GapMind for Amino acid biosynthesis


GapMind for Amino acid biosynthesis

Searching NCBI assemblies for 'Desulfovibrio vulgaris'

Found 5 assemblies, please choose one:

Desulfovibrio vulgaris Hildenborough (GCF_902167245.1)
Desulfovibrio vulgaris RCH1 (GCF_000166115.1)
Desulfovibrio vulgaris Hildenborough (GCF_000195755.1)
Desulfovibrio vulgaris Miyazaki F (GCF_000021385.1)
Desulfovibrio vulgaris DP4 (GCF_000015485.1)

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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).

For more information, see the preprint.

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