prs, hisG, hisI?, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD?
Overview: Histidine biosynthesis in GapMind is based on the MetaCyc pathway (link).
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate | Class of gap | Known gap? |
|---|---|---|---|---|---|
| prs | ribose-phosphate diphosphokinase | BM299_RS07610 | |||
| hisG | ATP phosphoribosyltransferase | BM299_RS10825 | |||
| hisI? | phosphoribosyl-ATP pyrophosphatase | BM299_RS07660 | known gap | ||
| hisE | phosphoribosyl-AMP cyclohydrolase | BM299_RS02185 | |||
| hisA | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase | BM299_RS02175 | BM299_RS02180 | ||
| hisF | imidazole glycerol phosphate synthase, cyclase subunit | BM299_RS02180 | BM299_RS02175 | ||
| hisH | imidazole glycerol phosphate synthase, amidotransferase subunit | BM299_RS02170 | |||
| hisB | imidazoleglycerol-phosphate dehydratase | BM299_RS02165 | |||
| hisC | histidinol-phosphate aminotransferase | BM299_RS02160 | BM299_RS07475 | ||
| hisN | histidinol-phosphate phosphatase | BM299_RS15995 | BM299_RS02165 | ||
| hisD? | histidinal/histidinol dehydrogenase | spurious |
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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:
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