GapMind for catabolism of small carbon sources

 

Protein SMc00966 in Sinorhizobium meliloti 1021

Annotation: SMc00966 acetyl-COA acyltransferase

Length: 397 amino acids

Source: Smeli in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-arginine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-citrulline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
2-deoxy-D-ribonate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
2-deoxy-D-ribose catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-leucine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-lysine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
phenylacetate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-phenylalanine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-proline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-tyrosine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 99% 264.6 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
L-isoleucine catabolism fadA med acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized) 41% 97% 264.2 β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) 43% 260.8
4-hydroxybenzoate catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
4-hydroxybenzoate catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
phenylacetate catabolism paaJ1 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
phenylacetate catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
L-phenylalanine catabolism paaJ1 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
L-phenylalanine catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
L-tryptophan catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 98% 260.8 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 98% 235 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 98% 235 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 98% 235 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 41% 264.2

Sequence Analysis Tools

View SMc00966 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNASSDPARTPVVIAALRTPVGRVNGSLAAVEPARLAALLIERIIADTGIDRAEIDDVLV
GNAANSAGNLARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGT
ESASRAHIRLRPPLTRGEEPQPVKRARMAPDSIGDPDMGVAAENVATACGISRERQDRFA
LESHRRAVAAEAEGRFSREIVPVPTPEGPIARDECPRANASAETLSRLRPVFVAGGTVTA
GNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGLGPVPAMAKLRARN
PALDVARVDFIEFNEAFASQVLGSLDQLDIAPERVNRDGGAIALGHPYGASGAILVVRLF
SQMLAASSPAEGLAMMGIGGGMGIAAHFSSCRPDQAA

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