Finding step gntA for D-gluconate catabolism in Acidovorax sp. GW101-3H11
3 candidates for gntA: gluconate TRAP transporter, small permease component
Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
hi | Ac3H11_3228 | Tripartite ATP-independent periplasmic transporter, DctQ component | C4-dicarboxylate ABC transporter permease (characterized, see rationale) | 100% | 100% | 328.2 | TRAP transporter DctQ subunit, component of The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ | 33% | 84.7 |
hi | Ac3H11_3521 | TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter | TRAP dicarboxylate transport system, small permease component (DctQ-like) (characterized, see rationale) | 44% | 88% | 134 | TRAP transporter DctQ subunit, component of The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ | 46% | 120.2 |
med | Ac3H11_1229 | TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter | TRAP dicarboxylate transport system, small permease component (DctQ-like) (characterized, see rationale) | 48% | 73% | 130.2 | TRAP transporter DctQ subunit, component of The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ | 42% | 127.9 |
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.
Also see fitness data for the candidates
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 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