Three types of qualifiers are used in the flat text file and advanced search to describe information that is not based on experimental findings:
- By similarity
The term ‘Potential’ indicates that there is some logical or conclusive evidence that the given annotation could apply. This non-experimental qualifier is often used to present results from protein sequence analysis software tools, which are only annotated if the result makes sense in the biological context of a given protein. A typical example is the annotation of N-glycosylation sites in secreted proteins.
The term ‘Probable’ indicates stronger evidence than the qualifier ‘Potential’. This qualifier implies that there must be at least some experimental evidence, which indicates, that the information is expected to be found in the natural environment of a protein.
When some biological information was experimentally obtained for a given protein (or part of it), it may be transferred to other protein family members within a certain taxonomic range, dependent on the biological event or characteristic. The propagated information is tagged with the ‘By similarity’ qualifier.
Non-experimental qualifiers are also assigned to biologically important sites found within conserved domains e.g. active sites within an enzymatic domain or disulfide bonds that stabilize the structure of extracellular modules.