Found 159 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | ON16_RS06350 | ON16_RS08585 |
4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | | |
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 | | |
arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
arginine | rocD: ornithine aminotransferase | ON16_RS01580 | ON16_RS10080 |
arginine | rocE: L-arginine permease | | |
aspartate | dauA: dicarboxylic acid transporter DauA | ON16_RS04725 | |
cellobiose | bgl: cellobiase | | |
cellobiose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
citrate | acn: aconitase | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ON16_RS02565 | ON16_RS02765 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | ON16_RS02570 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | ON16_RS02570 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
citrulline | rocD: ornithine aminotransferase | ON16_RS01580 | ON16_RS10080 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | ON16_RS05670 | ON16_RS05665 |
D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | | |
deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | ON16_RS02075 | |
deoxyinosine | deoB: phosphopentomutase | ON16_RS11465 | ON16_RS01800 |
deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | ON16_RS05575 | ON16_RS14140 |
deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | ON16_RS14135 | ON16_RS05580 |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ON16_RS01385 | ON16_RS13885 |
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) | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | | |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | ON16_RS00635 | |
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 | dauA: fumarate transporter DauA | ON16_RS04725 | |
galactose | galK: galactokinase (-1-phosphate forming) | ON16_RS07545 | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | ON16_RS07555 | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | ON16_RS14200 | ON16_RS03880 |
galacturonate | uxaA: D-altronate dehydratase | ON16_RS00840 | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | edd: phosphogluconate dehydratase | | |
gluconate | gntA: gluconate TRAP transporter, small permease component | ON16_RS14510 | |
gluconate | gntB: gluconate TRAP transporter, large permease component | ON16_RS02245 | ON16_RS01180 |
gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | ON16_RS11725 | ON16_RS01170 |
gluconate | gntK: D-gluconate kinase | ON16_RS04670 | ON16_RS02710 |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ON16_RS08890 | |
glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
glucose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | ON16_RS14245 | ON16_RS01170 |
glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | ON16_RS13930 | ON16_RS01120 |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | ON16_RS10455 | ON16_RS09350 |
histidine | PA5504: L-histidine ABC transporter, permease component | ON16_RS10460 | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ON16_RS11550 | ON16_RS10820 |
isoleucine | acn: (2R,3S)-2-methylcitrate dehydratase | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ON16_RS10830 | ON16_RS05710 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ON16_RS01680 | ON16_RS09985 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ON16_RS02795 | ON16_RS01840 |
isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | ON16_RS01850 | ON16_RS02805 |
isoleucine | prpB: 2-methylisocitrate lyase | | |
isoleucine | prpC: 2-methylcitrate synthase | ON16_RS03845 | |
isoleucine | prpD: 2-methylcitrate dehydratase | | |
isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
L-lactate | L-LDH: L-lactate dehydrogenase | ON16_RS03045 | |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
L-malate | Dshi_1195: TRAP transporter for succinate, fumarate, L-malate, and 2-oxoglutarate, substrate-binding component | | |
lactose | galK: galactokinase (-1-phosphate forming) | ON16_RS07545 | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | ON16_RS07555 | |
lactose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | aacS: acetoacetyl-CoA synthetase | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | ON16_RS10820 | ON16_RS15360 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ON16_RS08580 | ON16_RS01650 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | ON16_RS05710 | ON16_RS10830 |
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) | ON16_RS02795 | ON16_RS01840 |
leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | ON16_RS01850 | ON16_RS02805 |
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 | lat: L-lysine 6-aminotransferase | ON16_RS10080 | ON16_RS01580 |
lysine | lysN: 2-aminoadipate transaminase | ON16_RS13900 | ON16_RS05675 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
maltose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
maltose | susB: alpha-glucosidase (maltase) | ON16_RS06835 | |
mannitol | mt2d: mannitol 2-dehydrogenase | ON16_RS09985 | ON16_RS01680 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | man-isomerase: D-mannose isomerase | | |
mannose | STP6: mannose:H+ symporter | | |
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 | ON16_RS09320 | |
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) | ON16_RS08890 | |
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 | ON16_RS10830 | ON16_RS05710 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ON16_RS05710 | ON16_RS10830 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ON16_RS05715 | ON16_RS04985 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ON16_RS05715 | ON16_RS04985 |
phenylacetate | paaK: phenylacetate-CoA ligase | | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
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 | ON16_RS10830 | ON16_RS05710 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ON16_RS05710 | ON16_RS10830 |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ON16_RS05715 | ON16_RS04985 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | ON16_RS05715 | ON16_RS04985 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | put1: proline dehydrogenase | | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
propionate | acn: (2R,3S)-2-methylcitrate dehydratase | | |
propionate | prpB: 2-methylisocitrate lyase | | |
propionate | prpC: 2-methylcitrate synthase | ON16_RS03845 | |
propionate | prpD: 2-methylcitrate dehydratase | | |
propionate | prpE: propionyl-CoA synthetase | | |
propionate | putP: propionate transporter; proline:Na+ symporter | ON16_RS13915 | |
putrescine | gabD: succinate semialdehyde dehydrogenase | ON16_RS01115 | |
putrescine | gabT: gamma-aminobutyrate transaminase | ON16_RS10080 | ON16_RS01580 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ON16_RS01580 | ON16_RS10080 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | ON16_RS08360 | |
putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | ON16_RS08350 | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ON16_RS01385 | ON16_RS09985 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | ON16_RS00840 | |
rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | ON16_RS01680 | ON16_RS13885 |
rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | serP: L-serine permease SerP | | |
sorbitol | sdh: sorbitol dehydrogenase | ON16_RS01680 | ON16_RS09985 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
succinate | dauA: succinate:H+ symporter DauA | ON16_RS04725 | |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
threonine | adh: acetaldehyde dehydrogenase (not acylating) | | |
threonine | ltaE: L-threonine aldolase | ON16_RS09800 | ON16_RS04170 |
threonine | tdcC: L-threonine:H+ symporter TdcC | | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | | |
thymidine | deoB: phosphopentomutase | ON16_RS11465 | ON16_RS01800 |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | glk: glucokinase | ON16_RS08410 | ON16_RS02730 |
trehalose | treF: trehalase | | |
tryptophan | tnaA: tryptophanase | | |
tryptophan | trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP | | |
tyrosine | aacS: acetoacetyl-CoA synthetase | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | ON16_RS11550 | ON16_RS15360 |
valine | acn: (2R,3S)-2-methylcitrate dehydratase | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ON16_RS05710 | ON16_RS09920 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | ON16_RS02795 | ON16_RS01840 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | ON16_RS01850 | ON16_RS02805 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ON16_RS01115 | |
valine | prpB: 2-methylisocitrate lyase | | |
valine | prpC: 2-methylcitrate synthase | ON16_RS03845 | |
valine | prpD: 2-methylcitrate dehydratase | | |
valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | | |
xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
xylitol | xdhA: xylitol dehydrogenase | ON16_RS15695 | ON16_RS04320 |
xylose | xylA: xylose isomerase | | |
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