GapMind for catabolism of small carbon sources

 

Protein Echvi_3909 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_3909 Fucose permease

Length: 469 amino acids

Source: Cola in FitnessBrowser

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-cellobiose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
D-galactose catabolism HP1174 hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
D-glucose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
lactose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
D-maltose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
sucrose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
trehalose catabolism MFS-glucose hi Glucose/galactose porter (characterized) 45% 94% 315.8 D-mannitol and D-mannose transporter (MFS superfamily) 43% 267.3
D-mannose catabolism gluP med 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) 41% 98% 283.5 Glucose/galactose porter 45% 315.8
D-fructose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 38% 89% 260.8 Glucose/galactose porter 45% 315.8
sucrose catabolism fruP lo MFS transporter, FHS family, L-fucose permease (characterized, see rationale) 38% 89% 260.8 Glucose/galactose porter 45% 315.8
N-acetyl-D-glucosamine catabolism nagP lo N-acetylglucosamine porter, NagP (characterized) 32% 99% 205.7 Glucose/galactose porter 45% 315.8
D-glucosamine (chitosamine) catabolism nagP lo N-acetylglucosamine porter, NagP (characterized) 32% 99% 205.7 Glucose/galactose porter 45% 315.8
L-fucose catabolism fucP lo L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized) 34% 95% 189.9 Glucose/galactose porter 45% 315.8

Sequence Analysis Tools

View Echvi_3909 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

MASVTISKETEDNNVEFDSGQQYLGPLFLVTMLFFMWGFITCMNDILIPHLQQVFTLQNW
QAMLIQTAFFGAYFFISLGYYLISITKGDPIGRIGYKNGIILGLVISAVGCLFFYPAASL
VSFGFFLFALFVLASGITILQIAANPYVTILGKPSGASSRLNMTQAFNSLGTTIAPLIGG
YLIFGAIGDVDISADSVKMPYVALALTLLLIALIFKLFKLPEIGSQGVIISDSGALKHRH
LMLGIGAIFAYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFWGGAMVGRFFGAVA
LADFKHNLNRFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVVIIIGQFIPNRTLW
LFGITGIGLLVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGLGKYTAQASSLLVM
AIVGGAIVPLLQGLLADISGSVQLSFLVPLACYLYIVFYGMKGYRVEEG

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