GapMind for catabolism of small carbon sources


Protein Echvi_3632 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: FitnessBrowser__Cola:Echvi_3632

Length: 548 amino acids

Source: Cola in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galacturonate catabolism uxaA hi Altronate dehydratase (EC (characterized) 58% 100% 649 D-arabinoate dehydratase (EC; also involved in L-fucose catabolism 38% 219.5
D-galacturonate catabolism garD lo Galactarate dehydratase (L-threo-forming); GalcD; EC (characterized) 34% 65% 196.8 Altronate dehydratase (EC 58% 649.0
L-fucose catabolism fucD lo L-fuconate dehydratase; L-rhamnonate dehydratase (EC; EC (characterized) 32% 73% 152.1 Altronate dehydratase (EC 58% 649.0
L-rhamnose catabolism LRA3 lo L-fuconate dehydratase; L-rhamnonate dehydratase (EC; EC (characterized) 32% 73% 152.1 Altronate dehydratase (EC 58% 649.0

Sequence Analysis Tools

View Echvi_3632 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

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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