SUPERFAMILY 1.75 HMM library and genome assignments server


Sm-like ribonucleoproteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Sm-like fold [ 50181] (5)
Superfamily:   Sm-like ribonucleoproteins [ 50182] (6)
Families:   Sm motif of small nuclear ribonucleoproteins, SNRNP [ 50183] (8)
  Pleiotropic translational regulator Hfq [ 74939]
  Mechanosensitive channel protein MscS (YggB), middle domain [ 82090]
  PF1955-like [ 141294]
  LSM14 N-terminal domain-like [ 141297]
  YgdI/YgdR-like [ 159052] (6)


Superfamily statistics
Genomes (2,976) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,246 0 31
Proteins 21,186 0 31


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 aromatic compound metabolic process00Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0012890.004861Least InformativeInherited
Biological Process (BP)gene expression00Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization2.378e-082.975e-13Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis1.881e-067.333e-09Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.057590.05495Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.20610.163Moderately InformativeInherited
Biological Process (BP)RNA processing00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly9.416e-120InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process1.562e-062.867e-06InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.1320.1185InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)rRNA processing7.025e-060.000261Highly InformativeDirect
Biological Process (BP)mRNA processing00Highly InformativeDirect
Biological Process (BP)RNA splicing00Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization00Highly InformativeDirect
Molecular Function (MF)binding0.17371Least InformativeInherited
Molecular Function (MF)nucleic acid binding09.183e-10Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)intracellular organelle part4.104e-142.699e-13Least InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle0.051590.06281Least InformativeInherited
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)cytoplasmic part10.9567Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.13720.2686Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)cytoplasmic mRNA processing body1.014e-070Highly InformativeDirect
Cellular Component (CC)spliceosomal complex00Highly InformativeDirect
Cellular Component (CC)small nucleolar ribonucleoprotein complex3.364e-061.088e-10Highly InformativeDirect
Cellular Component (CC)small nuclear ribonucleoprotein complex00Highly InformativeDirect
Cellular Component (CC)N-terminal protein acetyltransferase complex7.11e-083.443e-11Highly InformativeDirect
Cellular Component (CC)methylosome1.486e-150Highly InformativeDirect
Cellular Component (CC)SMN-Sm protein complex00Highly InformativeDirect

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 aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004861 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.975e-13 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 7.333e-09 Moderately Informative Direct
Biological Process (BP) ion transport 0.2553 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8884 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.05495 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.163 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.199 Moderately Informative Inherited
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) microtubule-based process 0.0005073 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 2.867e-06 Informative Direct
Biological Process (BP) transmembrane transport 0.0336 Informative Inherited
Biological Process (BP) organelle assembly 0.005518 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.003786 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.9761 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.05782 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.1185 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.1303 Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 2.058e-05 Highly Informative Direct
Biological Process (BP) rRNA processing 0.000261 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001037 Highly Informative Direct
Biological Process (BP) RNA splicing 0 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 0.0005733 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 9.183e-10 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.6112 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) ion gated channel activity 0.00404 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 2.699e-13 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.06281 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.9567 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2686 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.1706 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) small nucleolar ribonucleoprotein complex 1.088e-10 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0001514 Highly Informative Direct
Cellular Component (CC) nuclear body 2.943e-05 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0 Highly Informative Direct
Cellular Component (CC) N-terminal protein acetyltransferase complex 3.443e-11 Highly Informative Direct
Cellular Component (CC) methylosome 0 Highly Informative Direct
Cellular Component (CC) SMN-Sm protein complex 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0006805Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004778Least InformativeInherited
Worm Phenotype (WP)growth variant0.6646Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant9.03e-10Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant2.312e-07Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant2.447e-05Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal4.89e-05Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect9.095e-05Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000126Moderately InformativeDirect
Worm Phenotype (WP)cell death variant0.003144Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.004011Moderately InformativeInherited
Worm Phenotype (WP)VPC competence variant3.978e-12InformativeDirect
Worm Phenotype (WP)sick6.581e-09InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant7.676e-09InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant1.601e-07InformativeDirect
Worm Phenotype (WP)alimentary system development variant2.516e-07InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective3.521e-06InformativeDirect
Worm Phenotype (WP)protein expression variant0.0001238InformativeDirect
Worm Phenotype (WP)brood size variant0.0003806InformativeDirect
Worm Phenotype (WP)vulva development variant0.0003874InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0005688InformativeDirect
Worm Phenotype (WP)cell division variant0.03473InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.4437InformativeInherited
Worm Phenotype (WP)cell corpse number variant0.4769InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)P granule defective3.737e-15Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest8.142e-09Highly InformativeDirect
Worm Phenotype (WP)protein subcellular localization variant4.034e-08Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant4.441e-05Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.000121Highly InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.0006577Highly InformativeDirect
Worm Phenotype (WP)germline proliferation variant0.6633Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.5076Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.2317InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

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

Document: FP 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)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)embryo0.001119Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.1283Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0.0003012Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000467InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0.0006646Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0006859Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0008606Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processStress response0InformativeDirect
Biological processmRNA splicing0InformativeDirect
Biological processTranslation regulation5.112e-07InformativeDirect
Biological processrRNA processing5.308e-07InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationIon channel2.179e-13InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010920 SSF50182 Protein matches
Abstract

This domain is found as the core structure in Lsm (like-Sm) proteins and bacterial Lsm-related Hfq proteins, and as the middle domain of the mechanosensitive channel protein MscS. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology.

Lsm proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [PubMed10801455, PubMed12438310]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. These snRNPs consist of seven Sm proteins (B/Bż, D1, D2, D3, E, F and G), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) [PubMed15130578]. Other snRNPs, such as U7 snRNP, can contain different Lsm proteins. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins.

The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA [PubMed12093755]. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.

The middle domain of the mechanosensitive channel of small conductance protein (MscS or YggB) structurally resembles an Lsm protein. MscS is a mechanosensitive channel present in the membrane of bacteria, archaea and eukarya that responds both to stretching of the cell membrane and to membrane depolarisation [PubMed12446901]. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region. The C-terminal cytoplasmic region can be further divided into middle and C-terminal domains, which together create a framework that connects to the cytoplasm through distinct openings. The middle domain exhibits an Lsm-like structure, consisting of five beta-strands that pack together with those of other subunits to form a barrel-like sheet extending around the entire protein.


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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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 25 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 Sm-like ribonucleoproteins 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 25 hidden Markov models representing the Sm-like ribonucleoproteins 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]