GapMind for Amino acid biosynthesis


Protein GFF2666 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF2666

Length: 406 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 10 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argD'B hi Succinylornithine transaminase (EC (characterized) 79% 100% 672.2
L-arginine biosynthesis argD'B hi astC: succinylornithine transaminase family (EC (TIGR03246) 100% 708.1
L-arginine biosynthesis argD hi succinylornithine transaminase (EC (characterized) 79% 100% 666.8
L-proline biosynthesis argD hi succinylornithine transaminase (EC (characterized) 79% 100% 666.8
L-lysine biosynthesis dapC hi Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC; EC (characterized) 63% 100% 523.1
L-lysine biosynthesis lysJ med [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC (characterized) 42% 92% 274.2 Succinylornithine transaminase (EC 79% 672.2
L-proline biosynthesis OAT lo Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC (characterized) 38% 94% 259.2 Succinylornithine transaminase (EC 79% 672.2
L-arginine biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC; EC (uncharacterized) 39% 95% 253.8 Succinylornithine transaminase (EC 79% 672.2
L-proline biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC; EC (uncharacterized) 39% 95% 253.8 Succinylornithine transaminase (EC 79% 672.2
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC (characterized) 35% 95% 205.3 Succinylornithine transaminase (EC 79% 672.2
glycine biosynthesis agx1 lo beta-alanine-pyruvate transaminase (EC; alanine-glyoxylate transaminase (EC (characterized) 31% 81% 178.7 Succinylornithine transaminase (EC 79% 672.2

Sequence Analysis Tools

View GFF2666 at FitnessBrowser

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