GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Pedobacter sp. GW460-11-11-14-LB5

Best path

prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD

Also see fitness data for the top candidates

Rules

Overview: Histidine biosynthesis in GapMind is based on the MetaCyc pathway (link).

11 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
prs ribose-phosphate diphosphokinase CA265_RS24735 CA265_RS03655
hisG ATP phosphoribosyltransferase CA265_RS03640
hisI phosphoribosyl-ATP pyrophosphatase CA265_RS03605 CA265_RS03635
hisE phosphoribosyl-AMP cyclohydrolase CA265_RS03605 CA265_RS03635
hisA isomerase HisA CA265_RS03615 CA265_RS19260
hisF IGP synthase, cyclase subunit CA265_RS03610 CA265_RS19260
hisH IGP synthase, amidotransferase subunit CA265_RS03620 CA265_RS19265
hisB IGP dehydratase CA265_RS03625
hisC histidinol-phosphate aminotransferase CA265_RS03630 CA265_RS11675
hisN histidinol-phosphate phosphatase CA265_RS03625 CA265_RS06215
hisD histidinol dehydrogenase CA265_RS03635

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 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, 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