Found 129 low-confidence and 64 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 | | |
| 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 | ATZ99_RS08525 | ATZ99_RS01480 |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcA: arginine deiminase | | |
| arginine | arcC: carbamate kinase | ATZ99_RS05315 | |
| arginine | davD: glutarate semialdehyde dehydrogenase | | |
| arginine | davT: 5-aminovalerate aminotransferase | ATZ99_RS11410 | ATZ99_RS04550 |
| arginine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ATZ99_RS09725 | |
| arginine | gcdG: succinyl-CoA:glutarate CoA-transferase | ATZ99_RS05180 | |
| arginine | gcdH: glutaryl-CoA dehydrogenase | ATZ99_RS09730 | |
| arginine | rocD: ornithine aminotransferase | ATZ99_RS04550 | ATZ99_RS11410 |
| arginine | rocE: L-arginine permease | | |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | ATZ99_RS04040 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ATZ99_RS10665 | ATZ99_RS01735 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | ATZ99_RS01740 | ATZ99_RS10670 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | ATZ99_RS01740 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | ATZ99_RS01745 | |
| citrulline | arcC: carbamate kinase | ATZ99_RS05315 | |
| citrulline | davD: glutarate semialdehyde dehydrogenase | | |
| citrulline | davT: 5-aminovalerate aminotransferase | ATZ99_RS11410 | ATZ99_RS04550 |
| citrulline | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ATZ99_RS09725 | |
| citrulline | gcdG: succinyl-CoA:glutarate CoA-transferase | ATZ99_RS05180 | |
| citrulline | gcdH: glutaryl-CoA dehydrogenase | ATZ99_RS09730 | |
| citrulline | rocD: ornithine aminotransferase | ATZ99_RS04550 | ATZ99_RS11410 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | ATZ99_RS07525 | ATZ99_RS03660 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | ATZ99_RS05600 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | ATZ99_RS05610 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | ATZ99_RS05615 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ATZ99_RS08105 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | ATZ99_RS10385 | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | ATZ99_RS01725 | ATZ99_RS08105 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | ATZ99_RS08525 | ATZ99_RS01480 |
| 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 | dctP: fumarate TRAP transporter, substrate-binding component DctP | ATZ99_RS03640 | ATZ99_RS01145 |
| fumarate | dctQ: fumarate TRAP transporter, small permease component DctQ | ATZ99_RS03635 | |
| galactose | galE: UDP-glucose 4-epimerase | ATZ99_RS03470 | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | edd: phosphogluconate dehydratase | ATZ99_RS06640 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | ATZ99_RS03650 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | ATZ99_RS03485 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | ATZ99_RS03485 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | ATZ99_RS06845 | ATZ99_RS10420 |
| glycerol | dhaD: glycerol dehydrogenase | ATZ99_RS01725 | ATZ99_RS05100 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | ATZ99_RS09910 | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ATZ99_RS09730 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ATZ99_RS09725 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ATZ99_RS08105 | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | ATZ99_RS08565 | ATZ99_RS04370 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ATZ99_RS04375 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | ATZ99_RS01400 | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | ATZ99_RS02490 | |
| isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | ATZ99_RS09620 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctP: L-malate TRAP transporter, substrate-binding component DctP | ATZ99_RS03640 | ATZ99_RS01145 |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | ATZ99_RS03635 | |
| lactose | galE: UDP-glucose 4-epimerase | ATZ99_RS03470 | |
| 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 | liuA: isovaleryl-CoA dehydrogenase | ATZ99_RS09730 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ATZ99_RS01400 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | ATZ99_RS09725 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ATZ99_RS02490 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | ATZ99_RS09760 | ATZ99_RS09790 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | ATZ99_RS03485 | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannose | manA: mannose-6-phosphate isomerase | ATZ99_RS02285 | ATZ99_RS01035 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | ATZ99_RS03485 | |
| 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 | ATZ99_RS09725 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ATZ99_RS09725 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ATZ99_RS10405 | ATZ99_RS00630 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ATZ99_RS10405 | ATZ99_RS00630 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | ATZ99_RS09725 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| 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 | ATZ99_RS09725 | |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ATZ99_RS09725 | |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ATZ99_RS10405 | ATZ99_RS00630 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | ATZ99_RS10405 | ATZ99_RS00630 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | ATZ99_RS09725 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| proline | davD: glutarate semialdehyde dehydrogenase | | |
| proline | davT: 5-aminovalerate aminotransferase | ATZ99_RS11410 | ATZ99_RS04550 |
| proline | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ATZ99_RS09725 | |
| proline | gcdG: succinyl-CoA:glutarate CoA-transferase | ATZ99_RS05180 | |
| proline | gcdH: glutaryl-CoA dehydrogenase | ATZ99_RS09730 | |
| proline | proY: proline:H+ symporter | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | ATZ99_RS01400 | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | ATZ99_RS02490 | |
| propionate | prpE: propionyl-CoA synthetase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | ATZ99_RS10955 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ATZ99_RS10390 | ATZ99_RS00645 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ATZ99_RS05100 | ATZ99_RS08105 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | ATZ99_RS09640 | ATZ99_RS01175 |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | ATZ99_RS01950 | ATZ99_RS01940 |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | ATZ99_RS00555 | ATZ99_RS10355 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | ATZ99_RS02935 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | ATZ99_RS08105 | ATZ99_RS05100 |
| succinate | dctP: succinate TRAP transporter, component DctP | ATZ99_RS03640 | ATZ99_RS01145 |
| succinate | dctQ: succinate TRAP transporter, small permease component DctQ | ATZ99_RS03635 | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | ATZ99_RS03485 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | ATZ99_RS00555 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ATZ99_RS09730 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ATZ99_RS09725 | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | ATZ99_RS08565 | ATZ99_RS04370 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ATZ99_RS04375 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | ATZ99_RS01400 | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | ATZ99_RS02490 | |
| valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
| xylitol | EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl) | ATZ99_RS08620 | |
| xylitol | EIIB-Axl: xylitol PTS, enzyme IIB (EIIB-Axl) | ATZ99_RS08615 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | ATZ99_RS03645 | ATZ99_RS08530 |
| 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