GapMind for Amino acid biosynthesis

 

Protein AZOBR_RS31185 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS31185 ribose-phosphate pyrophosphokinase

Length: 311 amino acids

Source: azobra in FitnessBrowser

Candidate for 1 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine biosynthesis prs hi Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized) 53% 99% 325.9
L-histidine biosynthesis prs hi prs: ribose-phosphate diphosphokinase (EC 2.7.6.1) (TIGR01251) 100% 374.8

Sequence Analysis Tools

View AZOBR_RS31185 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKVLAGNSNRPLAEAISTCLGVPLTKASIRRFSDMEVFVEILENVRGEDVFVVQSTSFPA
NDNLMELLVTIDALRRGSARRITAVLPYYGYARQDRKTGPRTPISAKLVANLITQAGANR
VLTMDLHAGQIQGFFDIPTDNLMAAPVFEKDIRATFEDIGEVTMVSPDVGGVVRARSLAK
RLDADLAIIDKRRERAGVSEVMNIIGDVKNRRCILLDDIVDSGGTLCNAAVALMDAGAKS
VHAYCTHGVLSGGAVARVAVSPLEQLVTTDSIQATEAVRVSRNIRQLTIAPLLADAITRI
SEERSVSSLFS

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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