GapMind for catabolism of small carbon sources

 

Protein WP_011385011.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS13240 acyl-CoA synthetase

Length: 541 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-lactate catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
acetate catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
2'-deoxyinosine catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
2-deoxy-D-ribose catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
ethanol catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-threonine catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
thymidine catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-tryptophan catabolism acs med Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 53% 97% 588.6 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
propionate catabolism prpE med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 42% 97% 426 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
2-deoxy-D-ribonate catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 30% 93% 208 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
2-deoxy-D-ribose catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 30% 93% 208 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-leucine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 30% 93% 208 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-phenylalanine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 30% 93% 208 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4
L-tyrosine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 30% 93% 208 3-(methylthio)propionyl-CoA ligase (EC 6.2.1.44) 68% 760.4

Sequence Analysis Tools

View WP_011385011.1 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSSNPYELGLDRNAANFVALTPLTFLERAAAVWPDRLAVIHGPVRRTWAETFVRCRKLAA
ALTARGIGLGDTVALMGANTPETFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKI
LITDREFSPVVKKALAALGRTIPVIDIDDPQFKGGELLGEKNYEQLLDEAASEAPWTLPT
DEWQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCNGWC
FPWTMAVVAGTSVCLRHVRVDAIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEGISHAV
KVMTAGAAPPAPVIAGMERMGWEVTHVYGLTECYGPTVQCVWHDKWNGLSIDEKAQIKAR
QGVRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEAFAGGWFH
TGDLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVARPDEKWGE
TPCAFIALKDGAEATEADIITFCRERMAHFKVPRTIVFGGLPKTSTGKVQKFMLRQKAKE
L

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