SUPERFAMILY 1.75 HMM library and genome assignments server


Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   N-cbl like [ 47667] (5)
Superfamily:   Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [ 47676]
Families:   Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 [ 47677] (2)


Superfamily statistics
Genomes (485) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,932 2,792 3
Proteins 2,916 2,771 3


Functional annotation
General category Regulation
Detailed category DNA-binding

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) cellular aromatic compound metabolic process 1.563e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 1.046e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 5.099e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.15e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.002514 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.02296 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1082 Least Informative Inherited
Biological Process (BP) localization 0.5817 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.001064 Least Informative Inherited
Biological Process (BP) gene expression 2.689e-12 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 1.877e-12 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 3.088e-10 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.832e-09 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0007896 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 2.337e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 9.814e-09 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.867e-09 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 2.322e-09 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.008121 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.01672 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 2.487e-08 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.03107 Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0 Highly Informative Direct
Biological Process (BP) phagocytosis 9.421e-06 Highly Informative Direct
Molecular Function (MF) binding 0.6389 Least Informative Inherited
Molecular Function (MF) enzyme binding 0.0002403 Informative Direct
Molecular Function (MF) protein binding transcription factor activity 7.152e-10 Highly Informative Direct
Molecular Function (MF) protein phosphatase binding 3.001e-09 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001297 Least Informative Direct
Cellular Component (CC) protein complex 0.05872 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2639 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3659 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0002477 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.036e-05 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0.01985 Informative Inherited
Cellular Component (CC) chromosome 0.001711 Informative Inherited
Cellular Component (CC) chromatin 1.582e-08 Highly Informative Direct
Cellular Component (CC) protein serine/threonine phosphatase complex 4.043e-10 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)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA 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)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

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
Cellular componentChromosome1.106e-09InformativeDirect
DomainZinc-finger4.824e-15Moderately InformativeDirect
DomainCoiled coil0.0002522Moderately InformativeDirect
Molecular functionZinc6.02e-10Least InformativeDirect
Molecular functionDNA-binding8.427e-12Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0003005InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationRepressor1.191e-07Moderately InformativeDirect
Post-translational modificationActivator6.465e-07Moderately InformativeDirect
Post-translational modificationMethyltransferase9.932e-05InformativeDirect
Post-translational modificationPhosphoprotein4.161e-05Least InformativeDirect
Post-translational modificationAcetylation4.342e-05Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010990 SSF47676 Protein matches
Abstract

This entry represents the conserved N-terminal domain found in the transcription elongation factors TFIIS, elongin A and CRSP70 [PubMed10811649]. The N-terminal domain in these transcription factors is conserved from yeast to man, and has a 4-helical bundle fold with a left-handed twist within a left-handed superhelix. TFIIS is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription [PubMed10723030]. TFIIS contains three structural domains termed I, II and III, where the N-terminal domain is domain I. Similarly, elongin A is a mammalian transcription elongation factor that forms the active subunit of the Elongin complex, which stimulates the rate of elongation by RNA polymerase II by suppressing the transient pausing of the polymerase at many sites along the DNA template [PubMed17112477]. CRSP70 is an essential subunit of the CRSP complex, which is required for the activity of the enhancer-binding protein Sp1 [PubMed9989412].


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) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 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 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 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) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]