GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Hydrogenovibrio halophilus DSM 15072

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 A377_RS0106745
hisG ATP phosphoribosyltransferase A377_RS0108545
hisI phosphoribosyl-ATP pyrophosphatase A377_RS0106850 A377_RS0108550
hisE phosphoribosyl-AMP cyclohydrolase A377_RS0104075 A377_RS0108550
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase A377_RS0106860 A377_RS0106855
hisF imidazole glycerol phosphate synthase, cyclase subunit A377_RS0106855 A377_RS0106860
hisH imidazole glycerol phosphate synthase, amidotransferase subunit A377_RS0106865 A377_RS0106855
hisB imidazoleglycerol-phosphate dehydratase A377_RS0106870
hisC histidinol-phosphate aminotransferase A377_RS0102575 A377_RS0110540
hisN histidinol-phosphate phosphatase A377_RS0108600 A377_RS0106870
hisD histidinal/histidinol dehydrogenase A377_RS0108550

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