Found 159 low-confidence and 48 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 | 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 | | |
alanine | cycA: L-alanine symporter CycA | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | Q366_RS17895 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | | |
asparagine | glt: aspartate:proton symporter Glt | | |
aspartate | glt: aspartate:proton symporter Glt | | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | arcC: carbamate kinase | | |
citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | | |
citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | | |
citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | Q366_RS06940 | Q366_RS06100 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | Q366_RS13490 | Q366_RS12750 |
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 | | |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | Q366_RS07185 | Q366_RS03910 |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | Q366_RS09940 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Q366_RS02280 | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | garK: glycerate 2-kinase | Q366_RS03210 | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | Q366_RS03850 | Q366_RS09470 |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | Q366_RS10385 | Q366_RS17050 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | Q366_RS17895 | |
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 | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | Q366_RS13505 | Q366_RS17050 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
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) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | Q366_RS13505 | Q366_RS17050 |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
glycerol | dhaK': dihydroxyacetone kinase, ATP dependent (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | permease: L-histidine permease | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | Q366_RS11450 | Q366_RS06780 |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | Q366_RS18135 | Q366_RS07650 |
isoleucine | epi: methylmalonyl-CoA epimerase | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | Q366_RS09470 | Q366_RS02355 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | Q366_RS13525 | Q366_RS04655 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Q366_RS04660 | |
isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | Q366_RS04650 | Q366_RS13530 |
isoleucine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | Q366_RS05475 | |
isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | Q366_RS09820 | |
isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
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 | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | Q366_RS11450 | Q366_RS08980 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | Q366_RS05475 | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | Q366_RS18135 | Q366_RS07650 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | Q366_RS09820 | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | Q366_RS13525 | Q366_RS04655 |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Q366_RS04660 | |
leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | Q366_RS04650 | Q366_RS13530 |
leucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
lysine | cadA: lysine decarboxylase | | |
lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | Q366_RS18135 | Q366_RS13010 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
lysine | gcdH: glutaryl-CoA dehydrogenase | Q366_RS06780 | Q366_RS11450 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | Q366_RS19250 | Q366_RS00665 |
maltose | malA: 6-phospho-alphaglucosidase | | |
maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
mannitol | mt2d: mannitol 2-dehydrogenase | Q366_RS02280 | Q366_RS02355 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | Q366_RS11055 | |
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 | Q366_RS17050 | Q366_RS13505 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | | |
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 | Q366_RS18135 | Q366_RS07650 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Q366_RS18135 | Q366_RS07650 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | Q366_RS00870 | Q366_RS02505 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | Q366_RS02505 | Q366_RS00870 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | Q366_RS07650 | Q366_RS18135 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
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 | Q366_RS18135 | Q366_RS07650 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Q366_RS18135 | Q366_RS07650 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | Q366_RS00870 | Q366_RS02505 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | Q366_RS02505 | Q366_RS00870 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | Q366_RS07650 | Q366_RS18135 |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | proW: proline ABC transporter, permease component ProW | Q366_RS03740 | |
proline | put1: proline dehydrogenase | Q366_RS04815 | |
propionate | epi: methylmalonyl-CoA epimerase | | |
propionate | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | Q366_RS05475 | |
propionate | pccB: propionyl-CoA carboxylase, beta subunit | Q366_RS09820 | |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabT: gamma-aminobutyrate transaminase | Q366_RS07000 | Q366_RS13500 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Q366_RS07000 | Q366_RS19250 |
pyruvate | dctM: pyruvate TRAP transporter, large permease component | Q366_RS17980 | Q366_RS12825 |
pyruvate | dctP: pyruvate TRAP transporter, substrate-binding component | Q366_RS17970 | |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | Q366_RS17975 | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | Q366_RS09470 | Q366_RS02280 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | Q366_RS02355 | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | sdaB: L-serine ammonia-lyase | | |
serine | serP: L-serine permease SerP | | |
sorbitol | sdh: sorbitol dehydrogenase | Q366_RS02280 | Q366_RS09470 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | ams: sucrose hydrolase (invertase) | Q366_RS08470 | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | Q366_RS19510 | Q366_RS19515 |
threonine | gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) | Q366_RS19525 | |
threonine | ltaE: L-threonine aldolase | Q366_RS19665 | |
threonine | tdcC: L-threonine:H+ symporter TdcC | | |
thymidine | deoA: thymidine phosphorylase DeoA | Q366_RS01905 | |
thymidine | deoB: phosphopentomutase | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupC: thymidine permease NupC | Q366_RS09940 | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | Q366_RS17640 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | Q366_RS11450 | Q366_RS06780 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | Q366_RS18135 | |
valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | Q366_RS18135 | Q366_RS13010 |
valine | epi: methylmalonyl-CoA epimerase | | |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | Q366_RS13525 | Q366_RS04655 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Q366_RS04660 | |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | Q366_RS04650 | Q366_RS13530 |
valine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Q366_RS17050 | Q366_RS13505 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | Q366_RS05475 | |
valine | pccB: propionyl-CoA carboxylase, beta subunit | Q366_RS09820 | |
valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
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