GapMind for catabolism of small carbon sources

 

Protein WP_010537714.1 in Bacteroides faecis MAJ27

Annotation: NCBI__GCF_000226135.1:WP_010537714.1

Length: 309 amino acids

Source: GCF_000226135.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylT lo D-xylose-proton symporter (characterized) 40% 66% 221.9 Glucose/fructose:H+ symporter, GlcP 37% 216.9
D-cellobiose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
D-glucose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
lactose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
D-maltose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
sucrose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
trehalose catabolism MFS-glucose lo Glucose transporter GlcP; Glucose/H(+) symporter (characterized) 38% 63% 202.6 D-xylose-proton symporter 40% 221.9
D-galactose catabolism galP lo Galactose-proton symporter; Galactose transporter (characterized) 35% 62% 199.5 D-xylose-proton symporter 40% 221.9
myo-inositol catabolism iolT lo Minor myo-inositol transporter, IolT2, of 478 aas (characterized) 31% 63% 183 D-xylose-proton symporter 40% 221.9
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 35% 51% 176.4 D-xylose-proton symporter 40% 221.9
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% 60% 147.5 D-xylose-proton symporter 40% 221.9
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% 60% 147.5 D-xylose-proton symporter 40% 221.9
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 31% 59% 142.9 D-xylose-proton symporter 40% 221.9

Sequence Analysis Tools

View WP_010537714.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MKSAINFSYLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGS
IVGVLFAGILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIV
SPLYISEVSVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVT
EVWRGMLGMEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNE
TKSVLTSETKSEWALLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGD
SLFYQVLVG

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:

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:

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