Potential Gaps in catabolism of small carbon sources in Pseudomonas stutzeri A1501
Found 76 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 | PST_RS08460 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabT: gamma-aminobutyrate transaminase | PST_RS00340 | PST_RS03780 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | PST_RS20430 | PST_RS11850 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | PST_RS20445 | PST_RS11845 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | PST_RS20440 | PST_RS11845 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | PST_RS20435 | PST_RS11840 |
| citrulline | gabT: gamma-aminobutyrate transaminase | PST_RS00340 | PST_RS03780 |
| citrulline | odc: L-ornithine decarboxylase | PST_RS05085 | PST_RS11335 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | PST_RS13100 | |
| D-serine | cycA: D-serine:H+ symporter CycA | PST_RS13100 | |
| D-serine | dsdA: D-serine ammonia-lyase | PST_RS11835 | PST_RS02100 |
| deoxyinosine | deoB: phosphopentomutase | PST_RS16655 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | PST_RS08795 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | PST_RS04405 | PST_RS10140 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | PST_RS08835 | PST_RS18325 |
| 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 | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| 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 | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PST_RS20850 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | PST_RS13990 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | PST_RS04165 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lysine | patA: cadaverine aminotransferase | PST_RS08350 | PST_RS00235 |
| lysine | patD: 5-aminopentanal dehydrogenase | PST_RS08835 | PST_RS18325 |
| mannose | manP: mannose PTS system, EII-CBA components | PST_RS05060 | |
| 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 | PST_RS19495 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PST_RS20850 | |
| 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 | PST_RS09740 | PST_RS06175 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | PST_RS03120 | PST_RS09740 |
| phenylacetate | paaK: phenylacetate-CoA ligase | PST_RS14845 | PST_RS00545 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | PST_RS08835 | PST_RS03120 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | PST_RS08835 | |
| phenylacetate | ppa: phenylacetate permease ppa | PST_RS07285 | PST_RS19425 |
| putrescine | gabT: gamma-aminobutyrate transaminase | PST_RS00340 | PST_RS03780 |
| rhamnose | aldA: lactaldehyde dehydrogenase | PST_RS08835 | PST_RS18325 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PST_RS19390 | PST_RS10930 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sucrose | ams: sucrose hydrolase (invertase) | PST_RS17335 | PST_RS02530 |
| thymidine | deoA: thymidine phosphorylase DeoA | PST_RS04400 | PST_RS09460 |
| thymidine | deoB: phosphopentomutase | PST_RS16655 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | PST_RS17335 | PST_RS02530 |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | PST_RS08440 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | PST_RS08445 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | PST_RS08450 | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | PST_RS13015 | PST_RS18935 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | PST_RS12265 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | PST_RS12260 | |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | PST_RS12255 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | PST_RS12250 | PST_RS11065 |
| xylose | xylA: xylose isomerase | | |
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