New documentation for IKR

New Documentation for IKR: Inferred from Key Residues

Current IKR documentation is located here

IKR: Inferred from Key Residues

A type of phylogenetic evidence characterized by the loss of key sequence residues. All annotations that apply this evidence code should use the 'NOT' qualifier. This evidence code has been renamed; it was previously referred to as IMR (inferred from Missing Residues).

This evidence code is often used to annotate a gene product when, although homologous to a particular protein family, it has lost essential catalytic residues and is very unlikely to have enzymatic activity, and therefore is unlikely to carry out the associated function or participate in the expected associated process.

This annotation statement can be supported by a PubMed reference which describes the sequence analysis efforts, or by a GO Reference, which describes the process a curator undertook to become sufficiently convinced of the sequence mutation.

Do not use this code if there is experimental evidence available from a publication to support a NOT-evidenced annotation.

Example 1:

Rat HPT (P06866) is homologous to serine proteases and contains a match to the peptidase S1 domain. However further sequence analysis by a curator established it has lost all essential catalytic residues, making it unable to carry out serine protease activity.

Annotation: UniProtKB:P06866 NOT GO:0004252 serine-type endopeptidase activity IKR GO_REF:0000XXX UniProtKB

Example 2:

PMID:12568721

The authors describe the determination of serine protease activity of proteins from the D. melanogaster S1 serine protease gene family, by determining the presence of conserved His, Asp, Ser catalytic triad residues in retrieved sequences. If all three residues were present in the conserved TAAHC, DIAL, and GDSGGP motifs, the sequence was considered to have serine protease activity. Any sequence lacking one of the key residues was identified as an a serine protease homolog, lacking proteolytic activity.

Annotation:

FB:FBgn0033192 NOT GO:0004252 serine-type endopeptidase activity IKR PMID:12568721 FlyBase

New GO_REF draft to be used with IKR-evidenced annotations

GO_REF:0000XXX

Manual determination of the loss of activity or location by curator judgment of sequence residues. Method for supplying a NOT-qualified, IKR-evidenced GO annotation to a gene product, when general sequence homology considerations would suggest a function or location, but where a curator has subsequently determined that the absence of key sequence residues means it is unable to carry out this suggested activity, involvement in a process or cellular component location.

This reference should only be used used when an IKR-evidenced annotation has been made based on curator judgement from manually reviewing the sequence of the gene product and where no publication can be found to support the curators conclusion. It is preferable to cite a peer-reviewed publication (such as a PubMed identifier) for IKR-evidenced annotations whenever possible.

Curators will have carefully reviewed the sequence of the annotated protein, and established that the key residues known to be required for an expected activity or location are not present.

For more information on the IKR evidence code, please see documentation [here http:nonexistantlink].