RS03395 | SE16_RS08920 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SE16_RS12950 | SE16_RS15150 |
lysine | hglS: D-2-hydroxyglutarate synthase | | |
lysine | lysN: 2-aminoadipate transaminase | SE16_RS11185 | SE16_RS07105 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | SE16_RS11695 | |
maltose | aglE: maltose ABC transporter, substrate-binding component AglK | SE16_RS03550 | |
maltose | aglF: maltose ABC transporter, permease component 1 (AglF) | SE16_RS03545 | SE16_RS12355 |
maltose | aglK: maltose ABC transporter, ATPase component AglK | SE16_RS08755 | SE16_RS02415 |
mannitol | mt2d: mannitol 2-dehydrogenase | SE16_RS00340 | SE16_RS11575 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | SE16_RS11915 | SE16_RS05930 |
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 | SE16_RS08700 | SE16_RS04050 |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | SE16_RS13090 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | SE16_RS13330 | |
phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
phenylacetate | paaK: phenylacetate-CoA ligase | SE16_RS07830 | SE16_RS13575 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | SE16_RS08735 | SE16_RS14460 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | SE16_RS12945 | SE16_RS14780 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | SE16_RS12950 | SE16_RS15160 |
phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | SE16_RS13330 | |
phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
phenylalanine | paaK: phenylacetate-CoA ligase | SE16_RS07830 | SE16_RS13575 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | SE16_RS08735 | SE16_RS14460 |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | pfor: phenylacetaldeyde:ferredoxin oxidoreductase | SE16_RS04100 | |
phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | SE16_RS05650 | SE16_RS03115 |
phenylalanine | PPDCbeta: phenylpyruvate decarboxylase, beta subunit | SE16_RS03110 | SE16_RS05650 |
proline | HSERO_RS00870: proline ABC transporter, substrate-binding component | SE16_RS12950 | SE16_RS15160 |
proline | HSERO_RS00885: proline ABC transporter, permease component 1 | SE16_RS12930 | SE16_RS14795 |
proline | HSERO_RS00900: proline ABC transporter, ATPase component 2 | SE16_RS12945 | SE16_RS14780 |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | SE16_RS08915 | SE16_RS03415 |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabT: gamma-aminobutyrate transaminase | SE16_RS01285 | SE16_RS14690 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | SE16_RS01285 | SE16_RS14690 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | SE16_RS04050 | SE16_RS08700 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | dctM: pyruvate TRAP transporter, large permease component | SE16_RS04130 | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | SE16_RS00340 | SE16_RS13660 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | SE16_RS13660 | SE16_RS00340 |
rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | SE16_RS14345 | SE16_RS03810 |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SE16_RS12950 | SE16_RS15150 |
serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | SE16_RS12935 | SE16_RS14790 |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | SE16_RS12945 | SE16_RS14780 |
serine | sdaB: L-serine ammonia-lyase | SE16_RS15125 | |
sorbitol | sdh: sorbitol dehydrogenase | SE16_RS13660 | SE16_RS11575 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
succinate | sdc: succinate:Na+ symporter Sdc | | |
sucrose | aglE: sucrose ABC transporter, substrate-binding component AglK | SE16_RS03550 | |
sucrose | aglF: sucrose ABC transporter, permease component 1 (AglF) | SE16_RS03545 | SE16_RS12355 |
sucrose | aglK: sucrose ABC transporter, ATPase component AglK | SE16_RS08755 | SE16_RS02415 |
sucrose | ams: sucrose hydrolase (invertase) | SE16_RS01195 | SE16_RS04190 |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SE16_RS12950 | SE16_RS15150 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | SE16_RS12935 | SE16_RS14790 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | SE16_RS12945 | SE16_RS14780 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | SE16_RS08075 | SE16_RS08085 |
thymidine | deoB: phosphopentomutase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | aglF: trehalose ABC transporter, permease component 1 (AglF) | SE16_RS03545 | SE16_RS12355 |
trehalose | aglK: trehalose ABC trehalose, ATPase component AglK | SE16_RS08755 | SE16_RS02415 |
trehalose | treF: trehalase | SE16_RS04190 | SE16_RS14730 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tyrosine | aacS: acetoacetyl-CoA synthetase | SE16_RS01120 | SE16_RS04000 |
tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | SE16_RS12945 | SE16_RS14780 |
tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | SE16_RS12930 | SE16_RS14795 |
tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | SE16_RS12950 | SE16_RS15160 |
tyrosine | fahA: fumarylacetoacetate hydrolase | SE16_RS14345 | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | SE16_RS08930 | SE16_RS05905 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | SE16_RS14460 | SE16_RS08740 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | SE16_RS12950 | SE16_RS15150 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | SE16_RS04050 | SE16_RS08700 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | SE16_RS09795 | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | SE16_RS08915 | SE16_RS03415 |
xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
xylitol | xdhA: xylitol dehydrogenase | SE16_RS01205 | SE16_RS11160 |
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