GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Thiomicrospira cyclica ALM1

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 THICY_RS07000
hisG ATP phosphoribosyltransferase THICY_RS02425
hisI phosphoribosyl-ATP pyrophosphatase THICY_RS07815 THICY_RS02430
hisE phosphoribosyl-AMP cyclohydrolase THICY_RS07470 THICY_RS02430
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase THICY_RS07805 THICY_RS07810
hisF imidazole glycerol phosphate synthase, cyclase subunit THICY_RS07810 THICY_RS07805
hisH imidazole glycerol phosphate synthase, amidotransferase subunit THICY_RS07800 THICY_RS07810
hisB imidazoleglycerol-phosphate dehydratase THICY_RS07795
hisC histidinol-phosphate aminotransferase THICY_RS04220 THICY_RS02435
hisN histidinol-phosphate phosphatase THICY_RS03595 THICY_RS07795
hisD histidinal/histidinol dehydrogenase THICY_RS02430

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