PANDIT+

KeywordFamilyClanGene   

Entry: Potex_coat (PF06184) * this family does not contain any human sequence in the seed alignment although some of the annotation data are human specific [read more]

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Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

Potexvirus coat protein

This family consists of several Potexvirus coat proteins.
 
Literature1. Ban N, McPherson A; Nat Struct Biol 1995;2:882-890.The structure of satellite panicum mosaic virus at 1.9 A resolution. PUBMED:7552713
 
 
InterPro entry IPR010392
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 2 aligned sequences:

  COAT_SPMV/5-157   Q65390_9VIRU/1-150  

The full alignment for this family in the Pfam database contains 45 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Panicum mosaic satellite virus (1);   Bamboo mosaic virus satellite RNA (1);  

The full alignment covers 3 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-1117.31-1103.354425-1103.354207-1103.509938-1103.354446

Tree Length  

100.00100100100100

κ  

0.960.2349420.2389920.3358430.245917

ω-ratio  

ω=0.00373p0=0.573702 ~ ω0=0.001953
p1=0.426298 ~ ω1=1
p0=0.57395 ~ ω0=0.002142
p1=0.345185 ~ ω1=1
p2=0.080865 ~ ω2=1.842211
ω~Β(0.242343,10.173968)p0=0.613581 ~ ω~Β(0.521575,99)
p1=0.386419 ~ ω=1.95038

P-value for testing  
positive selection  

M1 vs M2: P-value=0.999782
family classification: conserved
M7 vs M8: P-value=0.855994
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-1114.84303-1114.85303

Mean ω-ratio  

ω = 0.24605ω = 0.04704

Coeff. of variation  
of ω-ratio  

CVω = 1.18913CVω = 1.13917
 

Annotations

InteractionsThis family has 1 known interaction:
PF06184;

StructuresThis family has 5 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Cellular component
 viral capsid[GO:0019028]
Molecular Function
 structural molecule activity[GO:0005198]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Glycolysis / Gluconeogenesis [KEGG]
Pentose phosphate pathway [KEGG]
Starch and sucrose metabolism [KEGG]
Butanoate metabolism [KEGG]
Lipid Metabolism
Fatty acid metabolism [KEGG]
Amino Acid Metabolism
Methionine metabolism [KEGG]
Valine, leucine and isoleucine degradation [KEGG]
Metabolism of Other Amino Acids
Selenoamino acid metabolism [KEGG]
Genetic Information Processing
Translation
Aminoacyl-tRNA biosynthesis [KEGG]
Folding, Sorting and Degradation
Type III secretion system [KEGG]
Cellular Processes
Cell Motility
Flagellar assembly [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

none


HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data
 
Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment
 
Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment