GapMind for catabolism of small carbon sources

 

Protein 6935813 in Shewanella amazonensis SB2B

Annotation: Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)

Length: 387 amino acids

Source: SB2B 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) 100% 100% 758.8 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-isoleucine catabolism fadA med fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16) (TIGR02445) 100% 730.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
4-hydroxybenzoate catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 45% 100% 302.8 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
phenylacetate catabolism paaJ1 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 45% 100% 302.8 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
phenylacetate catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 45% 100% 302.8 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
L-phenylalanine catabolism paaJ1 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 45% 100% 302.8 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
L-phenylalanine catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 45% 100% 302.8 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
4-hydroxybenzoate catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 44% 100% 298.9 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
L-tryptophan catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 44% 100% 298.9 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
4-hydroxybenzoate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-arginine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-citrulline catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
2-deoxy-D-ribonate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
2-deoxy-D-ribose catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-leucine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-lysine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
phenylacetate catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-phenylalanine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-proline catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
L-tyrosine catabolism atoB med acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized) 44% 100% 291.2 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 48% 334.7
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 100% 241.5 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 100% 241.5 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 40% 100% 241.5 Acetyl-CoA C-acyltransferase (EC 2.3.1.16) 100% 758.8

Sequence Analysis Tools

View 6935813 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

MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ
TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH
MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS
IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA
LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ
DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM
EHKDATLGLATMCIGLGQGIATVFERV

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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 paper from 2022 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