Potential Gaps in catabolism of small carbon sources in Rhizobium leguminosarum 3841
Found 31 low-confidence and 33 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | RL_RS24230 | RL_RS17010 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | RL_RS34025 | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RL_RS19315 | RL_RS18225 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RL_RS19340 | RL_RS34940 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RL_RS19330 | RL_RS14685 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | RL_RS21170 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RL_RS29450 | RL_RS30850 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | RL_RS30845 | RL_RS14220 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | RL_RS29460 | RL_RS30840 |
| citrulline | arcC: carbamate kinase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | RL_RS20910 | RL_RS27845 |
| deoxyinosine | H281DRAFT_01112: deoxynucleoside transporter, permease component 2 | RL_RS25585 | RL_RS33885 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | RL_RS25350 | RL_RS04790 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | RL_RS05180 | RL_RS36000 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | RL_RS29275 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fdh: L-fucose 1-dehydrogenase | RL_RS02715 | RL_RS01620 |
| fucose | HSERO_RS05250: ABC transporter for L-fucose, ATPase component | RL_RS23960 | RL_RS36695 |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | RL_RS34865 | RL_RS09080 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | RL_RS02705 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | udh: D-galacturonate dehydrogenase | RL_RS36800 | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | RL_RS30660 | RL_RS36795 |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | RL_RS18270 | RL_RS03385 |
| glucuronate | uxaC: D-glucuronate isomerase | RL_RS00530 | |
| lactose | lacE: lactose ABC transporter, substrate-binding component | | |
| lactose | lacG: lactose ABC transporter, permease component 2 | RL_RS27255 | RL_RS36230 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | RL_RS01945 | RL_RS29885 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | RL_RS28875 | RL_RS13210 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | RL_RS29450 | RL_RS11410 |
| lysine | lysN: 2-aminoadipate transaminase | RL_RS17735 | RL_RS29560 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | RL_RS04995 | RL_RS33825 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | RL_RS21735 | RL_RS32985 |
| 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 | RL_RS35585 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | RL_RS33285 | RL_RS01945 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | RL_RS03115 | RL_RS22285 |
| phenylacetate | paaK: phenylacetate-CoA ligase | RL_RS35425 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | RL_RS01945 | RL_RS33285 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | RL_RS19340 | RL_RS34940 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | RL_RS19315 | RL_RS18225 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | RL_RS32145 | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RL_RS19315 | RL_RS18225 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RL_RS19340 | RL_RS34940 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RL_RS19330 | RL_RS14685 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RL_RS19315 | RL_RS18225 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RL_RS19340 | RL_RS34940 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RL_RS19330 | RL_RS14685 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | RL_RS03175 | RL_RS33285 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RL_RS04070 | RL_RS06630 |
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