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)cellular nitrogen compound metabolic process0.0012630.0000006387Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0024410.0001001Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0034370.08401Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0088080.0008275Least InformativeInherited
Biological Process (BP)biosynthetic process0.001690.00001155Least InformativeInherited
Biological Process (BP)primary metabolic process0.049240.004289Least InformativeInherited
Biological Process (BP)peptide metabolic process0.0000000079850.0000000000006855Moderately InformativeDirect
Biological Process (BP)gene expression0.0000010620.000000000005344Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00000049110.00000002906Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000000022630.000000000000001945Moderately InformativeDirect
Biological Process (BP)ribosome biogenesis0.000000012020.000000002218InformativeDirect
Molecular Function (MF)structural molecule activity0.000000000000010620Moderately InformativeDirect
Cellular Component (CC)macromolecular complex0.0000095870.00003976Least InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0000081120.00000000501Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0035280.000006927Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.00000011810.048Least InformativeInherited
Cellular Component (CC)ribosome0.00000000032280.0000000000001083Moderately InformativeDirect
Cellular Component (CC)cytosolic part0.00000000023090.000000001155Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit00InformativeDirect
Cellular Component (CC)cytosolic ribosome00.007587InformativeInherited

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 0.00001155 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000006387 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0001001 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0008275 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.08401 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.004289 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.0000000000006855 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000005344 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000002906 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.000000000000001945 Moderately Informative Direct
Biological Process (BP) ribosome biogenesis 0.000000002218 Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Cellular Component (CC) macromolecular complex 0.00003976 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.00000000501 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000006927 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.048 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribosome 0.0000000000001083 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.000000001155 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1492 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.004708 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.007587 Informative Inherited

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP 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)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular 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)D bilateral stage0Least 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)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect

Document: AP 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]