Found 143 low-confidence and 59 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | BED41_RS12235 | BED41_RS12250 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | BED41_RS05590 | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BED41_RS05565 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | BED41_RS15810 | BED41_RS00575 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | BED41_RS05590 | |
| acetate | actP: cation/acetate symporter ActP | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | BED41_RS04255 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcC: carbamate kinase | BED41_RS02530 | |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | BED41_RS04030 | BED41_RS14585 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | BED41_RS04025 | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | BED41_RS01765 | BED41_RS00575 |
| asparagine | ans: asparaginase | BED41_RS06480 | BED41_RS06455 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| cellobiose | glk: glucokinase | BED41_RS11630 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | BED41_RS03110 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BED41_RS04030 | BED41_RS14585 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BED41_RS04025 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BED41_RS04025 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BED41_RS04025 | |
| citrulline | arcC: carbamate kinase | BED41_RS02530 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | BED41_RS01765 | BED41_RS00575 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | BED41_RS03180 | BED41_RS03890 |
| 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 | BED41_RS12420 | BED41_RS03945 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | BED41_RS05600 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | scrK: fructokinase | BED41_RS11630 | |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | BED41_RS15810 | BED41_RS00575 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | BED41_RS04255 | |
| 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 | dauA: fumarate transporter DauA | BED41_RS11550 | |
| 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 | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | BED41_RS14455 | |
| 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 | BED41_RS13860 | BED41_RS02620 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BED41_RS02370 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| 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 | BED41_RS05565 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | BED41_RS15550 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpO: glycerol 3-phosphate oxidase | BED41_RS10295 | BED41_RS00390 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | BED41_RS07200 | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | BED41_RS14585 | BED41_RS04410 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | BED41_RS06505 | BED41_RS10185 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BED41_RS10750 | BED41_RS01565 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BED41_RS04590 | BED41_RS03690 |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | BED41_RS03700 | BED41_RS12750 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | BED41_RS04295 | BED41_RS10175 |
| 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 | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | BED41_RS11630 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BED41_RS02945 | BED41_RS10185 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BED41_RS04295 | BED41_RS10175 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BED41_RS04590 | BED41_RS03690 |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | BED41_RS03700 | BED41_RS12750 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | BED41_RS15810 | BED41_RS00575 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | BED41_RS04025 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | BED41_RS04030 | BED41_RS14585 |
| lysine | lysN: 2-aminoadipate transaminase | BED41_RS02430 | BED41_RS04460 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | BED41_RS03890 | BED41_RS03180 |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | BED41_RS06615 | |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BED41_RS02370 | |
| 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 | BED41_RS02945 | BED41_RS06505 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BED41_RS02945 | BED41_RS06505 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | BED41_RS06185 | BED41_RS10750 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BED41_RS10190 | BED41_RS01560 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BED41_RS10190 | BED41_RS01560 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BED41_RS02945 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | BED41_RS13925 | BED41_RS12745 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BED41_RS03695 | BED41_RS12755 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BED41_RS08725 | BED41_RS04590 |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | BED41_RS03700 | BED41_RS01970 |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | putP: proline:Na+ symporter | BED41_RS02995 | BED41_RS11250 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | BED41_RS04295 | BED41_RS10175 |
| propionate | prpE: propionyl-CoA synthetase | BED41_RS15085 | BED41_RS14140 |
| propionate | putP: propionate transporter; proline:Na+ symporter | BED41_RS02995 | BED41_RS11250 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | BED41_RS15810 | BED41_RS11335 |
| putrescine | gabT: gamma-aminobutyrate transaminase | BED41_RS03030 | BED41_RS01535 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BED41_RS03030 | BED41_RS01535 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BED41_RS15810 | BED41_RS00575 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BED41_RS15810 | BED41_RS00575 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BED41_RS06185 | BED41_RS00875 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | BED41_RS14455 | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | BED41_RS05565 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | BED41_RS05600 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BED41_RS08725 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BED41_RS03695 | BED41_RS12755 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BED41_RS08710 | BED41_RS01970 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BED41_RS13925 | BED41_RS12745 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BED41_RS10750 | BED41_RS01565 |
| succinate | dauA: succinate:H+ symporter DauA | BED41_RS11550 | |
| sucrose | scrK: fructokinase | BED41_RS11630 | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BED41_RS08725 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BED41_RS03695 | BED41_RS12755 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BED41_RS08710 | BED41_RS01970 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BED41_RS13925 | BED41_RS12745 |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | BED41_RS11630 | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tryptophan | ecfA1: energy-coupling factor transporter, ATPase 1 (A1) component | BED41_RS05230 | BED41_RS05235 |
| tryptophan | ecfA2: energy-coupling factor transporter, ATPase 2 (A2) component | BED41_RS05235 | BED41_RS14585 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP | | |
| 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 | BED41_RS06505 | BED41_RS10185 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BED41_RS04590 | BED41_RS03690 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BED41_RS03700 | BED41_RS12750 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BED41_RS13905 | BED41_RS10130 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | BED41_RS04295 | BED41_RS10175 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | BED41_RS08700 | BED41_RS01565 |
| 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