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 (451) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,468 1,225 5
Proteins 1,457 1,220 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 process8.069e-134.008e-15Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00046359.278e-12Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.0097424.402e-06Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.02811.596e-05Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0089072.814e-06Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.015329.285e-06Least InformativeInherited
Biological Process (BP)response to stimulus4.106e-050.1636Least InformativeInherited
Biological Process (BP)regulation of cellular process0.067330.07318Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.43981Least InformativeInherited
Biological Process (BP)cellular response to stress1.716e-056.352e-06Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process04.1e-13Moderately InformativeDirect
Biological Process (BP)regulation of cellular component organization3.099e-154.276e-09Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process4.683e-101.504e-05Moderately InformativeDirect
Biological Process (BP)regulation of molecular function0.0024250.02692Moderately InformativeInherited
Biological Process (BP)organelle organization0.010851.86e-10Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process0.084940.3794Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.22071Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process0.51251Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.0013280.02085Moderately InformativeInherited
Biological Process (BP)signal transduction0.49051Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.026140.4541Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.22080.881Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.065490.5962Moderately InformativeInherited
Biological Process (BP)positive regulation of macromolecule biosynthetic process2.024e-090.0009754InformativeDirect
Biological Process (BP)positive regulation of phosphorus metabolic process6.175e-111.221e-06InformativeDirect
Biological Process (BP)regulation of cell cycle process00InformativeDirect
Biological Process (BP)positive regulation of gene expression2.024e-090.0007512InformativeDirect
Biological Process (BP)cell cycle process00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process1.182e-073.526e-08InformativeDirect
Biological Process (BP)regulation of organelle organization00InformativeDirect
Biological Process (BP)intracellular signal transduction4.72e-089.13e-05InformativeDirect
Biological Process (BP)negative regulation of molecular function0.00053470.000101InformativeDirect
Biological Process (BP)negative regulation of cellular component organization00InformativeDirect
Biological Process (BP)negative regulation of protein metabolic process3.879e-146.037e-10InformativeDirect
Biological Process (BP)chromosome organization3.839e-051.293e-11InformativeDirect
Biological Process (BP)positive regulation of nitrogen compound metabolic process3.193e-090.001171InformativeInherited
Biological Process (BP)positive regulation of cellular biosynthetic process4.977e-090.001519InformativeInherited
Biological Process (BP)response to DNA damage stimulus0.0033970.003902InformativeInherited
Biological Process (BP)negative regulation of cellular metabolic process0.067890.5591InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle00.01884InformativeInherited
Biological Process (BP)regulation of protein phosphorylation0.14590.1311InformativeInherited
Biological Process (BP)positive regulation of protein metabolic process0.0013470.0006245InformativeInherited
Biological Process (BP)nuclear division1.116e-111.266e-07Highly InformativeDirect
Biological Process (BP)chromosome segregation2.1e-060Highly InformativeDirect
Biological Process (BP)regulation of proteolysis4.778e-061.554e-08Highly InformativeDirect
Biological Process (BP)negative regulation of cellular catabolic process5.244e-091.215e-12Highly InformativeDirect
Biological Process (BP)regulation of protein ubiquitination01.103e-13Highly InformativeDirect
Biological Process (BP)negative regulation of protein modification process3.099e-151.124e-10Highly InformativeDirect
Biological Process (BP)spindle checkpoint9.769e-065.661e-05Highly InformativeDirect
Biological Process (BP)regulation of protein catabolic process07.835e-15Highly InformativeDirect
Biological Process (BP)signal transduction in response to DNA damage3.306e-101.077e-10Highly InformativeDirect
Biological Process (BP)negative regulation of cell cycle00Highly InformativeDirect
Biological Process (BP)regulation of ligase activity8.634e-111.536e-12Highly InformativeDirect
Biological Process (BP)mitotic cell cycle0.24211Highly InformativeInherited
Biological Process (BP)mitotic cell cycle checkpoint0.38460.9029Highly InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)protein complex01.337e-10Least InformativeDirect
Cellular Component (CC)intracellular organelle part08.33e-05Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle10.8927Least InformativeInherited
Cellular Component (CC)cytoskeleton0.014990.8281Moderately InformativeInherited
Cellular Component (CC)nuclear part1.153e-050.005372Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex1.747e-097.407e-06InformativeDirect
Cellular Component (CC)chromosome7.033e-090InformativeDirect
Cellular Component (CC)microtubule cytoskeleton00.0004389InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex1.539e-083.854e-08Highly InformativeDirect
Cellular Component (CC)kinetochore00Highly InformativeDirect
Cellular Component (CC)spindle04.288e-10Highly InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex3.487e-137.84e-09Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex00Highly 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 4.402e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.596e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.008e-15 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.814e-06 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 9.278e-12 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 9.285e-06 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.07318 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1636 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.4928 Least Informative Inherited
Biological Process (BP) developmental process 0.467 Least Informative Inherited
Biological Process (BP) reproduction 1.452e-11 Moderately Informative Direct
Biological Process (BP) organelle organization 1.86e-10 Moderately Informative Direct
Biological Process (BP) cellular response to stress 6.352e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 4.1e-13 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 4.276e-09 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.504e-05 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.02692 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.3794 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.02085 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.4541 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.881 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.5962 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.04475 Moderately Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.0009754 Informative Direct
Biological Process (BP) positive regulation of phosphorus metabolic process 1.221e-06 Informative Direct
Biological Process (BP) regulation of cell cycle process 0 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.0007512 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 3.526e-08 Informative Direct
Biological Process (BP) regulation of organelle organization 0 Informative Direct
Biological Process (BP) intracellular signal transduction 9.13e-05 Informative Direct
Biological Process (BP) chordate embryonic development 1.95e-08 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.000101 Informative Direct
Biological Process (BP) single organism reproductive process 0.0006513 Informative Direct
Biological Process (BP) cellular process involved in reproduction 1.716e-14 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0006245 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 6.037e-10 Informative Direct
Biological Process (BP) chromosome organization 1.293e-11 Informative Direct
Biological Process (BP) regulation of reproductive process 3.384e-08 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.001171 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.001519 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.003902 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.5591 Informative Inherited
Biological Process (BP) sexual reproduction 0.3396 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01202 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.01884 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.1311 Informative Inherited
Biological Process (BP) nuclear division 1.266e-07 Highly Informative Direct
Biological Process (BP) chromosome segregation 0 Highly Informative Direct
Biological Process (BP) meiosis 1.158e-06 Highly Informative Direct
Biological Process (BP) spermatogenesis 7.529e-11 Highly Informative Direct
Biological Process (BP) female gamete generation 7.229e-11 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 1.554e-08 Highly Informative Direct
Biological Process (BP) negative regulation of cellular catabolic process 1.215e-12 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 1.103e-13 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 1.124e-10 Highly Informative Direct
Biological Process (BP) spindle checkpoint 5.661e-05 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 7.835e-15 Highly Informative Direct
Biological Process (BP) signal transduction in response to DNA damage 1.077e-10 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 1.536e-12 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 8.213e-11 Highly Informative Direct
Biological Process (BP) negative regulation of reproductive process 4.529e-10 Highly Informative Direct
Biological Process (BP) mitotic cell cycle 1 Highly Informative Inherited
Biological Process (BP) cell cycle phase 0.0218 Highly Informative Inherited
Biological Process (BP) mitotic cell cycle checkpoint 0.9029 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 1.337e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 8.33e-05 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8927 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.8281 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1975 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.005372 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 7.407e-06 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0004389 Informative Direct
Cellular Component (CC) nuclear ubiquitin ligase complex 3.854e-08 Highly Informative Direct
Cellular Component (CC) kinetochore 0 Highly Informative Direct
Cellular Component (CC) spindle 4.288e-10 Highly Informative Direct
Cellular Component (CC) cullin-RING ubiquitin ligase complex 7.84e-09 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0002027 Highly Informative Direct
Cellular Component (CC) condensed chromosome 0.1283 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

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) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
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 cycle4.744e-15Moderately InformativeDirect
Biological processDifferentiation1.281e-12Moderately InformativeDirect
Biological processDNA damage2.526e-06Moderately InformativeDirect
Biological processTranscription regulation0.0001183Moderately InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processMitosis0InformativeDirect
Biological processSpermatogenesis0Highly InformativeDirect
Biological processOogenesis0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton5.002e-12Moderately InformativeDirect
Cellular componentChromosome0InformativeDirect
Post-translational modificationPhosphoprotein6.01e-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 ]