GapMind for catabolism of small carbon sources

 

Protein 200845 in Shewanella oneidensis MR-1

Annotation: SO1680 enoyl-CoA hydratase/isomerase family protein (NCBI ptt file)

Length: 257 amino acids

Source: MR1 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ech hi enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 66% 92% 321.2 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
4-hydroxybenzoate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 98% 170.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 38% 161.4
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 38% 96% 161.4 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 38% 96% 161.4 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 38% 96% 161.4 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 38% 96% 161.4 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 100% 156 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 100% 156 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 100% 156 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 37% 91% 153.3 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
4-hydroxybenzoate catabolism badK lo BadK (characterized) 34% 98% 128.6 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
phenylacetate catabolism badK lo BadK (characterized) 34% 98% 128.6 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-phenylalanine catabolism badK lo BadK (characterized) 34% 98% 128.6 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 118.2 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 118.2 enoyl-CoA hydratase (EC 4.2.1.17) 66% 321.2

Sequence Analysis Tools

View 200845 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

MDYLVERIEGHTAILTMNNPPANTWTAQSLQALKAKVLELNANKDIYALVLTGEGNKFFS
AGADLKLFSDGDKGNAASMAKHFGEAFETLSQFRGVSIAAINGYAMGGGLEVALACDIRI
AETQAVMALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERVNAAQALNLRLVEEVV
ETGEALNAAIALAAKVANQSPSSVTACKTLIQAGRQMPRSQALPIEHELFVGLFDTEDQA
EGVNAFLEKRKADWKNR

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