Found 166 low-confidence and 42 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 | CALNI_RS02700 | CALNI_RS01945 |
2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | CALNI_RS02695 | CALNI_RS01940 |
4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | CALNI_RS00150 | |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | CALNI_RS02455 | CALNI_RS03360 |
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 | | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | put1: proline dehydrogenase | CALNI_RS04420 | |
arginine | rocD: ornithine aminotransferase | CALNI_RS07435 | CALNI_RS03705 |
arginine | rocE: L-arginine permease | | |
arginine | rocF: arginase | | |
asparagine | ans: asparaginase | | |
asparagine | dauA: dicarboxylic acid transporter DauA | CALNI_RS10365 | CALNI_RS08970 |
aspartate | dauA: dicarboxylic acid transporter DauA | CALNI_RS10365 | CALNI_RS08970 |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
cellobiose | glk: glucokinase | CALNI_RS05430 | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CALNI_RS09160 | CALNI_RS09555 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CALNI_RS09165 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CALNI_RS09165 | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | citrullinase: putative citrullinase | CALNI_RS07315 | |
citrulline | put1: proline dehydrogenase | CALNI_RS04420 | |
citrulline | rocD: ornithine aminotransferase | CALNI_RS07435 | CALNI_RS03705 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | CALNI_RS06795 | CALNI_RS05660 |
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 | CALNI_RS00005 | |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | CALNI_RS00150 | |
deoxyinosine | deoB: phosphopentomutase | CALNI_RS07265 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CALNI_RS06140 | |
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) | CALNI_RS00150 | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | CALNI_RS00150 | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | CALNI_RS06140 | CALNI_RS06835 |
fructose | 1pfk: 1-phosphofructokinase | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | CALNI_RS07450 | |
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 | CALNI_RS10365 | CALNI_RS08970 |
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 | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
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) | CALNI_RS02050 | |
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 | | |
glucuronate | garR: tartronate semialdehyde reductase | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | CALNI_RS03655 | |
glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
glycerol | glpK: glycerol kinase | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | permease: L-histidine permease | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CALNI_RS01695 | CALNI_RS01740 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CALNI_RS06140 | CALNI_RS07770 |
isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CALNI_RS03490 | |
isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CALNI_RS02830 | CALNI_RS01155 |
isoleucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | CALNI_RS01390 | |
L-lactate | L-LDH: L-lactate dehydrogenase | CALNI_RS02315 | |
L-lactate | SfMCT: L-lactate transporter SfMCT | CALNI_RS01295 | |
L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | CALNI_RS08605 | |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | CALNI_RS05430 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | CALNI_RS01695 | CALNI_RS01740 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CALNI_RS02830 | CALNI_RS02480 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | CALNI_RS01690 | CALNI_RS06640 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | CALNI_RS02825 | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CALNI_RS03490 | |
leucine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | CALNI_RS01390 | |
lysine | davA: 5-aminovaleramidase | | |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | davD: glutarate semialdehyde dehydrogenase | CALNI_RS00150 | |
lysine | davT: 5-aminovalerate aminotransferase | CALNI_RS03705 | CALNI_RS07435 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
lysine | gcdH: glutaryl-CoA dehydrogenase | CALNI_RS01695 | CALNI_RS01740 |
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 | 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 | CALNI_RS09785 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | CALNI_RS00150 | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CALNI_RS02050 | |
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 | CALNI_RS01690 | CALNI_RS06640 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CALNI_RS01690 | |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CALNI_RS01735 | CALNI_RS06825 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CALNI_RS01735 | CALNI_RS06825 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | CALNI_RS01690 | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | CALNI_RS03840 | |
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 | CALNI_RS01690 | CALNI_RS06640 |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CALNI_RS01690 | |
phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CALNI_RS01735 | CALNI_RS06825 |
phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | CALNI_RS01735 | CALNI_RS06825 |
phenylalanine | paaZ1: oxepin-CoA hydrolase | CALNI_RS01690 | |
phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
proline | proY: proline:H+ symporter | | |
proline | put1: proline dehydrogenase | CALNI_RS04420 | |
propionate | mctC: propionate:H+ symporter | CALNI_RS03840 | |
propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CALNI_RS02830 | CALNI_RS01155 |
propionate | prpE: propionyl-CoA synthetase | CALNI_RS01435 | CALNI_RS04325 |
putrescine | gabD: succinate semialdehyde dehydrogenase | CALNI_RS00150 | |
putrescine | gabT: gamma-aminobutyrate transaminase | CALNI_RS07435 | CALNI_RS03705 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CALNI_RS07435 | CALNI_RS03705 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CALNI_RS00150 | |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | CALNI_RS00315 | CALNI_RS06810 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CALNI_RS06140 | CALNI_RS06835 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
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 | CALNI_RS06835 | CALNI_RS07770 |
sucrose | scrK: fructokinase | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | pccA: propionyl-CoA carboxylase, alpha subunit | CALNI_RS02830 | CALNI_RS01155 |
threonine | phtA: L-threonine uptake permease PhtA | CALNI_RS10225 | |
threonine | tdcE: 2-ketobutyrate formate-lyase | | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | CALNI_RS00150 | |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | CALNI_RS07265 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | glk: glucokinase | CALNI_RS05430 | |
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 | CALNI_RS00220 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | CALNI_RS01695 | CALNI_RS01740 |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CALNI_RS03490 | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CALNI_RS00150 | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
valine | pccA: propionyl-CoA carboxylase, alpha subunit | CALNI_RS02830 | CALNI_RS01155 |
valine | vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC | CALNI_RS01390 | |
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 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