| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1eg3_Ai |
d1eg3a1 | A121-A144,A195-A250 | All alpha proteins | EF Hand-like | EF-hand | EF-hand modules in multidomain proteins | Dystrophin |
1paq_Ac |
d1paqa_ | A544-A582,A583-A704 | All alpha proteins | alpha-alpha superhelix | ARM repeat | MIF4G domain-like | Translation initiation factor eIF-2b epsilon |
Justification for analogy
In 1eg3, helix 1 and 4 in the first EF domain and helix 1 and 2 in the second EF domain form a right-handed superhelix, which is an interface motif.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 66 | 0.10606 | 3.23700 | 54.16667 | -6.40973 |
| dali | 67 | 0.13433 | 3.24716 | 54.47761 | -7.50856 |
| tm | 57 | 0.07018 | 3.12587 | 56.14035 | -10.79402 |
| fast | 49 | 0.08163 | 4.03491 | 47.44898 | -4.16030 |
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 1eg3_Ai --------------ldLLSLSAACDALDQHNl---kQNDqpRVLSFKTGIISLCk----------------aHLEDKYRYLFKQVAsstgfcDQRRLGLLLHDSIQIPRQLGE-------------------------------------------------------- 1paq_Ac dfekegiatveramenNHDLDTALLELNTLRmsmnvTYH--EVRIATITALLRRvyhfiatqtlgpkdavvkVFNQWGLLFKRQAF------DEEEYIDLMNIIMEKIVEQSFdkpdlilfsalvslydndiieedviykwwdnvstdprydevkkltvkwvewlqnad
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1eg3_Ai -------------lDLLS-LSAACDALDQHN---lKQNDqpRVLSFKTGIISL----------------ckaHLEDKYRYLFKQVAsstgfcDQRRLGLLLHDSIQ-IPRQLGE------------------------------------------------------- 1paq_Ac dfekegiatveramENNHdLDTALLELNTLRmsmnVTYH--EVRIATITALLRrvyhfiatqtlgpkdavvkVFNQWGLLFKRQAF------DEEEYIDLMNIIMEkIVEQSFDkpdlilfsalvslydndiieedviykwwdnvstdprydevkkltvkwvewlqnad
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1eg3_Ai LDLLSLSAACDALDQHNLKQNDQ-PRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLG------E------------------------------------------------------------------------------------------------- 1paq_Ac ---------------------DFE-KEGIATVERAMENNHDLDTALLELNTL-RMSMNVTYHEVRIATITALLRRVYHFIATQTLGPKDAVVKVFNQWGLLFKRQAFDEEEYIDLMNIIMEKIVEQSFDKPDLILFSALVSLYDNDIIEEDVIYKWWDNVSTDPRYDEVKKLTVKWVEWLQNAD
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1eg3_Ai LDLLS--LSAACDALDQHNLKQNDQPR---------------------------------------------------------VLSFKTGIISLCKA---HLEDKYRYLFKQVASSTGFCD-----------QRRLGLLLHDSIQIPRQLGE--------------------------------------- 1paq_Ac -----DFEKEGIATVERA---------MENNHDLDTALLELNTLRMSMNVTYHEVRIATITALLRRVYHFIATQTLGPKDAVVKVFNQWGLLFKR---QAFDEEEYIDLMNIIM--------EKIVEQSFDKPDLILFSALVSLYDN------DIIEEDVIYKWWDNVSTDPRYDEVKKLTVKWVEWLQNAD