Finding step frcA for D-fructose catabolism in Serinicoccus profundi MCCC 1A05965
4 candidates for frcA: fructose ABC transporter, ATPase component FrcA
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | GQY_RS0101930 | ATP-binding cassette domain-containing protein | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 44% | 96% | 386.3 | m-Inositol ABC transporter, ATPase component (itaA) | 44% | 415.6 |
| med | GQY_RS0104125 | sugar ABC transporter ATP-binding protein | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 45% | 94% | 378.6 | Inositol transport system ATP-binding protein | 46% | 412.9 |
| med | GQY_RS0105970 | ATP-binding cassette domain-containing protein | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 40% | 96% | 335.9 | ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production | 63% | 600.5 |
| lo | GQY_RS0108980 | ABC transporter ATP-binding protein | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 34% | 89% | 265 | 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 | 48% | 461.5 |
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 frcA
- Curated sequence Q9F9B0: Fructose import ATP-binding protein FrcA; EC 7.5.2.-. FrcA, component of Fructose/mannose/ribose porter
- UniProt sequence A0A0C4Y5F6: SubName: Full=ABC-type sugar transport system, ATP-binding protein {ECO:0000313|EMBL:AJG18103.1}; EC=3.6.3.17 {ECO:0000313|EMBL:AJG18103.1};
- Comment: FrcABC from Rhizobium meliloti. A distantly related system in Ralstonia eutropha H16 is required for fructose utilization (PMID:21478317), and fitness data confirms that the homologs in Cupriavidus basilensis 4G11 are important during growth on fructose (frcA = RR42_RS03360 = A0A0C4Y5F6; frcC = RR42_RS03365 = A0A0C4Y7K0; frcB = RR42_RS03370 = A0A0C4Y591)
Or cluster all characterized frcA 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