Potential Gaps in catabolism of small carbon sources in Sinorhizobium meliloti 1021
Found 25 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | SMc01869 | SMc04407 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | SM_b20724 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SMc02260 | SM_b21138 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | SMa0492 | SMc02257 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | SMc02258 | SMc00139 |
| D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | SMc01950 | |
| D-alanine | dadA: D-alanine dehydrogenase | SM_b20267 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | SMa1872 | SM_b20432 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | SMc02041 | SMc00372 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | SMc01637 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | SM_b21107 | SMa1351 |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | SMa0717 | SMc04142 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | gudD: D-glucarate dehydratase | SMa0056 | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | SMc04142 | SMa0717 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | SM_b20753 | SMa1400 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | SMc02260 | SMa0083 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | SMc01498 | SMc01626 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | SMc02227 | SMc00727 |
| phenylacetate | paaK: phenylacetate-CoA ligase | SMc00261 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | SMc01951 | SMc02359 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | SMc01946 | SMc00078 |
| phenylalanine | paaH: 3-hydroxyadipyl-CoA dehydrogenase | SMc02227 | SMc00727 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SMc01946 | SMc00078 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | SMc01951 | SMc02359 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | SMc01946 | SMc00078 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | SMc01951 | SMc02359 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | SM_b20753 | SMa1400 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | SM_b20752 | SMc01669 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | SMc00781 | SMc00094 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | SM_b20751 | SMc00274 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | SM_b20072 | SM_b20712 |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | SM_b20713 | SM_b20503 |
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