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Cyclin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Cyclin-like [ 47953]
Superfamily:   Cyclin-like [ 47954] (3)
Families:   Cyclin [ 47955] (8)
  Transcription factor IIB (TFIIB), core domain [ 47965]
  Retinoblastoma tumor suppressor domains [ 47969]


Superfamily statistics
Genomes (724) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 25,919 62,218 69
Proteins 16,028 38,298 37


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) biological regulation 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0003207 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0008157 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.2566 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.04961 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01599 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1403 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01422 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.1433 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02586 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2453 Least Informative Inherited
Biological Process (BP) regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000000005731 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000000008632 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000003316 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000001153 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0000003187 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000000388 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000005476 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0006643 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6662 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5077 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.789 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.005434 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2654 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5859 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.6723 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.7937 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7759 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.01299 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.002802 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0 Informative Direct
Biological Process (BP) regulation of cell cycle 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000000000002873 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000000000007138 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000000001125 Informative Direct
Biological Process (BP) post-embryonic development 0.0001073 Informative Direct
Biological Process (BP) response to radiation 0.000286 Informative Direct
Biological Process (BP) mitotic cell cycle 0.000531 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 1 Informative Inherited
Biological Process (BP) regulation of cell differentiation 1 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.3612 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.005863 Informative Inherited
Biological Process (BP) chromosome organization 0.1499 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.005396 Informative Inherited
Biological Process (BP) cell development 0.3284 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.01173 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
Biological Process (BP) embryo development 0.5228 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.002924 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.04777 Informative Inherited
Biological Process (BP) epithelium development 0.5564 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.1469 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.2312 Informative Inherited
Biological Process (BP) proteolysis 0.2285 Informative Inherited
Biological Process (BP) growth 0.003459 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.7366 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.002241 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.002396 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.1621 Informative Inherited
Biological Process (BP) DNA metabolic process 0.01561 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1567 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.8024 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.8093 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.9047 Informative Inherited
Biological Process (BP) cell cycle checkpoint 0 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0 Highly Informative Direct
Biological Process (BP) nuclear division 0.00000000005546 Highly Informative Direct
Biological Process (BP) response to UV 0.000000001132 Highly Informative Direct
Biological Process (BP) anatomical structure maturation 0.0000001679 Highly Informative Direct
Biological Process (BP) regulation of microtubule-based process 0.00001076 Highly Informative Direct
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.0001059 Highly Informative Direct
Biological Process (BP) cell maturation 0.0005785 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.4058 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 0.1121 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.1209 Highly Informative Inherited
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 0.9924 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle phase transition 0.01456 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.007386 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.1305 Highly Informative Inherited
Biological Process (BP) appendage development 0.3753 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.8897 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.9857 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 0.007544 Highly Informative Inherited
Biological Process (BP) cellular protein catabolic process 0.01693 Highly Informative Inherited
Biological Process (BP) regeneration 0.01453 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.006476 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.1359 Highly Informative Inherited
Biological Process (BP) germ cell development 0.02148 Highly Informative Inherited
Biological Process (BP) positive regulation of mitotic cell cycle 0.1247 Highly Informative Inherited
Biological Process (BP) DNA replication 0.01605 Highly Informative Inherited
Biological Process (BP) nuclear chromosome segregation 1 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.248 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000002952 Least Informative Direct
Molecular Function (MF) transferase activity 0.8101 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.3084 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.005931 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.0003329 Informative Direct
Molecular Function (MF) RNA binding 1 Informative Inherited
Molecular Function (MF) enzyme binding 0.002494 Informative Inherited
Molecular Function (MF) DNA binding 0.04147 Informative Inherited
Molecular Function (MF) enzyme activator activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.1534 Informative Inherited
Molecular Function (MF) kinase regulator activity 0 Highly Informative Direct
Molecular Function (MF) kinase binding 0.00000003981 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00003667 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00005774 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.02834 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.9931 Highly Informative Inherited
Cellular Component (CC) protein complex 0.00000000605 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000005258 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.00925 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000664 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0005187 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.02896 Moderately Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.000002535 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000198 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.01148 Informative Inherited
Cellular Component (CC) transcription elongation factor complex 0.000000000005559 Highly Informative Direct
Cellular Component (CC) SCF ubiquitin ligase complex 0.0000007184 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.000001702 Highly Informative Direct
Cellular Component (CC) RNA polymerase II transcription factor complex 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processTranscription regulation0.00000000000001911Moderately InformativeDirect
Biological processMitosis0.000000000000211InformativeDirect
Biological processMeiosis0.000000000002629InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.00004211Moderately InformativeDirect
DiseaseTumor suppressor0.0000003854Moderately InformativeDirect
DomainRepeat0.00000000003788Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.0000001351Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationChromatin regulator0.00007026InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationOxidation0.000003355InformativeDirect
Post-translational modificationMyristate0.0006238InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011028 SSF47954 Protein matches
Abstract

This domain is also found as the core domain in transcription factor IIB (TFIIB) and in the retinoblastoma tumour suppressor.


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 26 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 Cyclin-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 26 hidden Markov models representing the Cyclin-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]