NTR: SHP box

[ValWood]

name: SHP box child of SO:0100017 conserved Cdc48-interaction motif. The consensus sequence is F.GK..[RK]LG.

PMID: 27655872 PMID: 17083136

note to self rbd2 PMID:27655872

• dysferlin and ubx3

(aa242-251)

[ValWood]

Note from the author:

Thank you for creating a sequence feature in SO. I would suggest consensus for the SHP box as: F[PI]GKG[TK][RK]LG[GT] then relaxed to F.GKG.[RK]LG

Thank you,

Jiwon

(If these are out of scope I can put then in our in house vocabulary instead)

[nicoleruiz]

Does F[PI]GKG[TK][RK]LG[GT] represent consensus across yeast and F.GKG.[RK]LG represent consensus between yeast and humans?

[ValWood]

F[PI]GKG[TK][RK]LG[GT] is the consensus reported in the paper, but I noticed that it did not pull in ubx3 a known cdc48 cofactor cdc48, with a SHP box I added a bit more ambiguity to cover this, which was confirmed by the authors.

I haven't checked other species, but as the conservation for specific proteins in different families is closer than within species conservation for different families, I imagine the relaxed consensus will work better species wide.

ubx3 has FSGKGQRLG

looking further afield it might be necessary to relax the K to polar [CDEHKNQRST]

F.G[CDEHKNQRST]G.[RK]LG (picks up plant ubx3 orthologs). Or you could go with the initially reported and it could be refined later....

Val

[nicoleruiz]

I'll go with the consensus sequences suggested by the author of the paper. We can always change it later if we need to.

Is this ok for the term definition?

A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence F.GKG.[RK]LG.

[ValWood]

Yep, sounds good,

Thanks

Val

[nicoleruiz]

SO:0002159 SHP_box has been added.

[ValWood]

Thanks!