GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Denitrovibrio acetiphilus DSM 12809

Best path

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

Rules

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 DACET_RS00355  
hisG ATP phosphoribosyltransferase DACET_RS11565  
hisI phosphoribosyl-ATP pyrophosphatase DACET_RS15160 DACET_RS02055  
hisE phosphoribosyl-AMP cyclohydrolase DACET_RS01410 DACET_RS02055  
hisA 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase DACET_RS14095 DACET_RS15155  
hisF imidazole glycerol phosphate synthase, cyclase subunit DACET_RS15155  
hisH imidazole glycerol phosphate synthase, amidotransferase subunit DACET_RS14100 DACET_RS15155  
hisB imidazoleglycerol-phosphate dehydratase DACET_RS14105  
hisC histidinol-phosphate aminotransferase DACET_RS14925 DACET_RS00755  
hisN? histidinol-phosphate phosphatase DACET_RS14105 DACET_RS05830 known gap
hisD histidinal/histidinol dehydrogenase DACET_RS02055  

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.

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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