d1okra_d1m98a1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1okr_Ai	d1okra_	A92-A123,B92-B122	All alpha proteins	DNA/RNA-binding 3-helical bundle	"Winged helix" DNA-binding domain	Penicillinase repressor	Methicillin resistance regulatory protein MecI
1m98_Ac	d1m98a1	A17-A52,A131-A164	All alpha proteins	Orange carotenoid protein, N-terminal domain	Orange carotenoid protein, N-terminal domain	Orange carotenoid protein, N-terminal domain	Orange carotenoid protein, N-terminal domain

Justification for analogy
The motif is composed of two alpha-hairpins. In 1okr, the C-terminal extension has three helices and is probably a duplicated DNA/RNA-binding 3-helix bundle, only adapted to dimerization. The motif uses two helices from each chain and is an interface motif. In 1m98, the motif covers two entire duplicates and thus is not an interface motif. So the alpha-hairpins in 1okr and 1m98 are probably analogs.

Alignment-based scores
Aligner	Aligned Length	Sequence Identity	RMSD	GDT-TS	COMPASS
manual	59	0.06780	3.23307	58.89831	-5.78693
dali	56	0.07143	2.76469	60.71429	-5.54925
tm	56	0.03571	2.64647	63.39286	-8.77505
fast	51	0.07843	2.51341	62.74510	-5.05677

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   KGGFNSLVLNFVEKedLSQDEIEELRNILNKK------KGGFNSLVLNFVEKEdlSQDEIEELRNILNK-----
1m98_Ac   AADVVPATIARFKQ--LSAEDQLALIWFAYLEmgktitLSANANAILVTIQGI--DPGQQITVLRNCVVdmgfd

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

1okr_Ai   KGGFNSLVLNFVEkedLSQDEIEELRNILNKK------kgGFNSLVLNFVEKedLSQDEIEELRNILNK-----
1m98_Ac   AADVVPATIARFK--qLSAEDQLALIWFAYLEmgktitlsANANAILVTIQG--IDPGQQITVLRNCVVdmgfd

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

1okr_Ai   KGGFNSLVLNF-VEKEDLSQDEIEELRNILN-KK------KGGFNSLVLNF-VEKEDLSQDEIEELRNILNK-----
1m98_Ac   AADVVPATIARFK--QLSA-EDQLALIWFAYLEMGKTITL-SANANAILVTIQ--GIDP-GQQITVLRNCVVDMGFD

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

1okr_Ai   KGG---FNSLVLNFVEKEDLSQDEIEELRNILNKKKGG----------FNSLVLNFVEKEDLSQDEIEELRNILNK------
1m98_Ac   ---AADVVPATIARFKQ--LSAEDQLALIWFAYL----EMGKTITLSANANAILVTIQGI--DPGQQITVLRNCV-VDMGFD