GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Methylosarcina fibrata AML-C10

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 A3OW_RS0120450 A3OW_RS0107025
hisG ATP phosphoribosyltransferase A3OW_RS0118685
hisI phosphoribosyl-ATP pyrophosphatase A3OW_RS0101480 A3OW_RS0118680
hisE phosphoribosyl-AMP cyclohydrolase A3OW_RS0101485 A3OW_RS0118680
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase A3OW_RS0101495 A3OW_RS0101490
hisF imidazole glycerol phosphate synthase, cyclase subunit A3OW_RS0101490 A3OW_RS0101495
hisH imidazole glycerol phosphate synthase, amidotransferase subunit A3OW_RS0101500 A3OW_RS0101490
hisB imidazoleglycerol-phosphate dehydratase A3OW_RS0101505
hisC histidinol-phosphate aminotransferase A3OW_RS0108105 A3OW_RS0118675
hisN histidinol-phosphate phosphatase A3OW_RS0104935 A3OW_RS0101505
hisD histidinal/histidinol dehydrogenase A3OW_RS0118680

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