GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Calditerrivibrio nitroreducens DSM 19672

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 Known gap?
prs ribose-phosphate diphosphokinase CALNI_RS01175  
hisG ATP phosphoribosyltransferase CALNI_RS01480  
hisI phosphoribosyl-ATP pyrophosphatase CALNI_RS01305 CALNI_RS06400  
hisE phosphoribosyl-AMP cyclohydrolase CALNI_RS07385 CALNI_RS06400  
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase CALNI_RS09815 CALNI_RS01310  
hisF imidazole glycerol phosphate synthase, cyclase subunit CALNI_RS01310  
hisH imidazole glycerol phosphate synthase, amidotransferase subunit CALNI_RS09820 CALNI_RS01310  
hisB imidazoleglycerol-phosphate dehydratase CALNI_RS09825  
hisC histidinol-phosphate aminotransferase CALNI_RS00445 CALNI_RS10710  
hisN? histidinol-phosphate phosphatase CALNI_RS09825 known gap
hisD histidinal/histidinol dehydrogenase CALNI_RS06400  

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