Potential Gaps in catabolism of small carbon sources in Allochromatium vinosum DSM 180
Found 172 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | | |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | ALVIN_RS10770 | ALVIN_RS07410 |
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 | ALVIN_RS08825 | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
arginine | rocD: ornithine aminotransferase | ALVIN_RS09555 | ALVIN_RS00500 |
arginine | rocE: L-arginine permease | | |
arginine | rocF: arginase | | |
asparagine | ans: asparaginase | | |
cellobiose | cbp: cellobiose phosphorylase | ALVIN_RS05720 | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ALVIN_RS04190 | ALVIN_RS12190 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
citrulline | rocD: ornithine aminotransferase | ALVIN_RS09555 | ALVIN_RS00500 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
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 | ALVIN_RS11025 | |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | | |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | ALVIN_RS02485 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | ALVIN_RS07460 | |
deoxyribonate | aacS: acetoacetyl-CoA synthetase | ALVIN_RS06980 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ALVIN_RS07710 | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | garK: glycerate 2-kinase | ALVIN_RS02370 | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | ALVIN_RS07245 | ALVIN_RS05065 |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
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 | 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 | ALVIN_RS02390 | |
galacturonate | uxaA: D-altronate dehydratase | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
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) | ALVIN_RS00245 | ALVIN_RS01205 |
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 | ALVIN_RS12050 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | ALVIN_RS08215 | |
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 | | |
isoleucine | Bap2: L-isoleucine permease Bap2 | | |
isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ALVIN_RS03100 | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ALVIN_RS09405 | ALVIN_RS00330 |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | ALVIN_RS14785 | |
L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | ALVIN_RS14780 | |
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 | aacS: acetoacetyl-CoA synthetase | ALVIN_RS06980 | |
leucine | leuT: L-leucine:Na+ symporter LeuT | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | | |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ALVIN_RS08270 | ALVIN_RS09480 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | ALVIN_RS03100 | |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | | |
lysine | hglS: D-2-hydroxyglutarate synthase | | |
lysine | lat: L-lysine 6-aminotransferase | ALVIN_RS09555 | ALVIN_RS06090 |
lysine | lysN: 2-aminoadipate transaminase | ALVIN_RS01795 | ALVIN_RS09555 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
maltose | MAL11: maltose permease | | |
maltose | susB: alpha-glucosidase (maltase) | ALVIN_RS04180 | ALVIN_RS01235 |
mannitol | mt2d: mannitol 2-dehydrogenase | ALVIN_RS09405 | ALVIN_RS00330 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | ALVIN_RS04565 | ALVIN_RS11305 |
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 | ALVIN_RS01565 | |
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) | ALVIN_RS00245 | ALVIN_RS01205 |
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 | ALVIN_RS03100 | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ALVIN_RS03100 | |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | ALVIN_RS00330 | ALVIN_RS09405 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ALVIN_RS00315 | |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ALVIN_RS00315 | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | ALVIN_RS03100 | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | ALVIN_RS10780 | ALVIN_RS14785 |
phenylalanine | aacS: acetoacetyl-CoA synthetase | ALVIN_RS06980 | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | maiA: maleylacetoacetate isomerase | ALVIN_RS00355 | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
proline | ectP: proline transporter EctP | ALVIN_RS06905 | |
proline | put1: proline dehydrogenase | | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
propionate | mctC: propionate:H+ symporter | ALVIN_RS10780 | ALVIN_RS14785 |
putrescine | gabD: succinate semialdehyde dehydrogenase | ALVIN_RS15285 | |
putrescine | gabT: gamma-aminobutyrate transaminase | ALVIN_RS09555 | ALVIN_RS06090 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ALVIN_RS06090 | ALVIN_RS09555 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
rhamnose | aldA: lactaldehyde dehydrogenase | | |
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 | sdaB: L-serine ammonia-lyase | ALVIN_RS11025 | |
serine | serP: L-serine permease SerP | | |
sorbitol | sdh: sorbitol dehydrogenase | ALVIN_RS09405 | ALVIN_RS00330 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | phtA: L-threonine uptake permease PhtA | ALVIN_RS14360 | |
threonine | tdcE: 2-ketobutyrate formate-lyase | | |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | | |
thymidine | deoA: thymidine phosphorylase DeoA | ALVIN_RS06925 | |
thymidine | deoB: phosphopentomutase | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aacS: acetoacetyl-CoA synthetase | ALVIN_RS06980 | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | ALVIN_RS00355 | |
valine | acdH: isobutyryl-CoA dehydrogenase | | |
valine | Bap2: L-valine permease Bap2 | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ALVIN_RS03100 | |
valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ALVIN_RS03100 | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
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 | | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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About GapMind
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.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory