GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS13830 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS13830 acetyl-CoA synthetase

Length: 634 amino acids

Source: BFirm in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
propionate catabolism prpE hi propionate-CoA ligase (EC 6.2.1.17) (characterized) 62% 100% 803.1 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) 40% 458.4
propionate catabolism prpE hi prpE: propionate--CoA ligase (EC 6.2.1.17) (TIGR02316) 100% 1095.5 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) 40% 458.4
4-hydroxybenzoate catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
L-lactate catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
acetate catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
2'-deoxyinosine catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
2-deoxy-D-ribose catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
ethanol catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
L-threonine catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
thymidine catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1
L-tryptophan catabolism acs med Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; EC 6.2.1.1; Acetate--CoA ligase; Acyl-activating enzyme (uncharacterized) 40% 94% 486.9 propionate-CoA ligase (EC 6.2.1.17) 62% 803.1

Sequence Analysis Tools

View BPHYT_RS13830 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

MTSYRDFHRRSIEDPEAFWRDEARRIHWHTPFDTVLDRSNPPFARWFVGGRTNLCHNAVD
RHLAERAQQNALVYVSTETGIERRYTYAELYGEVNRMAAVMRSLDVKRGDVVLLYLPMIP
EALFAMLACARLGAIHSVVFGGFAAPNLAARIDDAKPVLIVTADAGARGGKVIDYTPLMD
EALARAQHKTPRVLLIDRQLAPERLNASYLVAYEPLREQFFDAHVPCEWLESNEPSYVLY
TSGTTGKPKGVQRDVGGYAVALAASMEHIFQGKAGDVMFTASDVGWVVGHSYIVYAPLIA
GLTTVMYEGTPIRPDGGIWWRLVAHHRINLMFTAPTALRVLKKQDPALLKQADLTSLRAL
FLAGEPLDEPTAAWIAGALDKPVIDNYWQTETGWPMLAIPRGVEALPTRLGSPGVPSAGF
NLTLRNELTGEPCPPGEKGVLTLDYPLPPGCMSTVWGDDKRFVSTYWSSIPNQQVYSTFD
WGVQDEDGYVTILGRTDDVINVAGHRLGTREIEEALSSHAAVAEVAVVGVTDPLKGQAAM
AFVVLRDAQAYADTKKRSKLDAELTATVDRQLGAIARPSRVVVVPMLPKTRSGKLLRRAI
AALAEGREPGDLPTIEDPAALQQVREALDDGAGK

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