GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Pelobacter propionicus DSM 2379

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 Class of gap Known gap?
prs ribose-phosphate diphosphokinase PPRO_RS03640    
hisG ATP phosphoribosyltransferase PPRO_RS14615 PPRO_RS15100    
hisI phosphoribosyl-ATP pyrophosphatase PPRO_RS15165 PPRO_RS15095    
hisE? phosphoribosyl-AMP cyclohydrolase PPRO_RS15095 spurious  
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase PPRO_RS15175 PPRO_RS15170    
hisF imidazole glycerol phosphate synthase, cyclase subunit PPRO_RS15170 PPRO_RS15175    
hisH imidazole glycerol phosphate synthase, amidotransferase subunit PPRO_RS15180 PPRO_RS15170    
hisB imidazoleglycerol-phosphate dehydratase PPRO_RS15085    
hisC histidinol-phosphate aminotransferase PPRO_RS15090 PPRO_RS07560    
hisN? histidinol-phosphate phosphatase PPRO_RS15085 PPRO_RS00085   known gap
hisD histidinal/histidinol dehydrogenase PPRO_RS15095    

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