GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Sinorhizobium fredii NGR234

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 NGR_RS22655
hisG ATP phosphoribosyltransferase NGR_RS13390
hisI phosphoribosyl-ATP pyrophosphatase NGR_RS28105 NGR_RS12475
hisE phosphoribosyl-AMP cyclohydrolase NGR_RS17535 NGR_RS12475
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase NGR_RS28115 NGR_RS28110
hisF imidazole glycerol phosphate synthase, cyclase subunit NGR_RS28110 NGR_RS28115
hisH imidazole glycerol phosphate synthase, amidotransferase subunit NGR_RS28120 NGR_RS28110
hisB imidazoleglycerol-phosphate dehydratase NGR_RS28130
hisC histidinol-phosphate aminotransferase NGR_RS27510 NGR_RS24690
hisN histidinol-phosphate phosphatase NGR_RS25515 NGR_RS07740
hisD histidinal/histidinol dehydrogenase NGR_RS12475 NGR_RS07705

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