SUPERFAMILY 1.75 HMM library and genome assignments server


Nucleoplasmin-like core domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Nucleoplasmin-like/VP (viral coat and capsid proteins) [ 88632] (7)
Superfamily:   Nucleoplasmin-like core domain [ 69203]
Families:   Nucleoplasmin-like core domain [ 69204] (3)


Superfamily statistics
Genomes (118) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 459 460 3
Proteins 459 460 3


Functional annotation
General category Information
Detailed category Chromatin structure

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) cellular component organization or biogenesis 1.726e-12 Least Informative Direct
Biological Process (BP) regulation of cellular process 4.491e-06 Least Informative Direct
Biological Process (BP) developmental process 0.0008624 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.006402 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.009786 Least Informative Inherited
Biological Process (BP) localization 0.002606 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7522 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.00337 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003823 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.006349 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.01225 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.03344 Least Informative Inherited
Biological Process (BP) regulation of catalytic activity 7.333e-15 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 1.635e-11 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.614e-09 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 5.079e-09 Moderately Informative Direct
Biological Process (BP) organic substance transport 1.184e-08 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1.533e-08 Moderately Informative Direct
Biological Process (BP) homeostatic process 2.654e-08 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.337e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 2.086e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0001032 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0001202 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0001514 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0002389 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000418 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0005122 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.5426 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.197 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.002414 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.07555 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.0224 Moderately Informative Inherited
Biological Process (BP) regulation of kinase activity 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 1.086e-14 Informative Direct
Biological Process (BP) regulation of organelle organization 1.065e-13 Informative Direct
Biological Process (BP) regulation of cell cycle 3.248e-12 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 9.641e-12 Informative Direct
Biological Process (BP) growth 2.922e-09 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 1.002e-08 Informative Direct
Biological Process (BP) nitrogen compound transport 2.313e-08 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 2.854e-07 Informative Direct
Biological Process (BP) organelle localization 5.987e-07 Informative Direct
Biological Process (BP) response to DNA damage stimulus 4.441e-06 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 5.683e-06 Informative Direct
Biological Process (BP) microtubule-based process 6.172e-06 Informative Direct
Biological Process (BP) cell cycle process 7.92e-05 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001479 Informative Direct
Biological Process (BP) positive regulation of cell proliferation 0.0001879 Informative Direct
Biological Process (BP) cytoskeleton organization 0.06236 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.004415 Informative Inherited
Biological Process (BP) chromosome organization 0.25 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.003784 Informative Inherited
Biological Process (BP) establishment of RNA localization 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 1.884e-13 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 3.142e-13 Highly Informative Direct
Biological Process (BP) cell growth 4.086e-11 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 3.335e-10 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 2.04e-09 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 1.403e-08 Highly Informative Direct
Biological Process (BP) nuclear export 9.777e-08 Highly Informative Direct
Biological Process (BP) aging 4.998e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.000274 Highly Informative Direct
Molecular Function (MF) binding 4.168e-07 Least Informative Direct
Molecular Function (MF) nucleic acid binding 4.505e-09 Moderately Informative Direct
Molecular Function (MF) RNA binding 1.134e-05 Informative Direct
Molecular Function (MF) unfolded protein binding 8.734e-12 Highly Informative Direct
Molecular Function (MF) transcription factor binding 4.448e-08 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 9.122e-10 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 9.773e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.663e-07 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.8001 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 5.97e-08 Moderately Informative Direct
Cellular Component (CC) nuclear part 3.263e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.101e-06 Moderately Informative Direct
Cellular Component (CC) cytosol 0.000107 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.02191 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) nucleolus 7.049e-12 Informative Direct
Cellular Component (CC) nucleoplasm part 0.103 Informative Inherited
Cellular Component (CC) nuclear body 0 Highly Informative Direct
Cellular Component (CC) centrosome 9.278e-12 Highly Informative Direct
Cellular Component (CC) nucleolar part 4.604e-11 Highly Informative Direct

Document: GO annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentNucleus0Least InformativeDirect
Molecular functionRNA-binding8.707e-05Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein3.459e-12Least InformativeDirect
Post-translational modificationAcetylation2.315e-06Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR004301 SSF69203 Protein matches
Abstract Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.

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) · 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 3 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 Nucleoplasmin-like core 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 3 hidden Markov models representing the Nucleoplasmin-like core 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) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]