d1aa7a_d1b68a_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1aa7_Ai	d1aa7a_	A51-A88,A120-A158	All alpha proteins	Influenza virus matrix protein M1	Influenza virus matrix protein M1	Influenza virus matrix protein M1	Influenza virus matrix protein M1
1b68_Ac	d1b68a_	A23-A85,A86-A162	All alpha proteins	Four-helical up-and-down bundle	Apolipoprotein	Apolipoprotein	Apolipoprotein E

Justification for analogy
The motif in 1aa7 uses helices from the two different domains and the linker helix, and is an interface motif. Although the first domain in 1aa7_A is also a 4-helix up-and-down bundle, this bundle cannot be homologous to the 4-helix bundle in 1b68, because they are mirror images, i.e. superimpose helix 1 and 2 in 1b68 and 1aa7, helix 3 and 4 are on different sides of the plane formed by helix 1 and 2.

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

1aa7_Ai   ---ilSPLTKGILGFVFTLTVpser-----glqrRRFVQNALNgng--------------------------------SAGALASCMGLIYNRmg---------------avTTEVAFGLVCATCEQIADSQ------
1b68_Ac   gqrweLALGRFWDYLRWVQTLseqvqeellssqvTQELRALMDetmkelkaykseleeqltaeetrarlskelqaaqaRLGADMEDVRGRLVQyrgevqamlgqsteelrvrLASHLRKLRKRLLRDADDLQkrlavy

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

1aa7_Ai   ---iLSPLTKGILGFVFTLTVPS-ERGL----QRRRFVQNALN--------------------------------gngSAGALASCMGLIYNRM---------------gaVTTEVAFGLVCATCEQIADSQ------
1b68_Ac   gqrwELALGRFWDYLRWVQTLSEqVQEEllssQVTQELRALMDetmkelkaykseleeqltaeetrarlskelqaaqaRLGADMEDVRGRLVQYrgevqamlgqsteelrvRLASHLRKLRKRLLRDADDLQkrlavy

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

1aa7_Ai   -ILSPLTKGILGFVFTLTV--PS------E--R-----G--LQRR--RFVQNALN---------------------GNGSAGALASCMGLIYNR-MGA--------------------------V-T-TEVAFGLVCATCEQIADSQ
1b68_Ac   G-Q---RW-ELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTAEETRARLSK---ELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY-

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

1aa7_Ai   ILS------PLTKGILGFVFTLTVPSERGLQRR---------------RFVQNALNGNG------------------------------------SAGALASCMGLIYNRMGAVT---------------------TEVAFGLVCATCEQIADSQ------
1b68_Ac   ---GQRWELALGRFWDYLRWVQT----------LSEQVQEELLSSQVTQELRALM----DETMKELKAYKSELEEQLTAEETRARLSKELQAAQARLGADMEDVRGRLV------QYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY