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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 (2,991) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 21,704 87,223 31
Proteins 21,639 86,892 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)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000000067730.0000000008185Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)biological regulation0.61671Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0029080.001776Least InformativeInherited
Biological Process (BP)gene expression00Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0000002620.0000000000006231Moderately InformativeDirect
Biological Process (BP)cellular component assembly0.0013580.000004743Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.0000071430.1716Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.000009790.002734Moderately InformativeInherited
Biological Process (BP)negative regulation of gene expression0.00000020520.00002239InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization00InformativeDirect
Biological Process (BP)ncRNA processing11InformativeInherited
Biological Process (BP)ribosome biogenesis11InformativeInherited
Biological Process (BP)mRNA processing00Highly InformativeDirect
Biological Process (BP)RNA splicing00Highly InformativeDirect
Biological Process (BP)rRNA metabolic process0.00010030.001998Highly InformativeInherited
Molecular Function (MF)binding0.00020970.1768Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)RNA binding00InformativeDirect
Cellular Component (CC)macromolecular complex00Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000000000061470.00000003707Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0080920.01015Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.025650.01966Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)transferase complex0.049630.09275Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.000098640.04985Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein granule0.0040260.000000001119InformativeInherited
Cellular Component (CC)nucleoplasm part11InformativeInherited
Cellular Component (CC)spliceosomal complex00Highly InformativeDirect
Cellular Component (CC)small nucleolar ribonucleoprotein complex0.0000085690.0000000001838Highly InformativeDirect
Cellular Component (CC)nuclear body0.00026570.00001481Highly InformativeDirect
Cellular Component (CC)small nuclear ribonucleoprotein complex00Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex0.0003110.0002849Highly InformativeDirect
Cellular Component (CC)methylosome0.0000000000000026430Highly InformativeDirect
Cellular Component (CC)SMN-Sm protein complex00Highly InformativeDirect
Cellular Component (CC)pole plasm0.00000033860Highly 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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000008185 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) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.001776 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) cellular component assembly 0.000004743 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0000000000006231 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.002734 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1716 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9708 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.7466 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.8776 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000371 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00002239 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0005108 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Informative Direct
Biological Process (BP) organelle assembly 0.08031 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.01071 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.03533 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) ribosome biogenesis 1 Informative Inherited
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0 Highly Informative Direct
Biological Process (BP) negative regulation of cellular amide metabolic process 0.0001882 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.007007 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.001998 Highly Informative Inherited
Molecular Function (MF) binding 0.1768 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) passive transmembrane transporter activity 0.06003 Informative Inherited
Molecular Function (MF) gated channel activity 0.01176 Highly Informative Inherited
Molecular Function (MF) ion channel activity 0.03417 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00000003707 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01015 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.01966 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.09275 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.04985 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.000000001119 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) small nucleolar ribonucleoprotein complex 0.0000000001838 Highly Informative Direct
Cellular Component (CC) nuclear body 0.00001481 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0.0002849 Highly Informative Direct
Cellular Component (CC) methylosome 0 Highly Informative Direct
Cellular Component (CC) SMN-Sm protein complex 0 Highly Informative Direct
Cellular Component (CC) pole plasm 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the face0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the voice0.0008826InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0000001238Least InformativeDirect
Worm Phenotype (WP)cell development variant0.000001037Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000007711Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.002344Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.002431Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.006246Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.6048Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.000000000005826Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.000003551Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00004102Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00004105Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.000181Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0005777Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.001623Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.001916Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.002948Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.005131Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.05354Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.4276Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.5042Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.8618Moderately InformativeInherited
Worm Phenotype (WP)cell number increased0.00000000000003584InformativeDirect
Worm Phenotype (WP)vulva cell fate specification variant0.00000000000807InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000000718InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000008535InformativeDirect
Worm Phenotype (WP)sick0.000000008628InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000001133InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0000001336InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.00003582InformativeDirect
Worm Phenotype (WP)brood size variant0.00007406InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000105InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.0004143InformativeDirect
Worm Phenotype (WP)pigmentation variant0.000799InformativeDirect
Worm Phenotype (WP)cell stress response variant0.001191InformativeInherited
Worm Phenotype (WP)pattern protein expression variant0.002957InformativeInherited
Worm Phenotype (WP)endosome morphology variant0.003625InformativeInherited
Worm Phenotype (WP)nuclear positioning variant0.03272InformativeInherited
Worm Phenotype (WP)life span variant0.0357InformativeInherited
Worm Phenotype (WP)mitosis variant0.03754InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.6116InformativeInherited
Worm Phenotype (WP)cell proliferation increased0Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.00000000002405Highly InformativeDirect
Worm Phenotype (WP)recycling endosome localization variant0.00000116Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.00003401Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.00006458Highly InformativeDirect
Worm Phenotype (WP)organism heat response variant0.0001213Highly InformativeDirect
Worm Phenotype (WP)no oocytes0.0001714Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.0002902Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.0003109Highly InformativeDirect
Worm Phenotype (WP)P granule defective0.0004431Highly InformativeDirect
Worm Phenotype (WP)unfolded protein response variant0.0004768Highly InformativeDirect
Worm Phenotype (WP)shortened life span0.0009756Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.0002746Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0.07111Least InformativeInherited
Xenopus ANatomical entity (XAN)egg0.00005136Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0.06522Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0000546InformativeDirect

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 stage0.0006669Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0006883Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0008609Least 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 processing0InformativeDirect
Biological processrRNA processing0.0000002081InformativeDirect
Biological processTranslation regulation0.000001411InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationIon channel0.00000000000006168InformativeDirect
Post-translational modificationMethylation0.000001296Moderately InformativeDirect

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) · Human Phenotype (HP) · Worm Phenotype (WP) · 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]