GapMind for catabolism of small carbon sources

 

Protein WP_012755213.1 in Rhizobium leguminosarum WSM1325

Annotation: NCBI__GCF_000023185.1:WP_012755213.1

Length: 401 amino acids

Source: GCF_000023185.1 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
4-hydroxybenzoate catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
4-hydroxybenzoate catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-isoleucine catabolism fadA med acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized) 42% 99% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
phenylacetate catabolism paaJ1 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
phenylacetate catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-phenylalanine catabolism paaJ1 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-phenylalanine catabolism paaJ2 med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-tryptophan catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 45% 98% 268.9 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
4-hydroxybenzoate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-arginine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-citrulline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
2-deoxy-D-ribonate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
2-deoxy-D-ribose catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-leucine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-lysine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
phenylacetate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-phenylalanine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-proline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6
L-tyrosine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 42% 98% 266.2 Putative acetyl-CoA C-acetyltransferase YhfS; EC 2.3.1.- 45% 291.6

Sequence Analysis Tools

View WP_012755213.1 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

MSYAFQPDEDWQPVVVAAYRSPIGRAFGSLATVAAEDLLAPIMHRILLETGIAPDTIDDV
LVGNAAGGGGNIARLAALTAGLPMSVPGVAIDRQCGSGLEAIIMAARLIQAKAGACFLAG
GVESVSTAPWRVERPKANGMPPRFYGRARFSPETIGDPEMGIAAENVARQFGISRQRQDE
FALRSHRLAVAAAEAGIFRPEIVEISTGHGPIERDECPRASTSLEALANLRPVFLADGSV
TAGNACPLNDGACLVLVMSRGMARSMGVEKGLAFIDSAAAGVDPNLLGIGPVASTRKLLK
RQPELSLLDIDAIEFNEAFAAQVLASLDQLAIPADAINKDGGAIALGHPFGASGAILVTR
LYSQLIRNTGEVGAPGATALAMIGIGGGIGLTAMFEATQLS

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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