SUPERFAMILY 1.75 HMM library and genome assignments server


Rap30/74 interaction domains superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   triple barrel [ 50915]
Superfamily:   Rap30/74 interaction domains [ 50916]
Families:   Rap30/74 interaction domains [ 50917] (2)


Superfamily statistics
Genomes (429) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,135 1,233 2
Proteins 1,077 1,162 2


Functional annotation
General category Information
Detailed category Transcription

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) biosynthetic process 4.078e-06 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 6.785e-06 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 8.076e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.67e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 4.397e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0002123 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0007483 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.02502 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.146e-10 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 1.213e-10 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 1.229e-10 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 6.248e-10 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1.376e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 1.632e-09 Moderately Informative Direct
Biological Process (BP) gene expression 4.037e-09 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 1.676e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.251e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.328e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0001716 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0009112 Moderately Informative Direct
Biological Process (BP) transcription, DNA-dependent 2.099e-14 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 3.064e-06 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.0003525 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.000565 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0009566 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 1.04e-07 Highly Informative Direct
Cellular Component (CC) protein complex 0.0002243 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.001681 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.007876 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 9.83e-07 Moderately Informative Direct
Cellular Component (CC) nuclear part 3.706e-05 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 4.609e-12 Informative Direct
Cellular Component (CC) nucleoplasm part 5.305e-05 Informative Direct
Cellular Component (CC) transcription factor complex 1.48e-13 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0.0001469Least InformativeDirect
Post-translational modificationHelicase1.303e-14InformativeDirect
Post-translational modificationPhosphoprotein4.768e-12Least InformativeDirect
Post-translational modificationAcetylation9.107e-05Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011039 SSF50916 Protein matches
Abstract

Transcription factor IIF (TFIIF), which is essential for eukaryotic transcription by RNA polymerase II. (PolII), consists of a heterodimer of Rap30 (beta) and Rap74 (alpha) subunits [PubMed11183778]. Rap30 and Rap74 have multiple domains that bind to PolII, TFIIB, TAF250 and DNA in interactions that are essential for transcription initiation and elongation. The N-terminal interactions domains of Rap30 and Rap74 are responsible for establishing the dimer interface between the two subunits, this interface being important for TFIIF function [PubMed12354769].


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) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 Rap30/74 interaction domains 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 Rap30/74 interaction domains 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) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]