GapMind for catabolism of small carbon sources

 

Protein GFF12 in Marinobacter adhaerens HP15

Annotation: HP15_12 enoyl-CoA hydratase/isomerase

Length: 270 amino acids

Source: Marino in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 99% 200.7 short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) 41% 180.6
propionate catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 99% 200.7 short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) 41% 180.6
L-threonine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 99% 200.7 short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) 41% 180.6
L-valine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 42% 99% 200.7 short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) 41% 180.6
L-isoleucine catabolism ech med short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) (characterized) 41% 84% 180.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
4-hydroxybenzoate catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-arginine catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-citrulline catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-lysine catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
phenylacetate catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-phenylalanine catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-proline catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-valine catabolism ech med Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 40% 94% 164.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 95% 163.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 95% 163.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 95% 163.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
4-hydroxybenzoate catabolism badK med BadK (characterized) 41% 95% 150.2 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
phenylacetate catabolism badK med BadK (characterized) 41% 95% 150.2 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-phenylalanine catabolism badK med BadK (characterized) 41% 95% 150.2 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 40% 83% 169.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.5 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 42% 200.7

Sequence Analysis Tools

View GFF12 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

MSLPEKVVESINDAVNVCRDGNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRV
IVIRGEGERGLCAGADIKERRGPENSLQVRKRMECARWIESIDQTTKPVIVAIHGYCMGG
GLELALACDIRYASPNAVMALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAA
RARSIGLVTRVAETQESLLQEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLEL
DLFALLAPTEDAREAASAFSERRSPNFIGE

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, 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