| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1lq7_Aa |
d1lq7a_ | A1-A67 | Designed proteins | Designed single chain three-helix bundle | Designed single chain three-helix bundle | Designed single chain three-helix bundle | Alpha3W |
1gqe_Ac |
d1gqea_ | A4-A117 | Multi-domain proteins (alpha and beta) | Release factor | Release factor | Release factor | Polypeptide chain release factor 2 (RF2) |
Justification for analogy
1lq7 is an artificial protein, so it is analog to the natural protein 1gqe.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 61 | 0.18033 | 1.45817 | 83.60656 | 0.35158 |
| dali | 63 | 0.19048 | 1.60904 | 82.14286 | 0.33429 |
| tm | 67 | 0.08955 | 2.16710 | 68.28358 | 0.01394 |
| fast | 65 | 0.13846 | 3.23155 | 49.23077 | 0.16144 |
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 1lq7_Aa gsrvKALEEKVKALEEKVKALGg-------------------------------------------GGRIEELKKKWEELKKKIEEL--gGGG-EVKKVEEEVKKLEEEIKKL---- 1gqe_Ac ---iNPVNNRIQDLTERSDVLRgyldydakkerleevnaeleqpdvwneperaqalgkerssleavVDTLDQMKQGLEDVSGLLELAveaDDEeTFNEAVAELDALEEKLAQLefrr
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lq7_Aa gsrvKALEEKVKALEEKVKALG-------------------------------------------GGGRIEELKKKWEELKKKIEELG--GGGE-VKKVEEEVKKLEEEIKKL---- 1gqe_Ac ---iNPVNNRIQDLTERSDVLRgyldydakkerleevnaeleqpdvwneperaqalgkerssleaVVDTLDQMKQGLEDVSGLLELAVeaDDEEtFNEAVAELDALEEKLAQLefrr
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lq7_Aa GS-RVKALEEKVKALEEKVKALGG--G--------------------------------G-RIEELKKKWEELKKKIEE-LG-G-------GG-E-VKKVEEEVKKLEEEIKKL 1gqe_Ac INPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRR
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lq7_Aa GS---RVKALEEKVKALEEKVKALGG---------------------------------------GGRIEELKKKWEELKKKIEELGGG---GEVKKVEEEVKKLEEEIKKL---- 1gqe_Ac --INPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRR