| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1chm_Ah |
d1chma1 | A62-A118 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Creatinase/prolidase N-terminal domain | Creatinase/prolidase N-terminal domain | Creatinase |
1g62_Ac |
d1g62a_ | A12-A100 | Alpha and beta proteins (a+b) | Pentein, beta/alpha-propeller | Pentein | Ribosome anti-association factor eIF6 (aIF6) | Ribosome anti-association factor eIF6 (aIF6) |
Justification for analogy
The motif in 1chm: one helix and one strand do not belong to the RNaseH core. The "Creatinase/prolidase N-terminal domain" superfamily has only two
proteins, and in the other protein (1n51) the inserted strand and helix are much deteriorated. Strictly speaking, this motif may not be a hybrid,
since it is present in all members in this superfamily.
However, since d1chma1 and d1g62a_ are drastically different structures, the motif in d1chma1 and the motif in d1g62a_ are very unlikely to be
homologs and are probably analogs.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 42 | 0.11905 | 3.31203 | 53.57143 | -5.21531 |
| dali | 39 | 0.07692 | 3.59758 | 50.64103 | -11.61107 |
| tm | 38 | 0.05263 | 2.80343 | 59.86842 | -8.01165 |
| fast | 30 | 0.03333 | 2.30021 | 65.83333 | -6.11432 |
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 1chm_Ah -fgrPYALVVteddVISISANIDGGQPWRRTv-----gTDNIVYTDw---------------------qrDNYFAAIQQALpka--------- 1g62_Ac eigvFSKLTN----TYCLVAVGGSENFYSAFeaelgdaIPIVHTTIagtriigrmtagnrrgllvptqttDQELQHLRNSLpdsvkiqrveer
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1chm_Ah -fgRPYALVVteddvISISANIDGG-QPWRRTV----gTDNIVYTDWQR-dNYFA-----------------------------aiqqalpka 1g62_Ac eigVFSKLTN----tYCLVAVGGSEnFYSAFEAelgdaIPIVHTTIAGTriIGRMtagnrrgllvptqttdqelqhlrnslpdsvkiqrveer
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1chm_Ah --------------------------------------------F-GR--PYALVVTEDDVISISA--NI--DGGQPWRRTVGTDNIVYTDWQRDNYFAAIQQALPKA 1g62_Ac EIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGNR----RGLLVPTQTTDQELQHLRNSLPDSVKIQRV--E-ER------------
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1chm_Ah FGRP---------------------------------------------------YALVVTEDDV--ISISANIDGG----QPWRRTVGT-DNIVYTDWQRDNYFAAIQQALPKA- 1g62_Ac ----EIGVFSKLTNTYCLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGN------RRGLLVPTQTTDQELQHLRNSLPDSVKIQRVEE-----------------R