GapMind for catabolism of small carbon sources

 

Protein WP_066329840.1 in Flavobacterium glycines Gm-149

Annotation: NCBI__GCF_900100165.1:WP_066329840.1

Length: 452 amino acids

Source: GCF_900100165.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 45% 94% 359 Arabinose-proton symporter; Arabinose transporter 35% 278.5
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 45% 94% 359 Arabinose-proton symporter; Arabinose transporter 35% 278.5
D-xylose catabolism xylT lo D-xylose-proton symporter (characterized) 33% 98% 266.2 D-fructose transporter, sugar porter family 45% 359.0
myo-inositol catabolism iolT lo Inositol transporter 1 (characterized) 34% 88% 241.9 D-fructose transporter, sugar porter family 45% 359.0
D-cellobiose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
D-galactose catabolism galP lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
D-glucose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
lactose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
D-maltose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
sucrose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
trehalose catabolism MFS-glucose lo Galactose-proton symporter; Galactose transporter (characterized) 32% 95% 240 D-fructose transporter, sugar porter family 45% 359.0
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 33% 93% 223.8 D-fructose transporter, sugar porter family 45% 359.0
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 30% 89% 201.8 D-fructose transporter, sugar porter family 45% 359.0
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 30% 89% 201.8 D-fructose transporter, sugar porter family 45% 359.0
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 31% 90% 187.2 D-fructose transporter, sugar porter family 45% 359.0
D-cellobiose catabolism cdt lo The cellobiose/cellodextrin transporter, Cdt-1 (characterized) 31% 54% 128.6 D-fructose transporter, sugar porter family 45% 359.0

Sequence Analysis Tools

View WP_066329840.1 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

MNKILLWSVTAALAGFLFGFDTVVISGADKQLQLLWHSSDAFHGLIVMAMALWGTVIGAI
FGAIPTNKLGRKKTLFWIGILYFVSAIGAAFANDPYVFAAFRFIGGLGVGASTIAAPAYV
SEIAPADKRGRLVALYQFNIVLGILIAFISNYFLKDIGENAWRWMIGVQAIPSLIYILFI
ITIPESPRWLLSRNRDTEAGKVLFEIDPLASIEDLIDDSRENGVTKHENIFMKKYRFPLM
LAFLMAFFNQFSGINAFLYYAPRIFEEAGLGQNTALLSSIGIGITNLIFTLVGVSLIDKL
GRKVLMYIGSLGYIISLGLVSASFYFNWGGLSVPVFLFLFIASHAIGQGAVIWVFISEIF
PNHIRAAGQAFGSSVHWVLAAIIPSLIPMLFSEIGPSVVFLIFTLMMVLQLLFVMFLMPE
TKGISLETLSENLTNKNIDKNEIKKTSIADIL

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