GapMind for Amino acid biosynthesis


Finding step PPYAT for L-phenylalanine biosynthesis in Dyella japonica UNC79MFTsu3.2

5 candidates for PPYAT: tyrosine:phenylpyruvate aminotransferase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi N515DRAFT_3488 aromatic-amino-acid transaminase Aromatic-amino-acid aminotransferase (EC (characterized) 51% 99% 391 Aspartate aminotransferase (EC 46% 356.3
med N515DRAFT_0573 branched-chain amino acid aminotransferase branched-chain-amino-acid transaminase (EC (characterized) 58% 100% 357.5 Branched-chain amino acid aminotransferase (EC 62% 385.2
med N515DRAFT_2015 branched-chain amino acid aminotransferase branched-chain-amino-acid transaminase (EC (characterized) 57% 99% 345.9 Branched-chain amino acid aminotransferase (EC 100% 622.9
lo N515DRAFT_1217 transcriptional regulator, GntR family Aromatic-amino-acid aminotransferase (EC (characterized) 30% 97% 191.4 uncharacterized HTH-type transcriptional regulator yjiR 39% 323.9
lo N515DRAFT_2186 alanine-synthesizing transaminase Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC (characterized) 30% 93% 160.6 valine-3-methyl-2-oxovalerate transaminase (EC 43% 331.6

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

Also see fitness data for the candidates

Definition of step PPYAT

Or cluster all characterized PPYAT proteins

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, 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