SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,234) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,972 0 11
Proteins 4,954 0 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)cellular macromolecule metabolic process0.0033550.01164Least InformativeInherited
Biological Process (BP)biosynthetic process0.011810.0005875Least InformativeInherited
Biological Process (BP)protein metabolic process0.0051080.007735Least InformativeInherited
Biological Process (BP)gene expression2.699e-061.151e-06Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00010667.087e-07Moderately InformativeDirect
Molecular Function (MF)structural molecule activity4.65e-059.245e-09Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome7.171e-061.875e-12InformativeDirect
Cellular Component (CC)intracellular organelle part0.1072.436e-06Least InformativeInherited
Cellular Component (CC)cytoplasmic part2.658e-070.4452Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.024531.217e-09Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex1.222e-051.008e-06Moderately InformativeDirect
Cellular Component (CC)cytosol0.051980.2152Moderately InformativeInherited
Cellular Component (CC)cytosolic large ribosomal subunit6.941e-130.0007251InformativeDirect

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 0.0005875 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.01164 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.007735 Least Informative Inherited
Biological Process (BP) gene expression 1.151e-06 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 7.087e-07 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 9.245e-09 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.875e-12 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.217e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 2.436e-06 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.4452 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9362 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1.008e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 1.255e-05 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0002661 Moderately Informative Direct
Cellular Component (CC) cytosol 0.2152 Moderately Informative Inherited
Cellular Component (CC) cytosolic large ribosomal subunit 0.0007251 Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranslation regulation0InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

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) · Arabidopsis Plant Ontology (AP) · 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]