PANDIT+

KeywordFamilyClanGene   

Entry: Ribosomal_L11 (PF00298)

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Pfam summary

Description

Ribosomal protein L11, RNA binding domain

 
Literature1. Markus MA, Hinck AP, Huang S, Draper DE, Torchia DA; Nat Struct Biol 1997;4:70-77.High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA. PUBMED:8989327
2. Hinck AP, Markus MA, Huang S, Grzesiek S, Kustonovich I, Draper DE; J Mol Biol 1997;274:101-113.The RNA binding domain of ribosomal protein L11: Three- dimensional structure of the RNA-bound form of the protein and its interaction with 23S rRNA. PUBMED:9398519
 
 
InterPro entry IPR000911
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 13 aligned sequences:

  RK11_SPIOL/142-210   RL11_BACSU/70-138   RL11_ECOLI/71-139   RL11_HALN1/66-134   RL11_LIBAS/71-139   RL11_STRGR/74-142   RL11_SULAC/68-136   RL11_SYNY3/71-139   RL11_THEMA/70-138   RL11_THETH/70-138   RL12_HUMAN/75-143   RL12_YEAST/75-143   RM11_CAEEL/86-155  

The full alignment for this family in the Pfam database contains 1967 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.

  Caenorhabditis elegans (1);   Homo sapiens (1);   Thermotoga maritima (1);   Sulfolobus acidocaldarius (1);   Candidatus Liberibacter asiaticus (1);   Escherichia coli K12 (1);   Spinacia oleracea (1);   Saccharomyces cerevisiae (1);   Thermus thermophilus (1);   Synechocystis sp. PCC 6803 (1);   Streptomyces griseus (1);   Halobacterium salinarum (1);   Bacillus subtilis (1);  

The full alignment covers 1013 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  

-2718.83-2714.402439-2714.390706-2695.608138-2695.262538

Tree Length  

211.38211.37529211.37529211.37529211.37529

κ  

1.171.1369011.1340291.1738581.146607

ω-ratio  

ω=0.01612p0=0.971298 ~ ω0=0.01645
p1=0.028702 ~ ω1=1		p0=0.971636 ~ ω0=0.018095
p1=0.020812 ~ ω1=1
p2=0.007552 ~ ω2=6.31776		ω~Β(1.930068,99)p0=0.993905 ~ ω~Β(2.299825,92.054991)
p1=0.006095 ~ ω=21.25173

P-value for testing  
positive selection  

M1 vs M2: P-value=0.988336
domain classification: conserved		M7 vs M8: P-value=0.707796
domain 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  

 -2762.76956-2738.43024

Mean ω-ratio  

ω = 0.24426ω = 0.02707

Coeff. of variation  
of ω-ratio  

 CVω = 3.33041CVω = 0.85332
 

Annotations

InteractionsThis domain has 2 known interactions:
PF03946; PF06325;
StructuresThis domain has 120 structures:
Notation: PDB_ID (PDB chain, PDB residues)
More...
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
Metabolism
Energy Metabolism
Methane metabolism [KEGG]
Nitrogen metabolism [KEGG]
Lipid Metabolism
Glycerolipid metabolism [KEGG]
Nucleotide Metabolism
Pyrimidine metabolism [KEGG]
Amino Acid Metabolism
Alanine and aspartate metabolism [KEGG]
Metabolism of Other Amino Acids
Cyanoamino acid metabolism [KEGG]
Xenobiotics Biodegradation and Metabolism
Trinitrotoluene degradation [KEGG]
Drug metabolism - other enzymes [KEGG]
Genetic Information Processing
Translation
Ribosome [KEGG]
Environmental Information Processing
Membrane Transport
Phosphotransferase system (PTS) [KEGG]
DisProt- disorder annotation inferred from homologous DisProt sequences
DP00512
Intrinsically disordered region starting at position 16 with length 12
 
ρD/ρO = 1.3099 (p-value = 3.1608e-13)
 

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.

Homo sapiens
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
 
180475 (1) 611826 (1)