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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 (719) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,690 28,397 69
Proteins 15,889 17,576 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) macromolecule metabolic process 0.2206 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.1446 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03003 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01435 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.07198 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1479 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.04799 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02651 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.137 Least Informative Inherited
Biological Process (BP) regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000000008617 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.0000000001782 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000002984 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000008428 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.00001737 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0008331 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.5259 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.645 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.01881 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.01325 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.6775 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4958 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9701 Moderately Informative Inherited
Biological Process (BP) response to stress 0.01444 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.6062 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.009964 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.002178 Moderately Informative Inherited
Biological Process (BP) signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.002888 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) regulation of cell cycle 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000000000003551 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000001377 Informative Direct
Biological Process (BP) regulation of protein modification process 0.00000000002337 Informative Direct
Biological Process (BP) organelle fission 0.0000000001758 Informative Direct
Biological Process (BP) response to radiation 0.00002106 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.01434 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
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 0.2886 Informative Inherited
Biological Process (BP) cell development 0.1842 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.6954 Informative Inherited
Biological Process (BP) embryo development 0.4785 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.00192 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.1502 Informative Inherited
Biological Process (BP) proteolysis 0.4781 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.2813 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.001198 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.002601 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.00329 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.01166 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.01356 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.1156 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.1174 Informative Inherited
Biological Process (BP) DNA metabolic process 0.02108 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.7808 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.8847 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.9523 Informative Inherited
Biological Process (BP) cell cycle phase transition 0 Highly Informative Direct
Biological Process (BP) cell cycle checkpoint 0 Highly Informative Direct
Biological Process (BP) response to UV 0.000000002723 Highly Informative Direct
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.0001262 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0001955 Highly Informative Direct
Biological Process (BP) regulation of protein serine/threonine kinase activity 0.0002278 Highly Informative Direct
Biological Process (BP) cell maturation 0.0003477 Highly Informative Direct
Biological Process (BP) regulation of nuclear division 0.0005661 Highly Informative Direct
Biological Process (BP) cell division 0.0006734 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle 0.002351 Highly Informative Inherited
Biological Process (BP) germ cell development 0.02306 Highly Informative Inherited
Biological Process (BP) muscle structure development 0.6958 Highly Informative Inherited
Biological Process (BP) modification-dependent protein catabolic process 0.005849 Highly Informative Inherited
Biological Process (BP) regeneration 0.01851 Highly Informative Inherited
Biological Process (BP) positive regulation of mitotic cell cycle 0.2698 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.01273 Highly Informative Inherited
Biological Process (BP) positive regulation of cell cycle process 0.6446 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3557 Highly Informative Inherited
Biological Process (BP) DNA replication 0.02829 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.08597 Highly Informative Inherited
Biological Process (BP) chromosome organization 0.009542 Highly Informative Inherited
Biological Process (BP) nuclear chromosome segregation 1 Highly Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3536 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.3708 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000002325 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) protein binding 0.000000000847 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.1573 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.01072 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.0007394 Informative Direct
Molecular Function (MF) RNA binding 1 Informative Inherited
Molecular Function (MF) enzyme activator activity 1 Informative Inherited
Molecular Function (MF) enzyme binding 0.005117 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.07794 Informative Inherited
Molecular Function (MF) DNA binding 0.01338 Informative Inherited
Molecular Function (MF) protein kinase regulator activity 0 Highly Informative Direct
Molecular Function (MF) kinase binding 0.00000002936 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000312 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00001189 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.01141 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.998 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000001184 Least Informative Direct
Cellular Component (CC) protein complex 0.0000002274 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.04641 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.9651 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000224 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0009785 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.1012 Moderately Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase complex 0.0000004026 Informative Direct
Cellular Component (CC) nucleoplasm part 0.000001736 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.000011 Informative Direct
Cellular Component (CC) site of polarized growth 0.0005753 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.01111 Informative Inherited
Cellular Component (CC) transcription elongation factor complex 0.000000000003444 Highly Informative Direct
Cellular Component (CC) centrosome 0.0000002312 Highly Informative Direct
Cellular Component (CC) SCF ubiquitin ligase complex 0.000000799 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.0397Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.006997Moderately InformativeInherited
Disease Ontology (DO)respiratory system cancer0.007185InformativeInherited
Disease Ontology (DO)retinal cell cancer0.000000004641Highly InformativeDirect
Disease Ontology (DO)laryngeal carcinoma0.00000787Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.00006278Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.04326Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.2403Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.2467Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.4582Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.831Least InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.002959Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.00306Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.0372Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.04049Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.1155Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.1317Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.1892Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system physiology0.2135Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.2281Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.2659Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.2885Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.5785Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.7712Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.7909Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.0005857InformativeDirect
Mammalian Phenotype (MP)increased carcinoma incidence0.003816InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.00539InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.01278InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.01963InformativeInherited
Mammalian Phenotype (MP)abnormal urine homeostasis0.04981InformativeInherited
Mammalian Phenotype (MP)abnormal eye physiology0.1443InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.4638InformativeInherited
Mammalian Phenotype (MP)abnormal neuron number0.5578InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.000428Highly InformativeDirect
Mammalian Phenotype (MP)increased urinary system tumor incidence0.0008478Highly InformativeDirect
Mammalian Phenotype (MP)abnormal embryonic growth/weight/body size0.003296Highly InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell number0.007386Highly InformativeInherited
Mammalian Phenotype (MP)abnormal retinal ganglion cell morphology0.01273Highly InformativeInherited
Mammalian Phenotype (MP)decreased sensory neuron number0.01797Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.07798Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.001231Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.07437Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.1416Least InformativeInherited
Worm Phenotype (WP)retarded heterochronic variations1Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.000004881Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.07874Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.0956Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1446Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.2131Moderately InformativeInherited
Worm Phenotype (WP)pigmentation variant0.0001096InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0.0004812InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0005372InformativeDirect
Worm Phenotype (WP)protein modification variant0.04723InformativeInherited
Worm Phenotype (WP)gonad development variant0.1593InformativeInherited
Worm Phenotype (WP)cell number increased0.4062InformativeInherited
Worm Phenotype (WP)nuclear number variant0.0000005712Highly InformativeDirect
Worm Phenotype (WP)nucleus defective early emb0.000003419Highly InformativeDirect
Worm Phenotype (WP)slow embryonic development0.0001488Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0002439Highly InformativeDirect
Worm Phenotype (WP)division axis defective0.001071Highly InformativeInherited
Worm Phenotype (WP)cytoplasmic appearance defective early emb0.03047Highly InformativeInherited
Worm Phenotype (WP)pronucleus centrosomes defective early emb0.1881Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.09871Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.0004582InformativeDirect
Yeast Phenotype (YP)budding0.02317Highly InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)mitotic cell cycle defective0.00005104InformativeDirect

Document: FP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.279Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2949Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.487Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.02685Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3314Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.04003InformativeInherited
Zebrafish Anatomy (ZA)cranial nerve II0.0001128Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cell0.0008072Least 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 phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processTranscription regulation0.0000000000000156Moderately InformativeDirect
Biological processMitosis0.00000000000003114InformativeDirect
Biological processMeiosis0.000000000022InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.000032Moderately InformativeDirect
DiseaseTumor suppressor0.0000004817Moderately InformativeDirect
DomainRepeat0.00000000003007Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.0000001128Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0.0001022InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationMyristate0.0006045InformativeDirect
Post-translational modificationOxidation0.000001338Highly InformativeDirect

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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · 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 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]