GapMind for catabolism of small carbon sources

 

Protein BWI76_RS17580 in Klebsiella michiganensis M5al

Annotation: BWI76_RS17580 MFS transporter

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSLIMNLNLQQRKRLHQITLVATFGGLLFGYDTGVINGAFSSLKQYMALTPTTEGLVMSV
LLIGAALGSVFGGKFADFFGRRKYLLFLSFIFFIGALMSALAPDITVLLISRFILGYAVG
GASVTAPTFISEVAPTEMRGKLTGLNEVAIVIGQLAAFAINAIIGILWGHLPDVWRYMLM
VQTIPAICLFIGMLRSPESPRWLISKNRHEEALEILKQIRPLERATKEFNDITTLIKAEA
DKKLHSQNAFITILQTPWIFKLLLVGVIWAALQQTTGVNVIMYYGTEILSSAGFSERTSL
ICNVLNGVFSVGGMLFGVLFLVDRFKRKTIIIYGFALMATLHLIIAGVDYTLVGDIKATA
IWLLGAMFVGVMQGTMGFITWVVLAELFPLKFRGLSMGISVFFMWVMNAIVSYLFPLLQA
KLGLGPVFLIFAAINYLAIVFVITALPETSNKSLEQLEEELSANKSTAGFNTATKESGL

This GapMind analysis is from Sep 17 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:

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:

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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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