The ConSurf Server
SERVER FOR THE IDENTIFICATION OF FUNCTIONAL REGIONS IN BIOPOLYMERS
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Variable
Average
Conserved
Insufficient Data
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1 11 21 31 41 A L H W R A A G A A T V L L V I V L L A G S Y L A V L A E R G A P G A Q L I T Y P R A L W W S V E T |
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51 61 71 81 91 A T T V G Y G D L Y P V T L W G R C V A V V V M V A G I T S F G L V T A A L A T W F V G R E Q |
ChimeraX- View ConSurf results with full-size NGL viewer
- View ConSurf results with FirstGlance in Jmol (How to see conservation of key amino acids)
Running Parameters
- Homologues Search:
- Homologues were collected from UNIREF90 database.
- Homologues search algorithm is HMMER.
- E-value cutoff is 0.0001.
- 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 35%.
- 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.
Homologues, Alignment and Phylogeny
- 27326 homologues were collected from the UNIREF90 database using HMMER.
- Of these, 17401 homologues passed the thresholds (min/max similarity, coverage, etc), 8893 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 : 1.32
- Lower bound : 0.07
- Upper bound : 2.83
- Residue variety per position in the MSA (The table is best viewed with an editor that respects Comma-Separated Values)
- View MSA and phylogenetic tree using WASABI
- Download Phylogenetic Tree (Newick format)
- The best evolutionary model was selected to be: LG. See details here
Related Links
- PDBsum - a pictorial database that provides an at-a-glance overview
- Proteopedia - an interactive encyclopedia of proteins
- Articles about ConSurf in Proteopedia
- FirstGlance in Jmol, a viewer adapted to ConSurf results