GapMind for Amino acid biosynthesis

 

Protein WP_013092629.1 in Paraburkholderia atlantica CCGE1002

Annotation: NCBI__GCF_000092885.1:WP_013092629.1

Length: 413 amino acids

Source: GCF_000092885.1 in NCBI

Candidate for 6 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metB hi O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized) 67% 98% 544.3 methionine gamma-lyase (EC 4.4.1.11); alliin lyase (EC 4.4.1.4) 35% 258.1
L-methionine biosynthesis metZ hi O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized) 67% 98% 544.3 methionine gamma-lyase (EC 4.4.1.11); alliin lyase (EC 4.4.1.4) 35% 258.1
L-methionine biosynthesis metY hi O-acetylhomoserine (Thiol)-lyase (characterized, see rationale) 54% 99% 436 methionine gamma-lyase (EC 4.4.1.11); alliin lyase (EC 4.4.1.4) 35% 258.1
L-methionine biosynthesis metC lo Cystathionine beta-lyase MetC; CBL; Beta-cystathionase MetC; Cysteine lyase MetC; Cysteine-S-conjugate beta-lyase MetC; EC 4.4.1.13 (characterized) 34% 99% 216.9 O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) 67% 544.3
L-cysteine biosynthesis cysK lo Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized) 32% 97% 214.2 O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) 67% 544.3
L-cysteine biosynthesis CGL lo cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized) 34% 98% 212.2 O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) 67% 544.3

Sequence Analysis Tools

View WP_013092629.1 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

MDKQGFTTGIVHGDRTAGTEHGALRQPVHTSVQYGFERVEDLIGVFQGTKKGGFNYARQG
TPTTAALERKITSLEEGVGTVCFSTGMAGITATFLTLLRAGDHLVSSRYVFGNTNSLFGT
LRALGVEVTTVDACRLDDVKNAIRPNTRMVFVETIANPGTQIPDLQGIGDVCRERGIAYV
VDNTITSPALFKPKAVGASLVINSLTKTIAGHGAALGGAVTDTGLFDWSAYPNIADDYRR
SGAKDQGLLQIRKKGLRDMGASLSSEQAHSIAMGAETLALRVRQSSDNALALAQFLEGHE
AIGKVFYPGLKSHPQYDIAQTLFKGASWLLSFELLNVDRMIEVVNALKLPVKATGLGDTR
TLIIPVAPTIFFEAGPETRKAMGISDGMLRLSAGIEDIDDLIADFAQALKLAA

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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