d1knza_d1rp3a3

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1knz_Ai
d1knza_A7-A58,B7-B58Multi-domain proteins (alpha and beta)NSP3 homodimerNSP3 homodimerNSP3 homodimerNSP3 homodimer
1rp3_Ac
d1rp3a3A1-A58,A59-A86All alpha proteinsSigma2 domain of RNA polymerase sigma factorsSigma2 domain of RNA polymerase sigma factorsSigma2 domain of RNA polymerase sigma factorsSigma factor sigma-28 (FliA)

Justification for analogy
The motif in 1knz: 4-helix bundle uses corresponding parts from the two monomers, so it is an interface motif.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual710.112683.3772053.16901-1.21546
dali740.108113.4527852.36486-1.14406
tm680.073532.6230860.29412-1.64845
fast690.072464.0275940.94203-1.27847

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

1knz_Ai   -----TQQMAVSIINSSFEAAVVAATSALENMGi-EYDYQDIYSRVKNKFDFVMDDSgtqqmavsIINSSFEAAVVAATSALENMGieydyqdiysrvknkfdfvmddsg
1rp3_Ac   mknpySNQIEREELILKYLPLVKAIATNIKKHLpeDVDIRDLISYGVIGLIKAVDNLs-----teNPKRAEAYIKLRIKGAIYDYLrsldf-------------------

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

1knz_Ai   -----TQQMAVSIINSSFEAAVVAATSALEnMGIE--YDYQDIYSRVKNKFDFVMDDSGtqqmavSIINSSFEAAVVAATSALENMGIeydyqdiysrvknkfdfvmddsg
1rp3_Ac   mknpySNQIEREELILKYLPLVKAIATNIK-KHLPedVDIRDLISYGVIGLIKAVDNLS-----tENPKRAEAYIKLRIKGAIYDYLR-------------------sldf

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

1knz_Ai   ------------TQQ-MAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDS-G----TQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSG
1rp3_Ac   MKNPYSNQIERE-ELI-LK--YLPLVKAIATNIKKHL----PEDV---DIRDLISYGVIGLIKAVDNLST--ENPKRAEAYIKLRIKGAIYDYLRSLDF-----------------------

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

1knz_Ai   --TQQMAVSIINSSFEAAVVA---ATSALENMGI---EYDYQDIYSRVKNKFDFVMDDSGTQQMAVSI---INSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSG------
1rp3_Ac   MKNPYSNQIEREELILKYLPLVKAIATNIKKH--LPEDVDIRDLISYGVIGLIKAVDNLS--------TENPKRAEAYIKLRIKGAIYDY-------------------------LRSLDF