GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Azospirillum sp. B510

Best path

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


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 AZL_RS11895 AZL_RS31030
hisG ATP phosphoribosyltransferase AZL_RS29220
hisI phosphoribosyl-ATP pyrophosphatase AZL_RS15360 AZL_RS11510
hisE phosphoribosyl-AMP cyclohydrolase AZL_RS06805 AZL_RS29225
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase AZL_RS15370 AZL_RS15365
hisF imidazole glycerol phosphate synthase, cyclase subunit AZL_RS15365 AZL_RS15370
hisH imidazole glycerol phosphate synthase, amidotransferase subunit AZL_RS15380 AZL_RS15365
hisB imidazoleglycerol-phosphate dehydratase AZL_RS15385
hisC histidinol-phosphate aminotransferase AZL_RS17465 AZL_RS06835
hisN histidinol-phosphate phosphatase AZL_RS02265 AZL_RS12635
hisD histidinal/histidinol dehydrogenase AZL_RS29225

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