Found 141 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | dctM: 2-oxoglutarate TRAP transporter, large permease component DctM | BEN30_RS06695 | BEN30_RS10015 |
| 2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | BEN30_RS06700 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BEN30_RS11380 | BEN30_RS17090 |
| 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 | | |
| alanine | alsT: L-alanine symporter AlsT/DagA | BEN30_RS15485 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | BEN30_RS04095 | |
| 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 | BEN30_RS09690 | BEN30_RS03080 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BEN30_RS09705 | BEN30_RS03085 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BEN30_RS09700 | BEN30_RS09705 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BEN30_RS09695 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | BEN30_RS05850 | BEN30_RS08600 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | BEN30_RS03095 | BEN30_RS06480 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | BEN30_RS03080 | BEN30_RS09690 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BEN30_RS14845 | BEN30_RS03755 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BEN30_RS03605 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | BEN30_RS08040 | BEN30_RS11070 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | BEN30_RS10155 | BEN30_RS07830 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | BEN30_RS08615 | |
| 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 | galE: UDP-glucose 4-epimerase | BEN30_RS09955 | BEN30_RS10850 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | BEN30_RS07830 | BEN30_RS10155 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| 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) | BEN30_RS17110 | |
| 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 | BEN30_RS01430 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | BEN30_RS03095 | BEN30_RS06480 |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BEN30_RS03085 | BEN30_RS09705 |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BEN30_RS03090 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | BEN30_RS10945 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BEN30_RS00415 | BEN30_RS03325 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BEN30_RS04700 | BEN30_RS00220 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | L-LDH: L-lactate dehydrogenase | BEN30_RS01760 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctM: L-malate TRAP transporter, large permease component DctM | BEN30_RS06695 | BEN30_RS10015 |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | BEN30_RS06700 | |
| lactose | galE: UDP-glucose 4-epimerase | BEN30_RS09955 | BEN30_RS10850 |
| 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 | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | BEN30_RS03095 | BEN30_RS06480 |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BEN30_RS03085 | BEN30_RS09705 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BEN30_RS03090 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | BEN30_RS00415 | BEN30_RS03325 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BEN30_RS04290 | BEN30_RS05880 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BEN30_RS17440 | BEN30_RS02890 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BEN30_RS04280 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | BEN30_RS02180 | BEN30_RS06940 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BEN30_RS00445 | BEN30_RS04700 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BEN30_RS10105 | |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mt1d: mannitol 1-dehydrogenase | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| 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 | BEN30_RS09465 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BEN30_RS17110 | |
| 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 | BEN30_RS17440 | BEN30_RS00545 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BEN30_RS17440 | BEN30_RS02890 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | BEN30_RS00445 | BEN30_RS04700 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BEN30_RS00215 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BEN30_RS00215 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | BEN30_RS09995 | BEN30_RS00555 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BEN30_RS17440 | BEN30_RS00545 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | BEN30_RS06385 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | BEN30_RS00175 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | BEN30_RS10155 | BEN30_RS07830 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | BEN30_RS10970 | |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | BEN30_RS01580 | BEN30_RS09230 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | BEN30_RS01585 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BEN30_RS17165 | BEN30_RS04700 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | BEN30_RS04700 | BEN30_RS00220 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | BEN30_RS04390 | |
| sorbitol | sdh: sorbitol dehydrogenase | BEN30_RS04700 | BEN30_RS00220 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BEN30_RS08700 | BEN30_RS08705 |
| threonine | ltaE: L-threonine aldolase | BEN30_RS14880 | |
| threonine | snatA: L-threonine transporter snatA | BEN30_RS04390 | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | BEN30_RS07830 | BEN30_RS10155 |
| thymidine | deoB: phosphopentomutase | | |
| 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 | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | BEN30_RS06385 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | BEN30_RS00175 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BEN30_RS00415 | BEN30_RS03325 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BEN30_RS17440 | BEN30_RS02890 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BEN30_RS10175 | BEN30_RS10155 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BEN30_RS09195 | BEN30_RS09215 |
| 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