GapMind for catabolism of small carbon sources

 

Protein CA265_RS06590 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS06590 acetyl-CoA acetyltransferase

Length: 391 amino acids

Source: Pedo557 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 hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-arginine catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-citrulline catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
2-deoxy-D-ribonate catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
2-deoxy-D-ribose catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-leucine catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-lysine catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
phenylacetate catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-phenylalanine catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-proline catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-tyrosine catabolism atoB hi Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized) 59% 99% 448
L-isoleucine catabolism fadA hi acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 54% 100% 397.9
L-isoleucine catabolism fadA hi acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 434.5
4-hydroxybenzoate catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 40% 100% 262.3 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
4-hydroxybenzoate catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 40% 100% 262.3 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
phenylacetate catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 40% 100% 262.3 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
L-phenylalanine catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 40% 100% 262.3 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
L-tryptophan catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 40% 100% 262.3 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
phenylacetate catabolism paaJ1 lo 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 38% 100% 250.4 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
L-phenylalanine catabolism paaJ1 lo 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 38% 100% 250.4 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 37% 98% 206.8 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 37% 98% 206.8 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 37% 98% 206.8 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 59% 448.0

Sequence Analysis Tools

View CA265_RS06590 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

MKEVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIEKAGLKPEQIQEVYMGNVLSAN
LGQAPATQAAKFAGLPDLPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESMSNV
PYYLDKARNGYRLGHGQITDGLVKDGLWDVYNDYHMGSAAELCATECNINREAQDNFAIS
SYKRAQAAQTSGKFANEIVAIEVKDRKGDITLVDTDDEPTAVKFDKIPSLKPVFKKDGTV
TAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPSKAIPLALH
KANVNINDVDFFEINEAFAVVSIANNQLLALNDNQVNVNGGAVSLGHPLGASGARIVVTL
LSVLAQNDGKIGVAGICNGGGGASALVIGKL

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