PANDIT+

KeywordFamilyClanGene   

Entry: Ribosomal_L29e (PF01779)

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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

Ribosomal L29e protein family

 
Literature
 
 
InterPro entry IPR002673
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 6 aligned sequences:

  O14461_SCHPO/1-40   O45226_CAEEL/3-42   RL29_DROME/3-42   RL29_HUMAN/2-41   RL29_SCHPO/3-41   RL29_YEAST/2-41  

The full alignment for this family in the Pfam database contains 210 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.

  Schizosaccharomyces pombe (2);   Homo sapiens (1);   Caenorhabditis elegans (1);   Saccharomyces cerevisiae (1);   Drosophila melanogaster (1);  

The full alignment covers 145 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  

-591.70-585.714424-585.714424-574.822986-574.822999

Tree Length  

14.2114.2142914.2142914.2142914.21429

κ  

1.051.3315841.3315840.9555520.955549

ω-ratio  

ω=0.02937p0=0.747604 ~ ω0=0.028954
p1=0.252396 ~ ω1=1		p0=0.747604 ~ ω0=0.028954
p1=0.227001 ~ ω1=1
p2=0.025395 ~ ω2=1		ω~Β(0.40733,6.483296)p0=0.999999 ~ ω~Β(0.40733,6.483275)
p1=1e-06 ~ ω=1.575068

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved		M7 vs M8: P-value=1
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  

 -573.86736-573.6823

Mean ω-ratio  

ω = 0.08146ω = 0.05297

Coeff. of variation  
of ω-ratio  

 CVω = 6.10671CVω = 1.03203
 

Annotations

InteractionsThis family has 0 known interactions:
StructuresThis family has 0 structures:
Notation: PDB_ID (PDB chain, PDB residues)
Gene Ontologies
Cellular component
 ribosome[GO:0005840]
 intracellular[GO:0005622]
Biological Process
 translation[GO:0006412]
Molecular Function
 structural constituent of ribosome[GO:0003735]
KEGG Pathways - for genes coding for sequences from full alignment
Genetic Information Processing
Translation
Ribosome [KEGG]
 

Expression data (explanation)

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

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Drosophila melanogaster
HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

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
 
601832 (1)