Potential Gaps in catabolism of small carbon sources in Dyella japonica UNC79MFTsu3.2
Found 84 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | N515DRAFT_0574 | |
| 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 | araVsh: L-arabinose ABC transporter, ATPase component AraV(Sh) | N515DRAFT_2413 | N515DRAFT_3232 |
| arginine | rocD: ornithine aminotransferase | N515DRAFT_3630 | N515DRAFT_3308 |
| arginine | rocE: L-arginine permease | N515DRAFT_2630 | N515DRAFT_3653 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | citrullinase: putative citrullinase | N515DRAFT_1536 | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | N515DRAFT_1085 | N515DRAFT_2216 |
| citrulline | rocD: ornithine aminotransferase | N515DRAFT_3630 | N515DRAFT_3308 |
| D-alanine | dadA: D-alanine dehydrogenase | N515DRAFT_3723 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | N515DRAFT_3582 | N515DRAFT_1999 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | N515DRAFT_2630 | N515DRAFT_3653 |
| D-serine | dsdA: D-serine ammonia-lyase | N515DRAFT_0537 | N515DRAFT_0565 |
| deoxyinosine | deoB: phosphopentomutase | N515DRAFT_1372 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | N515DRAFT_0396 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | N515DRAFT_1253 | N515DRAFT_0334 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | N515DRAFT_2085 | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | N515DRAFT_1222 | N515DRAFT_1918 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | N515DRAFT_0596 | N515DRAFT_4388 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | N515DRAFT_1231 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpF: glycerol facilitator glpF | N515DRAFT_3908 | N515DRAFT_1366 |
| histidine | hutH: histidine ammonia-lyase | N515DRAFT_2941 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | N515DRAFT_0492 | N515DRAFT_0941 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | N515DRAFT_2630 | N515DRAFT_3653 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | N515DRAFT_0356 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | N515DRAFT_0355 | N515DRAFT_0481 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | N515DRAFT_2156 | N515DRAFT_0354 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | N515DRAFT_0356 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | N515DRAFT_0355 | N515DRAFT_0481 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | N515DRAFT_2156 | N515DRAFT_0354 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | N515DRAFT_3630 | N515DRAFT_3308 |
| lysine | lysN: 2-aminoadipate transaminase | N515DRAFT_0006 | N515DRAFT_3308 |
| lysine | lysP: L-lysine:H+ symporter LysP | N515DRAFT_2630 | N515DRAFT_3653 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | N515DRAFT_3582 | N515DRAFT_1999 |
| maltose | susB: alpha-glucosidase (maltase) | N515DRAFT_3393 | N515DRAFT_3389 |
| mannitol | mt2d: mannitol 2-dehydrogenase | N515DRAFT_0039 | N515DRAFT_1104 |
| mannitol | PLT5: polyol transporter PLT5 | N515DRAFT_1228 | N515DRAFT_0382 |
| mannose | gluP: mannose:Na+ symporter | N515DRAFT_1918 | N515DRAFT_1222 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | N515DRAFT_0211 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | N515DRAFT_1228 | N515DRAFT_0382 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | N515DRAFT_1231 | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | N515DRAFT_2630 | N515DRAFT_3653 |
| 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 | N515DRAFT_1164 | N515DRAFT_0930 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | N515DRAFT_1164 | N515DRAFT_0930 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | N515DRAFT_2688 | N515DRAFT_0938 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | N515DRAFT_2688 | N515DRAFT_0938 |
| phenylacetate | paaK: phenylacetate-CoA ligase | N515DRAFT_1417 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | N515DRAFT_1164 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | N515DRAFT_3653 | N515DRAFT_2630 |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | N515DRAFT_1530 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | N515DRAFT_3308 | N515DRAFT_1751 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | N515DRAFT_3308 | N515DRAFT_1751 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | N515DRAFT_3729 | N515DRAFT_2488 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | N515DRAFT_1006 | N515DRAFT_1583 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | N515DRAFT_1231 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | N515DRAFT_2873 | N515DRAFT_1253 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | N515DRAFT_2630 | N515DRAFT_3653 |
| sorbitol | sdh: sorbitol dehydrogenase | N515DRAFT_0461 | N515DRAFT_1253 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | N515DRAFT_1228 | N515DRAFT_0382 |
| sucrose | ams: sucrose hydrolase (invertase) | N515DRAFT_3393 | N515DRAFT_3391 |
| threonine | RR42_RS28305: L-threonine:H+ symporter | N515DRAFT_2630 | N515DRAFT_3653 |
| thymidine | deoB: phosphopentomutase | N515DRAFT_1372 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | treF: trehalase | N515DRAFT_3393 | N515DRAFT_1888 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | N515DRAFT_3653 | N515DRAFT_2630 |
| tryptophan | kynB: kynurenine formamidase | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | | |
| tryptophan | mhpE: 4-hydroxy-2-oxovalerate aldolase | N515DRAFT_0574 | |
| tryptophan | nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase | N515DRAFT_3729 | N515DRAFT_0379 |
| tryptophan | nbaF: 2-aminomuconate deaminase | N515DRAFT_3727 | N515DRAFT_4323 |
| tryptophan | nbaG: 2-oxo-3-hexenedioate decarboxylase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | N515DRAFT_2630 | N515DRAFT_3653 |
| valine | acdH: isobutyryl-CoA dehydrogenase | N515DRAFT_0492 | N515DRAFT_0941 |
| valine | Bap2: L-valine permease Bap2 | N515DRAFT_2630 | N515DRAFT_3653 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | N515DRAFT_1164 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | N515DRAFT_0356 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | N515DRAFT_0355 | N515DRAFT_0481 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | N515DRAFT_2156 | N515DRAFT_0354 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | N515DRAFT_1164 | N515DRAFT_0416 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | N515DRAFT_3729 | N515DRAFT_0379 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | N515DRAFT_1074 | N515DRAFT_2996 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | N515DRAFT_1228 | N515DRAFT_0382 |
| xylitol | xdhA: xylitol dehydrogenase | N515DRAFT_0039 | N515DRAFT_1006 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 17 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