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.


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 (3,228) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 5,626 91,831 24
Proteins 5,068 89,922 24


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

Document:
Function annotation of SCOP domain superfamilies

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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0.1016Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.312Moderately InformativeInherited
Phenotypic Abnormality (PA)Gait disturbance0InformativeDirect
Phenotypic Abnormality (PA)Abnormal reflex0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature of the limbs0.001332InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.003931InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism behavior variant0.004515Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.01223Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.01318Least InformativeInherited
Worm Phenotype (WP)cell development variant0.01982Least InformativeInherited
Worm Phenotype (WP)blast cell physiology variant0.03645Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.03648Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.09858Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.000002084Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00004129Moderately InformativeDirect
Worm Phenotype (WP)germ cell differentiation variant0.0002781Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0006732Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.001442Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.002042Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.002124Moderately InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.005084Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.0000001553InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000164InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000004238InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00001658InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00001805InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.00008246InformativeDirect
Worm Phenotype (WP)transgene expression increased0.0007007InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000002602Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)lethal0Moderately InformativeDirect

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)urogenital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least 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)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

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-oxygen bonds0InformativeDirect

Document: EC 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 15 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 15 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]