GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_3009 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_3009 acetyl-CoA C-acetyltransferase

Length: 427 amino acids

Source: Dyella79 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
L-isoleucine catabolism fadA med 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized) 38% 97% 288.1 3-keto-acyl-CoA-thiolase 37% 243.8
L-isoleucine catabolism fadA hi acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 378.2 3-keto-acyl-CoA-thiolase 37% 243.8
4-hydroxybenzoate catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-arginine catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-citrulline catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
2-deoxy-D-ribonate catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
2-deoxy-D-ribose catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-leucine catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-lysine catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
phenylacetate catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-phenylalanine catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-proline catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
L-tyrosine catabolism atoB lo Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 32% 99% 198.7 3-keto-acyl-CoA-thiolase 37% 243.8
4-hydroxybenzoate catabolism paaJ2 lo subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 32% 100% 188.3 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
4-hydroxybenzoate catabolism pcaF lo subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 32% 100% 188.3 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
phenylacetate catabolism paaJ2 lo subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 32% 100% 188.3 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
L-phenylalanine catabolism paaJ2 lo subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 32% 100% 188.3 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
L-tryptophan catabolism pcaF lo subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 32% 100% 188.3 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
phenylacetate catabolism paaJ1 lo 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 32% 99% 175.6 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
L-phenylalanine catabolism paaJ1 lo 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 32% 99% 175.6 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 31% 98% 169.5 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 31% 98% 169.5 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 31% 98% 169.5 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 38% 288.1

Sequence Analysis Tools

View N515DRAFT_3009 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

MDNTPKRVGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERFRLHGEELGEVAMGAV
IKHSSEWNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSD
TTSDVPIVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGD
HCERMAKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVPFRGLKRDGFLRADSSMEK
LGTLKPAFDKISGHGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVAAVD
FVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCRNRLG
LEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISICTAGGMG
VTAILER

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