GapMind for Amino acid biosynthesis

 

chorismate biosynthesis in Shewanella oneidensis MR-1

Best path

aroG, aroB, aroD, aroE, aroL, aroA, aroC?

Also see fitness data for the top candidates

Rules

Overview: Chorismate is the starting point for the biosynthesis of the aromatic amino acids phenylalanine, tryptophan, and tyrosine. Chorismate biosynthesis in GapMind is based on MetaCyc pathways chorismate biosynthesis I (link), from D-erythrose-4-phosphate and phosphoenolpyruvate, or II (link), from D-glyceraldeyde-3-phosphate and L-asparatate. Both pathways are identical after they reach 3-dehydroquinate.

13 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
aroG 3-deoxy-7-phosphoheptulonate synthase SO0756 SO2646  
aroB 3-dehydroquinate synthase SO0287  
aroD 3-dehydroquinate dehydratase SO0512  
aroE shikimate dehydrogenase SO0040  
aroL shikimate kinase SO0286  
aroA 3-phosphoshikimate 1-carboxyvinyltransferase SO2404  
aroC? chorismate synthase SO3078.2 spurious
Alternative steps:
aroA' 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase  
aroB' dehydroquinate synthase II  
asd aspartate semi-aldehyde dehydrogenase SO3070  
asp-kinase aspartate kinase SO3415 SO4055  
fbp 6-deoxy-5-ketofructose 1-phosphate synthase SO0933  
tpiA D-glyceraldehyde-3-phosphate phospholyase SO1200 SO0932  

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 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