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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 (723) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,885 28,397 69
Proteins 16,007 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) single-organism cellular process 0.0002117 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.1491 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.05188 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.2496 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01411 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01508 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1424 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02709 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1905 Least Informative Inherited
Biological Process (BP) regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000000000003389 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000002804 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000005301 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000001345 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0000003724 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000005496 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000006154 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0006982 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8975 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.6447 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5961 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5561 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6539 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.00845 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.8456 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) system development 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) multi-organism process 0.003676 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0229 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.002588 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2903 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell cycle 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0 Informative Direct
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000000000004403 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000000000005433 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000006249 Informative Direct
Biological Process (BP) response to radiation 0.00005894 Informative Direct
Biological Process (BP) mitotic cell cycle 0.0004636 Informative Direct
Biological Process (BP) post-embryonic development 0.0005767 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.01182 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 0.4502 Informative Inherited
Biological Process (BP) chromosome organization 0.1528 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.7381 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
Biological Process (BP) embryo development 0.4137 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.3157 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.1456 Informative Inherited
Biological Process (BP) growth 0.003568 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.007004 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) proteolysis 0.249 Informative Inherited
Biological Process (BP) tissue development 0.9684 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.001697 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.1246 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.03589 Informative Inherited
Biological Process (BP) DNA metabolic process 0.01759 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.00201 Informative Inherited
Biological Process (BP) cell development 0.2067 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.004745 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.001597 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 0.00000000005696 Highly Informative Direct
Biological Process (BP) response to UV 0.000000003638 Highly Informative Direct
Biological Process (BP) regulation of microtubule-based process 0.000009193 Highly Informative Direct
Biological Process (BP) regulation of nuclear division 0.00009467 Highly Informative Direct
Biological Process (BP) cell maturation 0.0005842 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle 0.008162 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 0.1241 Highly Informative Inherited
Biological Process (BP) germ cell development 0.02313 Highly Informative Inherited
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 1 Highly Informative Inherited
Biological Process (BP) muscle structure development 0.6956 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 0.007681 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle phase transition 0.02588 Highly Informative Inherited
Biological Process (BP) proteolysis involved in cellular protein catabolic process 0.01156 Highly Informative Inherited
Biological Process (BP) regeneration 0.02718 Highly Informative Inherited
Biological Process (BP) negative regulation of cytoskeleton organization 0.006449 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.1192 Highly Informative Inherited
Biological Process (BP) positive regulation of mitotic cell cycle phase transition 0.002119 Highly Informative Inherited
Biological Process (BP) DNA replication 0.01769 Highly Informative Inherited
Biological Process (BP) nuclear chromosome segregation 1 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000001213 Least Informative Direct
Molecular Function (MF) transferase activity 0.8004 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00561 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.265 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.0003264 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.1569 Informative Inherited
Molecular Function (MF) enzyme activator activity 1 Informative Inherited
Molecular Function (MF) enzyme binding 0.002218 Informative Inherited
Molecular Function (MF) RNA binding 1 Informative Inherited
Molecular Function (MF) DNA binding 0.02982 Informative Inherited
Molecular Function (MF) protein kinase regulator activity 0 Highly Informative Direct
Molecular Function (MF) kinase binding 0.00000005052 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00001753 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00002927 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.02647 Highly Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.9792 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000001216 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.008433 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000002303 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0002015 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.02365 Moderately Informative Inherited
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.000002077 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00003557 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.0129 Informative Inherited
Cellular Component (CC) transcription elongation factor complex 0.000000000006307 Highly Informative Direct
Cellular Component (CC) SCF ubiquitin ligase complex 0.0000007836 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.000002618 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 cancer0.03919Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.007077Moderately InformativeInherited
Disease Ontology (DO)respiratory system cancer0.007153InformativeInherited
Disease Ontology (DO)retinal cell cancer0.000000004237Highly InformativeDirect
Disease Ontology (DO)laryngeal carcinoma0.000008015Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0.00004228Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.03796Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.2365Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.2387Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.4892Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.862Least InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.002642Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.002707Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03488Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.04725Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.08512Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.1292Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.1368Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.187Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system physiology0.1994Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.2385Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.2657Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.295Moderately InformativeInherited
Mammalian Phenotype (MP)decreased hematopoietic cell number0.3188Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4991Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.5757Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.794Moderately InformativeInherited
Mammalian Phenotype (MP)increased carcinoma incidence0.003539InformativeInherited
Mammalian Phenotype (MP)abnormal metencephalon morphology0.0051InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.0124InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.02022InformativeInherited
Mammalian Phenotype (MP)abnormal erythroid lineage cell morphology0.03055InformativeInherited
Mammalian Phenotype (MP)abnormal urine homeostasis0.04867InformativeInherited
Mammalian Phenotype (MP)abnormal eye physiology0.13InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.2897InformativeInherited
Mammalian Phenotype (MP)abnormal sensory neuron morphology0.4665InformativeInherited
Mammalian Phenotype (MP)abnormal neuron number0.5661InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic stem cell morphology0.0003393Highly InformativeDirect
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.0006127Highly InformativeDirect
Mammalian Phenotype (MP)increased urinary system tumor incidence0.0008016Highly InformativeDirect
Mammalian Phenotype (MP)abnormal myeloid cell number0.007721Highly InformativeInherited
Mammalian Phenotype (MP)abnormal embryo size0.0094Highly InformativeInherited
Mammalian Phenotype (MP)abnormal retinal ganglion cell morphology0.01343Highly InformativeInherited
Mammalian Phenotype (MP)decreased sensory neuron number0.01788Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fibroblast proliferation0.07736Highly 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 variant0.001957Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.09168Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.1757Least InformativeInherited
Worm Phenotype (WP)retarded heterochronic variations1Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.000004446Moderately InformativeDirect
Worm Phenotype (WP)protein expression variant0.009057Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.09462Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1009Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1747Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.2049Moderately InformativeInherited
Worm Phenotype (WP)pigmentation variant0.0001092InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0.0002333InformativeDirect
Worm Phenotype (WP)embryonic cell organization biogenesis variant0.0004996InformativeDirect
Worm Phenotype (WP)protein modification variant0.1034InformativeInherited
Worm Phenotype (WP)gonad development variant0.1553InformativeInherited
Worm Phenotype (WP)cell number increased0.383InformativeInherited
Worm Phenotype (WP)embryonic cell morphology variant0.000002012Highly InformativeDirect
Worm Phenotype (WP)slow embryonic development0.0001662Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0003745Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic appearance defective early emb0.02974Highly InformativeInherited
Worm Phenotype (WP)pronuclear nuclear appearance defective early emb0.04864Highly InformativeInherited
Worm Phenotype (WP)multiple nuclei0.6514Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.09888Moderately InformativeInherited
Yeast Phenotype (YP)subcellular morphology0.0004618InformativeDirect
Yeast Phenotype (YP)budding0.02304Highly 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 defective0.00006534InformativeDirect

Document: FP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0.2699Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.2802Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.4887Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.02665Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.3452Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.03945InformativeInherited
Zebrafish Anatomy (ZA)cranial nerve II0.00009512Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cell0.0008321Least 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 groups0.1165Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.000001021Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.0000002779InformativeDirect

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 regulation0.00000000000002045Moderately InformativeDirect
Biological processMitosis0.00000000000004796InformativeDirect
Biological processMeiosis0.00000000002766InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.00003967Moderately InformativeDirect
DiseaseTumor suppressor0.0000004183Moderately InformativeDirect
DomainRepeat0.00000000003187Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.0000001191Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0.00006951InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationOxidation0.000002457InformativeDirect
Post-translational modificationMyristate0.000612InformativeDirect

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 ]