SUPERFAMILY 1.75 HMM library and genome assignments server


The spindle assembly checkpoint protein mad2 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   The spindle assembly checkpoint protein mad2 [ 56018]
Superfamily:   The spindle assembly checkpoint protein mad2 [ 56019]
Families:   The spindle assembly checkpoint protein mad2 [ 56020]


Superfamily statistics
Genomes (497) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,605 1,796 5
Proteins 1,591 1,783 5


Functional annotation
General category Processes_IC
Detailed category Cell cycle, Apoptosis

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process2.749e-104.871e-09Least InformativeDirect
Biological Process (BP)regulation of cellular process1.209e-127.009e-07Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00061581.432e-09Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0054661.466e-05Least InformativeInherited
Biological Process (BP)response to stimulus1.784e-050.2666Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.5151Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0057241.898e-05Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.025060.000217Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.010495.479e-05Least InformativeInherited
Biological Process (BP)cellular response to stress8.752e-062.426e-06Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process1.946e-098.986e-12Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity0.00015640.0002149Moderately InformativeDirect
Biological Process (BP)regulation of cellular component organization9.589e-154.394e-09Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process3.031e-090.0001575Moderately InformativeDirect
Biological Process (BP)regulation of phosphate metabolic process10.001925Moderately InformativeInherited
Biological Process (BP)signal transduction0.57331Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.29721Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.01690.4448Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.0012940.04545Moderately InformativeInherited
Biological Process (BP)organelle organization0.016636.816e-10Moderately InformativeInherited
Biological Process (BP)regulation of cell cycle process7.348e-061.359e-06InformativeDirect
Biological Process (BP)cell cycle process00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process6.469e-071.608e-06InformativeDirect
Biological Process (BP)regulation of organelle organization01.922e-15InformativeDirect
Biological Process (BP)intracellular signal transduction1.821e-070.0004195InformativeDirect
Biological Process (BP)negative regulation of catalytic activity0.00025062.117e-05InformativeDirect
Biological Process (BP)positive regulation of phosphate metabolic process8.997e-109.211e-06InformativeDirect
Biological Process (BP)negative regulation of cellular component organization05.894e-13InformativeDirect
Biological Process (BP)negative regulation of protein metabolic process5.447e-131.158e-08InformativeDirect
Biological Process (BP)chromosome organization3.554e-051.035e-11InformativeDirect
Biological Process (BP)mitotic cell cycle0.028941InformativeInherited
Biological Process (BP)response to DNA damage stimulus0.00091040.00136InformativeInherited
Biological Process (BP)positive regulation of protein modification process0.039530.02135InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle3.086e-070.02978InformativeInherited
Biological Process (BP)regulation of protein phosphorylation0.17060.1442InformativeInherited
Biological Process (BP)chromosome segregation2.838e-060Highly InformativeDirect
Biological Process (BP)regulation of mitosis5.46e-135.754e-07Highly InformativeDirect
Biological Process (BP)regulation of proteolysis1.19e-073.278e-09Highly InformativeDirect
Biological Process (BP)negative regulation of cellular catabolic process1.798e-099.056e-13Highly InformativeDirect
Biological Process (BP)regulation of protein ubiquitination01.105e-12Highly InformativeDirect
Biological Process (BP)negative regulation of protein modification process7.796e-142.186e-09Highly InformativeDirect
Biological Process (BP)spindle checkpoint1.193e-058.81e-05Highly InformativeDirect
Biological Process (BP)regulation of protein catabolic process02.842e-13Highly InformativeDirect
Biological Process (BP)negative regulation of cell cycle00Highly InformativeDirect
Biological Process (BP)regulation of ligase activity1.095e-112.557e-13Highly InformativeDirect
Biological Process (BP)negative regulation of mitotic cell cycle phase transition00.1391Highly InformativeInherited
Biological Process (BP)mitosis0.052970.8852Highly InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)protein complex01.498e-08Least InformativeDirect
Cellular Component (CC)intracellular organelle part05.752e-06Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle10.6677Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0092740.8839Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.22940.103Moderately InformativeInherited
Cellular Component (CC)nuclear part7.904e-060.001222Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex3.132e-091.197e-05InformativeDirect
Cellular Component (CC)chromosome8.059e-100InformativeDirect
Cellular Component (CC)microtubule cytoskeleton02.213e-14InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex2.397e-087.478e-08Highly InformativeDirect
Cellular Component (CC)kinetochore00Highly InformativeDirect
Cellular Component (CC)spindle01.576e-10Highly InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex6.019e-133.376e-08Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex00Highly InformativeDirect
Cellular Component (CC)nuclear chromosome part0.00050330.0002504Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 1.898e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000217 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.871e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.466e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 7.009e-07 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1.432e-09 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 5.479e-05 Least Informative Direct
Biological Process (BP) response to stimulus 0.2666 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.7563 Least Informative Inherited
Biological Process (BP) developmental process 0.7203 Least Informative Inherited
Biological Process (BP) reproduction 3.938e-10 Moderately Informative Direct
Biological Process (BP) organelle organization 6.816e-10 Moderately Informative Direct
Biological Process (BP) cellular response to stress 2.426e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 8.986e-12 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0002149 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 4.394e-09 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0001575 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.001925 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.4448 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.0685 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.04545 Moderately Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 9.109e-07 Informative Direct
Biological Process (BP) regulation of cell cycle process 1.359e-06 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 1.608e-06 Informative Direct
Biological Process (BP) regulation of organelle organization 1.922e-15 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0004195 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 2.117e-05 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 9.211e-06 Informative Direct
Biological Process (BP) cellular process involved in reproduction 3.095e-14 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 5.894e-13 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 1.158e-08 Informative Direct
Biological Process (BP) chromosome organization 1.035e-11 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 4.782e-07 Informative Direct
Biological Process (BP) mitotic cell cycle 1 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.00136 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.02135 Informative Inherited
Biological Process (BP) sexual reproduction 0.4167 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001134 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01705 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.02978 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.1442 Informative Inherited
Biological Process (BP) chromosome segregation 0 Highly Informative Direct
Biological Process (BP) regulation of mitosis 5.754e-07 Highly Informative Direct
Biological Process (BP) meiosis 2.67e-07 Highly Informative Direct
Biological Process (BP) spermatogenesis 1.83e-09 Highly Informative Direct
Biological Process (BP) female gamete generation 8.464e-10 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 3.278e-09 Highly Informative Direct
Biological Process (BP) negative regulation of cellular catabolic process 9.056e-13 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 1.105e-12 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 2.186e-09 Highly Informative Direct
Biological Process (BP) spindle checkpoint 8.81e-05 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 2.842e-13 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 2.557e-13 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 3.206e-09 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.1391 Highly Informative Inherited
Biological Process (BP) mitosis 0.8852 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 1.498e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.752e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.6677 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.8839 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.103 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.001222 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 1.197e-05 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 2.213e-14 Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 7.478e-08 Highly Informative Direct
Cellular Component (CC) kinetochore 0 Highly Informative Direct
Cellular Component (CC) spindle 1.576e-10 Highly Informative Direct
Cellular Component (CC) cullin-RING ubiquitin ligase complex 3.376e-08 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0002504 Highly Informative Direct
Cellular Component (CC) condensed chromosome 0.06131 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal cell death0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal reproductive system morphology0.004213Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.01071Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.01825Moderately InformativeInherited
Mammalian Phenotype (MP)decreased germ cell number0.0002442InformativeDirect
Mammalian Phenotype (MP)abnormal male germ cell morphology0.0003901InformativeDirect
Mammalian Phenotype (MP)abnormal sex determination0.0004513InformativeDirect
Mammalian Phenotype (MP)abnormal spermatogenesis0.0005826InformativeDirect
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.0009474InformativeDirect
Mammalian Phenotype (MP)abnormal sex gland morphology0.001482InformativeInherited
Mammalian Phenotype (MP)abnormal fertility/fecundity0.007271InformativeInherited
Mammalian Phenotype (MP)abnormal oogenesis3.712e-06Highly InformativeDirect
Mammalian Phenotype (MP)azoospermia7.673e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight3.991e-05Highly InformativeDirect
Mammalian Phenotype (MP)small testis0.0002465Highly InformativeDirect
Mammalian Phenotype (MP)abnormal male reproductive system physiology0.001816Highly 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 variant0Least InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant2.604e-05Moderately InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant9.872e-08InformativeDirect
Worm Phenotype (WP)meiotic chromosome segregation variant0Highly InformativeDirect
Worm Phenotype (WP)aneuploidy0.02146Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle9.13e-15Moderately InformativeDirect
Biological processDifferentiation2.552e-12Moderately InformativeDirect
Biological processDNA damage3.405e-07Moderately InformativeDirect
Biological processTranscription regulation0.0001823Moderately InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processMitosis0InformativeDirect
Biological processSpermatogenesis0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton3.47e-13Moderately InformativeDirect
Cellular componentChromosome0InformativeDirect
Post-translational modificationPhosphoprotein6.067e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003511 SSF56019 Protein matches
Abstract The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.

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-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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 1 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 The spindle assembly checkpoint protein mad2 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 1 hidden Markov models representing the The spindle assembly checkpoint protein mad2 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-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]