Analysis of p.(Gly4544Val) variant, USH2A gene, usherin protein (5202 residues)
Ortholog conservation: |
Number of sequences | AAPI* | AAPIR** | Number of divergencies | Number of mutant | Number of gaps | Conservation of G4544 | Conservation - gap |
---|---|---|---|---|---|---|---|
17 | 55.91% | 45.55% | 8 details |
0 details |
0 details |
9 / 17 (52.94%) | 9 / 17 (52.94%) |
*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 4544). 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.
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Domain conservation: |
The residue belongs to the domain Fibronectin type-III 31.
4529 |
| 4627 |
|
|||
Fibronectin type-III 31 of usherin domain alignment including p.G4544 residue.
Number of sequences | AAPID*** (from aa 4529 to aa 4627) |
AAPIR! | Number of divergencies | Number of mutant | Number of gaps | Conservation of G4544 | Conservation - gap |
---|---|---|---|---|---|---|---|
2036 | 17.77% | 11.69% | 1831 details |
5 | 4 | 201 / 2036 (9.87%) | 201 / 2032 (9.89%) |
If we just consider Fibronectin type-III domain of usherin, we can add that:
on 35 sequences, conservation is 7/35 (20.00%),
or 7/35 (20.00%) 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.
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Secondary structure analysis: |
Residu G4544 is predicted to belong to a loop. Probability is 0.773.
Direct environment is as follow:
L | Q | A | R | G4544 | P | Q | E | I |
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+).
PDB template | Sequence identity* | Molprobity bad rotamers | Molprobity Ramachandran outliers | Molprobity Ramachandran favored |
---|---|---|---|---|
2ED8 | 27.7 % | 1/84 - 1.2 % | 4/104 - 3.8 % | 95/104 - 91.3 % |
* between target and template
Otherwise, see detailed Molprobity output
G4544 | V4544 |
---|---|
distance: 2.77 Å / angle: 1.67 rad between O and THR 4627 OG1 | distance: 3.08 Å / angle: 1.63 rad between O and THR 4627 OG1 |
G4544 | V4544 |
---|---|
none | none |
G4544 (wild-type) | V4544 (mutant) |
---|---|
JSmol Legends: The residue at the position 4544 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 4544 are labelled in blue. Amino acids involved in steric clashes with the residue 4544 are labelled in red.
Additional ressources: |
See accession numbers of sequences used or references.
Execution time: 2 wallclock secs ( 0.74 usr 0.01 sys + 1.55 cusr 0.61 csys = 2.91 CPU)