Finding step rbsA for D-ribose catabolism in Desulfotomaculum hydrothermale Lam5
3 candidates for rbsA: D-ribose ABC transporter, ATPase component RbsA
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | DESHY_RS05390 | sugar ABC transporter ATP-binding protein | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) | 46% | 98% | 454.5 | RbsA, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 48% | 450.3 |
| lo | DESHY_RS00685 | ABC transporter ATP-binding protein | Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 35% | 95% | 310.8 | Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement | 43% | 417.9 |
| lo | DESHY_RS05820 | ABC transporter ATP-binding protein | Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale) | 33% | 50% | 113.2 | nodulation ATP-binding protein I | 48% | 215.3 |
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 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