GapMind for Amino acid biosynthesis

 

Definition of L-phenylalanine biosynthesis

As rules and steps, or see full text

Rules

Overview: Phenylalanine biosynthesis in GapMind is based on MetaCyc pathways L-phenylalanine biosynthesis I (link), II (link), and III (link). Pathways I and III proceed via 3-phenyl-2-oxopropanoate, but with different amino acids providing the amino group for the conversion to phenylalanine. In pathway II, L-arogenate is the intermediate (the aminotransferase reaction occurs before the dehydratase reaction).

Steps

PPYAT: tyrosine:phenylpyruvate aminotransferase

cmutase: chorismate mutase

preph-dehydratase: prephenate dehydratase

ilvE: phenylalanine transaminase

ptransferase: prephenate aminotransferase

aro-dehydratase: arogenate dehydratase

Links

Downloads

Related tools

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, the preprint on GapMind for carbon sources, 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