Potential Gaps in catabolism of small carbon sources in Enterococcus termitis LMG 8895
Found 131 low-confidence and 25 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | csbX: 2-oxoglutarate permease csbX | BCR25_RS12665 | |
| 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 | | |
| acetate | ybhL: acetate uptake transporter YbhL | BCR25_RS02140 | |
| alanine | cycA: L-alanine symporter CycA | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcA: arginine deiminase | | |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | BCR25_RS16630 | BCR25_RS11310 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | BCR25_RS16635 | BCR25_RS11315 |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | BCR25_RS04380 | BCR25_RS04695 |
| arginine | rocD: ornithine aminotransferase | BCR25_RS02460 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BCR25_RS16630 | BCR25_RS11310 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BCR25_RS16635 | BCR25_RS04660 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BCR25_RS11315 | BCR25_RS04660 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BCR25_RS11315 | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | BCR25_RS04380 | BCR25_RS04695 |
| citrulline | rocD: ornithine aminotransferase | BCR25_RS02460 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | BCR25_RS18060 | BCR25_RS15870 |
| D-lactate | larD: D,L-lactic acid transporter | BCR25_RS03305 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BCR25_RS11385 | BCR25_RS17880 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | BCR25_RS08975 | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BCR25_RS01490 | BCR25_RS16985 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | BCR25_RS16865 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | BCR25_RS04695 | BCR25_RS04380 |
| 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 | | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | BCR25_RS18165 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | dddA: 3-hydroxypropionate dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | BCR25_RS08980 | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | hpcD: 3-hydroxypropionyl-CoA dehydratase | BCR25_RS08980 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BCR25_RS10140 | BCR25_RS08225 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pco: propanyl-CoA oxidase | BCR25_RS10110 | BCR25_RS10130 |
| L-lactate | SfMCT: L-lactate transporter SfMCT | BCR25_RS13135 | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | BCR25_RS08975 | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BCR25_RS10160 | BCR25_RS06445 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BCR25_RS08980 | |
| 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) | BCR25_RS04380 | BCR25_RS04695 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | BCR25_RS16635 | BCR25_RS11315 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | BCR25_RS18230 | BCR25_RS16630 |
| lysine | lat: L-lysine 6-aminotransferase | | |
| lysine | lysN: 2-aminoadipate transaminase | BCR25_RS02115 | BCR25_RS19265 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | BCR25_RS07760 | BCR25_RS10140 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | BCR25_RS02205 | BCR25_RS04390 |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| 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 | BCR25_RS08980 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BCR25_RS08980 | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | BCR25_RS10140 | BCR25_RS01490 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BCR25_RS08980 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | BCR25_RS08975 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
| 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 | | |
| proline | davD: glutarate semialdehyde dehydrogenase | BCR25_RS04695 | BCR25_RS04380 |
| proline | davT: 5-aminovalerate aminotransferase | BCR25_RS02460 | |
| proline | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
| proline | lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) | | |
| propionate | dddA: 3-hydroxypropionate dehydrogenase | | |
| propionate | hpcD: 3-hydroxypropionyl-CoA dehydratase | BCR25_RS08980 | |
| propionate | pco: propanyl-CoA oxidase | BCR25_RS10110 | BCR25_RS10130 |
| propionate | prpE: propionyl-CoA synthetase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | BCR25_RS16660 | BCR25_RS04695 |
| putrescine | gabT: gamma-aminobutyrate transaminase | BCR25_RS02460 | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BCR25_RS02460 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BCR25_RS04695 | BCR25_RS04380 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BCR25_RS04695 | BCR25_RS04380 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | BCR25_RS06875 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | BCR25_RS07760 | BCR25_RS14635 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | BCR25_RS15030 | BCR25_RS02845 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BCR25_RS09895 | BCR25_RS09900 |
| threonine | ltaE: L-threonine aldolase | BCR25_RS13185 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | malK: trehalose ABC transporter, ATPase component MalK | BCR25_RS09870 | BCR25_RS11970 |
| trehalose | treP: trehalose phosphorylase, inverting | BCR25_RS12865 | BCR25_RS15075 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | BCR25_RS08975 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | dddA: 3-hydroxypropionate dehydrogenase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | BCR25_RS08980 | |
| valine | hpcD: 3-hydroxypropionyl-CoA dehydratase | BCR25_RS08980 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BCR25_RS10100 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pco: propanyl-CoA oxidase | BCR25_RS10110 | BCR25_RS10130 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | BCR25_RS07760 | |
| 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