Finding step rbsB for D-ribose catabolism in Rhizobium freirei PRF 81
4 candidates for rbsB: D-ribose ABC transporter, substrate-binding component RbsB
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | RHSP_RS05955 | sugar ABC transporter substrate-binding protein | LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale) | 44% | 100% | 264.6 | RbsB, 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) | 32% | 149.1 |
| med | RHSP_RS08735 | substrate-binding domain-containing protein | D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized) | 35% | 97% | 164.9 | RbsB, 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) | 34% | 161.8 |
| lo | RHSP_RS23170 | D-ribose ABC transporter substrate-binding protein | Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 36% | 98% | 191 | Periplasmic erythritol binding protein, component of The erythritol uptake permease, EryEFG (Yost et al., 2006) (probably orthologous to 3.A.1.2.11) | 90% | 566.2 |
| lo | RHSP_RS24800 | rhamnose ABC transporter substrate-binding protein | LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale) | 31% | 92% | 105.9 | RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 90% | 589.7 |
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 rbsB
- Curated sequence CH_003593: D-ribose-binding periplasmic protein; EC 3.6.3.17. Ribose import binding protein RbsB. RbsB aka RBSP aka PRLB aka B3751, component of Ribose porter. ribose ABC transporter periplasmic binding protein. ribose ABC transporter periplasmic binding protein
- Curated sequence Q9X053: Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose
- UniProt sequence D8IUD0: SubName: Full=ABC-type sugar transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ63792.1};
- UniProt sequence A0A1N7UEH6: SubName: Full=LacI family transcriptional regulator {ECO:0000313|EMBL:AIB37521.1}; SubName: Full=Ribose transport system substrate-binding protein {ECO:0000313|EMBL:SFA82006.1}; SubName: Full=Sugar ABC transporter substrate-binding protein {ECO:0000313|EMBL:PRW85403.1};
- UniProt sequence A0A161ZH48: SubName: Full=LacI family transcriptional regulator {ECO:0000313|EMBL:KZN21272.1};
Or cluster all characterized rbsB 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