GapMind for catabolism of small carbon sources

 

Protein WP_011385596.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS16315 acyl-CoA dehydrogenase

Length: 392 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-arginine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-citrulline catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-lysine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
phenylacetate catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-phenylalanine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-proline catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 72% 98% 575.9 acyl-CoA oxidase (EC 1.3.3.6) 35% 235.0
L-isoleucine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 235 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 72% 575.9
propionate catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 235 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 72% 575.9
L-threonine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 235 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 72% 575.9
L-valine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 235 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 72% 575.9

Sequence Analysis Tools

View WP_011385596.1 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

MQHFKWDDPFLLEDQLSEDEKLIRDSAHAYCQEKLQPRVMKAFRDETFDREIMNEMGEMG
LLGPTIPEEYGGPGVNHVAYGLISREVERVDSGYRSAMSVQSSLVMHPIFSYGTEEQKKK
YLPRLATGEIIGCFGLTEPDAGSDPGGMRTRAKKVDGGYLLTGSKMWITNSPISDIAIVW
AKSDAHEGKIKGFIVEKGIKGFTTPKIEGKLSLRASITGEIVLDEAFVPDEALMPNASGL
GGPFGCLNKARYGIAWGVIGAAEFCWHAARQYMLDRKQFGRPLAANQIPQLKLANMMTEI
TLGLQACVRVGRMMDDHTWAPEAVSLIKRNNCGKALDIARMARDMHGGNGISEEFHVIRH
MVNLETVNTYEGAHDVHALILGRAMTGIQAFS

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