SUPERFAMILY 1.75 HMM library and genome assignments server


Amyloid beta a4 protein copper binding domain (domain 2) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Dodecin subunit-like [ 88797] (6)
Superfamily:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89811]
Families:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89812]


Superfamily statistics
Genomes (117) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 356 462 1
Proteins 356 461 1


Functional annotation
General category General
Detailed category Ion 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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 2.604e-14 Least Informative Direct
Biological Process (BP) response to stimulus 3.241e-11 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.433e-10 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 3.365e-10 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.49e-07 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1.184e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 4.938e-06 Least Informative Direct
Biological Process (BP) localization 2.46e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.1132 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.006035 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1249 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0 Moderately Informative Direct
Biological Process (BP) homeostatic process 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 3.75e-14 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 2.406e-11 Moderately Informative Direct
Biological Process (BP) system process 4.951e-11 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 1.53e-10 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 9.597e-10 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 3.413e-09 Moderately Informative Direct
Biological Process (BP) cell differentiation 4.186e-09 Moderately Informative Direct
Biological Process (BP) cellular localization 1.298e-05 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 1.979e-05 Moderately Informative Direct
Biological Process (BP) tissue development 0.9856 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6018 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2351 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.278 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.00235 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.002661 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.06753 Moderately Informative Inherited
Biological Process (BP) organ development 0.4898 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) metal ion homeostasis 0 Informative Direct
Biological Process (BP) regulation of kinase activity 0 Informative Direct
Biological Process (BP) single-organism behavior 0 Informative Direct
Biological Process (BP) alcohol metabolic process 0 Informative Direct
Biological Process (BP) cellular cation homeostasis 0 Informative Direct
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) regulation of mitotic cell cycle 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) generation of neurons 3.722e-15 Informative Direct
Biological Process (BP) phosphorylation 1.077e-14 Informative Direct
Biological Process (BP) locomotion 2.528e-13 Informative Direct
Biological Process (BP) vesicle-mediated transport 3.092e-13 Informative Direct
Biological Process (BP) microtubule-based process 1.383e-12 Informative Direct
Biological Process (BP) cell projection organization 9.403e-11 Informative Direct
Biological Process (BP) regulation of growth 3.384e-10 Informative Direct
Biological Process (BP) mitotic cell cycle 6.248e-10 Informative Direct
Biological Process (BP) central nervous system development 6.395e-10 Informative Direct
Biological Process (BP) cell-cell signaling 8.732e-10 Informative Direct
Biological Process (BP) single organism reproductive process 1.517e-09 Informative Direct
Biological Process (BP) cellular component movement 2.223e-07 Informative Direct
Biological Process (BP) programmed cell death 4.928e-07 Informative Direct
Biological Process (BP) transmission of nerve impulse 5.797e-07 Informative Direct
Biological Process (BP) cellular component morphogenesis 1.296e-06 Informative Direct
Biological Process (BP) regulation of nervous system development 7.558e-06 Informative Direct
Biological Process (BP) regulation of cell development 1.801e-05 Informative Direct
Biological Process (BP) response to oxidative stress 1.905e-05 Informative Direct
Biological Process (BP) negative regulation of developmental process 3.186e-05 Informative Direct
Biological Process (BP) muscle tissue development 0.0001726 Informative Direct
Biological Process (BP) cell cycle process 0.0007018 Informative Direct
Biological Process (BP) regulation of cell cycle process 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.002254 Informative Inherited
Biological Process (BP) muscle structure development 0.04949 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.001172 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.712 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.8418 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.9794 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0 Highly Informative Direct
Biological Process (BP) interphase 0 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) adult behavior 0 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) cellular transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0 Highly Informative Direct
Biological Process (BP) cell-type specific apoptotic process 2.201e-13 Highly Informative Direct
Biological Process (BP) chemotaxis 1.573e-12 Highly Informative Direct
Biological Process (BP) regulation of binding 1.432e-11 Highly Informative Direct
Biological Process (BP) developmental maturation 3.031e-11 Highly Informative Direct
Biological Process (BP) neuromuscular process 3.24e-10 Highly Informative Direct
Biological Process (BP) muscle fiber development 4.147e-10 Highly Informative Direct
Biological Process (BP) developmental growth 1.179e-09 Highly Informative Direct
Biological Process (BP) locomotory behavior 2.563e-08 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 6.705e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 1.621e-05 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in neuron differentiation 5.916e-05 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0005425 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) axon development 0.007652 Highly Informative Inherited
Biological Process (BP) learning or memory 0.004863 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.005683 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 1.493e-11 Moderately Informative Direct
Molecular Function (MF) DNA binding 3.031e-14 Informative Direct
Cellular Component (CC) membrane 5.936e-10 Least Informative Direct
Cellular Component (CC) cytoplasmic part 8.905e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.905 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.6197 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.09758 Least Informative Inherited
Cellular Component (CC) protein complex 0.03857 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 3.132e-15 Moderately Informative Direct
Cellular Component (CC) cell projection 7.862e-14 Moderately Informative Direct
Cellular Component (CC) vesicle 1.358e-06 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.0007831 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) neuron projection 0 Informative Direct
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) cell-cell junction 1.801e-06 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 2.522e-05 Informative Direct
Cellular Component (CC) coated vesicle 0.000369 Informative Direct
Cellular Component (CC) cilium part 1.303e-10 Highly Informative Direct
Cellular Component (CC) spindle 2.155e-08 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 2.972e-07 Highly Informative Direct
Cellular Component (CC) transport vesicle 0.0001258 Highly Informative Direct
Cellular Component (CC) neuromuscular junction 0.0001407 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)decreased body size0InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processNotch signaling pathway0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Coding sequence diversityAlternative splicing5.326e-12Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionZinc6.047e-08Least InformativeDirect
Molecular functionMetal-binding3.496e-05Least InformativeDirect
Molecular functionIron1.041e-06Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond2.404e-05Least InformativeDirect
Post-translational modificationProteoglycan4.253e-10InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011178 SSF89811 Protein matches
Abstract

This entry represents a copper-binding domain found within the extracellular domain, which is at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The copper-binding domain has a dodecin-like fold consisting of a 2-layer alpha/beta topology [PubMed12611883].

More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein.


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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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 Amyloid beta a4 protein copper binding domain (domain 2) 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 Amyloid beta a4 protein copper binding domain (domain 2) 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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]