GapMind for catabolism of small carbon sources

 

Protein 5209189 in Shewanella loihica PV-4

Annotation: Shew_1667 acetyl-CoA acetyltransferase (RefSeq)

Length: 396 amino acids

Source: PV4 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 hi 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized) 86% 100% 657.5
L-isoleucine catabolism fadA hi acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 417.5
4-hydroxybenzoate catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-arginine catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-citrulline catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
2-deoxy-D-ribonate catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
2-deoxy-D-ribose catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-leucine catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-lysine catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
phenylacetate catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-phenylalanine catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-proline catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
L-tyrosine catabolism atoB hi acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized) 62% 99% 477.6
4-hydroxybenzoate catabolism paaJ2 med Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 41% 99% 275 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
4-hydroxybenzoate catabolism pcaF med Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 41% 99% 275 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
phenylacetate catabolism paaJ2 med Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 41% 99% 275 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
L-phenylalanine catabolism paaJ2 med Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 41% 99% 275 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
L-tryptophan catabolism pcaF med Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 41% 99% 275 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
phenylacetate catabolism paaJ1 lo 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 38% 99% 249.2 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
L-phenylalanine catabolism paaJ1 lo 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 38% 99% 249.2 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 34% 99% 206.1 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 34% 99% 206.1 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 34% 99% 206.1 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) 86% 657.5

Sequence Analysis Tools

View 5209189 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

MSTEQTNQEIVIVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDAAGVQGGDVNEVLMG
CVLPAGLGQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGG
MESMSQAPYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADDFGITREA
MDNFALSSLQKANAAIESGAFKAEIVPVTVASRKGDLVVDTDEQPGNARPEKIPTLRPAF
AKDGTITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTAPVGA
MNKLLDKVNWSKDEVDLFEINEAFAMVTMLAISELGLDEAKVNVNGGACALGHPIGCSGA
RVLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV

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