Found 139 low-confidence and 59 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP | Q394_RS0107510 | |
| 2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | Q394_RS0111960 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | Q394_RS0102910 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | Q394_RS0102915 | Q394_RS0106645 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | Q394_RS0102920 | |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | Q394_RS0102925 | Q394_RS0106655 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | Q394_RS0102930 | Q394_RS0106660 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | Q394_RS0118285 | Q394_RS0118290 |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | Q394_RS0106625 | Q394_RS0103835 |
| arginine | gabT: gamma-aminobutyrate transaminase | Q394_RS0113995 | Q394_RS0111125 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | Q394_RS0113995 | Q394_RS0111125 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | Q394_RS0111975 | Q394_RS0104930 |
| asparagine | ans: asparaginase | | |
| cellobiose | bgl: cellobiase | Q394_RS0111225 | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Q394_RS0106625 | Q394_RS0103835 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | Q394_RS0118285 | Q394_RS0118290 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | Q394_RS0118295 | |
| citrulline | citrullinase: putative citrullinase | Q394_RS0100130 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | Q394_RS0111975 | Q394_RS0104930 |
| citrulline | rocD: ornithine aminotransferase | Q394_RS0113995 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | Q394_RS0103820 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | Q394_RS0103825 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | Q394_RS0103835 | Q394_RS0106625 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | Q394_RS0105245 | |
| deoxyinosine | deoB: phosphopentomutase | Q394_RS0100435 | Q394_RS0117455 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | Q394_RS0103490 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | Q394_RS0112845 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Q394_RS0118475 | |
| 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 | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | Q394_RS0117690 | Q394_RS0108955 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | Q394_RS0104930 | Q394_RS0111975 |
| 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 | | |
| 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) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Q394_RS0110770 | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | Q394_RS0117580 | Q394_RS0104930 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | Q394_RS0112085 | Q394_RS0113940 |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | Q394_RS0103145 | |
| glycerol | glpF: glycerol facilitator glpF | Q394_RS0117835 | |
| glycerol | glpK: glycerol kinase | | |
| histidine | hisJ: L-histidine ABC transporter, substrate-binding component HisJ | Q394_RS0118295 | |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | Q394_RS0118285 | Q394_RS0118290 |
| histidine | hisP: L-histidine ABC transporter, ATPase component HisP | Q394_RS0106625 | Q394_RS0103835 |
| histidine | hisQ: L-histidine ABC transporter, permease component 2 (HisQ) | Q394_RS0118290 | Q394_RS0118285 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | Q394_RS0112850 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | Q394_RS0114510 | Q394_RS0118475 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| 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 | Q394_RS0112845 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | Q394_RS0109800 | Q394_RS0109245 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | Q394_RS0112850 | |
| 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) | Q394_RS0117580 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | Q394_RS0118295 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | Q394_RS0118285 | Q394_RS0118290 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | Q394_RS0106625 | Q394_RS0103835 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | Q394_RS0118290 | Q394_RS0118285 |
| lysine | lat: L-lysine 6-aminotransferase | | |
| lysine | lysN: 2-aminoadipate transaminase | Q394_RS0100140 | Q394_RS0113995 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mt1d: mannitol 1-dehydrogenase | Q394_RS0103345 | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | Q394_RS0103645 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | Q394_RS0103650 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | Q394_RS0103655 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | Q394_RS0109195 | Q394_RS0108480 |
| 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 | Q394_RS0104830 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | Q394_RS0104930 | Q394_RS0117580 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Q394_RS0110770 | |
| 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 | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | Q394_RS0118420 | Q394_RS0100445 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | Q394_RS0118420 | Q394_RS0100445 |
| phenylacetate | paaK: phenylacetate-CoA ligase | Q394_RS0112845 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | Q394_RS0107750 | Q394_RS0105615 |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | Q394_RS0112845 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | Q394_RS0106530 | Q394_RS0102985 |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | Q394_RS0102930 | Q394_RS0106660 |
| phenylalanine | maiA: maleylacetoacetate isomerase | Q394_RS0116420 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | Q394_RS0111975 | Q394_RS0104930 |
| putrescine | gabT: gamma-aminobutyrate transaminase | Q394_RS0113995 | Q394_RS0111125 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Q394_RS0113995 | Q394_RS0111125 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Q394_RS0111975 | Q394_RS0104930 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | Q394_RS0115635 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | Q394_RS0104930 | Q394_RS0111975 |
| 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 | Q394_RS0117690 | Q394_RS0108955 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | Q394_RS0102930 | Q394_RS0106660 |
| serine | sdaB: L-serine ammonia-lyase | Q394_RS0105245 | |
| sorbitol | sdh: sorbitol dehydrogenase | Q394_RS0109205 | Q394_RS0109200 |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | Q394_RS0102910 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | Q394_RS0102915 | Q394_RS0106645 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | Q394_RS0102920 | |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | Q394_RS0102925 | Q394_RS0106655 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | Q394_RS0102930 | Q394_RS0106660 |
| threonine | ltaE: L-threonine aldolase | Q394_RS0103425 | |
| thymidine | deoA: thymidine phosphorylase DeoA | Q394_RS0109660 | |
| thymidine | deoB: phosphopentomutase | Q394_RS0100435 | Q394_RS0117455 |
| 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 | aacS: acetoacetyl-CoA synthetase | Q394_RS0112845 | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | Q394_RS0102930 | Q394_RS0106660 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | Q394_RS0106530 | Q394_RS0102985 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | Q394_RS0116420 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | Q394_RS0102915 | Q394_RS0106645 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Q394_RS0102910 | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | Q394_RS0102920 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Q394_RS0104930 | Q394_RS0111975 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | Q394_RS0114290 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | Q394_RS0118475 | Q394_RS0104545 |
| xylose | xylA: xylose isomerase | | |
| 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