Inputs and User Options

Input files

Download align file

Download tree file

Download PDB file

User Options

Phylogenetic tree: user tree

Selected PDB chain: A

Query sequence in the alignment: Mouse_SMAD1_NP_032565

Genetic code: Standard (NCBI transl_table=1)

Surface residues or all residues: ALL

Main results

Figure 1. The 3D locations of most conserved sites. The atoms of the most conserved sites are colored in blue. Yellow atoms belong to unconserved sites. White atoms (if present) belong to sites which are not included in the analysis. In total 124 sites have been included in the analysis. If you want to change the number of most conserved sites highlighted in blue, please change it below.

Change the number of most conserved sites:

Table 1. The estimated hyperparameters and log Bayes factor. The unit of characteristic length scale is angstrom while the signal standard deviation is unitless. The characteristic length scale measures the strength of the spatial correlation of site-specific substitution rates while the signal standard deviation measures the variability of substitution rates across sites. The statistical significance of the spatial correlation of substitution rates is determined by the log Bayes factor. If the log Bayes factor is greater than 8, the spatial correlation of substitutions rates may be considered to be significant in the dataset.

Characteristic length scale Signal standard deviation Log Bayes factor
9 1.1 9.18759

Table 2. The list of all analyzed sites and estimated substitution rates. The most conserved sites are colored in blue. The estimated substitution rates are the proxy of functionality. Lower values suggest that the sites are more conserved. The 50% credible intervals measure the reliability of the estimated substitution rates. Larger credible intervals suggest that the estimated substitution rates are less reliable.