d1a05a_d1j71a_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1a05_Ai	d1a05a_	A100-A110,A126-A137,A241-A281	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Dimeric isocitrate & isopropylmalate dehydrogenases	3-isopropylmalate dehydrogenase, IPMDH
1j71_Ac	d1j71a_	A192-A205,A206-A221,A222-A334	All beta proteins	Acid proteases	Acid proteases	Pepsin-like	Acid protease

Justification for analogy
The motif in 1a05: motif occurs at the interface of the two duplicates. The motif in 1j71: a core motif. Alternatively, this can be regarded as an interface motif because it uses corresponding elements from the two duplicates.

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

1a05_Ai   -------LYANLRPaqifdvdiLVVRELTg---------------GNMFGDILSDEasqltg--------siGMLPSASLGEG-RAMYEPIHGsa--------------------------------------------------------
1j71_Ac   svelrvhLGSINFD--------GTSVSTNadvvldsgttityfsqSTADKFARIVGatwdsrneiyrlpscdLSGDAVFNFDQgVKITVPLSElilkdsdssicyfgisrndanilgdnflrrayivydlddktislaqvkytsssdisal

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

1a05_Ai   ------lYANLRPaqifdvdILVVRELTG----------GNMFGDILSDEASQL------------tgsIGMLPSASLGEgRAMYEP---iHGSA------------------------------------------------------
1j71_Ac   svelrvhLGSINF-----dgTSVSTNADVvldsgttityFSQSTADKFARIVGAtwdsrneiyrlpscdLSGDAVFNFDQ-GVKITVplseLILKdsdssicyfgisrndanilgdnflrrayivydlddktislaqvkytsssdisal

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

1a05_Ai   -------LYANLRPAQIFDVDILVVRELTG-----------GNM-FGDILSDEASQL-----------TGS-IGMLPSASLG-EGRAMYEPI--HGSA------------------------------------------------------
1j71_Ac   SVELRVHLGSINFDG-------TSVSTNADVVLDSGTTITY-FSQSTADKFARIVGATWDSRNEIYRL-PSCDLSGDAVFNFDQGVKITVPLSELILKDSDSSICYFGISRNDANILGDNFLRRAYIVYDLDDKTISLAQVKYTSSSDISAL

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

1a05_Ai   L--------YANLRPAQIFDVD--ILVVRELTGGN--------------MFGDILSDEASQLTGSIG-----------------MLPSASLGEG-RAMYEPIHGSA-----------------------------------------------------------
1j71_Ac   -SVELRVHLGSINF--------DGTSVSTNA----DVVLDSGTTITYFSQSTADKFARIVG------ATWDSRNEIYRLPSCDLSGDAVFNFDQGVKITVPLS---ELILKDSDSSICYFGISRNDANILGDNFLRRAYIVYDLDDKTISLAQVKYTSSSDISAL