Found 107 low-confidence and 71 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | DNK54_RS02035 | DNK54_RS12245 |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | DNK54_RS02760 | DNK54_RS05865 |
| 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 | DNK54_RS01780 | DNK54_RS20170 |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | DNK54_RS05365 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | DNK54_RS05345 | DNK54_RS06380 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | DNK54_RS05350 | DNK54_RS06375 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcC: carbamate kinase | DNK54_RS18790 | DNK54_RS11255 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | DNK54_RS18915 | DNK54_RS15005 |
| asparagine | glt: aspartate:proton symporter Glt | DNK54_RS02110 | |
| aspartate | glt: aspartate:proton symporter Glt | DNK54_RS02110 | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | DNK54_RS05765 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | DNK54_RS07055 | DNK54_RS13505 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | DNK54_RS18790 | DNK54_RS11255 |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | DNK54_RS18915 | DNK54_RS15005 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | DNK54_RS16500 | |
| D-alanine | dadA: D-alanine dehydrogenase | DNK54_RS19485 | DNK54_RS16505 |
| D-lactate | D-LDH: D-lactate dehydrogenase | DNK54_RS05900 | DNK54_RS14340 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | DNK54_RS16500 | |
| D-serine | dsdA: D-serine ammonia-lyase | DNK54_RS16795 | DNK54_RS08260 |
| deoxyinosine | deoB: phosphopentomutase | DNK54_RS07650 | DNK54_RS20670 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DNK54_RS03205 | DNK54_RS10210 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | DNK54_RS18680 | |
| 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 | DNK54_RS17595 | DNK54_RS07665 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | DNK54_RS09135 | |
| 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 | DNK54_RS20065 | DNK54_RS18580 |
| galactose | galK: galactokinase (-1-phosphate forming) | DNK54_RS03760 | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | DNK54_RS15700 | DNK54_RS07650 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | DNK54_RS01540 | DNK54_RS01490 |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | DNK54_RS02515 | |
| galacturonate | udh: D-galacturonate dehydrogenase | DNK54_RS07630 | |
| 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) | DNK54_RS20650 | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | DNK54_RS01540 | DNK54_RS01490 |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | DNK54_RS02515 | |
| glucuronate | udh: D-glucuronate dehydrogenase | DNK54_RS07630 | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | DNK54_RS02110 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | DNK54_RS08050 | DNK54_RS14330 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | DNK54_RS05365 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | DNK54_RS05350 | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | DNK54_RS05345 | DNK54_RS06380 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | DNK54_RS01545 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | DNK54_RS07535 | DNK54_RS15085 |
| L-lactate | L-LDH: L-lactate dehydrogenase | DNK54_RS10835 | DNK54_RS20205 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galE: UDP-glucose 4-epimerase | DNK54_RS20065 | DNK54_RS18580 |
| lactose | galK: galactokinase (-1-phosphate forming) | DNK54_RS03760 | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | DNK54_RS17180 | DNK54_RS13290 |
| lactose | pgmA: alpha-phosphoglucomutase | DNK54_RS15700 | DNK54_RS07650 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | DNK54_RS00105 | DNK54_RS19555 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | DNK54_RS05365 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | DNK54_RS05350 | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | DNK54_RS05345 | DNK54_RS06380 |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | DNK54_RS01545 | |
| lysine | davA: 5-aminovaleramidase | DNK54_RS08055 | DNK54_RS14440 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | DNK54_RS18780 | DNK54_RS11350 |
| lysine | davT: 5-aminovalerate aminotransferase | DNK54_RS04735 | DNK54_RS11795 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | DNK54_RS12200 | DNK54_RS13740 |
| lysine | lysP: L-lysine:H+ symporter LysP | DNK54_RS16500 | |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | DNK54_RS20670 | |
| 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 | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | DNK54_RS15005 | DNK54_RS12190 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | DNK54_RS20650 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | DNK54_RS00105 | DNK54_RS19555 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | DNK54_RS15750 | DNK54_RS14305 |
| phenylacetate | paaK: phenylacetate-CoA ligase | DNK54_RS20210 | DNK54_RS15370 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | DNK54_RS19555 | DNK54_RS10265 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | DNK54_RS14905 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | DNK54_RS16500 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | DNK54_RS00105 | DNK54_RS19555 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | DNK54_RS15750 | DNK54_RS14305 |
| phenylalanine | paaK: phenylacetate-CoA ligase | DNK54_RS20210 | DNK54_RS15370 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | DNK54_RS19555 | DNK54_RS10265 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | DNK54_RS17595 | DNK54_RS07665 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | DNK54_RS14775 | |
| proline | put1: proline dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | DNK54_RS07535 | DNK54_RS15085 |
| putrescine | gabT: gamma-aminobutyrate transaminase | DNK54_RS04735 | DNK54_RS11795 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | DNK54_RS04735 | DNK54_RS11795 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | DNK54_RS17595 | DNK54_RS15005 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | DNK54_RS17595 | DNK54_RS07665 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | DNK54_RS10210 | DNK54_RS06790 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | DNK54_RS01490 | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| 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) | DNK54_RS05365 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | DNK54_RS05345 | DNK54_RS06380 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | DNK54_RS05350 | DNK54_RS06375 |
| sorbitol | scrK: fructokinase | DNK54_RS09130 | DNK54_RS00970 |
| sorbitol | sdh: sorbitol dehydrogenase | DNK54_RS18330 | DNK54_RS06325 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | dauA: succinate:H+ symporter DauA | DNK54_RS11475 | |
| sucrose | ams: sucrose hydrolase (invertase) | DNK54_RS00070 | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | DNK54_RS05365 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | DNK54_RS05345 | DNK54_RS06380 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | DNK54_RS05350 | DNK54_RS06375 |
| thymidine | deoB: phosphopentomutase | DNK54_RS07650 | DNK54_RS20670 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | | |
| trehalose | treF: trehalase | DNK54_RS07180 | DNK54_RS00070 |
| tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | DNK54_RS04850 | DNK54_RS20925 |
| tryptophan | andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc | | |
| tryptophan | andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | DNK54_RS16500 | |
| tryptophan | catB: muconate cycloisomerase | DNK54_RS09810 | |
| tryptophan | kyn: kynureninase | DNK54_RS06000 | |
| tryptophan | kynB: kynurenine formamidase | DNK54_RS20270 | DNK54_RS17010 |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | DNK54_RS09450 | DNK54_RS09790 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | DNK54_RS16500 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | DNK54_RS15005 | DNK54_RS17595 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | DNK54_RS16610 | |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | DNK54_RS05365 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | DNK54_RS05350 | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | DNK54_RS05345 | DNK54_RS06380 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | DNK54_RS01545 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | DNK54_RS07535 | DNK54_RS15085 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | DNK54_RS13675 | DNK54_RS20930 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | DNK54_RS01055 | |
| 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