GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Rhodanobacter denitrificans FW104-10B01

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 LRK54_RS03690 LRK54_RS01960
hisG ATP phosphoribosyltransferase LRK54_RS01610
hisI phosphoribosyl-ATP pyrophosphatase LRK54_RS01575 LRK54_RS01605
hisE phosphoribosyl-AMP cyclohydrolase LRK54_RS01575 LRK54_RS01605
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase LRK54_RS01585
hisF imidazole glycerol phosphate synthase, cyclase subunit LRK54_RS01580 LRK54_RS01585
hisH imidazole glycerol phosphate synthase, amidotransferase subunit LRK54_RS01590
hisB imidazoleglycerol-phosphate dehydratase LRK54_RS01595
hisC histidinol-phosphate aminotransferase LRK54_RS01600 LRK54_RS11155
hisN histidinol-phosphate phosphatase LRK54_RS01595 LRK54_RS04140
hisD histidinal/histidinol dehydrogenase LRK54_RS01605

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