GapMind for Amino acid biosynthesis


Protein 208494 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU2981 2-isopropylmalate synthase

Length: 509 amino acids

Source: 882 in MicrobesOnline

Candidate for 3 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-leucine biosynthesis leuA hi 2-isopropylmalate synthase (EC (characterized) 55% 97% 531.9 homocitrate synthase (EC 47% 447.6
L-leucine biosynthesis leuA med leuA: 2-isopropylmalate synthase (EC (TIGR00973) 100% 715.7 homocitrate synthase (EC 47% 447.6
L-lysine biosynthesis hcs med homocitrate synthase (EC (characterized) 47% 95% 447.6 2-isopropylmalate synthase (EC 55% 531.9
L-isoleucine biosynthesis cimA med (R)-citramalate synthase CimA; EC (characterized) 43% 100% 385.6 2-isopropylmalate synthase (EC 55% 531.9

Sequence Analysis Tools

View 208494 at MicrobesOnline

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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...



This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.



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 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, the preprint on GapMind for carbon sources, 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