Found 132 low-confidence and 88 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 | BUB04_RS10335 | BUB04_RS06490 |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | BUB04_RS05255 | BUB04_RS06485 |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BUB04_RS14925 | BUB04_RS10320 |
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 | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | rocE: L-arginine permease | | |
asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BUB04_RS05925 | BUB04_RS13795 |
asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BUB04_RS05930 | BUB04_RS14565 |
asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BUB04_RS05920 | |
asparagine | ans: asparaginase | BUB04_RS04620 | BUB04_RS16660 |
aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BUB04_RS05925 | BUB04_RS13795 |
aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BUB04_RS05930 | BUB04_RS14565 |
aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BUB04_RS05920 | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
cellobiose | glk: glucokinase | BUB04_RS16875 | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BUB04_RS05855 | BUB04_RS10875 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BUB04_RS05850 | BUB04_RS13795 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BUB04_RS06475 | BUB04_RS06465 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BUB04_RS03450 | |
citrulline | arcC: carbamate kinase | BUB04_RS05565 | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | BUB04_RS05915 | |
D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | BUB04_RS05920 | BUB04_RS12165 |
D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | BUB04_RS05930 | BUB04_RS14565 |
D-lactate | D-LDH: D-lactate dehydrogenase | BUB04_RS15385 | BUB04_RS07455 |
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 | BUB04_RS13615 | BUB04_RS01900 |
deoxyinosine | deoB: phosphopentomutase | BUB04_RS13695 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BUB04_RS04420 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | BUB04_RS10050 | BUB04_RS15270 |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | BUB04_RS08380 | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucO: L-lactaldehyde reductase | BUB04_RS10050 | BUB04_RS15270 |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
fumarate | dctA: fumarate:H+ symporter DctA | | |
galactose | galE: UDP-glucose 4-epimerase | BUB04_RS13365 | BUB04_RS13705 |
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 | kdgK: 2-keto-3-deoxygluconate kinase | BUB04_RS05935 | |
galacturonate | uxaA: D-altronate dehydratase | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | edd: phosphogluconate dehydratase | BUB04_RS09665 | |
gluconate | gntK: D-gluconate kinase | BUB04_RS08485 | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BUB04_RS16750 | |
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 | BUB04_RS11085 | |
glucuronate | garR: tartronate semialdehyde reductase | BUB04_RS05580 | BUB04_RS01755 |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | BUB04_RS07000 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BUB04_RS05925 | BUB04_RS13795 |
glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BUB04_RS05930 | BUB04_RS14565 |
glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BUB04_RS05920 | |
glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | BUB04_RS09120 | BUB04_RS01215 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | BUB04_RS05925 | BUB04_RS10880 |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | BUB04_RS05930 | BUB04_RS14565 |
histidine | hutG: N-formiminoglutamate formiminohydrolase | BUB04_RS18635 | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BUB04_RS03730 | BUB04_RS01095 |
isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BUB04_RS01335 | BUB04_RS01455 |
isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | BUB04_RS01340 | BUB04_RS01450 |
isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BUB04_RS01345 | BUB04_RS07775 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BUB04_RS07485 | BUB04_RS18395 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BUB04_RS13175 | BUB04_RS14530 |
isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | BUB04_RS13185 | BUB04_RS14540 |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BUB04_RS08790 | |
L-lactate | L-LDH: L-lactate dehydrogenase | BUB04_RS00940 | |
L-lactate | SfMCT: L-lactate transporter SfMCT | BUB04_RS12750 | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
lactose | galE: UDP-glucose 4-epimerase | BUB04_RS13365 | BUB04_RS13705 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | BUB04_RS16875 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BUB04_RS01335 | BUB04_RS01455 |
leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | BUB04_RS01340 | BUB04_RS01450 |
leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BUB04_RS01345 | BUB04_RS07775 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BUB04_RS08790 | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | BUB04_RS07705 | BUB04_RS01090 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | BUB04_RS00695 | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BUB04_RS13175 | BUB04_RS14530 |
leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | BUB04_RS13185 | BUB04_RS14540 |
lysine | cadA: lysine decarboxylase | | |
lysine | davD: glutarate semialdehyde dehydrogenase | BUB04_RS04110 | BUB04_RS05780 |
lysine | gcdH: glutaryl-CoA dehydrogenase | BUB04_RS03730 | BUB04_RS05240 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patD: 5-aminopentanal dehydrogenase | BUB04_RS04110 | BUB04_RS05780 |
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 | 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 | kdgK: 2-keto-3-deoxygluconate kinase | BUB04_RS05935 | |
myoinositol | uxaE: D-tagaturonate epimerase | | |
myoinositol | uxuA: D-mannonate dehydratase | | |
myoinositol | uxuB: D-mannonate dehydrogenase | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BUB04_RS16750 | |
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 | BUB04_RS03725 | BUB04_RS07705 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BUB04_RS09760 | BUB04_RS07705 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BUB04_RS03720 | BUB04_RS17410 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BUB04_RS03720 | BUB04_RS17410 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | BUB04_RS09760 | BUB04_RS15240 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | BUB04_RS02700 | BUB04_RS14475 |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BUB04_RS13180 | BUB04_RS02685 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BUB04_RS13175 | BUB04_RS02680 |
phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | BUB04_RS13185 | BUB04_RS12270 |
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 | BUB04_RS03725 | BUB04_RS07705 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BUB04_RS09760 | BUB04_RS07705 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BUB04_RS03720 | BUB04_RS17410 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | BUB04_RS03720 | BUB04_RS17410 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | BUB04_RS09760 | BUB04_RS15240 |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BUB04_RS05925 | BUB04_RS13795 |
proline | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BUB04_RS05930 | BUB04_RS14565 |
proline | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BUB04_RS05920 | |
proline | put1: proline dehydrogenase | BUB04_RS13170 | BUB04_RS16575 |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BUB04_RS08790 | |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabD: succinate semialdehyde dehydrogenase | BUB04_RS04110 | BUB04_RS05780 |
putrescine | gabT: gamma-aminobutyrate transaminase | BUB04_RS10885 | BUB04_RS02225 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BUB04_RS04110 | BUB04_RS05780 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | BUB04_RS15595 | |
rhamnose | fucO: L-lactaldehyde reductase | BUB04_RS10050 | BUB04_RS15270 |
rhamnose | rhaA: L-rhamnose isomerase | | |
rhamnose | rhaB: L-rhamnulokinase | | |
rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
rhamnose | rhaM: L-rhamnose mutarotase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BUB04_RS13175 | BUB04_RS02680 |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BUB04_RS13180 | BUB04_RS02685 |
serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BUB04_RS13185 | BUB04_RS12270 |
serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BUB04_RS02695 | BUB04_RS13190 |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BUB04_RS02700 | BUB04_RS14475 |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BUB04_RS18395 | BUB04_RS12055 |
succinate | sdc: succinate:Na+ symporter Sdc | | |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BUB04_RS13175 | BUB04_RS02680 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BUB04_RS13180 | BUB04_RS02685 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BUB04_RS13185 | BUB04_RS12270 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BUB04_RS02695 | BUB04_RS13190 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BUB04_RS02700 | BUB04_RS14475 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BUB04_RS03940 | BUB04_RS03935 |
threonine | gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) | BUB04_RS03950 | BUB04_RS16585 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | BUB04_RS13695 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupC: thymidine permease NupC | BUB04_RS04420 | |
trehalose | glk: glucokinase | BUB04_RS16875 | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | BUB04_RS03730 | BUB04_RS15245 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BUB04_RS13370 | BUB04_RS07705 |
valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | BUB04_RS01335 | BUB04_RS01455 |
valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | BUB04_RS01340 | BUB04_RS01450 |
valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BUB04_RS01345 | BUB04_RS07775 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BUB04_RS13175 | BUB04_RS14530 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BUB04_RS13185 | BUB04_RS14540 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BUB04_RS04110 | BUB04_RS13170 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BUB04_RS05580 | BUB04_RS01755 |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | BUB04_RS08790 | |
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 Apr 09 2024. 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