GapMind for Amino acid biosynthesis

 

Finding step serC for L-serine biosynthesis in Echinicola vietnamensis KMM 6221, DSM 17526

Manual classification of gap: diverged
Rationale: Echvi_1811 could be a diverged phosphoserine aminotransferase. It appears to be essential (PMID:29769716)

No candidates for serC: 3-phosphoserine aminotransferase

Definition of step serC

Or cluster all characterized serC proteins

Known gaps in related organisms

This GapMind analysis is from Mar 30 2021. The underlying query database was built on Mar 30 2021.

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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 paper from 2019 on GapMind for amino acid biosynthesis, 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