SUPERFAMILY 1.75 HMM library and genome assignments server

NAC domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   NAC domain [ 101940]
Superfamily:   NAC domain [ 101941]
Families:   NAC domain [ 101942]


Superfamily statistics
Genomes (59) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,243 5,335 1
Proteins 8,116 5,264 1


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)nucleic acid binding transcription factor activity00InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0.0002075 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.07585 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.004146 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.005878 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.02761 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.7386 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.229 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.000000000000001913 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000000000001414 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000000000001752 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.0000000003922 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000003232 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.000004947 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001454 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.00001466 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.1868 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.3363 Moderately Informative Inherited
Biological Process (BP) tissue development 0.1587 Moderately Informative Inherited
Biological Process (BP) organ development 0.08335 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.02526 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.2904 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cell wall organization or biogenesis 0.00000000001862 Informative Direct
Biological Process (BP) response to acid chemical 0.00001613 Informative Direct
Biological Process (BP) secondary metabolic process 0.0009772 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.6031 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.277 Informative Inherited
Biological Process (BP) response to lipid 0.006921 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.05622 Informative Inherited
Biological Process (BP) response to inorganic substance 0.03971 Informative Inherited
Biological Process (BP) response to water deprivation 0.000000001837 Highly Informative Direct
Biological Process (BP) response to salt stress 0.000000001894 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0.000002312 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00002841 Highly Informative Direct
Biological Process (BP) aging 0.00009825 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0001203 Highly Informative Direct
Biological Process (BP) response to cold 0.0003654 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.005413 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.00007405 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000002142 Highly Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot axis0.5339Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.9505Least InformativeInherited
Plant ANatomical entity (PAN)root system1Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure1Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)vascular system0.000000002055InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.0000002637InformativeDirect
Plant ANatomical entity (PAN)root tip0.0000004404InformativeDirect
Plant ANatomical entity (PAN)shoot axis stele0.0000005564Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0000005696Highly InformativeDirect
Plant ANatomical entity (PAN)primary root0.0002675Highly InformativeDirect
Plant ANatomical entity (PAN)plant axis elongation zone0.0002917Highly InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationDevelopmental protein0.0000008306Moderately InformativeDirect
Post-translational modificationActivator0.00009663Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003441 SSF101941 Protein matches
Abstract

The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) [PubMed9212461]. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [PubMed11114891,PubMed12175016].

The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D [PubMed10660065]. The DBD is contained within a 60 amino acid region located within subdomains D and E [PubMed12175016]. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [PubMed15083810].


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-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · 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 NAC 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 NAC 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-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]