GapMind for Amino acid biosynthesis

 

Protein WP_012568155.1 in Rhodospirillum centenum SW SW; ATCC 51521

Annotation: NCBI__GCF_000016185.1:WP_012568155.1

Length: 412 amino acids

Source: GCF_000016185.1 in NCBI

Candidate for 9 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine biosynthesis PPYAT lo aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized) 36% 92% 198.7 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-phenylalanine biosynthesis ptransferase lo aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized) 36% 92% 198.7 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-tyrosine biosynthesis ptransferase lo aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized) 36% 92% 198.7 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-tyrosine biosynthesis tyrB lo aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized) 36% 92% 198.7 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-lysine biosynthesis lysN lo Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized) 35% 91% 198 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-lysine biosynthesis dapX lo Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized) 31% 94% 179.9 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
glycine biosynthesis agx1 lo alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized) 30% 92% 175.6 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-valine biosynthesis ilvE lo Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized) 32% 91% 162.2 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8
L-lysine biosynthesis DAPtransferase lo LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized) 30% 98% 153.7 arginine-pyruvate transaminase (EC 2.6.1.84) 39% 213.8

Sequence Analysis Tools

View WP_012568155.1 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

MPILHDLPGLRPVVAGLEETRIVQMVQYGRGREGLIPLWVGEGDVPTPDFIREACDRAIR
DGRVFYTWQRGLPELREGLAAYLSGNHGVAVGMERITVASSGMQAIMLALQALVGPGDEV
VVVTPVWPNVMSAVTLLGGVVVPVPLEPGPGGWRLNPGRVAAAIGPRTRALFVNSPSNPT
GWMLDRDGLRDLWALARRTGIWLIADEVYGRLVYDRAPGQRAVAPSFLELAGPEDRLIVV
NSFSKNWAMTGWRLGWLVTPPALGLVLEKLVQINTSGTPEFIQMAGLAALEQGEDFLAAT
LERCRTGRGIVTAALASVPGVRLLPPAGAFYAFLAVPGVTDTLAFAKDLLDRCGVGLAPG
CAFGPGGEGHLRLCFASSAERLHAAMARLVPALDALAPAADRDSADRKNNAE

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

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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