SUPERFAMILY 1.75 HMM library and genome assignments server

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A heparin-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   SRCR-like [ 56486] (2)
Superfamily:   A heparin-binding domain [ 56491]
Families:   A heparin-binding domain [ 56492]


Superfamily statistics
Genomes (126) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 393 478 1
Proteins 391 475 1


Functional annotation
General category General
Detailed category Small molecule 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 0.00000000000007655 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000000008405 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000004505 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000006199 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002453 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000001089 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000004741 Least Informative Direct
Biological Process (BP) localization 0.00003462 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.1195 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.006055 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.119 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) single-organism developmental process 0.00000000000003782 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.00000000002936 Moderately Informative Direct
Biological Process (BP) system process 0.00000000005136 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0000000001571 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000000138 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.000000002865 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.000000005615 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000000007194 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00001347 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.00002122 Moderately Informative Direct
Biological Process (BP) tissue development 0.9882 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6022 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 0.2425 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.6839 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.7196 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.002337 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.002607 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.06786 Moderately Informative Inherited
Biological Process (BP) organ development 0.4918 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 0 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) synaptic transmission 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) 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) cellular chemical homeostasis 0 Informative Direct
Biological Process (BP) growth 0.000000000000003741 Informative Direct
Biological Process (BP) generation of neurons 0.000000000000007318 Informative Direct
Biological Process (BP) phosphorylation 0.00000000000001429 Informative Direct
Biological Process (BP) locomotion 0.0000000000003942 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000000000005315 Informative Direct
Biological Process (BP) microtubule-based process 0.000000000001464 Informative Direct
Biological Process (BP) cell projection organization 0.00000000009269 Informative Direct
Biological Process (BP) regulation of growth 0.0000000003465 Informative Direct
Biological Process (BP) central nervous system development 0.0000000007454 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000001518 Informative Direct
Biological Process (BP) apoptotic process 0.00000021 Informative Direct
Biological Process (BP) cellular component movement 0.0000002104 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000001284 Informative Direct
Biological Process (BP) regulation of nervous system development 0.000009472 Informative Direct
Biological Process (BP) response to oxidative stress 0.00002005 Informative Direct
Biological Process (BP) regulation of cell development 0.00002238 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00003128 Informative Direct
Biological Process (BP) muscle tissue development 0.0001763 Informative Direct
Biological Process (BP) regulation of cell cycle process 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.002288 Informative Inherited
Biological Process (BP) muscle structure development 0.05106 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.001412 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.7185 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.8435 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.9813 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) protein phosphorylation 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) cell part morphogenesis 0 Highly Informative Direct
Biological Process (BP) neuron projection development 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) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) cell-type specific apoptotic process 0.0000000000002804 Highly Informative Direct
Biological Process (BP) chemotaxis 0.000000000001216 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00000000001815 Highly Informative Direct
Biological Process (BP) developmental maturation 0.00000000003034 Highly Informative Direct
Biological Process (BP) neuromuscular process 0.0000000004448 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.0000000005387 Highly Informative Direct
Biological Process (BP) developmental growth 0.000000001038 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.00000003611 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0000002737 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.00000686 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00001543 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0006648 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) learning or memory 0.004392 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.006411 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000002888 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.00000000000006484 Informative Direct
Cellular Component (CC) membrane 0.00000000174 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00001765 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8275 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.5516 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1022 Least Informative Inherited
Cellular Component (CC) protein complex 0.04556 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.000000000000006075 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000000000000026 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000001078 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.0009468 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 0.000000000000001594 Informative Direct
Cellular Component (CC) cell junction 0.00001931 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.00002989 Informative Direct
Cellular Component (CC) coated vesicle 0.000395 Informative Direct
Cellular Component (CC) cilium part 0.0000000001624 Highly Informative Direct
Cellular Component (CC) spindle 0.0000000265 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000001965 Highly Informative Direct
Cellular Component (CC) transport vesicle 0.0001221 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 splicing0.000000000005225Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionZinc0.00000006005Least InformativeDirect
Molecular functionMetal-binding0.00003509Least InformativeDirect
Molecular functionIron0.000001044Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00002364Least InformativeDirect
Post-translational modificationProteoglycan0.0000000004272InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015849 SSF56491 Protein matches
Abstract

This entry represents a heparin-binding domain found at the N-terminal of the extracellular domain, which is itself found at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The core of the heparin-binding domain has an unusual disulphide-rich fold, consisting of a beta-x-alpha-beta-loop-beta topology [PubMed10201399].

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 A heparin-binding 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 1 hidden Markov models representing the A heparin-binding 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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]