Found 181 low-confidence and 36 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) | Synpcc7942_0489 | |
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 | Synpcc7942_1367 | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
acetate | actP: cation/acetate symporter ActP | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | gabD: succinate semialdehyde dehydrogenase | Synpcc7942_1857 | Synpcc7942_0489 |
arginine | gabT: gamma-aminobutyrate transaminase | Synpcc7942_0943 | Synpcc7942_0031 |
arginine | patA: putrescine aminotransferase (PatA/SpuC) | Synpcc7942_0943 | Synpcc7942_0031 |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | Synpcc7942_0489 | |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | Synpcc7942_0166 | |
cellobiose | bgl: cellobiase | Synpcc7942_0854 | Synpcc7942_0354 |
cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Synpcc7942_0249 | Synpcc7942_1680 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | Synpcc7942_0248 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | Synpcc7942_0248 | Synpcc7942_0247 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | citrullinase: putative citrullinase | Synpcc7942_2145 | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
citrulline | rocD: ornithine aminotransferase | Synpcc7942_0943 | Synpcc7942_0645 |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | Synpcc7942_0246 | |
D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | Synpcc7942_0248 | |
D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | Synpcc7942_0249 | Synpcc7942_1680 |
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 | adh: acetaldehyde dehydrogenase (not acylating) | Synpcc7942_0489 | |
deoxyinosine | deoB: phosphopentomutase | Synpcc7942_2132 | |
deoxyinosine | deoD: deoxyinosine phosphorylase | Synpcc7942_0923 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Synpcc7942_0684 | |
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) | Synpcc7942_0489 | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | Synpcc7942_0489 | |
fructose | 1pfk: 1-phosphofructokinase | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | aldA: lactaldehyde dehydrogenase | Synpcc7942_0489 | |
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 | | |
fumarate | dctA: fumarate:H+ symporter DctA | | |
galactose | galE: UDP-glucose 4-epimerase | Synpcc7942_0320 | Synpcc7942_2100 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | Synpcc7942_0017 | |
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 | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | | |
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 | aspA: L-aspartate ammonia-lyase | Synpcc7942_1007 | |
glycerol | dhaK': dihydroxyacetone kinase, ATP dependent (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | natB: L-histidine ABC transporter, substrate-binding component NatB | Synpcc7942_1861 | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | Synpcc7942_0597 | |
isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | Synpcc7942_0684 | Synpcc7942_1596 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
isoleucine | prpB: 2-methylisocitrate lyase | | |
isoleucine | prpC: 2-methylcitrate synthase | Synpcc7942_0612 | |
isoleucine | prpD: 2-methylcitrate dehydratase | | |
L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
lactose | galE: UDP-glucose 4-epimerase | Synpcc7942_0320 | Synpcc7942_2100 |
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 | aacS: acetoacetyl-CoA synthetase | | |
leucine | atoB: acetyl-CoA C-acetyltransferase | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | | |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | Synpcc7942_1379 | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | Synpcc7942_0597 | |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
lysine | hglS: D-2-hydroxyglutarate synthase | | |
lysine | lat: L-lysine 6-aminotransferase | Synpcc7942_0943 | |
lysine | lysN: 2-aminoadipate transaminase | Synpcc7942_2545 | Synpcc7942_0943 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
maltose | susB: alpha-glucosidase (maltase) | Synpcc7942_0150 | |
maltose | thuE: maltose ABC transporter, substrate-binding component ThuE | Synpcc7942_0950 | |
maltose | thuG: maltose ABC transporter, permease component 2 (ThuG) | Synpcc7942_0948 | Synpcc7942_0471 |
maltose | thuK: maltose ABC transporter, ATPase component ThuK | Synpcc7942_0960 | Synpcc7942_0947 |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
mannose | manA: mannose-6-phosphate isomerase | Synpcc7942_1608 | |
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 | Synpcc7942_1443 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | | |
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 | Synpcc7942_0597 | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Synpcc7942_0597 | |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | Synpcc7942_0684 | |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
phenylacetate | paaK: phenylacetate-CoA ligase | | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | maiA: maleylacetoacetate isomerase | | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
proline | put1: proline dehydrogenase | | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
propionate | prpB: 2-methylisocitrate lyase | | |
propionate | prpC: 2-methylcitrate synthase | Synpcc7942_0612 | |
propionate | prpD: 2-methylcitrate dehydratase | | |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabD: succinate semialdehyde dehydrogenase | Synpcc7942_1857 | Synpcc7942_0489 |
putrescine | gabT: gamma-aminobutyrate transaminase | Synpcc7942_0943 | Synpcc7942_0031 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Synpcc7942_0943 | Synpcc7942_0031 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Synpcc7942_0489 | |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | aldA: lactaldehyde dehydrogenase | Synpcc7942_0489 | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | Synpcc7942_0684 | Synpcc7942_1573 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | sdaB: L-serine ammonia-lyase | | |
sorbitol | scrK: fructokinase | Synpcc7942_0116 | |
sorbitol | sdh: sorbitol dehydrogenase | Synpcc7942_0684 | Synpcc7942_1573 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
succinate | sdc: succinate:Na+ symporter Sdc | | |
sucrose | scrK: fructokinase | Synpcc7942_0116 | |
sucrose | thuE: sucrose ABC transporter, substrate-binding component ThuE | Synpcc7942_0950 | |
sucrose | thuG: sucrose ABC transporter, permease component 2 (ThuG) | Synpcc7942_0948 | Synpcc7942_0471 |
sucrose | thuK: sucrose ABC transporter, ATPase component ThuK | Synpcc7942_0960 | Synpcc7942_0947 |
threonine | adh: acetaldehyde dehydrogenase (not acylating) | Synpcc7942_0489 | |
threonine | ltaE: L-threonine aldolase | Synpcc7942_0282 | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | Synpcc7942_0489 | |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | Synpcc7942_2132 | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | Synpcc7942_0950 | |
trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | Synpcc7942_0960 | Synpcc7942_0947 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aacS: acetoacetyl-CoA synthetase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
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 | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | Synpcc7942_0597 | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
valine | prpB: 2-methylisocitrate lyase | | |
valine | prpC: 2-methylcitrate synthase | Synpcc7942_0612 | |
valine | prpD: 2-methylcitrate dehydratase | | |
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