Analysis of p.(Asp1051Tyr) variant, VLGR1 gene, vlgr1 protein (6306 residues)
Ortholog conservation: |
Number of sequences | AAPI* | AAPIR** | Number of divergencies | Number of mutant | Number of gaps | Conservation of D1051 | Conservation - gap |
---|---|---|---|---|---|---|---|
20 | 65.35% | 48.82% | 0 details |
0 details |
0 details |
20 / 20 (100.00%) | 20 / 20 (100.00%) |
*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 1051). 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.
Informativity of this alignment: P0 = 0.0047, with an average substitution per position of 5.37.
This means that you have a probability of 0.9953 (99.53%) that position 1051 is invariant because it is functionally constrained.
More information here.
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Domain conservation: |
The residue belongs to the domain Calx-beta 8.
1051 |
| 1092 |
|
|||
Calx-beta 8 of vlgr1 domain alignment including p.D1051 residue.
Number of sequences | AAPID*** (from aa 1051 to aa 1092) |
AAPIR! | Number of divergencies | Number of mutant | Number of gaps | Conservation of D1051 | Conservation - gap |
---|---|---|---|---|---|---|---|
1938 | 33.66% | 75.79% | 74 details |
2 | 17 | 1847 / 1938 (95.30%) | 1847 / 1921 (96.15%) |
If we just consider Calx-beta domain of vlgr1, we can add that:
on 16 sequences, conservation is 15/16 (93.75%),
or 15/16 (93.75%) 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 D1051 is predicted to belong to a loop. Probability is 0.652.
Direct environment is as follow:
A | R | E | R | D1051 | F | I | P | V |
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 |
---|---|---|---|---|
3EAD | 31.5 % | 0/99 - 0 % | 0/112 - 0 % | 107/112 - 95.5 % |
* between target and template
Otherwise, see detailed Molprobity output
D1051 | Y1051 |
---|---|
distance: 3.20 Å / angle: 2.33 rad between N and THR 1046 O distance: 3.45 Å / angle: 2.00 rad between OD2 and THR 1046 OG1 distance: 2.78 Å / angle: 2.42 rad between O and ASN 1077 N distance: 3.40 Å / angle: 1.67 rad between OD1 and ARG 1050 NH1 distance: 3.48 Å / angle: 1.61 rad between OD2 and ARG 1050 NH1 | distance: 3.18 Å / angle: 2.34 rad between N and THR 1046 O distance: 3.12 Å / angle: 2.85 rad between OH and LYS 1044 O distance: 2.82 Å / angle: 2.40 rad between O and ASN 1077 N distance: 3.47 Å / angle: 2.09 rad between OH and GLU 1086 OE2 |
D1051 | Y1051 |
---|---|
3.48 Å between OD2 and ARG 1050 NH1 | none |
D1051 | Y1051 |
---|---|
2.41 Å between OD2 and THR 1046 N 2.61 Å between OD2 and ALA 1045 CA | 2.89 Å between CE2 and ALA 1045 CA 2.67 Å between CD2 and ALA 1045 CA |
D1051 (wild-type) | Y1051 (mutant) |
---|---|
JSmol Legends: The residue at the position 1051 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 1051 are labelled in blue. Amino acids involved in steric clashes with the residue 1051 are labelled in red.
Additional ressources: |
See accession numbers of sequences used or references.
Execution time: 3 wallclock secs ( 0.93 usr 0.01 sys + 1.56 cusr 0.60 csys = 3.10 CPU)