GapMind for Amino acid biosynthesis


Protein 208745 in Desulfovibrio vulgaris Hildenborough

Annotation: MicrobesOnline__882:208745

Length: 390 amino acids

Source: 882 in MicrobesOnline

Candidate for 10 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine biosynthesis PPYAT hi aspartate transaminase (EC (characterized) 47% 99% 354
L-tyrosine biosynthesis tyrB hi aspartate transaminase (EC (characterized) 47% 99% 354
L-phenylalanine biosynthesis ptransferase hi Aspartate/prephenate aminotransferase; AspAT / PAT; EC; EC (characterized) 48% 99% 348.6
L-tyrosine biosynthesis ptransferase hi Aspartate/prephenate aminotransferase; AspAT / PAT; EC; EC (characterized) 48% 99% 348.6
L-lysine biosynthesis lysN lo Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC; EC (characterized) 40% 95% 287.7 aspartate transaminase (EC 47% 354.0
L-lysine biosynthesis dapX lo Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized) 38% 94% 245.4 aspartate transaminase (EC 47% 354.0
glycine biosynthesis agx1 lo alanine—glyoxylate transaminase (EC (characterized) 33% 100% 227.3 aspartate transaminase (EC 47% 354.0
L-lysine biosynthesis DAPtransferase lo LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC (uncharacterized) 31% 97% 186.4 aspartate transaminase (EC 47% 354.0
L-lysine biosynthesis dapC lo succinyldiaminopimelate transaminase (EC (characterized) 32% 97% 170.2 aspartate transaminase (EC 47% 354.0
L-methionine biosynthesis metC lo kynurenine-oxoglutarate transaminase (EC (characterized) 32% 77% 162.9 aspartate transaminase (EC 47% 354.0

Sequence Analysis Tools

View 208745 at MicrobesOnline

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

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This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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