GapMind for Amino acid biosynthesis

 

L-phenylalanine biosynthesis in Bacteroides thetaiotaomicron VPI-5482

Best path

cmutase, preph-dehydratase, ilvE

Also see fitness data for the top candidates

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).

6 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
cmutase chorismate mutase BT3934 BT3936
preph-dehydratase prephenate dehydratase BT3936
ilvE phenylalanine transaminase BT2415 BT0735
Alternative steps:
aro-dehydratase arogenate dehydratase BT3936
PPYAT tyrosine:phenylpyruvate aminotransferase BT3375 BT2415
ptransferase prephenate aminotransferase BT2415 BT3375

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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