GapMind for catabolism of small carbon sources

 

Protein 3610436 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)

Length: 400 amino acids

Source: Dino 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 paaJ2 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 70% 100% 561.6 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
4-hydroxybenzoate catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 674.7 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
4-hydroxybenzoate catabolism pcaF hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 68% 100% 544.7 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 65% 505.8
4-hydroxybenzoate catabolism pcaF med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 674.7 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 65% 505.8
phenylacetate catabolism paaJ2 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 70% 100% 561.6 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
phenylacetate catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 674.7 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
L-phenylalanine catabolism paaJ2 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 70% 100% 561.6 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
L-phenylalanine catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 674.7 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
L-tryptophan catabolism pcaF hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 68% 100% 544.7 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 65% 505.8
L-tryptophan catabolism pcaF med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 674.7 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 65% 505.8
phenylacetate catabolism paaJ1 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 70% 100% 561.6 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
L-phenylalanine catabolism paaJ1 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 70% 100% 561.6 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 45% 325.5
L-isoleucine catabolism fadA hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 68% 100% 544.7 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 441.1 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
4-hydroxybenzoate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-arginine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-citrulline catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
2-deoxy-D-ribonate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
2-deoxy-D-ribose catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-leucine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-lysine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
phenylacetate catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-phenylalanine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-proline catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
L-tyrosine catabolism atoB med Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized) 45% 99% 325.5 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 67% 534.3
4-hydroxybenzoate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 42% 99% 266.9 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 68% 544.7
phenylacetate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 42% 99% 266.9 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 68% 544.7
L-phenylalanine catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 42% 99% 266.9 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 68% 544.7

Sequence Analysis Tools

View 3610436 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

MDAVICDGVRTPIGRYGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAG
EDNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMS
RAPFVMPKAESAFTRAATVHDTTIGWRFVNPKIAAMHGIDTMPQTADTVAAAYEISRADQ
DAFAARSQARWAAADAAGLFADEIVPVPVPQRGSAPILVDRDEHPRPGTDAARLAGLKGI
NGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGVAPRVMGIGPVP
ASRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNGGAIAMGHPLGM
SGARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILERV

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