d1mk5a_d1efub2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1mk5_Ai	d1mk5a_	A66-A99,A100-A116,B66-B99,B100-B116	All beta proteins	Streptavidin-like	Avidin/streptavidin	Avidin/streptavidin	Streptavidin
1efu_Bi	d1efub2	B55-B85,B123-B139,B140-B164,B245-B269	Alpha and beta proteins (a+b)	EF-Ts domain-like	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain

Justification for analogy
The motif in 1mk5: it uses corresponding core elements in two monomers and is an interface motif. The motif in 1efu: it uses corresponding core elements in two duplicates and is an interface motif. The two motifs are analogous because 1mk5 is a barrel but 1efu is a a+b structure.

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

1mk5_Ai   tdgsGTALGWTVAWKnnyrnaHSATTWSGQYVGg-------AEARINT-QWLLTSGttetdgsGTALGWTVAwknnyrnahsATTWSGQYVGg-------AEARI-NTQWLLTSgtte----
1efu_Bi   --vaADGVIKTKIDG------NYGIILEVNCQTdfvakdakIGENINIrRVAALEG-------DVLGSYQHG---------aRIGVLVAAKGadeellkeHNAEVtGFIRFEVGegiekvet

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

1mk5_Ai   tdGSGTALGWTVAwknnyrnahsATTWSGQYVGG-----------AEARI-NTQWLLTsgttetdgsgtALGWTVAWKnnyrnaHSATTWSGQYV----gGAEARINTQWLLTSGTTE------
1efu_Bi   vaADGVIKTKIDG----------NYGIILEVNCQtdfvakdakigENINIrRVAALEG-----------DVLGSYQHG-----aRIGVLVAAKGAdeellKEHNAEVTGFIRFEVGEGiekvet

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

1mk5_Ai   TDGSGTALGWTVAWKNNYRNAHSATTWSGQYV---G-----GAEARINTQWLLTSGTTETDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGG-------AEARI-NTQWLLTS--G-TT--E
1efu_Bi   --VAADGVIKTKIDG------NYGIILEVNCQTDFVAKDAKIGENINIRRVAALEG-------DVLGSYQHGA---------RIGVLVAAKGADEELLKEHNAEVTGFIRFEVGEGIEKVET-

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

1mk5_Ai   TDGS----GTALGWTVAWKNNYRNAHSA--TTWSGQYVGGA------------EARIN-TQWLLTSGTTETDGSGTA-LGWTVAWKNNYRN-AHSATTWSGQYVGGAE-----------ARINTQWLLTSGTTE---------
1efu_Bi   ----VAADGVIKTKID------------GNYGIILEVNCQ-TDFVAKDAKIGENINIRRVAALEG------------DVLGSYQH------GARIGVLVAAK------GADEELLKEHNAEVT-GFIRFEV---GEGIEKVET