SUPERFAMILY 1.75 HMM library and genome assignments server

S15/NS1 RNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   S15/NS1 RNA-binding domain [ 47059]
Superfamily:   S15/NS1 RNA-binding domain [ 47060] (3)
Families:   N-terminal, RNA-binding domain of nonstructural protein NS1 [ 47061]
  Ribosomal protein S15 [ 47064]
  a tRNA synthase domain [ 47068] (2)


Superfamily statistics
Genomes (3,220) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,524 50,670 24
Proteins 4,993 50,081 24


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0.000396 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0008539 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000001241 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0005949 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000294 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0008544 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.9337 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.01877 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.005753 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0001556 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000002477 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0001626 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000005192 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.3946 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.5701 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1643 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1154 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.4143 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.005731 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4289 Moderately Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.0000007673 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.005804 Informative Inherited
Molecular Function (MF) binding 0.244 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.000000001254 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00387 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.000002579 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0.00000000000008973 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0003196 Informative Direct
Cellular Component (CC) intracellular organelle part 0.4538 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.004948 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.02273 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.0000004081 Moderately Informative Direct
Cellular Component (CC) cytosol 0.02733 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.02497 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1088 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.000131 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.1559 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.0009921 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Tryptophan--tRNA ligase0.00000008695Highly InformativeDirect
Enzyme Commission (EC)Histidine--tRNA ligase0.000524Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)early embryonic lethal0.000005975Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0003563Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.001082Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.001674Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.0000001797InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000003813InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00001781InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00001924InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately 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

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processAngiogenesis0.0008916InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Coding sequence diversityAlternative splicing0.00000000000008634Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationIsopeptide bond0.0000000001535Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00008117Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009068 SSF47060 Protein matches
Abstract

The RNA-binding domains of the ribosomal protein S15 and the influenza virus non-structural protein NS1 share the same structural fold, consisting of three helices in an irregular array. S15 is one of 21 proteins in the small, bacterial 30S ribosomal subunit, and is required for assembly of the subunit through its binding to 16S rRNA [PubMed10742169]. The multifunctional glutamyl-prolyl-tRNA synthase (EPRS) contains three tandem repeats linking two catalytic domains, all three of which contribute to RNA-binding; the second repeated element bears structural resemblance to the S15/NS1 RNA-binding domain [PubMed11123902].


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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 9 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 S15/NS1 RNA-binding domain 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 9 hidden Markov models representing the S15/NS1 RNA-binding domain 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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]