GapMind for Amino acid biosynthesis

Searching NCBI assemblies for 'Desulfovibrio vulgaris'

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Related tools

• GapMind for catabolism of small carbon sources
• Clusters of characterized proteins
• PaperBLAST: Find papers about a protein or its homologs
• Curated BLAST for Genomes

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:

• ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
  • (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
• HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

Otherwise, a candidate is "medium confidence" if either:

• ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
• ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
• HMMer finds a hit (regardless of coverage or other bits).

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:

• our ignorance of proteins' functions,
• omissions in the gene models,
• frame-shift errors in the genome sequence, or
• the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
• the source code
• instructions for running GapMind on your computer
• 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