GapMind for Amino acid biosynthesis

 

L-tryptophan biosynthesis in Pelobacter propionicus DSM 2379

Best path

trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB

Rules

Overview: Tryptophan biosynthesis in GapMind is based on MetaCyc pathway L-tryptophan biosynthesis (link), from chorismate, glutamine, 5-phosphoribose-1-diphosphate, and serine.

8 steps (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
trpE anthranilate synthase subunit TrpE PPRO_RS07880 PPRO_RS13915
trpD_1 glutamine amidotransferase of anthranilate synthase PPRO_RS07875 PPRO_RS12485
trpD_2 anthranilate phosphoribosyltransferase PPRO_RS03485
PRAI phosphoribosylanthranilate isomerase PPRO_RS06400 PPRO_RS15175
IGPS indole-3-glycerol phosphate synthase PPRO_RS03480
trpA indoleglycerol phosphate aldolase PPRO_RS05700
trpB tryptophan synthase PPRO_RS06395 PPRO_RS06405
Alternative steps:
trpED anthranilate synthase, alpha proteobacterial clade

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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 (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:

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. 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