- Extract sequence from PDB file
- Select best evolutionary model
- Calculate conservation scores
- Project conservation scores onto the molecule
Running Messages:
- Please note: Before the analysis took place, modified nucleotides read from SEQRES field in the PDB were converted back to the original nucleotides:
2MG->G
H2U->U
M2G->G
OMC->C
OMG->G
YYG->G
PSU->U
5MC->C
7MG->G
5MU->U
1MA->A
.
For a description of modified nucleotides in PDB files click here.
- The sequence extracted from the ATOM field of the PDB file is shorter than the sequence extracted from the MSA file. The MSA sequence has 76 residues and the ATOM sequence has 62 residues. The calculation continues nevertheless.
- The Score of the alignment between the sequence extracted from the MSA file and the sequence extracted from the ATOM field of the PDB file is 75% identity.
See pairwise alignment. The calculation continues nevertheless.
- The best evolutionary model was selected to be: GTR. See details here
Final Results
- View ConSurf results with FirstGlance in Jmol [load results using color-blind friendly scale here]
Note: FirstGlance version was updated. In case you can't see the molecule and get warnings, press OK and afterwards press Ctrl+F5 keys to reload the new version. You can read more about the issue here.
- Secondary structure prediction for the RNA molecule (by RNAFold) colored by ConSurf scores (ps file pdf file)
- Secondary structure prediction for the RNA molecule (by RNAFold) colored by ConSurf scores [color blind friendly scale] (ps file pdf file)
- Download all ConSurf outputs in a click!
PDB Files
Create high resolution figures
Alignment
Alignment details
The average number of replacements between any two sequences in the alignment;
A distance of 0.01 means that on average, the expected replacement for every 100 positions is 1.
Average pairwise distance : 1.1434
Lower bound : 0.221843
Upper bound : 4.95762
Phylogenetic Tree