GapMind for catabolism of small carbon sources

 

Protein GFF4142 in Pseudomonas simiae WCS417

Annotation: PS417_21215 3-hydroxyacyl-CoA dehydrogenase

Length: 715 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
4-hydroxybenzoate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-arginine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-citrulline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-isoleucine catabolism ech med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-lysine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
phenylacetate catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
phenylacetate catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-phenylalanine catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-phenylalanine catabolism paaH med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
L-proline catabolism fadB med fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) 37% 98% 397.9
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 30% 97% 278.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 30% 97% 278.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 30% 97% 278.1 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 66% 115.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 66% 115.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 38% 66% 115.9 fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 37% 397.9

Sequence Analysis Tools

View GFF4142 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

MTQAIRYEKGQDGIVVLTLDMPGQSANTMNGAYREAMAAMVERLEAQKDDLAGVVITSAK
KTFFAGGDLNELIKVDKAHAKDFYDSVRELKAQLRRLETLGKPVVAAINGAALGGGWEIC
LACHYRVALDDKSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPQQAL
QAGLVNELAADRDELLAKSRAWILANPDAKQPWDNKGYQIPGGTPSSPKVAQMLAIAPSI
LRSKTQGCFPAPEKILCAAVEGAQVDFDTAHLIETRYFTELVTGQVAKNMIGTFWFQLNE
INAGSSRPQGFAPYVTRKVGVLGAGMMGAGIAYVSASAGIEVVLKDINLAAAEKGKAHSA
ALLDKKVSRGQLTAEQRETFLARIHPTATDEDLAGCDLIIEAVFEDRELKAKVSAAAQSV
VGADAVIASNTSTLPISGLATAVPDQTRFIGLHFFSPVDKMPLVEIIKGARTSDETLARG
FDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVAAPMIETEARKAGMPVGPL
AVSDEVSLSLMNHIRQQTAKDLQAEGKAVPTHPATAVIDLLVNEYQRMGKAAGGGFYDYP
SGGHKYLWPELKSRFERPDQRISPQDVRDRLLFIQAIETVRCVEEGVLMSTADANVGSIF
GIGFAPWSGGALQFINQYGLNDFIARARYLAEQYGERFMPPALLLEKAAQGDVFR

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