GapMind for catabolism of small carbon sources

 

Protein 353142 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT3616 fucose permease (NCBI ptt file)

Length: 418 amino acids

Source: Btheta 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
L-fucose catabolism fucP med L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized) 39% 92% 278.9 Glucose/galactose porter 37% 245.7
D-fructose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 35% 92% 254.6 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
sucrose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 35% 92% 254.6 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
D-cellobiose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
D-glucose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
lactose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
D-maltose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
sucrose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
trehalose catabolism MFS-glucose lo Glucose/galactose transporter (characterized, see rationale) 37% 96% 246.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
D-galactose catabolism HP1174 lo Glucose/galactose porter (characterized) 37% 96% 245.7 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9
D-mannose catabolism gluP lo The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized) 32% 99% 214.5 L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease 39% 278.9

Sequence Analysis Tools

View 353142 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

MKKNTYTIPLALVFSLFFLWAISSNLLPTMIRQLMKTCELNTFEASFTETAYWLAYFIFP
IPIAMFMKRYSYKAGIIFGLLLAAVGGLLFFPAAMLKEYWAYLCIFFIIATGMCFLETAA
NPYVTVLGAPETAPRRLNLAQSFNGLGAFIAAMFLSKLILSGTHYTRETLPVDYPGGWQA
YIQLETDAMKLPYLILALLLLAIAVVFVFSKLPKIGDEGAEPASGKKEKLIDFDVLKRSH
LRWGVIAQFFYNGGQTAINSLFLVYCCTYAGLPEDTATTFFGLYMLAFLLGRWIGTGLMV
KFRPQGMLLVYALMNILLCGVVMLWGGMIGLYAMLAISFFMSIMYPTQFSLALKGLGNQT
KSGSAFLVMAIVGNACLPQLTAYFMHVNEHIYYVAYGIPMICFAFCAYYGWKGYKVID

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 paper from 2022 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