GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1147 in Pseudomonas fluorescens FW300-N2E2

Annotation: Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

Length: 257 amino acids

Source: pseudo6_N2E2 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 hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-arginine catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-citrulline catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-isoleucine catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-lysine catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
phenylacetate catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-phenylalanine catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-proline catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
L-valine catabolism ech hi Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 76% 100% 398.3 AcuK 57% 286.2
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 62% 100% 316.6 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 62% 100% 316.6 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 62% 100% 316.6 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
4-hydroxybenzoate catabolism badK med BadK (characterized) 52% 100% 258.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism badK med BadK (characterized) 52% 100% 258.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism badK med BadK (characterized) 52% 100% 258.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 45% 100% 216.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 45% 100% 216.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 45% 100% 216.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 45% 100% 216.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 36% 79% 155.6 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 35% 100% 154.1 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 35% 100% 154.1 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 35% 100% 154.1 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 35% 99% 142.9 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 35% 99% 142.9 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 116.3 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 33% 94% 116.3 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
4-hydroxybenzoate catabolism badI lo BadI (characterized) 31% 98% 109.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
phenylacetate catabolism badI lo BadI (characterized) 31% 98% 109.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-phenylalanine catabolism badI lo BadI (characterized) 31% 98% 109.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 31% 54% 105.5 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 76% 398.3

Sequence Analysis Tools

View Pf6N2E2_1147 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

MSYETILLEIKDRVGLITLNRPQALNALNAQIVSELNQALDSLEADPKIGCIVLTGSKKA
FAAGADIKEMAELTYPQIYLDDLFSDSDRVANRRKPIIAAVNGFALGGGCELALMCDFIL
AGDNAKFGQPEVNLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEAERCGIVARIV
PADELLDDALKTAALIASKSVPISMMVKESVNRAFEVSLSEGVRFERRVFHAAFATQDQK
EGMAAFVAKRAAEFQDK

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