SUPERFAMILY 1.75 HMM library and genome assignments server


Spermadhesin, CUB domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   CUB-like [ 49853] (3)
Superfamily:   Spermadhesin, CUB domain [ 49854]
Families:   Spermadhesin, CUB domain [ 49855] (5)


Superfamily statistics
Genomes (189) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 18,950 16,534 8
Proteins 7,754 6,875 7


Functional annotation
General category General
Detailed category General

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) developmental process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) response to stimulus 5.608e-13 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 4.983e-08 Least Informative Direct
Biological Process (BP) protein metabolic process 5.886e-08 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0001461 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 0.3667 Least Informative Inherited
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) nervous system development 6.637e-09 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 4.619e-08 Moderately Informative Direct
Biological Process (BP) signal transduction 1.504e-06 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 2.417e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 3.42e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0001659 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.6759 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.05035 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.002442 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.06222 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.4728 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.01453 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2904 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.0562 Moderately Informative Inherited
Biological Process (BP) tissue development 0.03532 Moderately Informative Inherited
Biological Process (BP) reproduction 0.5032 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.3698 Moderately Informative Inherited
Biological Process (BP) immune system process 0.05193 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component movement 0 Informative Direct
Biological Process (BP) cell projection organization 0 Informative Direct
Biological Process (BP) regulation of locomotion 7.333e-15 Informative Direct
Biological Process (BP) locomotion 4.427e-14 Informative Direct
Biological Process (BP) regulation of anatomical structure size 6.436e-12 Informative Direct
Biological Process (BP) cardiovascular system development 2.952e-10 Informative Direct
Biological Process (BP) regulation of growth 3.514e-10 Informative Direct
Biological Process (BP) positive regulation of developmental process 4.541e-09 Informative Direct
Biological Process (BP) cellular component movement 1.983e-08 Informative Direct
Biological Process (BP) regulation of response to external stimulus 3.686e-08 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 5.071e-08 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 1.268e-07 Informative Direct
Biological Process (BP) regulation of nervous system development 1.945e-07 Informative Direct
Biological Process (BP) localization of cell 2.284e-07 Informative Direct
Biological Process (BP) single-organism behavior 6.941e-07 Informative Direct
Biological Process (BP) embryonic organ development 8.429e-06 Informative Direct
Biological Process (BP) immune effector process 8.969e-06 Informative Direct
Biological Process (BP) regulation of cell development 2.582e-05 Informative Direct
Biological Process (BP) tissue morphogenesis 3.409e-05 Informative Direct
Biological Process (BP) proteolysis 4.993e-05 Informative Direct
Biological Process (BP) defense response 5.659e-05 Informative Direct
Biological Process (BP) organ morphogenesis 9.06e-05 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0001026 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.000324 Informative Direct
Biological Process (BP) response to wounding 0.0004691 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0006145 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0008001 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.001321 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.6662 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.06392 Informative Inherited
Biological Process (BP) cell-cell signaling 0.3801 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.1556 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.04418 Informative Inherited
Biological Process (BP) generation of neurons 0.009488 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) response to lipid 0.1929 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.2341 Informative Inherited
Biological Process (BP) response to cytokine stimulus 0.04178 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.05311 Informative Inherited
Biological Process (BP) central nervous system development 0.5826 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.1321 Informative Inherited
Biological Process (BP) epithelium development 0.06174 Informative Inherited
Biological Process (BP) immune response 0.09255 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.006301 Informative Inherited
Biological Process (BP) regulation of immune response 0.6485 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9154 Informative Inherited
Biological Process (BP) regulation of neuron projection development 0 Highly Informative Direct
Biological Process (BP) regulation of cell size 0 Highly Informative Direct
Biological Process (BP) regulation of cell growth 0 Highly Informative Direct
Biological Process (BP) protein processing 0 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 1.823e-13 Highly Informative Direct
Biological Process (BP) chemotaxis 2.457e-13 Highly Informative Direct
Biological Process (BP) regulation of behavior 4.882e-13 Highly Informative Direct
Biological Process (BP) protein activation cascade 1.158e-11 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 4.631e-11 Highly Informative Direct
Biological Process (BP) positive regulation of growth 9.276e-11 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 2.651e-10 Highly Informative Direct
Biological Process (BP) humoral immune response 4.024e-10 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 4.158e-10 Highly Informative Direct
Biological Process (BP) activation of immune response 1.946e-09 Highly Informative Direct
Biological Process (BP) skeletal system development 5.043e-07 Highly Informative Direct
Biological Process (BP) pattern specification process 5.685e-07 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 2.783e-06 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 5.6e-06 Highly Informative Direct
Biological Process (BP) neuron projection development 9.929e-06 Highly Informative Direct
Biological Process (BP) female pregnancy 1.288e-05 Highly Informative Direct
Biological Process (BP) adult behavior 1.839e-05 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0001126 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.0001371 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.0002316 Highly Informative Direct
Biological Process (BP) epithelial tube morphogenesis 0.0003439 Highly Informative Direct
Biological Process (BP) angiogenesis 0.0009166 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.01149 Highly Informative Inherited
Biological Process (BP) developmental maturation 0.03959 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.3302 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 1 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.1275 Highly Informative Inherited
Biological Process (BP) negative regulation of growth 0.008633 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.005128 Highly Informative Inherited
Biological Process (BP) stem cell development 0.3189 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.08701 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.005777 Highly Informative Inherited
Biological Process (BP) innate immune response 0.002002 Highly Informative Inherited
Molecular Function (MF) binding 0.1843 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.003515 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.9136 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) receptor activity 3.374e-10 Informative Direct
Molecular Function (MF) molecular transducer activity 0.000151 Informative Direct
Molecular Function (MF) enzyme binding 0.5246 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.6181 Informative Inherited
Molecular Function (MF) kinase activity 0.7434 Informative Inherited
Molecular Function (MF) protein kinase activity 0.3196 Highly Informative Inherited
Cellular Component (CC) membrane 1.407e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8221 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 2.972e-15 Moderately Informative Direct
Cellular Component (CC) cell projection 5.839e-15 Moderately Informative Direct
Cellular Component (CC) vesicle 5.188e-11 Moderately Informative Direct
Cellular Component (CC) endomembrane system 2.697e-05 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 4.485e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.4192 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.1414 Moderately Informative Inherited
Cellular Component (CC) secretory granule 7.459e-08 Informative Direct
Cellular Component (CC) integral to membrane 4.943e-05 Informative Direct
Cellular Component (CC) cell surface 0.0003047 Informative Direct
Cellular Component (CC) neuron projection 0.03551 Informative Inherited
Cellular Component (CC) cell body 8.113e-10 Highly Informative Direct
Cellular Component (CC) axon part 0.01388 Highly Informative Inherited
Cellular Component (CC) cytoplasmic vesicle membrane 0.01234 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.0003183Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases8.539e-12InformativeDirect
Enzyme Commission (EC)Complement subcomponent C1s3.399e-12Highly InformativeDirect
Enzyme Commission (EC)Complement subcomponent C1r3.399e-12Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.4152Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.1962Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal innervation0.02658InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.09309InformativeInherited
Mammalian Phenotype (MP)biphasic excitatory postsynaptic current amplitude1.361e-07Highly InformativeDirect
Mammalian Phenotype (MP)decreased excitatory postsynaptic current amplitude2.242e-05Highly InformativeDirect
Mammalian Phenotype (MP)short excitatory postsynaptic current rise time0.0001203Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Purkinje cell innervation0.0002055Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)pericellular component development variant5.539e-07Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant7.493e-08InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)NF stage5.663e-06Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.0002608Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases7.696e-12InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.0002588InformativeDirect
Enzyme Commission (EC)Enteropeptidase4.305e-09Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

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KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDifferentiation0Moderately InformativeDirect
Biological processProtein transport0.000421Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processEndocytosis9.354e-12InformativeDirect
Biological processNeurogenesis6.047e-10InformativeDirect
Biological processAngiogenesis1.258e-08InformativeDirect
Biological processWnt signaling pathway6.398e-08InformativeDirect
Biological processCell adhesion7.751e-05InformativeDirect
Biological processFertilization2.365e-16Highly InformativeDirect
Biological processComplement pathway2.716e-13Highly InformativeDirect
Cellular componentMembrane1.306e-12Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle4.356e-06Moderately InformativeDirect
Cellular componentCoated pit3.163e-10Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.02619Least InformativeInherited
DomainEGF-like domain0InformativeDirect
DomainSushi0Highly InformativeDirect
DomainLaminin EGF-like domain2.864e-14Highly InformativeDirect
DomainKringle3.195e-09Highly InformativeDirect
DomainKelch repeat1.919e-07Highly InformativeDirect
Molecular functionZinc1.159e-05Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionLectin8.592e-05InformativeDirect
Post-translational modificationHydrolase4.438e-16Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationGrowth factor0InformativeDirect
Post-translational modificationSerine protease2.321e-06InformativeDirect
Post-translational modificationMetalloprotease8.767e-05InformativeDirect
Post-translational modificationMitogen0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues6.681e-12Moderately InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect
Post-translational modificationZymogen1.602e-10InformativeDirect
Post-translational modificationProteoglycan0.005565InformativeInherited
Post-translational modificationHeparan sulfate0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000859 SSF49854 Protein matches
Abstract

The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found almost exclusively in extracellular and plasma membrane-associated proteins, many of which are developmentally regulated [PubMed8510165, PubMed2026272]. These proteins are involved in a diverse range of functions, including complement activation, developmental patterning, tissue repair, axon guidance and angiogenesis, cell signalling, fertilisation, haemostasis, inflammation, neurotransmission, receptor-mediated endocytosis, and tumour suppression [PubMed17335815, PubMed17051152]. Many CUB-containing proteins are peptidases belonging to MEROPS peptidase families M12A (astacin) and S1A (chymotrypsin). Proteins containing a CUB domain include:

  • Mammalian complement subcomponents C1s/C1r, which form the calcium-dependent complex C1, the first component of the classical pathway of the complement system.
  • Cricetidae sp. (Hamster) serine protease Casp, which degrades type I and IV collagen and fibronectin in the presence of calcium.
  • Mammalian complement-activating component of Ra-reactive factor (RARF), a protease that cleaves the C4 component of complement.
  • Vertebrate enteropeptidase , a type II membrane protein of the intestinal brush border, which activates trypsinogen.
  • Vertebrate bone morphogenic protein 1 (BMP-1), a protein which induces cartilage and bone formation and expresses metalloendopeptidase activity.
  • Sea urchin blastula proteins BP10 and SpAN.
  • Caenorhabditis elegans hypothetical proteins F42A10.8 and R151.5.
  • Neuropilin (A5 antigen), a calcium-independent cell adhesion molecule that functions during the formation of certain neuronal circuits.
  • Fibropellins I and III from Strongylocentrotus purpuratus (Purple sea urchin).
  • Mammalian hyaluronate-binding protein TSG-6 (or PS4), a serum and growth factor induced protein.
  • Mammalian spermadhesins.
  • Xenopus laevis embryonic protein UVS.2, which is expressed during dorsoanterior development.

Several of the above proteins consist of a catalytic domain together with several CUB domains interspersed by calcium-binding EGF domains. Some CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding partners. For example, in the complement proteases, the CUB domains mediate dimerisation and binding to collagen-like regions of target proteins (e.g. C1q for C1r/C1s). The structure of CUB domains consists of a beta-sandwich with a jelly-roll fold. Almost all CUB domains contain four conserved cysteines that probably form two disulphide bridges (C1-C2, C3-C4). The CUB1 domains of C1s and Map19 have calcium-binding sites [PubMed17446170].


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) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 8 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 Spermadhesin, CUB domain 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 8 hidden Markov models representing the Spermadhesin, CUB domain 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) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]