GapMind for catabolism of small carbon sources

 

Protein WP_011383077.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS03265 enoyl-CoA hydratase

Length: 258 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 27 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 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
4-hydroxybenzoate catabolism paaF hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 64% 328.6
L-arginine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
L-citrulline catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
L-isoleucine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
L-lysine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
phenylacetate catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
phenylacetate catabolism paaF hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 64% 328.6
L-phenylalanine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
L-phenylalanine catabolism paaF hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) 64% 328.6
L-proline catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
L-valine catabolism ech hi trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 70% 100% 362.8 BadK 57% 291.2
4-hydroxybenzoate catabolism badK med BadK (characterized) 57% 100% 291.2 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
phenylacetate catabolism badK med BadK (characterized) 57% 100% 291.2 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-phenylalanine catabolism badK med BadK (characterized) 57% 100% 291.2 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 205.3 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 205.3 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 205.3 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 100% 205.3 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 37% 81% 159.5 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 33% 100% 116.7 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 33% 100% 116.7 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 33% 100% 116.7 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
4-hydroxybenzoate catabolism badI lo BadI (characterized) 33% 99% 115.5 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
phenylacetate catabolism badI lo BadI (characterized) 33% 99% 115.5 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
L-phenylalanine catabolism badI lo BadI (characterized) 33% 99% 115.5 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8
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% 63% 102.4 trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) 70% 362.8

Sequence Analysis Tools

View WP_011383077.1 at NCBI

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

MAFENITVETRGNVGVIALNRPKAMNALCAALISELGQALDAFEADDSIGAVVLTGSEKA
FAAGADIKEMASKSYMDVYLANFITDGWERVTKCRKPIVAAVAGFALGGGCEMAMMCDFI
IAGDNAKFGQPEITIGTIPGAGGTQRLTRAVGKSKAMEMCLTGRMMDAAEAERAGLVSRI
VPVAELLDEAVKAAGKIASLSRPIVMLCKESVNAAFETTLAQGVTFERRLFHSTFSTEDQ
KEGMAAFVEKRPAAFKNR

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