GapMind for catabolism of small carbon sources

 

Protein CCNA_01794 in Caulobacter crescentus NA1000

Annotation: CCNA_01794 enoyl-CoA hydratase/isomerase family

Length: 256 amino acids

Source: Caulo in FitnessBrowser

Candidate for 16 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 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-arginine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-citrulline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-lysine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
phenylacetate catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-phenylalanine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-proline catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
L-valine catabolism ech med 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 39% 87% 153.7 methylglutaconyl-CoA hydratase (EC 4.2.1.18) 36% 144.8
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 95% 149.1 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 95% 149.1 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 95% 149.1 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 36% 98% 144.8 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
4-hydroxybenzoate catabolism badI lo BadI (characterized) 31% 79% 90.9 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
phenylacetate catabolism badI lo BadI (characterized) 31% 79% 90.9 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
L-phenylalanine catabolism badI lo BadI (characterized) 31% 79% 90.9 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 32% 50% 76.3 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 39% 153.7

Sequence Analysis Tools

View CCNA_01794 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

MLLIERRGAIAIVTLNRPEAMNALSKALRLALHDAIVQLDQDPDVSVVILTGAGDRAFTA
GLDLKELGGDPAAMGAANDQDARSNPVRAVETCRKPVIGAINGVAITGGFELALACDVLL
ASENARFADTHARVGIMPGWGLSQKLSRLIGPYRAKELSLTGNFLDARTAADWGLVNRVT
TASELLPTALRMAQDMASIPVEALSFYKSLIDDGYAVAFGEGLALEHERSSAHNRTVTPE
RVEAQRRQVMERGRGQ

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