Discovery

Target ?

NCBI taxonomy IDs, separated by spaces, commas or newlines. A clade ID works too — it is expanded to every species below it that has a reference proteome, so 5820 covers all of Plasmodium. Look up an ID.

Background ?

Families present here are excluded from the results. More organisms means far stronger evidence — one background organism caps the best achievable p-value at about 0.04.

Measure ? Presence / absence asks only whether an organism has the family at all — one copy is the same as forty. That is the right question for a drug target.

Tendency uses copy number, so an expansion counts for more than a single copy. Use it when the signal is how much rather than whether.

Family type ? Pfam — protein domain families, computed in-house with pyhmmer. Always available.

KEGG orthologs (KOfam) — K numbers, which is what KEGG pathways are defined over. Only available for organisms that have been KOfam-annotated; if a taxon has none, it will look as though it carries no families at all.

KEGG pathway ? Optional, e.g. map00010 (Glycolysis). Keeps only orthologs belonging to that pathway.

Pathways are defined over K numbers, so this needs Family type: KEGG orthologs — with Pfam selected it is ignored and says so.

GO term ? Optional. Keeps only families whose proteins carry this GO term.

For KEGG, use Family type: KEGG orthologs and the KEGG pathway box — K numbers are annotated in the database itself.

Advanced query builder

Strictness & filters

Minimum share of the target group 1.0 = every target organism must carry it.

Maximum share of the background 0.0 = must be completely absent. Raise to see near-misses.

Reference version

E-value cutoff

Maximum families

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Target identification from a profile

The same test as below, asked about subclades rather than whole protein families. At family level a shared, ancient family is present in everything, so the answer is always “no candidate”. Split it into its paralogous subclades and the question becomes answerable.

Organisms in this profile

Click an organism to cycle it through target protected not used.

clear all

Or enter taxon / clade IDs

Target

Protect

A clade ID selects every organism in the profile that belongs to it, so 7742 covers all vertebrates present. Anything picked above is added to whatever these resolve to.

Question

Count

Min. prevalence in target

Max. prevalence in protected

Drug target identification

Insecticide target identification

Metagenomic marker discovery

Phenotype correlation

Target identification from a profile

Candidates