| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1dc1_Ah |
d1dc1a_ | A135-A206 | Alpha and beta proteins (a/b) | Restriction endonuclease-like | Restriction endonuclease-like | Restriction endonuclease BsobI | Restriction endonuclease BsobI |
1nf2_Ac |
d1nf2a_ | A81-A189 | Alpha and beta proteins (a/b) | HAD-like | HAD-like | Predicted hydrolases Cof | Hypothetical protein TM0651 |
Justification for analogy
The motif in 1dc1: compared to d1ckqa_ (same superfamiliy), two strands are insertion;
The motif in 1nf2: the inserted domain appears like a circular-permuted ferredoxin, and most of the elements in the motif come from this
ferredoxin-like part.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 55 | 0.09091 | 2.01788 | 70.45455 | -0.31274 |
| dali | 60 | 0.05000 | 2.26177 | 69.16667 | -0.49322 |
| tm | 62 | 0.06452 | 2.56321 | 72.17742 | -0.44730 |
| fast | 50 | 0.06000 | 2.05432 | 72.50000 | -0.35640 |
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 1dc1_Ah galaQQKLTRAIISALDIANIPYKWLDSrdkkyTNWMDK-------------------PEDDYELE--tFAKGISWTIN-------------------------gKHRTLMYnitvsl 1nf2_Ac -ekiPPEVAKDIIEYIKPLNVHWQAYID-----DVLYSEkdneeiksyarhsnvdyrvEPNLSELVskmGTTKLLLIDTperldelkeilserfkdvvkvfksfpTYLEIVPknv---
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1dc1_Ah galaQQKLTRAIISALDIANIPYKWLDSrdkkyTNWMDK-------------------PEDD-YELE-TFAKGISWTING-------------------------KHRTLMYNITvsl 1nf2_Ac -ekiPPEVAKDIIEYIKPLNVHWQAYID-----DVLYSEkdneeiksyarhsnvdyrvEPNLsELVSkMGTTKLLLIDTPerldelkeilserfkdvvkvfksfpTYLEIVPKNV---
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1dc1_Ah -GALAQQKLTRAIISALDIANIPYKWLDSRDKKYTNWMDK-------------------PED-DYELE-TFAKGISWTI---NGK----------------------HRTLMYNITVSL 1nf2_Ac E-K-IPPEVAKDIIEYIKPLNVHWQAYI-DD----VLYSEKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDTPERLDELKEILSERFKDVVKVFKSFPTYLEIVPKNV---
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1dc1_Ah GALAQ----QKLTRAIISALDIANIPYKWLDSRDKKY-TNWMDKPEDD-------------------------YELETF-AKGISWTING--------------------------KHRTLMYNITVSL-- 1nf2_Ac -----EKIPPEVAKDIIEYIKPLNVHWQAYI------DDVLYS-----EKDNEEIKSYARHSNVDYRVEPNLSELVSKMGTTKLLLIDT-PERLDELKEILSERFKDVVKVFKSFPTYLEIVPK-----NV