GapMind for catabolism of small carbon sources

 

Protein Dsui_2069 in Dechlorosoma suillum PS

Annotation: Dsui_2069 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

Length: 529 amino acids

Source: PS in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribonate catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 31% 90% 206.1 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
2-deoxy-D-ribose catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 31% 90% 206.1 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
L-leucine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 31% 90% 206.1 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
L-phenylalanine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 31% 90% 206.1 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
L-tyrosine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 31% 90% 206.1 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
propionate catabolism prpE lo acetate-CoA ligase (EC 6.2.1.1) (characterized) 31% 77% 178.3 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6
4-hydroxybenzoate catabolism hcl lo 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized) 31% 89% 176.4 Long-chain-fatty-acid--CoA ligase FadD13; Fatty acyl-CoA ligase; FACL; FACL13; Fatty acyl-CoA synthetase; ACS; FACS; Very-long-chain fatty-acyl-CoA synthetase; ACSVL; EC 6.2.1.3 38% 296.6

Sequence Analysis Tools

View Dsui_2069 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSRGLTLGDTLSWPARYFPDKPALIAWEGGDHDTPAQRRVWTYAQLNAEVNRHAHALLAL
GVQKGDVVAAFLYNTPAFVFSLLAAARVGAVFNPINYRLAAQELAFILEDGQAKVLLFEK
EGCEVVEKAREHGVPTAHWIYADSDAAPAFATARLDQLVRHQPATLPPVIVEENDNCILM
YTSGTTGRPKGVLHTHRSKLAHNAMMHQAMTLSREDVGLAVAPLNHTAELHTSFLPRLQL
GATQVLLRRFDAGEAWRLTEVEKVTHFFAAPTMVTLLLHHPDVASRDLSSLRLVEYGGAS
MAPHLIREWDKKVGAGLVQIYGTTEMGPCMSVLYPHEQLSHAGSAGLPSLNHDLLVARVK
ADGSPSDPADLAAPDEVGEILVRGPCMMGGYLNRPEANARALAFGWYHTGDLGSLDKEGY
LWIRDRIDHMINSGAENVYPREVEDALVEHPGVLEVAVVGEPDDTWGQVVAAHVVAKPGA
TLTQEALDHFLLEGDRLAHYKRPRRYHFIEALPKTTSGKIQKHLLRQAG

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