GapMind for Amino acid biosynthesis


L-histidine biosynthesis in Herbaspirillum seropedicae SmR1

Best path

prs, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD

Also see fitness data for the top candidates


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 HSERO_RS19570
hisG ATP phosphoribosyltransferase HSERO_RS20350
hisI phosphoribosyl-ATP pyrophosphatase HSERO_RS20305 HSERO_RS20345
hisE phosphoribosyl-AMP cyclohydrolase HSERO_RS20310 HSERO_RS20345
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase HSERO_RS20320 HSERO_RS20315
hisF imidazole glycerol phosphate synthase, cyclase subunit HSERO_RS20315 HSERO_RS21020
hisH imidazole glycerol phosphate synthase, amidotransferase subunit HSERO_RS20325 HSERO_RS21015
hisB imidazoleglycerol-phosphate dehydratase HSERO_RS20330
hisC histidinol-phosphate aminotransferase HSERO_RS23520 HSERO_RS20335
hisN histidinol-phosphate phosphatase HSERO_RS03150 HSERO_RS20330
hisD histidinal/histidinol dehydrogenase HSERO_RS20345

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