GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Pseudomonas fluorescens FW300-N2E2

Best path

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

Also see fitness data for the top candidates


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 Pf6N2E2_5216 Pf6N2E2_844
hisG ATP phosphoribosyltransferase Pf6N2E2_3253
hisI phosphoribosyl-ATP pyrophosphatase Pf6N2E2_3783 Pf6N2E2_3252
hisE phosphoribosyl-AMP cyclohydrolase Pf6N2E2_3782 Pf6N2E2_3252
hisA isomerase HisA Pf6N2E2_3839 Pf6N2E2_3838
hisF IGP synthase, cyclase subunit Pf6N2E2_3838 Pf6N2E2_3839
hisH IGP synthase, amidotransferase subunit Pf6N2E2_3841
hisB IGP dehydratase Pf6N2E2_3842
hisC histidinol-phosphate aminotransferase Pf6N2E2_3251 Pf6N2E2_2519
hisN histidinol-phosphate phosphatase Pf6N2E2_3940 Pf6N2E2_5785
hisD histidinol dehydrogenase Pf6N2E2_3252

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.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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