| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1knz_Ai |
d1knza_ | A7-A58,B7-B58 | Multi-domain proteins (alpha and beta) | NSP3 homodimer | NSP3 homodimer | NSP3 homodimer | NSP3 homodimer |
1rp3_Ac |
d1rp3a3 | A1-A58,A59-A86 | All alpha proteins | Sigma2 domain of RNA polymerase sigma factors | Sigma2 domain of RNA polymerase sigma factors | Sigma2 domain of RNA polymerase sigma factors | Sigma 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 | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 71 | 0.11268 | 3.37720 | 53.16901 | -1.21546 |
| dali | 74 | 0.10811 | 3.45278 | 52.36486 | -1.14406 |
| tm | 68 | 0.07353 | 2.62308 | 60.29412 | -1.64845 |
| fast | 69 | 0.07246 | 4.02759 | 40.94203 | -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