GapMind for catabolism of small carbon sources

 

Protein WP_035854742.1 in Dechloromonas agitata is5

Annotation: NCBI__GCF_000519045.1:WP_035854742.1

Length: 427 amino acids

Source: GCF_000519045.1 in NCBI

Candidate for 19 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 lo Trifunctional enzyme subunit beta, mitochondrial; TP-beta; EC 2.3.1.155; EC 2.3.1.16 (characterized) 35% 89% 246.1 3-keto-acyl-CoA-thiolase 71% 615.9
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 428.6 3-keto-acyl-CoA-thiolase 71% 615.9
4-hydroxybenzoate catabolism paaJ2 lo Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 39% 100% 252.3 3-keto-acyl-CoA-thiolase 71% 615.9
4-hydroxybenzoate catabolism pcaF lo Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 39% 100% 252.3 3-keto-acyl-CoA-thiolase 71% 615.9
phenylacetate catabolism paaJ2 lo Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 39% 100% 252.3 3-keto-acyl-CoA-thiolase 71% 615.9
L-phenylalanine catabolism paaJ2 lo Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 39% 100% 252.3 3-keto-acyl-CoA-thiolase 71% 615.9
L-tryptophan catabolism pcaF lo Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized) 39% 100% 252.3 3-keto-acyl-CoA-thiolase 71% 615.9
phenylacetate catabolism paaJ1 lo β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 38% 100% 248.4 3-keto-acyl-CoA-thiolase 71% 615.9
L-phenylalanine catabolism paaJ1 lo β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 38% 100% 248.4 3-keto-acyl-CoA-thiolase 71% 615.9
4-hydroxybenzoate catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-arginine catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-citrulline catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
2-deoxy-D-ribonate catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
2-deoxy-D-ribose catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-leucine catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-lysine catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
phenylacetate catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-phenylalanine catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-proline catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9
L-tyrosine catabolism atoB lo acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 37% 99% 236.9 3-keto-acyl-CoA-thiolase 71% 615.9

Sequence Analysis Tools

View WP_035854742.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MKTIYVVDGARTPFLKAQKGPGPFAASDLATQAGRALLLRQPFEPSDLDEVILGCAAPSP
DETNIGRMVALRLGCGKKVPGWTVMRNCASGMQAIDSAIANIQCGRSELVLAGGVDALSR
APLLYSDAMVRWFAGMMSLRTVGQKLQHFLKLRPAMLLTPVIGLMKGLTDPVVGLLMGQT
AENLAWKFGISRQQMDEFAVRSHQRSIAGRQAGHLAEIVPVVDGQGNVYADDDGVRADAT
LAGMAKPKPFFDKKYGNITAANSSQITDGAAWVLLASEEAVQKWGLKPIGKIVDSEWAGL
EPDQMGLGPVHASTPILQRHGLSLADIDYWELNEAFAAQVLACQAAWKDDAYCREQLDLP
GALGEIPEDRLNVDGGAVSIGHPVGASGARIVLHLLHVLRRNQARRGIATICIGGGLGGA
MLLETVN

This GapMind analysis is from Apr 09 2024. 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:

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