d1r2ja2d1ecmb_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1r2j_Ai	d1r2ja2	A49-A89,A207-A251	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	Protein FkbI
1ecm_Bc	d1ecmb_	B6-B67,B68-B100	All alpha proteins	Chorismate mutase II	Chorismate mutase II	Chorismate mutase domain of P-protein	Chorismate mutase domain of P-protein

Justification for analogy
The motif in 1r2j: the 3-helix bundle uses one helix from the C_terminal Bromodomain-like domain and two helices from the N-terminal all-alpha domain. The N-terminal all-alpha domain is basically a superhelix arrangement while the C-terminal Bromodomain-like domain is a up-and-down arrangement. So these are TWO domains instead of one big all-alpha domain. Therefore, the query motif is an interface motif using elements from both domains.

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

1r2j_Ai   --------------glglGSRENGEFTAHVGSL---------CSSLRSVMTSQGMAAWTVQRlglagsgaslpMLVAASLAYGRKSVAWGCVGILRACRTAAVAHartr
1ecm_Bc   pllalrekisaldekllaLLAERRELAVEVGKAkllshrpvrDIDRERDLLERLITLGKAHH----------lDAHYITRLFQLIIEDSVLTQQALLQQHLNKIN----

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

1r2j_Ai   -----------------glgLGSRENGEFTAHVgSLCSSLRSVmtSQGMAAWTVQRLGL-AGSGASLPMLVAASLAYGRKSVAWGCVGILRACRTAAvahartr
1ecm_Bc   pllalrekisaldekllallAERRELAVEVGKAkLLSHRPVRD--IDRERDLLERLITLgKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKIN-------

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

1r2j_Ai   --------------GLGLGSR-ENG-EF-TAH--VG---------SLCSSLRSVMTSQGMAAWTVQRLGLAGSGASLPMLVAASLAYGRKSVAWGCVGILRACRTAAVAHARTR
1ecm_Bc   PLLALREKISALDE----KLLALLAERRE-LAVEVGKAKLLSHRPVRDIDRERDLLERLITLGKAHHL--------------DAHYITRLFQLIIEDSVLTQQALLQQHLNKIN

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

1r2j_Ai   GLGLG---------------SRENGEFTAHVGSL-------------CSSLRSVMTSQGMAAWTVQRLGLAGSGASLPMLVAA---SLAYGRKSVAWGCVGILRACRTAAVAHARTR
1ecm_Bc   -----PLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLITLGKAH-----------------HLDAHYITRLFQLIIEDSVLTQQALLQQHLNKIN