Found 144 low-confidence and 47 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 | BM299_RS04570 | BM299_RS16955 |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | BM299_RS08865 | BM299_RS12820 |
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 | | |
alanine | cycA: L-alanine symporter CycA | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | BM299_RS05060 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | gabD: succinate semialdehyde dehydrogenase | BM299_RS16640 | |
arginine | gabT: gamma-aminobutyrate transaminase | BM299_RS02525 | BM299_RS00590 |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | | |
asparagine | glnP: L-asparagine ABC transporter, fused permease and substrate-binding components GlnP | | |
aspartate | glt: aspartate:proton symporter Glt | | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BM299_RS00225 | BM299_RS18035 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BM299_RS05465 | BM299_RS18040 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BM299_RS05465 | BM299_RS18040 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BM299_RS18045 | BM299_RS08595 |
citrulline | arcC: carbamate kinase | | |
citrulline | put1: proline dehydrogenase | BM299_RS03410 | |
citrulline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
citrulline | rocD: ornithine aminotransferase | BM299_RS04985 | BM299_RS08235 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | BM299_RS10985 | BM299_RS04225 |
D-lactate | glcF: D-lactate dehydrogenase, FeS subunit GlcF | BM299_RS10990 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | BM299_RS07595 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BM299_RS12585 | BM299_RS17970 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | garK: glycerate 2-kinase | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | BM299_RS10520 | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | BM299_RS05060 | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucO: L-lactaldehyde reductase | BM299_RS08815 | BM299_RS11945 |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
fumarate | Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components | BM299_RS04570 | BM299_RS16955 |
fumarate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | BM299_RS16950 | |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
galacturonate | uxaA: D-altronate dehydratase | BM299_RS07255 | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | gntA: gluconate TRAP transporter, small permease component | BM299_RS11935 | BM299_RS07270 |
gluconate | gntB: gluconate TRAP transporter, large permease component | BM299_RS09255 | BM299_RS11930 |
gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | BM299_RS11940 | BM299_RS09265 |
gluconate | gntK: D-gluconate kinase | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BM299_RS08430 | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP | | |
glycerol | dhaK': dihydroxyacetone kinase, ATP dependent (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | BM299_RS01320 | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | hutV: L-histidine ABC transporter, ATPase component HutV | BM299_RS08565 | BM299_RS03860 |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BM299_RS11335 | BM299_RS06015 |
isoleucine | Bap2: L-isoleucine permease Bap2 | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | BM299_RS07795 | BM299_RS07900 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BM299_RS06260 | |
L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | BM299_RS04190 | |
L-malate | Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components | BM299_RS04570 | BM299_RS16955 |
L-malate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | BM299_RS16950 | |
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 | leuT: L-leucine:Na+ symporter LeuT | BM299_RS01110 | |
leucine | liuA: isovaleryl-CoA dehydrogenase | BM299_RS06015 | BM299_RS06045 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BM299_RS06260 | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | BM299_RS10405 | BM299_RS07795 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BM299_RS10410 | BM299_RS09155 |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | cadA: lysine decarboxylase | | |
lysine | davD: glutarate semialdehyde dehydrogenase | | |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BM299_RS01175 | |
lysine | gcdH: glutaryl-CoA dehydrogenase | BM299_RS11335 | BM299_RS06045 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patD: 5-aminopentanal dehydrogenase | | |
maltose | malAP: maltose permease | BM299_RS01700 | |
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 | BM299_RS10520 | |
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 | BM299_RS02705 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BM299_RS08430 | |
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 | BM299_RS07795 | BM299_RS18360 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BM299_RS17115 | BM299_RS00890 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BM299_RS17115 | BM299_RS00890 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | BM299_RS00245 | BM299_RS10405 |
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 | BM299_RS07795 | BM299_RS18360 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BM299_RS17115 | BM299_RS00890 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | BM299_RS17115 | BM299_RS00890 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | BM299_RS00245 | BM299_RS10405 |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | hutV: proline ABC transporter, ATPase component HutV | BM299_RS08565 | BM299_RS03860 |
proline | hutW: proline ABC transporter, permease component HutW | BM299_RS03855 | BM299_RS08570 |
proline | put1: proline dehydrogenase | BM299_RS03410 | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BM299_RS06260 | |
putrescine | gabD: succinate semialdehyde dehydrogenase | BM299_RS16640 | |
putrescine | gabT: gamma-aminobutyrate transaminase | BM299_RS02525 | BM299_RS00590 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | fucO: L-lactaldehyde reductase | BM299_RS08815 | BM299_RS11945 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BM299_RS05100 | BM299_RS12585 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | BM299_RS07255 | BM299_RS11820 |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
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 | | |
sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | BM299_RS05100 | BM299_RS00600 |
succinate | Dshi_1194: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components | BM299_RS04570 | BM299_RS16955 |
succinate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | BM299_RS16950 | |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | BM299_RS10520 | |
threonine | pccA: propionyl-CoA carboxylase, alpha subunit | BM299_RS06260 | |
threonine | tdcC: L-threonine:H+ symporter TdcC | | |
threonine | tdcE: 2-ketobutyrate formate-lyase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
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 | BM299_RS11335 | BM299_RS06015 |
valine | Bap2: L-valine permease Bap2 | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BM299_RS10405 | BM299_RS07900 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BM299_RS16945 | |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | BM299_RS06260 | |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | BM299_RS10520 | |
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