Finding step mtlF for D-sorbitol (glucitol) catabolism in Phyllobacterium brassicacearum STM 196
5 candidates for mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | CU102_RS17060 | sugar ABC transporter permease | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 77% | 100% | 440.7 | | | |
| lo | CU102_RS11575 | sugar ABC transporter permease | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2 (characterized) | 31% | 98% | 145.2 | MalF, component of Maltose/trehalose porter | 37% | 201.1 |
| lo | CU102_RS04240 | sugar ABC transporter permease | ABC transporter for D-Sorbitol, permease component 2 (characterized) | 30% | 98% | 142.5 | ABC transporter for D-Trehalose, permease component 1 | 51% | 302.4 |
| lo | CU102_RS22260 | sugar ABC transporter permease | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 100% | 132.5 | ABC transporter for D-Glucosamine, permease component 2 | 86% | 506.1 |
| lo | CU102_RS20475 | sugar ABC transporter permease | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2 (characterized) | 31% | 92% | 126.3 | ABC-type maltose transporter (EC 7.5.2.1) | 35% | 189.1 |
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 mtlF
- Curated sequence O30492: MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK
- Curated sequence BPHYT_RS16110: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence GFF1304: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence GFF2492: ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 2
- Curated sequence Ac3H11_2943: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence AO356_00020: ABC transporter for D-Sorbitol, permease component 2
- Curated sequence Pf6N2E2_1962: ABC transporter for D-sorbitol, permease component 1
- Curated sequence O30832: SmoF, component of Hexitol (glucitol; mannitol) porter
- Ignore hits to AO353_25885 when looking for 'other' hits (ABC transporter for D-mannitol and D-mannose, permease component 1)
- Ignore hits to PfGW456L13_3041 when looking for 'other' hits (ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 2)
Or cluster all characterized mtlF 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