Potential Gaps in catabolism of small carbon sources in Stenotrophomonas chelatiphaga DSM 21508
Found 85 low-confidence and 27 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| arabinose | aldA: (glycol)aldehyde dehydrogenase | ABB28_RS16890 | ABB28_RS05980 |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | ABB28_RS13160 | |
| arabinose | KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase | | |
| arabinose | xacD: L-arabinonate dehydratase | ABB28_RS10335 | |
| arginine | gabT: gamma-aminobutyrate transaminase | ABB28_RS05895 | ABB28_RS13775 |
| arginine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | ABB28_RS16890 | ABB28_RS05980 |
| arginine | rocE: L-arginine permease | ABB28_RS14795 | |
| asparagine | glt: aspartate:proton symporter Glt | ABB28_RS07385 | ABB28_RS11690 |
| aspartate | glt: aspartate:proton symporter Glt | ABB28_RS07385 | ABB28_RS11690 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ABB28_RS12160 | ABB28_RS03690 |
| 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 | citrullinase: putative citrullinase | ABB28_RS16215 | |
| citrulline | gabT: gamma-aminobutyrate transaminase | ABB28_RS05895 | ABB28_RS13775 |
| citrulline | odc: L-ornithine decarboxylase | | |
| citrulline | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | ABB28_RS16890 | ABB28_RS05980 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | ABB28_RS14795 | |
| D-serine | cycA: D-serine:H+ symporter CycA | ABB28_RS14795 | |
| D-serine | dsdA: D-serine ammonia-lyase | ABB28_RS10275 | ABB28_RS14485 |
| deoxyinosine | deoB: phosphopentomutase | ABB28_RS16370 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | ABB28_RS03425 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ABB28_RS03140 | ABB28_RS10765 |
| 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 | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | ABB28_RS06360 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | ABB28_RS02945 | ABB28_RS16890 |
| 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 | ABB28_RS12315 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | ABB28_RS08240 | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | ABB28_RS12915 | ABB28_RS12320 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | kguD: 2-keto-6-phosphogluconate reductase | ABB28_RS15235 | ABB28_RS14455 |
| gluconate | kguK: 2-ketogluconokinase | | |
| gluconate | kguT: 2-ketogluconate transporter | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | ABB28_RS14520 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | ABB28_RS08240 | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | ABB28_RS12915 | ABB28_RS12320 |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | ABB28_RS13175 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | ABB28_RS07385 | ABB28_RS11690 |
| glycerol | glpF: glycerol facilitator glpF | ABB28_RS07840 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | ABB28_RS14795 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | ABB28_RS05105 | ABB28_RS10755 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| lysine | lat: L-lysine 6-aminotransferase | ABB28_RS13775 | ABB28_RS13760 |
| lysine | lysN: 2-aminoadipate transaminase | ABB28_RS13775 | ABB28_RS11865 |
| lysine | lysP: L-lysine:H+ symporter LysP | ABB28_RS14795 | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | ABB28_RS12370 | ABB28_RS06140 |
| mannitol | mt2d: mannitol 2-dehydrogenase | ABB28_RS02015 | ABB28_RS12825 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | gluP: mannose:Na+ symporter | ABB28_RS12315 | ABB28_RS14540 |
| 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 | ABB28_RS13215 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | ABB28_RS08195 | |
| 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 | ABB28_RS05820 | ABB28_RS04910 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ABB28_RS05820 | ABB28_RS13605 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | ABB28_RS04910 | ABB28_RS05820 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | ABB28_RS14985 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | ABB28_RS14570 | ABB28_RS17565 |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | ABB28_RS16890 | ABB28_RS05980 |
| propionate | lctP: propionate permease | ABB28_RS14460 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ABB28_RS05895 | ABB28_RS13775 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | ABB28_RS16890 | ABB28_RS05980 |
| rhamnose | aldA: lactaldehyde dehydrogenase | ABB28_RS02945 | ABB28_RS16890 |
| 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 | ABB28_RS06360 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | ABB28_RS16160 | ABB28_RS04570 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | ABB28_RS02135 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | ABB28_RS16370 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| tryptophan | tnaA: tryptophanase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ABB28_RS06925 | ABB28_RS04915 |
| valine | Bap2: L-valine permease Bap2 | ABB28_RS14795 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ABB28_RS04900 | ABB28_RS14605 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | ABB28_RS02015 | ABB28_RS10765 |
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