Found 156 low-confidence and 54 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 | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
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 | | |
alanine | TRIC: TRIC-type L-alanine transporter | GURA_RS01335 | |
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 | GURA_RS09920 | GURA_RS00600 |
arginine | patA: putrescine aminotransferase (PatA/SpuC) | GURA_RS11390 | GURA_RS01135 |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | GURA_RS00565 | GURA_RS16875 |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | | |
asparagine | glt: aspartate:proton symporter Glt | GURA_RS01960 | |
aspartate | glt: aspartate:proton symporter Glt | GURA_RS01960 | |
cellobiose | cbp: cellobiose phosphorylase | GURA_RS22075 | |
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 | GURA_RS05755 | GURA_RS19800 |
citrulline | put1: proline dehydrogenase | GURA_RS09480 | |
citrulline | rocD: ornithine aminotransferase | GURA_RS01135 | GURA_RS00600 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | GURA_RS11155 | GURA_RS03295 |
D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | GURA_RS22820 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | GURA_RS20520 | |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
deoxyinosine | deoB: phosphopentomutase | GURA_RS13880 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | GURA_RS08055 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | GURA_RS09505 | GURA_RS18385 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | garK: glycerate 2-kinase | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | GURA_RS12310 | GURA_RS06110 |
fructose | scrK: fructokinase | | |
fructose | Slc2a5: fructose:H+ symporter | | |
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 | GURA_RS04350 | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | GURA_RS01175 | |
galacturonate | udh: D-galacturonate dehydrogenase | GURA_RS11700 | |
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) | GURA_RS00610 | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | GURA_RS01175 | |
glucuronate | udh: D-glucuronate dehydrogenase | GURA_RS11700 | |
glutamate | gltP: L-glutamate:cation symporter GltP/GltT | GURA_RS01960 | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
glycerol | glpK: glycerol kinase | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | permease: L-histidine permease | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | GURA_RS15475 | GURA_RS15455 |
isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | GURA_RS14760 | GURA_RS06460 |
isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GURA_RS14750 | GURA_RS08200 |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | GURA_RS15480 | GURA_RS08095 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | GURA_RS09505 | GURA_RS18385 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | GURA_RS10795 | |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GURA_RS10805 | |
isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | GURA_RS10790 | |
isoleucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | GURA_RS06450 | GURA_RS04270 |
L-lactate | L-LDH: L-lactate dehydrogenase | GURA_RS11125 | |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | GURA_RS22820 | |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | GURA_RS04350 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | GURA_RS14760 | GURA_RS06460 |
leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GURA_RS14750 | GURA_RS08200 |
leucine | liuA: isovaleryl-CoA dehydrogenase | GURA_RS15475 | GURA_RS16870 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | GURA_RS14795 | GURA_RS09260 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | GURA_RS15480 | GURA_RS08130 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | GURA_RS10795 | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GURA_RS10805 | |
leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | GURA_RS10790 | |
leucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | GURA_RS06450 | GURA_RS04270 |
lysine | davA: 5-aminovaleramidase | GURA_RS01040 | GURA_RS07345 |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
lysine | gcdH: glutaryl-CoA dehydrogenase | GURA_RS16870 | GURA_RS15475 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
maltose | malA: 6-phospho-alphaglucosidase | | |
maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
mannose | manA: mannose-6-phosphate isomerase | GURA_RS16640 | |
mannose | STP6: mannose:H+ symporter | | |
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 | GURA_RS16875 | GURA_RS00565 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | GURA_RS00610 | |
NAG | nagP: N-acetylglucosamine transporter NagP | | |
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 | GURA_RS15480 | GURA_RS08130 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | GURA_RS08130 | GURA_RS15480 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | GURA_RS08100 | GURA_RS15490 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | GURA_RS08100 | GURA_RS15490 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | GURA_RS06815 | |
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 | GURA_RS15480 | GURA_RS08130 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | GURA_RS08130 | GURA_RS15480 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | GURA_RS08100 | GURA_RS15490 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | GURA_RS08100 | GURA_RS15490 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | proY: proline:H+ symporter | | |
proline | put1: proline dehydrogenase | GURA_RS09480 | |
propionate | mctC: propionate:H+ symporter | GURA_RS07225 | |
propionate | prpE: propionyl-CoA synthetase | GURA_RS08185 | GURA_RS08015 |
putrescine | gabT: gamma-aminobutyrate transaminase | GURA_RS09920 | GURA_RS00600 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | GURA_RS11390 | GURA_RS01135 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | GURA_RS00565 | GURA_RS16875 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | mctC: pyruvate symporter MctC | GURA_RS07225 | |
rhamnose | rhaA: L-rhamnose isomerase | | |
rhamnose | rhaB: L-rhamnulokinase | | |
rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
rhamnose | rhaM: L-rhamnose mutarotase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | snatA: L-serine transporter | GURA_RS03275 | |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | GURA_RS18385 | GURA_RS09505 |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
threonine | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | GURA_RS01730 | GURA_RS01725 |
threonine | lpd: dihydrolipoyl dehydrogenase | GURA_RS06450 | GURA_RS04270 |
threonine | snatA: L-threonine transporter snatA | GURA_RS03275 | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | GURA_RS00565 | GURA_RS16875 |
thymidine | deoA: thymidine phosphorylase DeoA | GURA_RS11300 | |
thymidine | deoB: phosphopentomutase | GURA_RS13880 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | GURA_RS15475 | GURA_RS15455 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | GURA_RS15480 | |
valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | GURA_RS14760 | GURA_RS06460 |
valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GURA_RS14750 | GURA_RS08200 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | GURA_RS10795 | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | GURA_RS10805 | |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | GURA_RS10790 | |
valine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | GURA_RS06450 | GURA_RS04270 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | GURA_RS00565 | GURA_RS09480 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | GURA_RS02990 | GURA_RS14275 |
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