Ortholog conservation: |
|
Number of sequences |
AAPI* |
AAPIR** |
Number of divergencies |
Number of mutant |
Number of gaps |
Conservation of Q58 |
Conservation - gap |
18 |
80.21% |
74.81% |
12 details |
9 details |
4 details |
2 / 18 (11.11%) |
2 / 14 (14.29%) |
Divergencies:
Pan troglodytes - R |
Cavia porcellus - R |
Mus musculus - R |
Rattus norvegicus - R |
Equus caballus - R |
Bos taurus - R |
Canis familiaris - R |
Felis catus - R |
Gallus gallus - R |
Danio rerio - V |
Takifugu rubripes - T |
Gasterosteus aculeatus - L |
Species having the mutant residue:
Pan troglodytes - R |
Cavia porcellus - R |
Mus musculus - R |
Rattus norvegicus - R |
Equus caballus - R |
Bos taurus - R |
Canis familiaris - R |
Felis catus - R |
Gallus gallus - R |
Following species have a gap at the position:
Monodelphis domestica |
Anolis carolinensis |
Taeniopygia guttata |
Oryzias latipes |
*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 58). AAPIR appears in green if it is more than 10% compared to AAPI, in red if less than 10%.
You can check the AAPIRs compared with AAPI of the whole alignment by clicking here.
The help page will tell you more.
Display alignment
Click on the alignment to zoom in and out.
| | | | | | | | | | | | | | | | | | | | | | | | | | | 58 | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Homo sapiens | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
Q |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Pan troglodytes | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Macaca mulatta | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
D |
S |
E |
R |
Q |
M |
M |
A |
Q |
T |
L |
Y |
M |
P |
M |
L |
V |
N |
G |
K |
A |
H |
V |
Q |
A |
S |
K |
Q |
T |
C |
T |
A |
L |
D |
Cavia porcellus | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Mus musculus | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Rattus norvegicus | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Equus caballus | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Bos taurus | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Canis familiaris | - |
- |
- |
- |
- |
- |
- |
L |
I |
S |
S |
V |
A |
I |
P |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Felis catus | H |
F |
F |
D |
T |
Y |
L |
L |
I |
S |
E |
D |
T |
P |
V |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
M |
D |
N |
D |
P |
L |
V |
F |
G |
V |
S |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
P |
D |
Monodelphis domestica | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
Anolis carolinensis | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
Gallus gallus | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
G |
S |
S |
V |
T |
Q |
L |
L |
A |
R |
D |
L |
D |
N |
D |
P |
L |
V |
F |
G |
V |
V |
G |
E |
E |
A |
S |
R |
F |
F |
A |
V |
E |
S |
V |
Taeniopygia guttata | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
Danio rerio | Y |
F |
F |
Q |
S |
Y |
L |
L |
V |
Y |
E |
D |
T |
P |
V |
G |
T |
S |
I |
T |
Q |
L |
Q |
A |
V |
D |
P |
D |
G |
E |
P |
L |
I |
F |
G |
V |
V |
G |
E |
E |
A |
M |
R |
Y |
F |
A |
V |
Q |
G |
T |
Oryzias latipes | - |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
- |
Takifugu rubripes | Y |
F |
F |
S |
T |
Y |
L |
L |
I |
Y |
E |
D |
M |
P |
V |
G |
S |
S |
V |
A |
Q |
L |
K |
A |
T |
D |
P |
E |
G |
E |
P |
L |
I |
Y |
G |
V |
S |
G |
E |
E |
A |
M |
K |
Y |
F |
S |
V |
N |
K |
D |
Gasterosteus aculeatus | F |
F |
F |
S |
T |
Y |
L |
L |
I |
Y |
E |
D |
A |
P |
V |
G |
S |
S |
V |
A |
Q |
L |
N |
A |
L |
D |
P |
E |
G |
E |
P |
L |
I |
Y |
G |
V |
S |
G |
E |
E |
A |
V |
R |
Y |
F |
S |
V |
N |
K |
D |
Species color legend (basic classification):
Great apes | Other monkeys | Prosimians | Other mammals | Lizards | Birds | Amphibians | Fishes | Insects | Nematods | Tunicates | Echinoderms
Show Venn diagram of alignment
Display WebLogo for the region
Click on the top-left corner to enlarge.
Display alignment phylogenetic tree
Click on the top-left corner to enlarge.
Download tree in Newick format (right-click on the link, and choose 'Save target as').
Display region alignment (21 residues, Fasta format)
Display methods
Ortholog sequences have been selected from the Ensembl(1) and
NCBI websites. Alignment has been performed with
ClustalW(2), version 1.83 or 2.0.7.
Trees have been built using Phylogeny.fr (3), based on the alignments.
Software used is PhyML 3.0 aLRT with default parameters. Pictures of trees have been made using Phylip at Mobyle.
AAPI and AAPIR have been calculated thanks to Bioperl.
WebLogos are drawn with WebLogo 3(14)
Accession numbers
Domain conservation: |
|
The residue belongs to the domain Cadherin 1.
Cadherin 1 of cadherin 23 domain alignment including p.Q58 residue.
Number of sequences |
AAPID*** (from aa 34 to aa 132) |
AAPIR! |
Number of divergencies |
Number of mutant |
Number of gaps |
Conservation of Q58 |
Conservation - gap |
1879 |
26.06% |
34.25% |
1667 details |
116 |
110 |
102 / 1879 (5.43%) |
102 / 1769 (5.77%) |
Divergencies
Residues present in more than 10% of the sequences are highlighted in blue.
A - 1.28% |
D - 0.64% |
E - 3.41% |
F - 1.76% |
G - 0.53% |
H - 4.26% |
I - 6.81% |
K - 2.61% |
L - 4.15% |
M - 1.60% |
N - 2.55% |
P - 0.16% |
R - 6.17% |
S - 13.68% |
T - 23.10% |
V - 13.15% |
W - 1.28% |
Y - 1.60% |
If we just consider Cadherin domain of cadherin 23, we can add that:
on 27 sequences, conservation is 1/27 (3.70%),
or 1/27 (3.70%) if you do not take the gaps into account.
***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
!AAPIR is here compared with AAPID.
Show Venn diagram of alignment
Display WebLogo for the region
Click on the top-left corner to enlarge.
Display complete alignment (Clustal format)
Display region alignment (21 residues, Fasta format)
Display methods
Secondary structure analysis: |
|
Residu Q58 is predicted to belong to an α helice. Probability is 0.761.
Direct environment is as follow:
Observed frequencies in α helices:
Q: 1.14
R: 1.11
The two residues are found equivalent in this type of structure.
Display methods
Predictions of secondary structures have been made with PsiPred(9)
, version 2.5, using Protein Multiple Sequences Alignments as input, in order to increase the accuracy of the prediction.
Amino acid frequencies have been calculated from a non redondant set defined by the RCSB. Details are provided
here.
3D analysis: |
|
Models provided and analysed by USMA must be considered as predictions, therefore be careful when interpreting the results. All efforts have been made to build structures of quality, however, they are provided with NO WARRANTY as to their accuracy with the real biological molecules studied.
Predicted wild type and mutant structures have been compared. You will find the results below. Please note that USMA's "3D engine" is unable to analyse interactions with non amino-acids molecules (e.g. ATP or Ca2+).
- Quick assessment of the overall quality of the structure:
PDB template |
Sequence identity* |
Molprobity bad rotamers |
Molprobity Ramachandran outliers |
Molprobity Ramachandran favored |
3MVS |
97.6 % |
2/187 - 1.1 % |
0/208 - 0 % |
205/208 - 98.6 % |
* between target and template
Otherwise, see detailed Molprobity output
- Download wild-type model (PDB format) or mutant prediction.
- Check 3D coverage of cadherin 23.
- This model is made of 1 α helices and of 12 β strands (and is mainly composed of strands (6 residues in helices against 80 in strands, for a total of 210 amino acids)).
- 3D model predicts Q58 to be located in a loop (which differs from PsiPred prediction) and R58 in a loop.
- The wild type residue is predicted to be exposed and the mutant residue to be exposed.
- The two residues have different charges, which can interfere with ionic bonds or potential inter- or intra-molecular interactions.
- Hydrogen bond network:
Q58 |
R58 |
distance: 2.92 Å / angle: 2.83 rad between N and PHE 30 O
distance: 3.03 Å / angle: 2.70 rad between O and PHE 30 N
| distance: 2.96 Å / angle: 2.84 rad between N and PHE 30 O
distance: 3.09 Å / angle: 2.68 rad between O and PHE 30 N
|
- The mutant residue is not predicted to introduce steric clashes.
- Pictures:
Click on the top-left corner to enlarge.
Legend: non-covalent bonds/steric clashes: - - - - colors: - - - -: h-bonds, - - - -: ionic bonds, - - - -: hydrophobic interactions; - - - -:clashes.
- If you are not satisfied with the pictures above, or just want to investigate further the structures, you can
display the JSmol applet of the wild-type (left) and mutant (right) structures.
Click on the JSmol applet's link to hide it.
You have a full access to Jmol commands with a simple right click on one applet.
JSmol Legends:
The residue at the position 58 is located in the center, labelled in yellow and surrounded by its neighboring residues (distance < 5 Å).
Amino acids involved in H-bonds with the residue 58 are labelled in blue.
Amino acids involved in steric clashes with the residue 58 are labelled in red.
Display methods
All 3D structures except two for harmonin and sans, and myosin VIIa and sans used in USMA are predictions. They are build by homology, (more),
using Domain Fishing(15) or Atome 2(25) for template recognition, modeller(16)
for model building and mutation, and PyMOL(17) and Jmol(18) for visualisation.
Each structure has been assessed with MolProbity(19).
Msms(20) is used to calculate solvent accessibility, and STRIDE(21) (plus stride2pdb)
for secondary structure assignment. When necessary, SCWRL4(22) was used to refine side chains conformations.
Secondary structure analyses in 3D models uses side chain interaction energies reviewed in (23), as well as amino-acids propensities for N-caps, N1-N3, helix middle, C3-C1 and C-caps extracted from (24)(PDB values).
Execution time: 3 wallclock secs ( 0.94 usr 0.01 sys + 1.60 cusr 0.63 csys = 3.18 CPU)