GapMind for catabolism of small carbon sources

 

Protein Echvi_4069 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_4069 Enoyl-CoA hydratase/carnithine racemase

Length: 261 amino acids

Source: Cola in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-arginine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-citrulline catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-lysine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
phenylacetate catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-phenylalanine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-proline catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-valine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 48% 97% 234.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 216.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 216.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 216.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 216.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-isoleucine catabolism ech med Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized) 43% 96% 193.4 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 216.5
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 98% 169.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 98% 169.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 98% 169.5 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 39% 85% 175.6 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
4-hydroxybenzoate catabolism badK lo BadK (characterized) 35% 99% 134 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
phenylacetate catabolism badK lo BadK (characterized) 35% 99% 134 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-phenylalanine catabolism badK lo BadK (characterized) 35% 99% 134 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 31% 99% 120.2 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 31% 99% 120.2 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 31% 99% 120.2 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 32% 50% 89.4 Crotonyl-CoA hydratase; EC 4.2.1.150 48% 234.6

Sequence Analysis Tools

View Echvi_4069 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAESTNILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGE
KAFVAGADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMAC
HMRIATSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLV
NYVTQTKAEAIQKAEEILQKIMTKAPLSIGMIIDCVNAVYSNDENGYLIEANSFARCVKS
EDYSEGTSAFLEKRKPNFKGE

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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