Finding step dctM for 2-oxoglutarate (alpha-ketoglutarate) catabolism in Planktomarina temperata RCA23
5 candidates for dctM: 2-oxoglutarate TRAP transporter, large permease component DctM
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | RCA23_RS04895 | TRAP transporter large permease | dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) | 48% | 82% | 323.9 | TrapT family, dctM subunit, C4-dicarboxylate transport, component of Transporter for lignin derived aromatic compounds, TarPQM | 32% | 199.1 |
| lo | RCA23_RS05635 | TRAP transporter large permease | TRAP transporter, subunit DctM (characterized, see rationale) | 30% | 99% | 220.3 | TrapT family, dctM subunit, C4-dicarboxylate transport, component of Transporter for lignin derived aromatic compounds, TarPQM | 40% | 352.1 |
| lo | RCA23_RS10410 | TRAP transporter large permease | dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) | 30% | 96% | 198.4 | TrapT family, dctM subunit, C4-dicarboxylate transport, component of Transporter for lignin derived aromatic compounds, TarPQM | 44% | 380.9 |
| lo | RCA23_RS03480 | TRAP transporter large permease | TRAP transporter, subunit DctM (characterized, see rationale) | 30% | 89% | 164.5 | Sialic acid TRAP transporter large permease protein SiaM | 31% | 225.3 |
| lo | RCA23_RS13345 | TRAP transporter large permease | alpha-ketoglutarate TRAP transporter, large permease component (characterized) | 33% | 58% | 148.7 | TrapT family, dctM subunit, C4-dicarboxylate transport, component of Transporter for lignin derived aromatic compounds, TarPQM | 45% | 391.3 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step dctM
- Curated sequence 6938090: alpha-ketoglutarate TRAP transporter, large permease component
- Curated sequence 5208943: dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component
- UniProt sequence I7DRS6: SubName: Full=TRAP transporter, subunit DctM {ECO:0000313|EMBL:AFO91751.1};
- Ignore hits to O07838 when looking for 'other' hits (C4-dicarboxylate TRAP transporter large permease protein DctM. DctM, component of Tripartite dicarboxylate:H+ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate))
- Ignore hits to Q9HU16 when looking for 'other' hits (C4-dicarboxylate TRAP transporter large permease protein DctM)
- Comment: O07838 and Q9HU16 are reported to transport various dicarboxylates, and transport of 2-oxoglutarate does not seem to have been tested, so they are marked ignore.
Or cluster all characterized dctM proteins
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