GapMind for catabolism of small carbon sources

 

Protein Ac3H11_2775 in Acidovorax sp. GW101-3H11

Annotation: Enoyl-CoA hydratase (EC 4.2.1.17)

Length: 279 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 29 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) 43% 99% 201.1 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 42% 177.9
propionate catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 43% 99% 201.1 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 42% 177.9
L-threonine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 43% 99% 201.1 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 42% 177.9
L-valine catabolism hpcD hi 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 43% 99% 201.1 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 42% 177.9
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 42% 98% 177.9 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
4-hydroxybenzoate catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-arginine catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-citrulline catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-lysine catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-proline catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-valine catabolism ech med Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 40% 97% 176.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 97% 172.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-isoleucine catabolism ech med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 97% 172.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 97% 172.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 41% 97% 172.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
4-hydroxybenzoate catabolism badK med BadK (characterized) 41% 98% 168.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism badK med BadK (characterized) 41% 98% 168.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism badK med BadK (characterized) 41% 98% 168.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 93% 125.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 93% 125.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized) 31% 66% 113.2 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
4-hydroxybenzoate catabolism badI lo BadI (characterized) 31% 95% 109 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism badI lo BadI (characterized) 31% 95% 109 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism badI lo BadI (characterized) 31% 95% 109 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 97% 91.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 97% 91.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 97% 91.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 43% 201.1

Sequence Analysis Tools

View Ac3H11_2775 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MMETSFHKPATPTRDEAAAPGNAVEVERRGGVGWIVLNRPDQINAINDDIRRGVPAALAE
LDSDPSVRVIVIRGAGARGFCAGADIKERRAAETSVQVRRRMQKSRWIEALDRTEKPVIA
AIHGYCMGGGMELALACDLRFAASDAVFALPETGLGLIPGGGGTQRLGAVVGPGRALDLL
LTGDRVDARRAFDIGLITRMADSADSLLAEVTALAERIAQKPPTATLFAKQAARAACHLD
LKSGLDLELDLFAMLVPMNDVKEAALAFREKRAPCFSGE

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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