SUPERFAMILY 1.75 HMM library and genome assignments server


Regulatory factor Nef superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Regulatory factor Nef [ 55670]
Superfamily:   Regulatory factor Nef [ 55671]
Families:   Regulatory factor Nef [ 55672]


Superfamily statistics
Genomes (0) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 0 20,584 3
Proteins 0 20,575 3


Functional annotation
General category Regulation
Detailed category Other regulatory function

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) response to stimulus 6.216e-06 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.5141 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.005974 Least Informative Inherited
Biological Process (BP) regulation of protein metabolic process 2.288e-14 Moderately Informative Direct
Biological Process (BP) multi-organism process 2.415e-12 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 2.223e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0004199 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.03239 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.05902 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.08134 Moderately Informative Inherited
Biological Process (BP) regulation of defense response 0 Informative Direct
Biological Process (BP) regulation of immune effector process 0 Informative Direct
Biological Process (BP) defense response 1.514e-12 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.828e-12 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 1.021e-06 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 1.149e-06 Informative Direct
Biological Process (BP) regulation of immune response 4.064e-06 Informative Direct
Biological Process (BP) response to other organism 0.01437 Informative Inherited
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0 Highly Informative Direct
Biological Process (BP) regulation of calcium-mediated signaling 0 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 5.59e-15 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 1.347e-12 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 1.919e-11 Highly Informative Direct
Biological Process (BP) pathogenesis 7.007e-09 Highly Informative Direct
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) receptor binding 6.658e-09 Informative Direct
Molecular Function (MF) enzyme binding 7.204e-09 Informative Direct
Molecular Function (MF) kinase binding 0 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 2.461e-12 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processVirulence0InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Developmental stageEarly protein0Least InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainSH3-binding0InformativeDirect
Post-translational modificationPhosphoprotein2.741e-07Least InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001558 SSF55671 Protein matches
Abstract

Human immunodeficiency virus (HIV) negative factor (Nef protein) accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases [PubMed9351809].


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) · 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 2 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 Regulatory factor Nef 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 2 hidden Markov models representing the Regulatory factor Nef 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) · UniProtKB KeyWords (KW) · Internal database links ]