Found 112 low-confidence and 66 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 | FRAAL_RS14880 | |
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 | FRAAL_RS02485 | |
acetate | dctA: organic acid/proton symporter DctA | FRAAL_RS06065 | |
alanine | cycA: L-alanine symporter CycA | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arabinose | xacB: L-arabinose 1-dehydrogenase | FRAAL_RS26370 | FRAAL_RS10545 |
arabinose | xacC: L-arabinono-1,4-lactonase | | |
arabinose | xacD: L-arabinonate dehydratase | FRAAL_RS29895 | |
arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
arginine | aguB: N-carbamoylputrescine hydrolase | FRAAL_RS06160 | FRAAL_RS00760 |
arginine | gabT: gamma-aminobutyrate transaminase | FRAAL_RS26530 | FRAAL_RS06200 |
arginine | patA: putrescine aminotransferase (PatA/SpuC) | FRAAL_RS22695 | FRAAL_RS06200 |
arginine | rocE: L-arginine permease | | |
asparagine | glt: aspartate:proton symporter Glt | FRAAL_RS06065 | |
aspartate | glt: aspartate:proton symporter Glt | FRAAL_RS06065 | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | FRAAL_RS26090 | FRAAL_RS24880 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | FRAAL_RS26085 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | FRAAL_RS26085 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
citrulline | put1: proline dehydrogenase | FRAAL_RS18995 | FRAAL_RS08175 |
citrulline | rocD: ornithine aminotransferase | FRAAL_RS26530 | FRAAL_RS06200 |
D-alanine | dadA: D-alanine dehydrogenase | FRAAL_RS24620 | |
D-lactate | D-LDH: D-lactate dehydrogenase | FRAAL_RS16885 | FRAAL_RS23870 |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | FRAAL_RS19290 | FRAAL_RS05015 |
deoxyinosine | deoB: phosphopentomutase | FRAAL_RS05230 | FRAAL_RS04860 |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | FRAAL_RS19180 | FRAAL_RS25580 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoP: deoxyribose transporter | | |
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 | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galP: galactose:H+ symporter GalP | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | FRAAL_RS24990 | |
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) | FRAAL_RS04865 | FRAAL_RS20020 |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
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 | FRAAL_RS14885 | FRAAL_RS24990 |
glucuronate | garR: tartronate semialdehyde reductase | FRAAL_RS35065 | FRAAL_RS26490 |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glutamate | yveA: L-glutamate:H+ symporter YveA | FRAAL_RS13090 | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | FRAAL_RS06805 | FRAAL_RS31395 |
glycerol | glpF: glycerol facilitator glpF | FRAAL_RS06150 | |
histidine | Ga0059261_1577: L-histidine transporter | FRAAL_RS16235 | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | FRAAL_RS14120 | FRAAL_RS00345 |
isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | FRAAL_RS14110 | FRAAL_RS22465 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | FRAAL_RS03125 | FRAAL_RS11430 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | FRAAL_RS03120 | FRAAL_RS20185 |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | FRAAL_RS05280 | FRAAL_RS13800 |
L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | FRAAL_RS16695 | FRAAL_RS15640 |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | FRAAL_RS14120 | FRAAL_RS00345 |
leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | FRAAL_RS14110 | FRAAL_RS22465 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | FRAAL_RS13800 | FRAAL_RS07215 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | FRAAL_RS25610 | FRAAL_RS13585 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | FRAAL_RS03125 | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | FRAAL_RS03120 | FRAAL_RS20185 |
lysine | cadA: lysine decarboxylase | FRAAL_RS26605 | FRAAL_RS28025 |
lysine | davD: glutarate semialdehyde dehydrogenase | FRAAL_RS14890 | FRAAL_RS18340 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | FRAAL_RS20775 | FRAAL_RS14895 |
lysine | gcdH: glutaryl-CoA dehydrogenase | FRAAL_RS13805 | FRAAL_RS12160 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | FRAAL_RS22695 | FRAAL_RS28020 |
maltose | MAL11: maltose permease | | |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
mannose | manA: mannose-6-phosphate isomerase | FRAAL_RS05545 | |
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 | FRAAL_RS08930 | FRAAL_RS13170 |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | FRAAL_RS04865 | FRAAL_RS20020 |
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 | FRAAL_RS25610 | FRAAL_RS13585 |
phenylacetate | paaK: phenylacetate-CoA ligase | FRAAL_RS11395 | FRAAL_RS13580 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | FRAAL_RS20785 | FRAAL_RS20780 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | FRAAL_RS03140 | FRAAL_RS21210 |
phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | FRAAL_RS03135 | FRAAL_RS13665 |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | FRAAL_RS03125 | FRAAL_RS11430 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | FRAAL_RS03120 | FRAAL_RS20185 |
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 | FRAAL_RS25610 | FRAAL_RS13585 |
phenylalanine | paaK: phenylacetate-CoA ligase | FRAAL_RS11395 | FRAAL_RS13580 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | FRAAL_RS20785 | FRAAL_RS20780 |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | FRAAL_RS00920 | FRAAL_RS14890 |
proline | HSERO_RS00870: proline ABC transporter, substrate-binding component | FRAAL_RS03120 | FRAAL_RS20185 |
proline | HSERO_RS00900: proline ABC transporter, ATPase component 2 | FRAAL_RS03140 | FRAAL_RS21210 |
proline | put1: proline dehydrogenase | FRAAL_RS18995 | FRAAL_RS08175 |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | FRAAL_RS05280 | FRAAL_RS13800 |
putrescine | gabT: gamma-aminobutyrate transaminase | FRAAL_RS26530 | FRAAL_RS06200 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | FRAAL_RS22695 | FRAAL_RS06200 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | FRAAL_RS11520 | FRAAL_RS03280 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | FRAAL_RS14885 | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | FRAAL_RS03140 | FRAAL_RS21210 |
serine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | FRAAL_RS03135 | FRAAL_RS13665 |
serine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | FRAAL_RS03125 | |
serine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | FRAAL_RS03120 | FRAAL_RS20185 |
serine | sdaB: L-serine ammonia-lyase | FRAAL_RS05015 | FRAAL_RS19290 |
sorbitol | scrK: fructokinase | FRAAL_RS17365 | FRAAL_RS22205 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | ams: sucrose hydrolase (invertase) | FRAAL_RS07960 | FRAAL_RS25690 |
sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
threonine | tdcC: L-threonine:H+ symporter TdcC | | |
thymidine | deoB: phosphopentomutase | FRAAL_RS05230 | FRAAL_RS04860 |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | lpqY: trehalose ABC transporter, substrate-binding lipoprotein component LpqY | FRAAL_RS16475 | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | FRAAL_RS03140 | FRAAL_RS21210 |
tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | FRAAL_RS03135 | FRAAL_RS13665 |
tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | FRAAL_RS03125 | |
tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | FRAAL_RS03120 | FRAAL_RS20185 |
tyrosine | fahA: fumarylacetoacetate hydrolase | FRAAL_RS25420 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | FRAAL_RS12225 | FRAAL_RS07100 |
valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | FRAAL_RS14120 | FRAAL_RS00345 |
valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | FRAAL_RS14110 | FRAAL_RS22465 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | FRAAL_RS03125 | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | FRAAL_RS03120 | FRAAL_RS20185 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | FRAAL_RS03130 | FRAAL_RS03425 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | FRAAL_RS06170 | FRAAL_RS13635 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | FRAAL_RS26490 | FRAAL_RS06570 |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | FRAAL_RS05280 | FRAAL_RS13800 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | FRAAL_RS23810 | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | FRAAL_RS19965 | |
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