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Ortholog conservation Domain conservation Secondary structure 3D structure More Home

Analysis of p.(Leu2004Phe) 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 L2004	Conservation - gap
  20	65.35%	62.88%	5 details	0 details	0 details	15 / 20 (75.00%)	15 / 20 (75.00%)

  
  
  

  Divergencies:

  Taeniopygia guttata - C

  Danio rerio - R

  Takifugu rubripes - Q

  Oryzias latipes - Q

  Gasterosteus aculeatus - Q

  The mutant residue cannot be found in the alignment.

  There is no gap in the alignment.

  *AAPI: Alignment Average Percentage Identity
  **AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 2004). 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.

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  Homo sapiens

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  Pan troglodytes

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  Pongo pygmaeus

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  Macaca mulatta

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  Cavia porcellus

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  Mus musculus

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  Rattus norvegicus

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  Canis familiaris

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  Equus caballus

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  Bos taurus

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  Monodelphis domestica

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  Ornithorhynchus anatinus

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  Anolis carolinensis

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  Gallus gallus

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  Taeniopygia guttata

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  Xenopus tropicalis

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  Danio rerio

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  Takifugu rubripes

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  Oryzias latipes

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  Gasterosteus aculeatus

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  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 Calx-beta 14.

  1966

  2079

  	Calx-beta domains are present as tandem repeats in vlgr1. Their role is unknown.

  
  
  
  
  

  Calx-beta 14 of vlgr1 domain alignment including p.L2004 residue.

  
  
  

  Number of sequences	AAPID*** (from aa 1966 to aa 2079)	AAPIR!	Number of divergencies	Number of mutant	Number of gaps	Conservation of L2004	Conservation - gap
  1938	33.66%	26.88%	1821 details	4	66	51 / 1938 (2.63%)	51 / 1872 (2.72%)

  
  
  

  Divergencies

  Residues present in more than 10% of the sequences are highlighted in blue.

  A - 1.96%	C - 0.10%	D - 11.76%	E - 1.81%	F - 0.21%	G - 0.67%	H - 1.03%	I - 1.91%	K - 11.09%	M - 0.77%
  N - 5.06%	P - 1.34%	Q - 1.29%	R - 17.39%	S - 17.60%	T - 16.87%	V - 2.06%	W - 0.05%	Y - 0.98%

  If we just consider Calx-beta domain of vlgr1, we can add that:
  
  on 16 sequences, conservation is 4/16 (25.00%),
  or 4/13 (30.77%) 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

  Alignments have all been extracted from Prosite⁽⁴⁾, except alignment of vlgr1 calx-beta domains which comes from Pfam⁽⁵⁾. Pictures of proteins have been performed using MyDomains - Image Creator. WebLogos are drawn with WebLogo 3⁽¹⁴⁾

• Secondary structure analysis:

  Residu L2004 is predicted to belong to a loop. Probability is 0.742.

  Direct environment is as follow:

  S	I	I	R	L2004	K	G	L	M

  
  
  

  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:

  No 3D model available at this position.

  Check 3D coverage of vlgr1

• Additional ressources:

  
  
  
  • UNIPROT annotations
    

    The variation is not reported in Uniprot.

  • Click on the LOVD picture to check if a variant is described at position 2004    
    
    
    
    
  • Graphical display of the region at NCBI (including SNPs)

See accession numbers of sequences used or references.

Execution time: 3 wallclock secs ( 0.74 usr 0.02 sys + 1.46 cusr 0.61 csys = 2.83 CPU)