GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1164 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1164 enoyl-CoA hydratase

Length: 260 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 31 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 med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-arginine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-citrulline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-lysine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
phenylacetate catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-phenylalanine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-proline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-valine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 49% 100% 241.1 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 100% 237.3 crotonase (EC 4.2.1.150) 48% 238.4
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 100% 237.3 crotonase (EC 4.2.1.150) 48% 238.4
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 100% 237.3 crotonase (EC 4.2.1.150) 48% 238.4
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 46% 100% 237.3 crotonase (EC 4.2.1.150) 48% 238.4
L-isoleucine catabolism ech med Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized) 46% 100% 207.6 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 46% 237.3
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 100% 195.3 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 100% 195.3 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 100% 195.3 crotonase (EC 4.2.1.150) 48% 238.4
4-hydroxybenzoate catabolism badK med BadK (characterized) 42% 97% 174.9 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism badK med BadK (characterized) 42% 97% 174.9 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism badK med BadK (characterized) 42% 97% 174.9 crotonase (EC 4.2.1.150) 48% 238.4
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 41% 98% 173.7 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 35% 96% 142.9 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 35% 96% 142.9 crotonase (EC 4.2.1.150) 48% 238.4
4-hydroxybenzoate catabolism badI lo BadI (characterized) 36% 98% 137.1 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism badI lo BadI (characterized) 36% 98% 137.1 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism badI lo BadI (characterized) 36% 98% 137.1 crotonase (EC 4.2.1.150) 48% 238.4
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 100% 124.8 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 100% 124.8 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 34% 100% 124.8 crotonase (EC 4.2.1.150) 48% 238.4
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 122.9 crotonase (EC 4.2.1.150) 48% 238.4
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 122.9 crotonase (EC 4.2.1.150) 48% 238.4
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 35% 71% 106.3 crotonase (EC 4.2.1.150) 48% 238.4

Sequence Analysis Tools

View N515DRAFT_1164 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

MAYRNLDIGNRGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDK
AFVAGADIAEMNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACH
LRVASEKARFGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVN
RVVAPEALDETVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTE
DMREGTTAFLEKRKAEFKGR

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