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 (470) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,167 1,267 3
Proteins 1,161 1,261 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 process0.0038440.006993Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0022710.02234Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.001020.001903Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.00097920.00166Least InformativeInherited
Biological Process (BP)biosynthetic process0.0017660.001112Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0017450.003345Least InformativeInherited
Biological Process (BP)gene expression0.0000042170.000003717Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.0000010450.000001488Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000047260.0000001835Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000027340.0000001855Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000026790.000001721Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000040840.0000001746Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000010110.0000007556Moderately InformativeDirect
Biological Process (BP)transcription, DNA-dependent0.0000000003420.00000000008978InformativeDirect
Biological Process (BP)transcription from RNA polymerase II promoter0.0000000000093180.00000000000234Highly InformativeDirect
Molecular Function (MF)protein binding transcription factor activity0.0000000000030660.000000001854Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0000078240.0000004461Least InformativeDirect
Cellular Component (CC)protein complex0.00000000013270.000000000000007667Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000000070420.000000000002469Least InformativeDirect
Cellular Component (CC)nuclear part0.00000000000011140Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.000000000000075340.00000007545Moderately InformativeDirect
Cellular Component (CC)nucleoplasm part00.00000000001172InformativeDirect

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) developmental process 0.2895 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.006993 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.02234 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1361 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4151 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.001903 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.00166 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001112 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.003345 Least Informative Inherited
Biological Process (BP) gene expression 0.000003717 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000001488 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0000001835 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000001855 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000001721 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0000001746 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000007556 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.03819 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.002332 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.002601 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.1016 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 0.00000000008978 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00003186 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.00000000000234 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00001621 Highly Informative Direct
Biological Process (BP) stem cell development 0.000000006518 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.000000001854 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000004461 Least Informative Direct
Cellular Component (CC) protein complex 0.000000000000007667 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000000000002469 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000007545 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000000001172 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 ]