d1okra_d1v9da_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1okr_Ai	d1okra_	A73-A108,B73-B108	All alpha proteins	DNA/RNA-binding 3-helical bundle	"Winged helix" DNA-binding domain	Penicillinase repressor	Methicillin resistance regulatory protein MecI
1v9d_Ac	d1v9da_	A829-A865,A866-A960	All alpha proteins	Formin homology 2 domain (FH2 domain)	Formin homology 2 domain (FH2 domain)	Formin homology 2 domain (FH2 domain)	Diaphanous protein homolog 1, dia1

Justification for analogy
The motif in 1okr: comes from two monomers, interface motif.

In the alignments below, two upper-case letters are aligned, while two lower-case letters are NOT aligned. The two sequences in an alignment are NOT continuous in most cases (see their ranges). The superpositions are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A.

MANUAL alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1okr_Ai   ----veeSDIKYKTSKNFINKVYkGGFNSLVLNFVEKedl-veeSDIKYKTSKNFInkvykggFNSLVLNFVEKEDl----------------------------------------------------------------
1v9d_Ac   vkelkvlDSKTAQNLSIFLGSFR-MPYQEIKNVILEVn--eavlTESMIQNLIKQMp------EPEQLKMLSELKEeyddlaeseqfgvvmgtvprlrprlnailfklqfseqvenikpeivsvtaaceelrksenfssll

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1okr_Ai   -------VEESDIKYKTSKNFINkvykGGFNSLVLNFVEKedlvEESDIkyKTSKNFINKVY------------kggfnslvLNFV--------------------------------------------------ekedl
1v9d_Ac   vkelkvlDSKTAQNLSIFLGSFR----MPYQEIKNVILEV---nEAVLT--ESMIQNLIKQMpepeqlkmlselkeeyddlaESEQfgvvmgtvprlrprlnailfklqfseqvenikpeivsvtaaceelrksenfssll

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1okr_Ai   ---VEESD-I-KYKTSKN-FINKVYKGGFNSLVLNFVEK--EDLVEESD-IKYKTSKNFINKVYKGG-FNSL-VLNFVEKEDL-------------------------------------------------------------
1v9d_Ac   VKE-LKVLDSKTAQNL-SIFLGSF-RMPYQEIKNVILEVNE----AVLTESMIQNLIKQM---PE-PE-QLKMLSELKEEYDDLAESEQFGVVMGTVPRLRPRLNAILFKLQFSEQVENIKPEIVSVTAACEELRKSENFSSLL

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1okr_Ai   VEESDIKYKTSKNFINKVYKG-----------------------------------------GFNSLVLNFVEKEDLV----------------------------------EESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDL----------------------------
1v9d_Ac   ---------------------VKELKVLDSKTAQNLSIFLGSFRMPYQEIKNVILEVNEAVLTESMIQNLIKQ-----MPEPEQLKMLSELKEEYDDLAESEQFGVVMGTVPRLRPRLNAILFKLQFSEQ-----------------VENIKPEIVSVTAACEELRKSENFSSLL