Found 65 low-confidence and 97 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | VV02_RS18825 | |
| 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 | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | VV02_RS14190 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | VV02_RS14195 | |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | VV02_RS14200 | |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | VV02_RS14205 | VV02_RS16280 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | VV02_RS14210 | VV02_RS16285 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | gguA: L-arabinose ABC transporter, ATPase component GguA | VV02_RS22655 | VV02_RS06875 |
| arabinose | gguB: L-arabinose ABC transporter, permease component GguB | VV02_RS22660 | VV02_RS06870 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | aguB: N-carbamoylputrescine hydrolase | VV02_RS18350 | VV02_RS17920 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | VV02_RS26180 | |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | VV02_RS12005 | VV02_RS13625 |
| aspartate | glt: aspartate:proton symporter Glt | VV02_RS15430 | |
| cellobiose | mglA: glucose ABC transporter, ATP-binding component (MglA) | VV02_RS22655 | VV02_RS06950 |
| cellobiose | mglC: glucose ABC transporter, permease component (MglC) | VV02_RS22660 | VV02_RS06870 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | VV02_RS23450 | |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | VV02_RS26180 | VV02_RS23015 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | VV02_RS09175 | VV02_RS09180 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | citrullinase: putative citrullinase | VV02_RS17920 | VV02_RS18350 |
| citrulline | rocD: ornithine aminotransferase | VV02_RS19810 | VV02_RS11190 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | VV02_RS12695 | |
| D-serine | cycA: D-serine:H+ symporter CycA | VV02_RS18730 | VV02_RS08520 |
| D-serine | dsdA: D-serine ammonia-lyase | VV02_RS25925 | VV02_RS19315 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | VV02_RS09990 | |
| deoxyinosine | deoB: phosphopentomutase | VV02_RS10190 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | VV02_RS10005 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | VV02_RS06890 | VV02_RS05780 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | VV02_RS06750 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | VV02_RS02315 | VV02_RS15985 |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | VV02_RS15600 | VV02_RS24825 |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galE: UDP-glucose 4-epimerase | VV02_RS25215 | VV02_RS10480 |
| galactose | gguA: galactose ABC transporter, ATPase component GguA | VV02_RS22655 | VV02_RS06875 |
| galactose | gguB: galactose ABC transporter, permease component GguB | VV02_RS22660 | VV02_RS06870 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | VV02_RS24420 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | mglA: glucose ABC transporter, ATP-binding component (MglA) | VV02_RS22655 | VV02_RS06950 |
| glucose | mglC: glucose ABC transporter, permease component (MglC) | VV02_RS22660 | VV02_RS06870 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | VV02_RS06880 | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | VV02_RS24550 | VV02_RS14890 |
| histidine | bgtA: L-histidine ABC transporter, ATPase component BgtA | VV02_RS19715 | VV02_RS13180 |
| histidine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | VV02_RS26180 | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | VV02_RS04765 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VV02_RS04850 | VV02_RS25110 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | VV02_RS14195 | VV02_RS16275 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | VV02_RS14190 | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | VV02_RS14200 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | VV02_RS10230 | VV02_RS05075 |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | VV02_RS16415 | VV02_RS23790 |
| lactose | galE: UDP-glucose 4-epimerase | VV02_RS25215 | VV02_RS10480 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VV02_RS04850 | VV02_RS25110 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | VV02_RS05075 | VV02_RS02890 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | VV02_RS14195 | VV02_RS16275 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | VV02_RS14190 | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | VV02_RS14200 | |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | VV02_RS26180 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | VV02_RS12055 | VV02_RS11195 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | VV02_RS03820 | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | VV02_RS13180 | VV02_RS19715 |
| lysine | patA: cadaverine aminotransferase | VV02_RS13625 | VV02_RS19810 |
| maltose | mglA: glucose ABC transporter, ATP-binding component (MglA) | VV02_RS22655 | VV02_RS06950 |
| maltose | mglC: glucose ABC transporter, permease component (MglC) | VV02_RS22660 | VV02_RS06870 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | VV02_RS20670 | VV02_RS10135 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | VV02_RS10145 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | VV02_RS10130 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | VV02_RS10125 | VV02_RS19595 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | VV02_RS10135 | VV02_RS02310 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | VV02_RS16445 | VV02_RS06945 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | VV02_RS06870 | VV02_RS06960 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | VV02_RS19060 | VV02_RS10365 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | VV02_RS20265 | VV02_RS23595 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | VV02_RS23595 | VV02_RS05335 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | VV02_RS23390 | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | VV02_RS14210 | VV02_RS16285 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | VV02_RS14195 | VV02_RS16275 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | VV02_RS14200 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | VV02_RS19060 | VV02_RS10365 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | VV02_RS20265 | VV02_RS23595 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | VV02_RS23595 | VV02_RS05335 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | VV02_RS10095 | VV02_RS09595 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | VV02_RS10230 | VV02_RS05075 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | VV02_RS12005 | VV02_RS13625 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaB: L-rhamnulokinase | VV02_RS00525 | |
| rhamnose | rhaM: L-rhamnose mutarotase | VV02_RS06895 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | VV02_RS14190 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | VV02_RS14195 | |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | VV02_RS14200 | |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | VV02_RS14205 | VV02_RS16280 |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | VV02_RS14210 | VV02_RS16285 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | VV02_RS13505 | VV02_RS15280 |
| sorbitol | mtlG: ABC transporter for polyols MtlEFGK, permease component MtlG | VV02_RS13510 | VV02_RS20685 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | VV02_RS07335 | VV02_RS20680 |
| sorbitol | scrK: fructokinase | VV02_RS20670 | VV02_RS10135 |
| sucrose | ams: sucrose hydrolase (invertase) | VV02_RS18540 | VV02_RS08840 |
| sucrose | mglA: glucose ABC transporter, ATP-binding component (MglA) | VV02_RS22655 | VV02_RS06950 |
| sucrose | mglC: glucose ABC transporter, permease component (MglC) | VV02_RS22660 | VV02_RS06870 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | VV02_RS14190 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | VV02_RS14195 | |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | VV02_RS14200 | |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | VV02_RS14205 | VV02_RS16280 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | VV02_RS14210 | VV02_RS16285 |
| thymidine | deoB: phosphopentomutase | VV02_RS10190 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | pgmB: beta-phosphoglucomutase | VV02_RS12930 | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | VV02_RS13500 | |
| trehalose | treP: trehalose phosphorylase, inverting | VV02_RS12925 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | VV02_RS08520 | VV02_RS18730 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | VV02_RS14210 | VV02_RS16285 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | VV02_RS14200 | |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | VV02_RS14195 | |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | | |
| tyrosine | hmgA: homogentisate dioxygenase | VV02_RS11310 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | VV02_RS25735 | VV02_RS23595 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VV02_RS04850 | VV02_RS25110 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | VV02_RS14195 | VV02_RS16275 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | VV02_RS14190 | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | VV02_RS14200 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | VV02_RS18370 | VV02_RS16495 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | VV02_RS10230 | VV02_RS05075 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | VV02_RS06875 | VV02_RS16435 |
| xylose | xylG: ABC transporter for xylose, ATP-binding component xylG | VV02_RS22655 | VV02_RS06950 |
| xylose | xylH: ABC transporter for xylose, permease component xylH | VV02_RS22660 | VV02_RS06870 |
| xylose | xyrA: xylitol reductase | VV02_RS10235 | VV02_RS25745 |
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