GapMind for Amino acid biosynthesis

 

Definition of L-serine biosynthesis

As rules and steps, or see full text

Rules

Overview: Serine biosynthesis in GapMind is based on MetaCyc pathway L-serine biosynthesis I (link). Pathway II (link) is not included because it is known only in plants. Also, MetaCyc states that the gene for the first step (EC 3.1.3.38) is not known. (Alkaline phosphatase from E. coli (phoA) is reported to be catalyze this reaction, but it has rather broad specificity.)

Steps

serA: 3-phosphoglycerate dehydrogenase

serC: 3-phosphoserine aminotransferase

serB: phosphoserine phosphatase

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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 (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:

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. 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:

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:

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