Potential Gaps in catabolism of small carbon sources in Shewanella halifaxensis HAW-EB4
Found 76 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | SHAL_RS03505 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | SHAL_RS10920 | |
| 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 | SHAL_RS11065 | SHAL_RS14225 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | SHAL_RS01320 | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocE: L-arginine permease | | |
| cellobiose | SSS-glucose: Sodium/glucose cotransporter | SHAL_RS03410 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SHAL_RS18035 | SHAL_RS20880 |
| 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 | odc: L-ornithine decarboxylase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | SHAL_RS04430 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | SHAL_RS05030 | SHAL_RS01660 |
| 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 | sglS: sodium/galactose cotransporter | SHAL_RS03410 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | SHAL_RS02065 | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | SHAL_RS18415 | SHAL_RS14515 |
| glucose | SSS-glucose: Sodium/glucose cotransporter | SHAL_RS03410 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | SHAL_RS02065 | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | SHAL_RS17255 | SHAL_RS04120 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | SHAL_RS20880 | SHAL_RS05080 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | SHAL_RS20870 | |
| lactose | lacP: lactose permease LacP | | |
| lysine | davA: 5-aminovaleramidase | SHAL_RS19790 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | SHAL_RS11015 | SHAL_RS00080 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | SHAL_RS15015 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | SSS-glucose: Sodium/glucose cotransporter | SHAL_RS03410 | |
| maltose | susB: alpha-glucosidase (maltase) | SHAL_RS00470 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | SHAL_RS04330 | |
| 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 | SHAL_RS10985 | SHAL_RS05605 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | SHAL_RS11015 | SHAL_RS14880 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | SHAL_RS11015 | SHAL_RS11185 |
| phenylacetate | paaK: phenylacetate-CoA ligase | SHAL_RS09490 | SHAL_RS17595 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | SHAL_RS11185 | SHAL_RS01130 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | SHAL_RS09040 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | SHAL_RS05075 | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | SHAL_RS13345 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | SHAL_RS13350 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | SHAL_RS05030 | SHAL_RS01660 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | SHAL_RS11070 | SHAL_RS09215 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | SHAL_RS02080 | SHAL_RS02065 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | SHAL_RS02940 | SHAL_RS10455 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | SHAL_RS02950 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | SHAL_RS02945 | SHAL_RS10460 |
| sorbitol | scrK: fructokinase | SHAL_RS07830 | |
| sorbitol | sdh: sorbitol dehydrogenase | SHAL_RS10445 | SHAL_RS11070 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | SSS-glucose: Sodium/glucose cotransporter | SHAL_RS03410 | |
| trehalose | SSS-glucose: Sodium/glucose cotransporter | SHAL_RS03410 | |
| trehalose | treF: trehalase | | |
| tryptophan | tnaA: tryptophanase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | SHAL_RS14885 | SHAL_RS15015 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | SHAL_RS11015 | SHAL_RS00080 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | SHAL_RS14870 | SHAL_RS09240 |
| xylose | Echvi_1871: sodium/xylose cotransporter | SHAL_RS03410 | |
| xylose | xyrA: xylitol reductase | | |
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