| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1pie_Ah |
d1piea1 | A96-A119,A131-A180 | Alpha and beta proteins (a+b) | Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | GHMP Kinase, N-terminal domain | Galactokinase |
1nxh_Ac |
d1nxha_ | A107-A126,A3-A106 | All alpha proteins | Hypothetical protein MTH393 | Hypothetical protein MTH393 | Hypothetical protein MTH393 | Hypothetical protein MTH393 |
Justification for analogy
The motif in 1pie: two helices come from the "Ribosomal protein S5 domain 2-like" core and the third helix comes from C-terminal
extension. hybrid motif.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 57 | 0.08772 | 3.52386 | 54.82456 | -0.57944 |
| dali | 61 | 0.04918 | 3.32606 | 56.96721 | -1.14273 |
| tm | 63 | 0.06349 | 3.17469 | 57.93651 | -0.99606 |
| fast | 52 | 0.07692 | 2.82242 | 56.25000 | -0.96880 |
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 1pie_Ah dgELWSNYVKGMIVMLKGAGyeid--------------------------------------------------------ptasglSSSASLELLVG--VVLDDLFNlNVPRLELVQLGQKTENDYIGvnsg 1nxh_Ac --REYSEALSEGRRRLHEILrs--egelmrlmkrrilesyrwqedvvkplsreleidveefqdilmdkldmsslealhprfesarpRCIREKLHSDLqlCWLVDVME-IISVDDAEALKDEITELVLAg---
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1pie_Ah dgeLWSNYVKGMIVMLKGAG----------------------------------------------------yeidptASGL--SSSASLELLVG-VVLDDLFNLNVPRLELVQLGQKTENdyIGVNsg 1nxh_Ac --rEYSEALSEGRRRLHEILrsegelmrlmkrrilesyrwqedvvkplsreleidveefqdilmdkldmsslealhprFESArpRCIREKLHSDLqLCWLVDVMEIISVDDAEALKDEITE--LVLA-g
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1pie_Ah DGELWSNYVKGMIVMLKGAGYE----------------------IDP---T---------------------------A--S-GL--SSSASLELL-VGVVLDD--LFNLNVPRLELVQLGQKTENDYIGVN-SG 1nxh_Ac -RE-YSEALSEGRRRLHEI-LRSEGELMRLMKRRILESYRWQED--VVKPLSRELEIDVEEFQDILMDKLDMSSLEALHPRFESARPRCIREKLHSDLQLCWLVDV--MEIISVDDAEALKDEITE--LVLAG--
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1pie_Ah DGE-LWSNYVKGMIVMLKGAGYEIDPTAS------------------------------------------------------------GLSSSASLELLVGVVL-DDLFNLN------VPRLELVQLGQKTENDYIGVNSG---- 1nxh_Ac ---REYSEALSEGRRRLHEI---------LRSEGELMRLMKRRILESYRWQEDVVKPLSRELEIDVEEFQDILMDKLDMSSLEALHPRFESARPRCIREKLHSDLQLCWL---VDVMEIISVDDAEALKDEITEL-------VLAG