GapMind for catabolism of small carbon sources

 

Protein 5207484 in Shewanella loihica PV-4

Annotation: Shew_0018 3-ketoacyl-CoA thiolase (RefSeq)

Length: 387 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 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 92% 100% 714.9 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-isoleucine catabolism fadA med fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16) (TIGR02445) 99% 720.9 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
4-hydroxybenzoate catabolism paaJ2 med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
4-hydroxybenzoate catabolism pcaF med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
phenylacetate catabolism paaJ1 med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
phenylacetate catabolism paaJ2 med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
L-phenylalanine catabolism paaJ1 med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
L-phenylalanine catabolism paaJ2 med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
L-tryptophan catabolism pcaF med 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized) 46% 100% 321.6 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
4-hydroxybenzoate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-arginine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-citrulline catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
2-deoxy-D-ribonate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
2-deoxy-D-ribose catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-leucine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-lysine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
phenylacetate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-phenylalanine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-proline catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
L-tyrosine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 45% 99% 293.5 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 45% 321.6
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 99% 235.3 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 99% 235.3 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 99% 235.3 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 92% 714.9

Sequence Analysis Tools

View 5207484 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

MKQAVIVDCIRTPMGRSKAGVFRNMRAESLSAELMKALLVRNPQLDPNTIEDVIWGCVQQ
TLEQGFNIARNAALLAGIPKQAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIVGGVEH
MGHVPMNHGVDFHPGLATNVAKASGMMGLTAEMLGKMHGITRQQQDEFAVRSHQRAHAAT
VEGRFANEIHAIEGHDANGALIKVMHDEVIRPETSLESLATLRPVFDPANGTVTAGTSSA
LSDGASAMLVMEEEKAKALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALQRAGLTMN
DIDLIELNEAFAAQSLPCVKDLGLMDLVDEKVNLNGGAIALGHPLGCSGARISTTLINLM
ESKDATLGLATMCIGLGQGIATVFERA

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