GapMind for catabolism of small carbon sources

 

Protein WP_061532136.1 in Collimonas arenae Ter10

Annotation: NCBI__GCF_001584165.1:WP_061532136.1

Length: 398 amino acids

Source: GCF_001584165.1 in NCBI

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; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized) 50% 99% 362.8 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 451.8 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
4-hydroxybenzoate catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-arginine catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-citrulline catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
2-deoxy-D-ribonate catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
2-deoxy-D-ribose catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-leucine catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-lysine catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
phenylacetate catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-phenylalanine catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-proline catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
L-tyrosine catabolism atoB med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized) 45% 92% 309.3 3-oxopimeloyl-CoA:CoA acetyltransferase 45% 303.1
4-hydroxybenzoate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 45% 99% 303.1 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
phenylacetate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 45% 99% 303.1 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
L-phenylalanine catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 45% 99% 303.1 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8
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) 43% 100% 297.4 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 50% 362.8

Sequence Analysis Tools

View WP_061532136.1 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

MSKQLQEAYIVSATRTPIGKAPRGMFKNTRPDDLLVRVMQSAMAQVPGLDPKLVQDAIIG
CSFPEGAQGLNMARNAVLLAGLPNTIGGVTVNRYCASGITAIAMAADRIRVGEADVMIAG
GAESMSMVPMMGFHPSINMNAFKDENVGMAYGMGLTAEKVAQQWKVSREAQDAFAVESHR
RAIAGQLAGEFKDETTSYDIIDRAPNLATGQIDLKTRTVDRDEGARAESSMETLGKLKAV
FAAKGTVTAGNSSQMSDGAGALILVSEKILKEHNLTPLARFVSFAVRGVPPEIMGIGPKE
AIPAALRAAGLTQDQLDWIELNEAFAAQALAVIQDLGLDPSKVNPLGGAIALGHPLGATG
AIRAATAIHGIRRRNQKYGMVTMCVGAGMGAAGIFERM

This GapMind analysis is from Sep 24 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:

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