Finding step gntA for D-gluconate catabolism in Marivita geojedonensis DPG-138
No candidates for gntA: gluconate TRAP transporter, small permease component
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step gntA
- UniProt sequence Q930R3: SubName: Full=TRAP-type small permease component {ECO:0000313|EMBL:AAK64790.1};
- UniProt sequence G8AR26: SubName: Full=TRAP dicarboxylate transport system, small permease component (DctQ-like) {ECO:0000313|EMBL:CCC99887.1};
- Curated sequence GFF2080: fusion of gluconokinase and the small permease component of the D-gluconate TRAP transporter
- UniProt sequence A0A165IVI0: SubName: Full=C4-dicarboxylate ABC transporter permease {ECO:0000313|EMBL:KZT13591.1};
- Comment: A TRAP type transporter for gluconate is described in Sinorhizobium meliloti (PMID:19060150). SMa0249 (gntA, Q930R3) is the small permease component. SMa0250 (gntB, Q930R2) is the large permease component. SMa0252 (gntC, Q930R1) is the periplasmic solute-binding component. Fitness data identified related systems in Azospirillum brasilense Sp245, Pseudomona stutzeri RCH2, Acidovorax sp. GW101-3H11. AZOBR_RS15925 = AZOBR_p130075 = G8AR26 is the small permease component; it was originally annotated as a pseudogene. AZOBR_RS15920 is the large permease component. AZOBR_RS15915 = G8AR24 is the solute receptor (DctP-like) . In psRCH2, these are Psest_2123, Psest_2124, Psest_2125 (GFF2080:GFF2082); the small permease component is fused to gluconokinase. In Acidovorax, these are Ac3H11_3228 (A0A165IVI0), Ac3H11_3227 (A0A165IWV9), Ac3H11_3226 (A0A165IVH1).
Or cluster all characterized gntA 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