d1k2fa_d1svb_2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1k2f_Ah	d1k2fa_	A152-A231,A269-A282	All beta proteins	TRAF domain-like	TRAF domain-like	SIAH, seven in absentia homolog	SIAH, seven in absentia homolog
1svb__c	d1svb_2	1-269,270-302	Membrane and cell surface proteins and peptides	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Viral glycoprotein, central and dimerisation domains	Envelope glycoprotein

Justification for analogy
The motif in 1k2f: uses part of the Ig core and the inserted strand; hybrid motif. The most important feature in Ig fold is the interlock composed of strands 2, 3, 5, 6 (if strands in a classic Ig is numbered from 1 to 7), like two scissors arranged mouth-to-mouth. The motif in 1svb: the first domain in 1svb is almost all meander, so it cannot be homologous to Ig-like proteins.

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

1k2f_Ah   -----HKSITTLQG----EDIVFLATdinlpgavDWVMMQSCF-GFHFMLVLE-KQEKYd---------------------------------------------------------------------------------gHQQFFAIVQLIG-------------------------trkqaenFAYRLELNGhr---------------------------------------------------------------------------------------------enGNLGINVTISMc-----
1svb__c   srcthLENRDFVTGtqgtTRVTLVLEl-------GGCVTITAEgKPSMDVWLDaIYQENpaktreyclhaklsdtkvaarcptmgpatlaeehqggtvckrdqsdrgwgnhcglfgkgsivacvkaaceakkkatghvydanKIVYTVKVEPHTgdyvaanethsgrktasftissektiltmgeyGDVSLLCRVasgvdlaqtvileldktvehlptawqvhrdwfndlalpwkhegaqnwnnaerlvefgaphavkmdvynlgdqtgvllkalagvpvahiegtkyhlksGHVTCEVGLEKlkmkgl

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

1k2f_Ah   -----HKSITTLQG----EDIVFLATdinlpgavDWVMMQSCF-GFHFMLVLEKqekydghqQ------------------------------------------------------------------------------------------FFAIVQLIGT-------------------------rkqAENFAYRLELNG---------------------------------------------------------------------------------------------hrenGNLGINVTISM-----c
1svb__c   srcthLENRDFVTGtqgtTRVTLVLE-------lGGCVTITAEgKPSMDVWLDA--------IyqenpaktreyclhaklsdtkvaarcptmgpatlaeehqggtvckrdqsdrgwgnhcglfgkgsivacvkaaceakkkatghvydankivYTVKVEPHTGdyvaanethsgrktasftissektiltmGEYGDVSLLCRVasgvdlaqtvileldktvehlptawqvhrdwfndlalpwkhegaqnwnnaerlvefgaphavkmdvynlgdqtgvllkalagvpvahiegtkyhlksGHVTCEVGLEKlkmkgl

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

1k2f_Ah   ----HKSITTLQG-------EDIVFLATDINLPGAVDWVMMQSCF--G-FHFMLVLEKQEKYDGH------------------------------------------------------------------------------Q----QFFAIVQLIG------------T-----------------RKQAENFAYRLEL-NG-HREN--G---------------------------------------------------------------------------------------NLGINVTIS-MC------
1svb__c   SRCTHLENRDFVTGTQGTTRVTLVLEL----------GGCVTITAEGKPSMDVWLDAIYQE--NPAKTREYCLHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDRGWGNHCGLFGKGSIVACVKAACEAKKKATGHVYDANKIVYTVKVEPHTGDYVAANETHSGRKTASFTISSEKTILTMGEY-GDVSLLCRVASGV--DLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGAQNWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTKYHLKSGHVTCEVGLEKLKMKGL

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

1k2f_Ah   -----HKSITTLQG-----EDIVFLATDINLPGAVDWV--------------------------------------------------------------------MMQSCF---------GFHFMLVLEKQEKYDGH----------------------QQFFAIVQLIGTRKQAENF--------------------------------AYRLELNGHRENG--------------------------------------------------------------------------------------------------NLGINVTISMC-------
1svb__c   SRCTHLENRDFVT-GTQGTTRVTLVLE-----------LGGCVTITAEGKPSMDVWLDAIYQENPAKTREYCLHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDR-GWGNHCGLFGKGSIV-----------ACVKAACEAKKKATGHVYDANKIVYTVKVEPHTG-------DYVAANETHSGRKTASFTISSEKTILTMGEYGDVSLLCRV-----ASGVDLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGAQNWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTKYHLKSGHVTCEVGLE--KLKMKGL