GapMind for catabolism of small carbon sources

 

Protein WP_043743408.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS04300 beta-ketoacyl-ACP reductase

Length: 240 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 badH lo BadH (characterized) 37% 99% 144.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
phenylacetate catabolism badH lo BadH (characterized) 37% 99% 144.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
L-phenylalanine catabolism badH lo BadH (characterized) 37% 99% 144.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 36% 97% 143.3 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 35% 96% 139 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 31% 92% 122.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
L-rhamnose catabolism LRA1 lo L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized) 33% 96% 122.1 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 87% 107.5 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 87% 107.5 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
lactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 87% 107.5 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 31% 95% 105.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 64% 305.8

Sequence Analysis Tools

View WP_043743408.1 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

MGRLAIVTGGTRGIGREISVTLKKAGYKVVANYGGNDEAAAKFTAETGIPSMKWDVGSYP
ACEAAIAKIVAEHGPVEIIVNNAGITRDATLHRMSYQMWEEVIHTNLTSCFNMARLAIDS
MRERGFGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGAAKNITVNAIAPGYV
DTDMVRAVPPAVLEKIIAKIPVGRLGRAEDIARCVMFLIADEADFITGSTLSVNGGQHMY

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