d1st6a8d1r5id_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1st6_Ah	d1st6a8	A875-A942,A1007-A1065	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin	alpha-catenin/vinculin	Vinculin
1r5i_Dc	d1r5id_	D1-D94,D95-D128	All alpha proteins	Superantigen MAM	Superantigen MAM	Superantigen MAM	Superantigen MAM

Justification for analogy
The motif in 1st6: comparing the 8 duplicates, we know that the helix before the last duplicate is an insertion. So the three helix bundle is a hybrid motif with one inserted helix and two core helices.

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

1st6_Ah   ------------------------ppppeekdeefpeqkageainQPMMMAARQLHDEARKWss------kgNDIIAAAKRMALLMAEMSRLVRggsggrtnisdeeseqaTEMLVHNAQNLMQSVKETVREAEAASIKIrtdagftlrwvrktpwy
1r5i_Dc   mklrvenpkkaqkhfvqnlnnvvftnkelediynlsnkeetkevlKLFKLKVNQFYRHAFGIvndynglleyKEIFNMMFLKLSVVFDTQRKEA----------------nNVEQIKRNIAILDEIMAKADNDLSYFISQnknf-------------

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

1st6_Ah   -------------ppppeeKDEEF----PEQK--AGEA-----iNQPMMMAARQLHDEARKWS------skgNDIIAAAKRMALLMAEMSRLVRggsggrtnisdeeseqaTEMLVHNAQNLMQSVKETVREAEAAS-IKIRTdagftlrwvrktpwy
1r5i_Dc   mklrvenpkkaqkhfvqnlNNVVFtnkeLEDIynLSNKeetkevLKLFKLKVNQFYRHAFGIVndynglleyKEIFNMMFLKLSVVFDTQRKEA----------------nNVEQIKRNIAILDEIMAKADNDLSYFiSQNKN--------------f

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

1st6_Ah   ----------------PPPP-EEKD-EEFPE-QK---A-GE-A--IN-Q-PMMMAARQLHDEARK-W---S--SKG-NDIIAAAKRMALLMAE-MSRLVRGGSGGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRT-DAGFTLRWVRKTPWY
1r5i_Dc   MKLRVENPKKAQKHFV---QN-LNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGL-LEYKEIFNMMFLKLSVVFDTQRKEAN-----------------NVEQIKRNIAILDEIMAKADNDLSYFISQNKN-------F-------

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

1st6_Ah   PPPPEEKDEEF------------------------PEQKAGEAINQ-------------------------PMMMAARQLHDEARKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGGRTNISD-----EESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWY--
1r5i_Dc   -----------MKLRVENPKKAQKHFVQNLNNVVFTNKE-------LEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLL-----EYKEIFNMMFLKLSVVFDTQR----------KEANNVEQIKRNIAILDEIMAKADNDLSYFISQNK----------------------NF