Protein BWI76_RS17580 in Klebsiella michiganensis M5al
Annotation: FitnessBrowser__Koxy:BWI76_RS17580
Length: 479 amino acids
Source: Koxy in FitnessBrowser
Candidate for 11 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| D-glucose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| lactose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| D-maltose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| myo-inositol catabolism | iolT | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Glucose transporter GlcP; Glucose/H(+) symporter | 38% | 297.7 |
| sucrose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| trehalose catabolism | MFS-glucose | hi | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) | 47% | 92% | 418.7 | Major myo-inositol transporter IolT | 46% | 401.4 |
| L-arabinose catabolism | araE | lo | Arabinose/xylose transporter, AraE (characterized) | 35% | 95% | 261.9 | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) | 47% | 418.7 |
| D-fructose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 30% | 93% | 213 | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) | 47% | 418.7 |
| sucrose catabolism | Slc2a5 | lo | The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) | 30% | 93% | 213 | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) | 47% | 418.7 |
| D-sorbitol (glucitol) catabolism | SOT | lo | Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized) | 30% | 92% | 208 | Myo-Inositol uptake porter, IolT1 (Km=0.2mM) | 47% | 418.7 |
Sequence Analysis Tools
View BWI76_RS17580 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MSLIMNLNLQQRKRLHQITLVATFGGLLFGYDTGVINGAFSSLKQYMALTPTTEGLVMSV
LLIGAALGSVFGGKFADFFGRRKYLLFLSFIFFIGALMSALAPDITVLLISRFILGYAVG
GASVTAPTFISEVAPTEMRGKLTGLNEVAIVIGQLAAFAINAIIGILWGHLPDVWRYMLM
VQTIPAICLFIGMLRSPESPRWLISKNRHEEALEILKQIRPLERATKEFNDITTLIKAEA
DKKLHSQNAFITILQTPWIFKLLLVGVIWAALQQTTGVNVIMYYGTEILSSAGFSERTSL
ICNVLNGVFSVGGMLFGVLFLVDRFKRKTIIIYGFALMATLHLIIAGVDYTLVGDIKATA
IWLLGAMFVGVMQGTMGFITWVVLAELFPLKFRGLSMGISVFFMWVMNAIVSYLFPLLQA
KLGLGPVFLIFAAINYLAIVFVITALPETSNKSLEQLEEELSANKSTAGFNTATKESGL
This GapMind analysis is from Apr 09 2024. 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