SUPERFAMILY 1.75 HMM library and genome assignments server


Mediator hinge subcomplex-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Mediator hinge subcomplex-like [ 140717]
Superfamily:   Mediator hinge subcomplex-like [ 140718] (2)
Families:   CSE2-like [ 140719]
  MED7 hinge region [ 140722]


Superfamily statistics
Genomes (430) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,110 871 3
Proteins 1,105 865 3


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

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)nitrogen compound metabolic process0.0045450.0004925Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0025720.001995Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0012080.0001016Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0011558.579e-05Least InformativeInherited
Biological Process (BP)biosynthetic process0.0020195.056e-05Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0020630.0002013Least InformativeInherited
Biological Process (BP)gene expression4.46e-066.026e-08Moderately InformativeDirect
Biological Process (BP)RNA metabolic process1.218e-062.455e-08Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process5.384e-062.293e-09Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process3.128e-062.365e-09Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process2.79e-062.459e-08Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process4.612e-062.103e-09Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process1.176e-051.169e-08Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent3.759e-104.677e-13InformativeDirect
Biological Process (BP)transcription from RNA polymerase II promoter1.088e-117.333e-15Highly InformativeDirect
Molecular Function (MF)binding0.0052010.01263Least InformativeInherited
Molecular Function (MF)transcription factor binding transcription factor activity4.446e-135.857e-12Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle6.046e-068.332e-10Least InformativeDirect
Cellular Component (CC)protein complex1.618e-100Least InformativeDirect
Cellular Component (CC)intracellular organelle part4.612e-091.521e-15Least InformativeDirect
Cellular Component (CC)nuclear part1.415e-140Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen9.088e-150Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part00InformativeDirect

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 0.0001016 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0004925 Least Informative Direct
Biological Process (BP) biosynthetic process 5.056e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 8.579e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002013 Least Informative Direct
Biological Process (BP) developmental process 0.1381 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001995 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.02007 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2157 Least Informative Inherited
Biological Process (BP) gene expression 6.026e-08 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 2.455e-08 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.293e-09 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 2.365e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.459e-08 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 2.103e-09 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.169e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.01527 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.004648 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.007434 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.0449 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 4.677e-13 Informative Direct
Biological Process (BP) negative regulation of developmental process 3.093e-05 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 7.333e-15 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 1.726e-05 Highly Informative Direct
Biological Process (BP) stem cell development 1.788e-09 Highly Informative Direct
Molecular Function (MF) binding 0.01263 Least Informative Inherited
Molecular Function (MF) transcription factor binding transcription factor activity 5.857e-12 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 8.332e-10 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1.521e-15 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct

Document: GO 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

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 2 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 Mediator hinge subcomplex-like 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 2 hidden Markov models representing the Mediator hinge subcomplex-like 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]