| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1miw_Ah |
d1miwa2 | A20-A27,A36-A47,A102-A131 | Alpha and beta proteins (a+b) | Nucleotidyltransferase | Nucleotidyltransferase | Poly A polymerase head domain-like | tRNA CCA-adding enzyme, head domain |
1gyf_Ac |
d1gyfa_ | A25-A33,A34-A47,A48-A86 | Alpha and beta proteins (a+b) | GYF domain | GYF domain | GYF domain | GYF domain from cd2bp2 protein |
Justification for analogy
The motif in 1miw: compare 1miw to d1fa0a4 (different family, same superfamily), a C-terminal beta-hairpin is insertion.
The motif in 1gyf: core motif.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 46 | 0.10870 | 3.22876 | 53.80435 | -9.10967 |
| dali | 41 | 0.00000 | 2.67554 | 60.36585 | -13.28426 |
| tm | 46 | 0.02174 | 2.72809 | 58.15217 | -11.37415 |
| fast | 37 | 0.02703 | 2.66235 | 55.40541 | -8.90982 |
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 1miw_Ah YDAYFVGG--RPIGDVDI-ATSArSLEEDLKRRDFtmnAIAMDE---YGTIIDPFG------- 1gyf_Ac DVMWEYKWenTGDAELYGpFTSA-QMQTWVSEGYFpdgVYCRKLdppGGQFYNSKRidfdlyt
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1miw_Ah -YDAYFVGGrpIGDVDIATS-aRSLEEDLK--RRDFtmnAIAMD-----eYGTIIDP------fg 1gyf_Ac dVMWEYKWEntGDAELYGPFtsAQMQTWVSegYFPD---GVYCRkldppgGQFYNSKridfdlyt
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1miw_Ah YDAYFVGG--RPIGDVDIATS-ARSLEEDLKR-RDFTMNAI-AMD---EYG-TIIDPF-------G 1gyf_Ac DVMWEYKWENTGDAELYGPFTS-AQMQTWVSEGYFPD--GVYCRKLDPPGGQFYNSKRIDFDLYT-
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1miw_Ah YDAYFVGGRPI------GDVDIATSA-----RSLEEDLKR--RDFTMNA-IAMDE---YGTIIDPFG-------- 1gyf_Ac DVMWEYK----WENTGDAELY-----GPFTSAQMQTWVSEGYFPDG---VYCRKLDPPGGQFYNSK-RIDFDLYT