Potential Gaps in catabolism of small carbon sources in Shewanella amazonensis SB2B
Found 86 low-confidence and 17 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 | | |
| 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 | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | aguB: N-carbamoylputrescine hydrolase | | |
| arginine | rocE: L-arginine permease | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Sama_1486 | Sama_1333 |
| 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 | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | Sama_3334 | Sama_0410 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | Sama_3278 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Sama_0517 | Sama_0389 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | Sama_0562 | Sama_1663 |
| fructose | fruP: fructose porter FruP | Sama_1403 | Sama_1663 |
| fucose | aldA: lactaldehyde dehydrogenase | Sama_2648 | Sama_3435 |
| 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 | Sama_1403 | Sama_1663 |
| fucose | fucU: L-fucose mutarotase FucU | | |
| 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 | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | Sama_3240 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | Sama_2235 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | Sama_0629 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | permease: L-histidine permease | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | Sama_1402 | |
| lysine | davA: 5-aminovaleramidase | Sama_0473 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | Sama_1378 | Sama_0032 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | Sama_0097 | Sama_1980 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| 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 | Sama_2756 | |
| 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 | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | Sama_1378 | Sama_2167 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Sama_3052 | Sama_3135 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | Sama_0031 | Sama_1375 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | Sama_0031 | Sama_1375 |
| phenylacetate | paaK: phenylacetate-CoA ligase | Sama_1934 | Sama_2897 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | Sama_1378 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | Sama_1523 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | Sama_1522 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | Sama_2648 | Sama_3435 |
| 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 | Sama_1980 | Sama_0097 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | Sama_1662 | |
| trehalose | treF: trehalase | Sama_1662 | |
| tryptophan | tnaA: tryptophanase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | Sama_1377 | Sama_1362 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | Sama_1378 | Sama_0032 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | Sama_1380 | Sama_1975 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | Sama_0097 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | | |
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