GapMind for Amino acid biosynthesis


Protein 3607880 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607880

Length: 388 amino acids

Source: Dino in FitnessBrowser

Candidate for 3 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argE lo Predicted argE by GapMind curators (no experimental data) 34% 97% 228 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 44% 304.7
L-proline biosynthesis argE lo Predicted argE by GapMind curators (no experimental data) 34% 97% 228 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 44% 304.7
L-lysine biosynthesis dapL lo N-acetyldiaminopimelate deacetylase; EC (uncharacterized) 37% 95% 224.2 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 44% 304.7

Sequence Analysis Tools

View 3607880 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

Fitness BLAST: loading...



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



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