Found 160 low-confidence and 42 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 | mhpE: 4-hydroxy-2-oxovalerate aldolase | CKL_RS10580 | |
| 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 | | |
| 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 | gabT: gamma-aminobutyrate transaminase | CKL_RS10130 | CKL_RS15175 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | CKL_RS11765 | CKL_RS10130 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| arginine | rocE: L-arginine permease | CKL_RS07600 | CKL_RS17165 |
| arginine | speB: agmatinase | CKL_RS11780 | |
| asparagine | ans: asparaginase | CKL_RS05075 | CKL_RS11315 |
| asparagine | ansP: L-asparagine permease AnsP | CKL_RS03175 | CKL_RS17165 |
| aspartate | glt: aspartate:proton symporter Glt | | |
| 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 | CKL_RS04820 | CKL_RS10155 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CKL_RS04815 | CKL_RS03475 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CKL_RS03475 | CKL_RS10140 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CKL_RS04810 | CKL_RS11640 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | put1: proline dehydrogenase | CKL_RS10110 | CKL_RS02190 |
| citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
| citrulline | rocD: ornithine aminotransferase | CKL_RS15175 | CKL_RS10130 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | CKL_RS02105 | CKL_RS02495 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | CKL_RS14730 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| 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 | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | CKL_RS10825 | |
| 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 | 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 | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | CKL_RS04980 | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| 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) | CKL_RS01560 | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | CKL_RS10825 | |
| 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 | dhaD: glycerol dehydrogenase | CKL_RS11770 | CKL_RS10135 |
| glycerol | dhaK: dihydroxyacetone:PEP phosphotransferase, subunit K | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | CKL_RS11780 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | CKL_RS04035 | CKL_RS03265 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CKL_RS03105 | CKL_RS02250 |
| isoleucine | dddA: 3-hydroxypropionate dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | CKL_RS02245 | CKL_RS12375 |
| isoleucine | hpcD: 3-hydroxypropionyl-CoA dehydratase | CKL_RS02245 | CKL_RS12375 |
| isoleucine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CKL_RS03830 | CKL_RS10300 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CKL_RS13405 | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | mleP: malate permease MleP | CKL_RS11105 | |
| 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 | CKL_RS14730 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | CKL_RS03105 | CKL_RS02250 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CKL_RS02210 | CKL_RS00540 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CKL_RS02245 | CKL_RS12375 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CKL_RS13405 | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | | |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | CKL_RS03105 | CKL_RS02250 |
| maltose | MAL11: maltose permease | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannose | manA: mannose-6-phosphate isomerase | CKL_RS16635 | CKL_RS18235 |
| 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 | CKL_RS17525 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CKL_RS01560 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | CKL_RS03175 | CKL_RS17165 |
| 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 | CKL_RS02245 | CKL_RS12375 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CKL_RS02245 | CKL_RS12375 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CKL_RS17985 | CKL_RS17990 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CKL_RS17995 | CKL_RS17985 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CKL_RS02245 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | CKL_RS17165 | CKL_RS03175 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| 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 | CKL_RS02245 | CKL_RS12375 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CKL_RS02245 | CKL_RS12375 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CKL_RS17985 | CKL_RS17990 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | CKL_RS17995 | CKL_RS17985 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | CKL_RS02245 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| proline | opuBA: proline ABC transporter, ATPase component OpuBA/BusAA | CKL_RS03815 | CKL_RS13695 |
| proline | put1: proline dehydrogenase | CKL_RS10110 | CKL_RS02190 |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
| propionate | dddA: 3-hydroxypropionate dehydrogenase | | |
| propionate | hpcD: 3-hydroxypropionyl-CoA dehydratase | CKL_RS02245 | CKL_RS12375 |
| propionate | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| propionate | prpE: propionyl-CoA synthetase | CKL_RS14730 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CKL_RS10130 | CKL_RS15175 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CKL_RS11765 | CKL_RS10130 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CKL_RS10300 | CKL_RS00520 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CKL_RS00520 | CKL_RS07515 |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | CKL_RS11645 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | CKL_RS17165 | CKL_RS03175 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | CKL_RS00520 | CKL_RS03830 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | CKL_RS07860 | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CKL_RS08700 | CKL_RS08705 |
| threonine | serP1: L-threonine uptake transporter SerP1 | CKL_RS17165 | CKL_RS03175 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treB: trehalose PTS system, EII-BC components TreB | | |
| trehalose | treC: trehalose-6-phosphate hydrolase | CKL_RS07860 | |
| trehalose | treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) | CKL_RS17460 | CKL_RS01510 |
| tryptophan | ecfA1: energy-coupling factor transporter, ATPase 1 (A1) component | CKL_RS01250 | CKL_RS01255 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | CKL_RS14730 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CKL_RS17165 | CKL_RS03175 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | CKL_RS11645 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CKL_RS03105 | CKL_RS02250 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CKL_RS02245 | |
| valine | dddA: 3-hydroxypropionate dehydrogenase | | |
| valine | hpcD: 3-hydroxypropionyl-CoA dehydratase | CKL_RS02245 | CKL_RS12375 |
| valine | iolA: malonate semialdehyde dehydrogenase (CoA-acylating) | | |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CKL_RS13405 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CKL_RS10825 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| 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 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