SUPERFAMILY 1.75 HMM library and genome assignments server


Mechanosensitive channel protein MscS (YggB), C-terminal domain 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:   Mechanosensitive channel protein MscS (YggB), C-terminal domain [ 82689]
Families:   Mechanosensitive channel protein MscS (YggB), C-terminal domain [ 82690]


Superfamily statistics
Genomes (2,192) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,607 39,328 2
Proteins 5,602 39,313 2


Functional annotation
General category Processes_IC
Detailed category 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) single-organism cellular process 0.16 Least Informative Inherited
Biological Process (BP) localization 0.03246 Least Informative Inherited
Biological Process (BP) ion transport 4.916e-06 Moderately Informative Direct
Biological Process (BP) transmembrane transport 3.111e-07 Informative Direct
Biological Process (BP) ion transmembrane transport 1.245e-08 Highly Informative Direct
Molecular Function (MF) transporter activity 5.585e-06 Moderately Informative Direct
Molecular Function (MF) ion gated channel activity 0.003668 Highly Informative Inherited
Cellular Component (CC) membrane 0.02791 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 3.296e-05 Moderately Informative Direct
Cellular Component (CC) integral to membrane 2.204e-05 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1.024e-06Least InformativeDirect
Biological processIon transport1.388e-12Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationIon channel0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011066 SSF82689 Protein matches
Abstract

Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya [PubMed12626684]. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL [PubMed12446901]. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. The C-terminal domain is the cytoplasmic region, and has a ferredoxin-like alpha/beta sandwich fold, where the last strand of the fold is flipped away and involved in oligomerization.


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) · 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 1 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 Mechanosensitive channel protein MscS (YggB), C-terminal 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 1 hidden Markov models representing the Mechanosensitive channel protein MscS (YggB), C-terminal 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) · UniProtKB KeyWords (KW) · Internal database links ]