GapMind for Amino acid biosynthesis

 

GapMind: Automated annotation of Amino acid biosynthesis

View 'gaps' in 35 bacteria that grow in minimal media, or choose a genome to analyze:

Genome database to search:

Example: Desulfovibrio vulgaris

Or upload a proteome in fasta format:

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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 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).

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