GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1577
hisG ATP phosphoribosyltransferase PfGW456L13_5001
hisI phosphoribosyl-ATP pyrophosphatase PfGW456L13_303 PfGW456L13_5000
hisE phosphoribosyl-AMP cyclohydrolase PfGW456L13_302 PfGW456L13_5000
hisA isomerase HisA PfGW456L13_359 PfGW456L13_358
hisF IGP synthase, cyclase subunit PfGW456L13_358 PfGW456L13_359
hisH IGP synthase, amidotransferase subunit PfGW456L13_361 PfGW456L13_4238
hisB IGP dehydratase PfGW456L13_362
hisC histidinol-phosphate aminotransferase PfGW456L13_4999 PfGW456L13_2177
hisN histidinol-phosphate phosphatase PfGW456L13_951 PfGW456L13_4205
hisD histidinol dehydrogenase PfGW456L13_5000

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:

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