GapMind for Amino acid biosynthesis


L-tryptophan biosynthesis in Nocardioides dokdonensis FR1436

Best path

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


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 Known gap?
trpE? anthranilate synthase subunit TrpE I601_RS03910 I601_RS05290 known gap
trpD_1 glutamine amidotransferase of anthranilate synthase I601_RS05295 I601_RS05300  
trpD_2 anthranilate phosphoribosyltransferase I601_RS13135  
PRAI phosphoribosylanthranilate isomerase I601_RS13625  
IGPS indole-3-glycerol phosphate synthase I601_RS18240  
trpA indoleglycerol phosphate aldolase I601_RS18230  
trpB tryptophan synthase I601_RS18235  
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.



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