Found 142 low-confidence and 83 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | BLU87_RS03510 | BLU87_RS07020 |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BLU87_RS05665 | |
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) | BLU87_RS11835 | |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLU87_RS11830 | BLU87_RS12680 |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BLU87_RS11820 | BLU87_RS12690 |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BLU87_RS11815 | BLU87_RS12695 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | BLU87_RS06340 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | put1: proline dehydrogenase | BLU87_RS12670 | BLU87_RS15955 |
arginine | putA: L-glutamate 5-semialdeyde dehydrogenase | BLU87_RS05345 | BLU87_RS15950 |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | BLU87_RS11585 | |
asparagine | yhiT: probable L-asparagine transporter YhiT | BLU87_RS04225 | |
aspartate | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | BLU87_RS03900 | |
aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BLU87_RS03910 | BLU87_RS11125 |
aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BLU87_RS03915 | BLU87_RS11120 |
aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BLU87_RS03905 | |
cellobiose | bgl: cellobiase | | |
cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BLU87_RS03915 | BLU87_RS11120 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BLU87_RS09590 | BLU87_RS11125 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BLU87_RS09590 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | citrullinase: putative citrullinase | BLU87_RS07975 | |
citrulline | put1: proline dehydrogenase | BLU87_RS12670 | BLU87_RS15955 |
citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | BLU87_RS05345 | BLU87_RS15950 |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | BLU87_RS03900 | |
D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | BLU87_RS03905 | |
D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | BLU87_RS03915 | BLU87_RS11120 |
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 | BLU87_RS11570 | BLU87_RS04710 |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | BLU87_RS03510 | BLU87_RS07020 |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BLU87_RS14010 | |
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) | BLU87_RS03510 | BLU87_RS07020 |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | BLU87_RS03510 | BLU87_RS07020 |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | BLU87_RS10700 | BLU87_RS10015 |
fructose | 1pfk: 1-phosphofructokinase | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | aldA: lactaldehyde dehydrogenase | BLU87_RS07020 | BLU87_RS05845 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | BLU87_RS06340 | |
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 | BLU87_RS06225 | BLU87_RS10400 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | BLU87_RS04510 | |
galactose | pgmA: alpha-phosphoglucomutase | BLU87_RS10530 | BLU87_RS06860 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | BLU87_RS01645 | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
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) | BLU87_RS15755 | |
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 | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | BLU87_RS01645 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | BLU87_RS03900 | |
histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | BLU87_RS03910 | BLU87_RS11125 |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | BLU87_RS03915 | BLU87_RS11120 |
histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | BLU87_RS03905 | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | BLU87_RS12445 | |
histidine | hutH: histidine ammonia-lyase | BLU87_RS00950 | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BLU87_RS11780 | BLU87_RS14575 |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | BLU87_RS11775 | BLU87_RS12270 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BLU87_RS14010 | BLU87_RS00915 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLU87_RS11835 | BLU87_RS03940 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BLU87_RS13655 | BLU87_RS06260 |
isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | BLU87_RS11655 | |
L-lactate | L-LDH: L-lactate dehydrogenase | BLU87_RS16460 | BLU87_RS11760 |
lactose | galE: UDP-glucose 4-epimerase | BLU87_RS06225 | BLU87_RS10400 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | BLU87_RS04510 | |
lactose | glk: glucokinase | BLU87_RS12610 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
lactose | pgmA: alpha-phosphoglucomutase | BLU87_RS10530 | BLU87_RS06860 |
leucine | liuA: isovaleryl-CoA dehydrogenase | BLU87_RS11780 | BLU87_RS14575 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BLU87_RS13655 | BLU87_RS06260 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | BLU87_RS11775 | BLU87_RS12270 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLU87_RS11835 | BLU87_RS03940 |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | BLU87_RS05845 | |
lysine | hglS: D-2-hydroxyglutarate synthase | | |
lysine | lat: L-lysine 6-aminotransferase | BLU87_RS01565 | BLU87_RS04965 |
lysine | lysN: 2-aminoadipate transaminase | BLU87_RS08685 | BLU87_RS01565 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
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 | manA: mannose-6-phosphate isomerase | BLU87_RS10525 | BLU87_RS03630 |
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 | BLU87_RS07850 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | BLU87_RS05845 | BLU87_RS07020 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BLU87_RS15755 | |
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 | BLU87_RS11775 | BLU87_RS12270 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BLU87_RS14585 | BLU87_RS11775 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BLU87_RS14570 | BLU87_RS04905 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BLU87_RS14570 | BLU87_RS04905 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | BLU87_RS11815 | BLU87_RS12695 |
phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | BLU87_RS11820 | BLU87_RS12690 |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BLU87_RS11830 | BLU87_RS12680 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BLU87_RS11835 | |
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 | BLU87_RS11775 | BLU87_RS12270 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BLU87_RS14585 | BLU87_RS11775 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BLU87_RS14570 | BLU87_RS04905 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | BLU87_RS14570 | BLU87_RS04905 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | proW: proline ABC transporter, permease component ProW | BLU87_RS10690 | |
proline | proX: proline ABC transporter, substrate-binding component ProX | BLU87_RS10695 | |
proline | put1: proline dehydrogenase | BLU87_RS12670 | BLU87_RS15955 |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | BLU87_RS05345 | BLU87_RS15950 |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BLU87_RS13655 | BLU87_RS06260 |
propionate | pccB: propionyl-CoA carboxylase, beta subunit | BLU87_RS11655 | |
propionate | prpE: propionyl-CoA synthetase | BLU87_RS12135 | BLU87_RS12405 |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabT: gamma-aminobutyrate transaminase | BLU87_RS01675 | BLU87_RS04965 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BLU87_RS01675 | BLU87_RS04965 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BLU87_RS07020 | BLU87_RS05845 |
putrescine | potA: putrescine ABC transporter, ATPase component (PotA/PotG) | BLU87_RS13055 | BLU87_RS09610 |
putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | BLU87_RS13050 | |
putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | BLU87_RS13045 | |
putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | BLU87_RS13060 | |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | BLU87_RS12845 | BLU87_RS12825 |
rhamnose | aldA: lactaldehyde dehydrogenase | BLU87_RS07020 | BLU87_RS05845 |
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) | BLU87_RS11835 | |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLU87_RS11830 | BLU87_RS12680 |
serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BLU87_RS11820 | BLU87_RS12690 |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BLU87_RS11815 | BLU87_RS12695 |
sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BLU87_RS14010 | BLU87_RS00915 |
sucrose | 1pfk: 1-phosphofructokinase | | |
sucrose | ams: sucrose hydrolase (invertase) | BLU87_RS09965 | |
sucrose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
threonine | adh: acetaldehyde dehydrogenase (not acylating) | BLU87_RS03510 | BLU87_RS07020 |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BLU87_RS11835 | |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLU87_RS11830 | BLU87_RS12680 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | BLU87_RS11820 | BLU87_RS12690 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | BLU87_RS11815 | BLU87_RS12695 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BLU87_RS06620 | BLU87_RS06615 |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | BLU87_RS03510 | BLU87_RS07020 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
trehalose | treF: trehalase | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | BLU87_RS03080 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | BLU87_RS11780 | BLU87_RS14575 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BLU87_RS11775 | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BLU87_RS11835 | BLU87_RS03940 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BLU87_RS05845 | BLU87_RS07020 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | BLU87_RS13655 | BLU87_RS06260 |
valine | pccB: propionyl-CoA carboxylase, beta subunit | BLU87_RS11655 | |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | BLU87_RS10015 | |
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