Potential Gaps in catabolism of small carbon sources in Pseudomonas taeanensis MS-3
Found 78 low-confidence and 22 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | TMS3_RS15105 | |
| acetate | actP: cation/acetate symporter ActP | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | TMS3_RS10120 | TMS3_RS14670 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | TMS3_RS17170 | TMS3_RS01655 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| cellobiose | bgl: cellobiase | | |
| citrulline | citrullinase: putative citrullinase | TMS3_RS01865 | TMS3_RS13415 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | deoB: phosphopentomutase | TMS3_RS07725 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | TMS3_RS21615 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | TMS3_RS00610 | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | TMS3_RS15350 | TMS3_RS10015 |
| 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 | garD: meso-galactarate dehydratase (L-threo-forming) GarD | TMS3_RS14680 | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | TMS3_RS20245 | |
| galacturonate | udh: D-galacturonate dehydrogenase | TMS3_RS23180 | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | TMS3_RS02845 | |
| 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 | TMS3_RS20245 | TMS3_RS10025 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | TMS3_RS14680 | |
| glucuronate | udh: D-glucuronate dehydrogenase | TMS3_RS23180 | |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | | |
| 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 | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | TMS3_RS01750 | TMS3_RS19250 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannose | manP: mannose PTS system, EII-CBA components | TMS3_RS19335 | |
| 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 | TMS3_RS01010 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | TMS3_RS02845 | |
| 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 | TMS3_RS14965 | TMS3_RS19290 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | TMS3_RS19290 | TMS3_RS18265 |
| phenylacetate | paaK: phenylacetate-CoA ligase | TMS3_RS13175 | TMS3_RS13170 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | TMS3_RS18265 | TMS3_RS19290 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | TMS3_RS00495 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | TMS3_RS00500 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | TMS3_RS15350 | TMS3_RS10015 |
| 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 | sdh: sorbitol dehydrogenase | TMS3_RS02465 | TMS3_RS22160 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| thymidine | deoA: thymidine phosphorylase DeoA | TMS3_RS16585 | |
| thymidine | deoB: phosphopentomutase | TMS3_RS07725 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | TMS3_RS24075 | TMS3_RS15125 |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | TMS3_RS15115 | TMS3_RS24890 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | TMS3_RS14965 | TMS3_RS21560 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | TMS3_RS14975 | TMS3_RS14715 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | TMS3_RS19335 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | TMS3_RS17150 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | TMS3_RS17145 | |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | TMS3_RS17140 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | TMS3_RS17135 | TMS3_RS02470 |
| 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