GapMind for catabolism of small carbon sources

 

Protein Echvi_3928 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: FitnessBrowser__Cola:Echvi_3928

Length: 252 amino acids

Source: Cola 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-sorbitol (glucitol) catabolism sdh lo Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized) 38% 98% 149.4 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 36% 98% 144.4 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
4-hydroxybenzoate catabolism badH lo BadH (characterized) 34% 100% 141.7 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
phenylacetate catabolism badH lo BadH (characterized) 34% 100% 141.7 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
L-phenylalanine catabolism badH lo BadH (characterized) 34% 100% 141.7 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 98% 137.1 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 98% 137.1 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 36% 96% 125.6 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
D-galactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 32% 96% 114.8 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
lactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 32% 96% 114.8 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 32% 97% 102.4 aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) 42% 198.4

Sequence Analysis Tools

View Echvi_3928 at FitnessBrowser

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

MSHLNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRSAEKVNVAAAELGVTGITADVL
ELAAIDAAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVFTIEKF
LPILKDGGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRVNAVNPGP
VYTPIFSKTGMSEDQLNGMAAAMQNRIPLKRYGKPEDIAELVAFLASDRASFITGAEYNI
DGGTNVNPLLVS

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:

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