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 (130) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 528 557 3
Proteins 528 556 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 0.000000000004239 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.000005648 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.0007848 Least Informative Direct
Biological Process (BP) developmental process 0.0009642 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.008343 Least Informative Inherited
Biological Process (BP) localization 0.003361 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003995 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.0129 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7723 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.03298 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8105 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.006601 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.003537 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3072 Least Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.000000000000005526 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000002949 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0000000108 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.00000001162 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00000001439 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000002908 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.00002617 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00004837 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0001158 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.000307 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000381 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0005387 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.6211 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.204 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001635 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.08124 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.0163 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.001985 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.03692 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.002889 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.08729 Moderately Informative Inherited
Biological Process (BP) regulation of cell cycle process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.00000000000001414 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0000000000003993 Informative Direct
Biological Process (BP) cytoplasmic transport 0.000000000002272 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.00000000001185 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00000000208 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000000007612 Informative Direct
Biological Process (BP) growth 0.00000001232 Informative Direct
Biological Process (BP) nitrogen compound transport 0.00000001609 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.00000002632 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.00000004779 Informative Direct
Biological Process (BP) organelle localization 0.0000006579 Informative Direct
Biological Process (BP) microtubule-based process 0.000001221 Informative Direct
Biological Process (BP) DNA repair 0.000003607 Informative Direct
Biological Process (BP) cell cycle process 0.00001063 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00002896 Informative Direct
Biological Process (BP) regulation of transferase activity 0.0008368 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.005415 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.004027 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.05155 Informative Inherited
Biological Process (BP) chromosome organization 0.2163 Informative Inherited
Biological Process (BP) establishment of RNA localization 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell cycle process 0.0000000000001285 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000000003407 Highly Informative Direct
Biological Process (BP) regulation of mRNA processing 0.0000000000004662 Highly Informative Direct
Biological Process (BP) cell growth 0.000000000003931 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.00000000003051 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.0000000002898 Highly Informative Direct
Biological Process (BP) aging 0.0000001277 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000002251 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0001851 Highly Informative Direct
Biological Process (BP) nuclear export 0.0006677 Highly Informative Direct
Molecular Function (MF) binding 0.000000001163 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000001007 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.00001486 Informative Direct
Molecular Function (MF) unfolded protein binding 0.000000000009921 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00000003923 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000001099 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000101 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000009 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.7808 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.00000004063 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000006262 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000167 Moderately Informative Direct
Cellular Component (CC) cytosol 0.000113 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.009158 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0 Informative Direct
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.003818 Informative Inherited
Cellular Component (CC) nuclear body 0 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0 Highly Informative Direct
Cellular Component (CC) nucleolar part 0.00000000001987 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-binding0.00008616Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein0.000000000003688Least InformativeDirect
Post-translational modificationAcetylation0.000002348Least 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 ]