SUPERFAMILY 1.75 HMM library and genome assignments server


Ribosomal protein S6 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Ribosomal protein S6 [ 54995]
Families:   Ribosomal protein S6 [ 54996]


Superfamily statistics
Genomes (2,988) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,217 0 13
Proteins 3,211 0 13


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 process0.00077520.06097Least InformativeInherited
Biological Process (BP)protein metabolic process0.00022560.002145Least InformativeInherited
Biological Process (BP)biosynthetic process0.00061870.003619Least InformativeInherited
Biological Process (BP)gene expression3.343e-064.48e-05Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process2.276e-062.772e-05Moderately InformativeDirect
Molecular Function (MF)structural molecule activity7.206e-096.715e-09Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome6.595e-102.074e-11InformativeDirect
Cellular Component (CC)intracellular organelle part0.027380.0169Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0081320.02307Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.015330.0005969Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex3.203e-052.681e-06Moderately InformativeDirect
Cellular Component (CC)small ribosomal subunit4.126e-081.163e-12InformativeDirect

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) cellular macromolecule metabolic process 0.06097 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.002145 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.003619 Least Informative Inherited
Biological Process (BP) gene expression 4.48e-05 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.772e-05 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 6.715e-09 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 2.074e-11 Informative Direct
Cellular Component (CC) cytoplasmic part 0.0005969 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0169 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02307 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 2.681e-06 Moderately Informative Direct
Cellular Component (CC) small ribosomal subunit 1.163e-12 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)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

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

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000529 SSF54995 Protein matches
Abstract

Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.


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 S6 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 S6 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 ]