Finding step rbsA for D-ribose catabolism in Lactobacillus silagei IWT126
No candidates for rbsA: D-ribose ABC transporter, ATPase component RbsA
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 rbsA
- Curated sequence CH_003578: ribose transport, ATP-binding protein RbsA; EC 3.6.3.17. Ribose import ATP-binding protein RbsA; EC 7.5.2.7. RbsA aka B3749, component of Ribose porter. ribose ABC transporter ATP binding subunit. ribose ABC transporter ATP binding subunit
- Curated sequence Q9X051: Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose
- UniProt sequence D8IUD1: SubName: Full=ABC-type sugar transport system, ATPase component protein {ECO:0000313|EMBL:ADJ63793.1};
- UniProt sequence A0A1N7TZ92: SubName: Full=Ribose ABC transporter ATPase {ECO:0000313|EMBL:ERH60791.1}; SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:PRW85404.1}; SubName: Full=Sugar ABC transporter ATPase {ECO:0000313|EMBL:AIB37520.1};
- UniProt sequence A0A166R419: SubName: Full=Sugar ABC transporter ATP-binding protein {ECO:0000313|EMBL:KZN21271.1};
- Comment: E. coli rbsABC and the related system from T. maritima. The fitness data also identified a related system in Herbaspirillum: rbsBAC = HSERO_RS11480 (D8IUD0), HSERO_RS11485 (D8IUD1), HSERO_RS11490 (D8IUD2); and in various Pseudomonas: rbsBAC = PS417_18405 (A0A1N7UEH6) PS417_18400 (A0A1N7TZ92) PS417_18395 (A0A1N7UNQ5) or Pf1N1B4_6035 (A0A161ZH48), Pf1N1B4_6034 (A0A166R419), Pf1N1B4_6033 (A0A166R405).
Or cluster all characterized rbsA 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