SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Ribosomal protein L1 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Ribosomal protein L1 [ 56807]
Superfamily:   Ribosomal protein L1 [ 56808]
Families:   Ribosomal protein L1 [ 56809]


Superfamily statistics
Genomes (3,247) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 5,055 22,009 11
Proteins 5,035 21,947 11


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)organonitrogen compound metabolic process0.0081960.0008489Least InformativeInherited
Biological Process (BP)biosynthetic process0.0015010.00001141Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.0011240.0000004356Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0032880.08311Least InformativeInherited
Biological Process (BP)primary metabolic process0.045560.003311Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0023110.00007642Least InformativeInherited
Biological Process (BP)peptide metabolic process0.0000000067930.0000000000006237Moderately InformativeDirect
Biological Process (BP)gene expression0.0000010830.000000000004097Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00000043130.00000003032Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000000018960Moderately InformativeDirect
Biological Process (BP)ribosome biogenesis0.000000010930.000000001805InformativeDirect
Molecular Function (MF)structural molecule activity0.0000000000000079790Moderately InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0000089670.000000005356Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00000010330.04284Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.0033660.000006482Least InformativeInherited
Cellular Component (CC)ribosome0.00000000026540.00000000000007397Moderately InformativeDirect
Cellular Component (CC)cytosolic part0.00000000019230.0000000008797Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit00InformativeDirect
Cellular Component (CC)cytosolic ribosome00.007456InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 0.00001141 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000004356 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00007642 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0008489 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.08311 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.003311 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.0000000000006237 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000004097 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000003032 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) ribosome biogenesis 0.000000001805 Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000005356 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000006482 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.04284 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribosome 0.00000000000007397 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.0000000008797 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1542 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.004764 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.007456 Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranslation regulation0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002143 SSF56808 Protein matches
Abstract

Ribosomal protein L1 is the largest protein from the large ribosomal subunit. In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [PubMed8635468, PubMed8607874], groups:

  • Eubacterial L1.
  • Algal and plant chloroplast L1.
  • Cyanelle L1.
  • Archaebacterial L1.
  • Vertebrate L10A.
  • Yeast SSM1.

InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 4 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Ribosomal protein L1 domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 4 hidden Markov models representing the Ribosomal protein L1 superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]