Potential Gaps in catabolism of small carbon sources in Frischella perrara PEB0191
Found 154 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | FPB0191_RS01850 | FPB0191_RS01940 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 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 | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
| arginine | rocD: ornithine aminotransferase | FPB0191_RS02585 | FPB0191_RS05315 |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | FPB0191_RS06345 | FPB0191_RS08935 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | FPB0191_RS05265 | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | FPB0191_RS05795 | FPB0191_RS05260 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | FPB0191_RS05255 | FPB0191_RS06795 |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | FPB0191_RS06790 | FPB0191_RS06925 |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | | |
| citrulline | rocD: ornithine aminotransferase | FPB0191_RS02585 | FPB0191_RS05315 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | FPB0191_RS08390 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | FPB0191_RS07025 | |
| 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 | | |
| fucose | aldA: lactaldehyde dehydrogenase | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | FPB0191_RS04880 | |
| 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 | | |
| 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) | FPB0191_RS00150 | |
| 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 | gdhA: glutamate dehydrogenase, NAD-dependent | | |
| glycerol | dhaL: dihydroxyacetone:PEP phosphotransferase, subunit L | FPB0191_RS04885 | |
| glycerol | dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | FPB0191_RS00570 | FPB0191_RS06285 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | FPB0191_RS06290 | FPB0191_RS00560 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | FPB0191_RS02855 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | FPB0191_RS02210 | FPB0191_RS04215 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | epi: methylmalonyl-CoA epimerase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | FPB0191_RS01165 | |
| isoleucine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | FPB0191_RS11230 | FPB0191_RS04225 |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctA: L-malate:H+ symporter DctA | FPB0191_RS01545 | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | FPB0191_RS02855 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | FPB0191_RS04225 | FPB0191_RS11230 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| 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 | FPB0191_RS11515 | FPB0191_RS02585 |
| lysine | lysN: 2-aminoadipate transaminase | FPB0191_RS11515 | FPB0191_RS05315 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| maltose | susB: alpha-glucosidase (maltase) | FPB0191_RS10970 | |
| mannitol | mak: mannose kinase | FPB0191_RS06935 | |
| mannitol | mt1d: mannitol 1-dehydrogenase | FPB0191_RS04895 | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | FPB0191_RS00150 | |
| 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 | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | FPB0191_RS02845 | FPB0191_RS01165 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | FPB0191_RS02985 | FPB0191_RS03365 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | FPB0191_RS02985 | FPB0191_RS03365 |
| 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 | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | FPB0191_RS01500 | FPB0191_RS02210 |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | FPB0191_RS07600 | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | | |
| propionate | epi: methylmalonyl-CoA epimerase | | |
| propionate | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | FPB0191_RS11230 | FPB0191_RS04225 |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | | |
| propionate | prpE: propionyl-CoA synthetase | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | FPB0191_RS10160 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | FPB0191_RS11515 | FPB0191_RS05315 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | FPB0191_RS11515 | |
| 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 | | |
| sorbitol | scrK: fructokinase | FPB0191_RS10250 | FPB0191_RS06935 |
| sorbitol | sdh: sorbitol dehydrogenase | FPB0191_RS01165 | FPB0191_RS08270 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | FPB0191_RS11540 | |
| threonine | tdh: L-threonine 3-dehydrogenase | FPB0191_RS10160 | FPB0191_RS04895 |
| threonine | tynA: aminoacetone oxidase | | |
| trehalose | treF: trehalase | FPB0191_RS10970 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | FPB0191_RS01500 | FPB0191_RS04215 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | FPB0191_RS01500 | FPB0191_RS04215 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | FPB0191_RS02855 | |
| valine | Bap2: L-valine permease Bap2 | FPB0191_RS02210 | FPB0191_RS04215 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | epi: methylmalonyl-CoA epimerase | | |
| valine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | FPB0191_RS11230 | FPB0191_RS04225 |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | FPB0191_RS07375 | |
| 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