| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1axn__i |
d1axn__ | 77-110,269-284 | All alpha proteins | Annexin | Annexin | Annexin | Annexin III |
1sf9_Ac |
d1sf9a_ | A11-A55,A56-A80 | All beta proteins | SH3-like barrel | Hypothetical protein YfhH | Hypothetical protein YfhH | Hypothetical protein YfhH |
Justification for analogy
In 1axn, the 3-helix bundle uses helix 5 in the 1st duplicate, helix 1 in the 2nd duplicate, and helix 2 in the
5th duplicate. This is an interface motif at the interface of three duplicates and in any one duplicate, the
arrangement of helix 1,2,5 is different than the arrangement in the interface motif.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 42 | 0.07143 | 2.10404 | 75.00000 | -2.87982 |
| dali | 48 | 0.06250 | 2.86106 | 68.75000 | -2.72103 |
| tm | 47 | 0.10638 | 2.40506 | 72.87234 | -2.88978 |
| fast | 43 | 0.06977 | 2.22959 | 72.09302 | -3.41166 |
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 1axn__i --------LSGHFEHLMVALVTPPAVFDAKQLKKSMKgagtn-----------DEFTLNRIMVSRSeid- 1sf9_Ac vdlgtenlYFQSNAMEKRYSQMTPHELNTEIALLSEKarkaeqhgiinelavlERKITMAKAYLLNpedy
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i --------LSGHFEHLMVALVTPPAVFDAKQLKKSMK-GAGT----------nDEFTLNRIMVSrSEID-- 1sf9_Ac vdlgtenlYFQSNAMEKRYSQMTPHELNTEIALLSEKaRKAEqhgiinelavlERKITMAKAYL-LNPEdy
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i ---------LSGHFEHLMVALVTPPAVFDAKQLKKSMKG-AGT-----------NDEF-TLNRIMVSRSEID- 1sf9_Ac VDLGTENLY-FQSNAMEKRYSQMTPHELNTEIALLSEKARKAEQHGIINELAVLER-KIT-MAKAYLLNPEDY
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1axn__i L---------SGHFEHLMVALVTPPAVFDAKQLKKSMKGAGTN-----------------DEFTLNRIMVSR-SEID 1sf9_Ac -VDLGTENLYFQSNAMEKRYSQMTPHELNTEIALLSE------KARKAEQHGIINELAVLERKITMAKAYLLNPEDY