cmutase, preph-dehydratase, PPYAT
Also see fitness data for the top candidates
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).
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| cmutase | chorismate mutase | Synpcc7942_1915 | Synpcc7942_0881 |
| preph-dehydratase | prephenate dehydratase | Synpcc7942_0881 | |
| PPYAT | phenylpyruvate aminotransferase | Synpcc7942_2545 | Synpcc7942_1794 |
| Alternative steps: | |||
| aro-dehydratase | arogenate dehydratase | Synpcc7942_0881 | |
| ptransferase | prephenate aminotransferase | Synpcc7942_1029 | Synpcc7942_2545 |
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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:
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