The ConSurf Server

SERVER FOR THE IDENTIFICATION OF FUNCTIONAL REGIONS IN BIOPOLYMERS

The ConSurf Server

SERVER FOR THE IDENTIFICATION OF FUNCTIONAL REGIONS IN BIOPOLYMERS

ConSurf Analysis for: Phe-tRNA

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Variable
Average
Conserved
Insufficient Data     Download Scale
ConSurf Results
1          11         21         31         41         
G C G G A T T T A G  C T C A G T T G G G  A G A G C G C C A G  A C T G A A G A T C  T G G A G G T C C T
51         61         71         
G T G T T C G A T C  C A C A G A A T T C  G C A C C A

High Resolution Figures: Pymol ChimeraX
View Colored Sequence in PDF format
View Colored Multiple Sequence Alignment
View Multiple Sequence Alignment in FASTA format
Per-Residue Details
Download all files

Running Parameters

  • Homologues Search:
    • Homologues were collected from NT database.
    • Homologues search algorithm is HMMER.
    • E-value cutoff is 0.001.
    • Number of Iterations is 1.
  • Homologues Thresholds:
    • CD-HIT cutoff is 95% (This is the maximal sequence identity between homologues).
    • Maximal number of final homologues is 150.
    • Maximal overlap between homologues is 10% (If overlap between two homologues exceeds 10%, the highest scoring homologue is chosen).
    • Coverage is 60% (This is the minimal percentage of the query sequence covered by the homologue).
    • Minimal sequence identity with the query sequence is 60%.
  • Alignment, Phylogeny and Conservation Scores:
    • Multiple Sequence Alignment was built using MAFFT.
    • Phylogenetic tree was built using Neighbor Joining with ML distance.
    • Conservation Scores were calculated with the Bayesian method.
    • Amino acid substitution model was chosen by best fit.

High Resolution Figures and PDB files

Homologues, Alignment and Phylogeny

    • 10627 homologues were collected from the NT database using HMMER.
    • Of these, 10254 homologues passed the thresholds (min/max similarity, coverage, etc), 219 of them are CD-HIT unique.
    • The calculations were conducted on 150 hits (query included), sampled from the unique hits. Click here if you wish to view the list of sequences which produced significant alignments, but were not chosen as hits.
  • 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 : 0.18
    • Lower bound : 0.0
    • Upper bound : 0.48
    • Residue variety per position in the MSA (The table is best viewed with an editor that respects Comma-Separated Values)

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