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Putative DNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Putative DNA-binding domain [ 46954]
Superfamily:   Putative DNA-binding domain [ 46955] (7)
Families:   Domains B1 and B5 of PheRS-beta, PheT [ 46956]
  DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain [ 46959]
  Dachshund-homology domain [ 74693] (2)
  DNA-binding N-terminal domain of transcription activators [ 46962] (4)
  Terminase gpNU1 subunit domain [ 74696]
  Excisionase-like [ 46891] (2)
  N-terminal subdomain of bacterial translation initiation factor IF2 [ 89006]


Superfamily statistics
Genomes (3,226) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,492 138,277 22
Proteins 22,651 136,690 20


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)regulation of metabolic process0.000031610.0001122Least InformativeDirect
Biological Process (BP)regulation of cellular process0.003261Least InformativeInherited
Biological Process (BP)regulation of gene expression0.00000067090Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.013890.00001201Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.00000015870.107Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.012540.000003293Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity0.0000000082430.000003403InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity0.0000000070650.000003263Highly InformativeDirect

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) regulation of metabolic process 0.0001122 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000000112 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000006727 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000001584 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000002516 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000002223 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000005024 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00004053 Least Informative Direct
Biological Process (BP) developmental process 0.00006149 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03488 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1499 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.0325 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000003293 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00001201 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000000007849 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000000001335 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000000201 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000002078 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00000002276 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000003058 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.000007099 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0004835 Moderately Informative Direct
Biological Process (BP) organ development 0.0008851 Moderately Informative Direct
Biological Process (BP) reproduction 0.0009334 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.456 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7697 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.107 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1676 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.888 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.03967 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2765 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.001092 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.001278 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.001796 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.003911 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2984 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.01193 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02339 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4251 Moderately Informative Inherited
Biological Process (BP) sensory organ development 0.000000000000003755 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0000000000003895 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0000000008165 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.000000001938 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.00000002227 Informative Direct
Biological Process (BP) cell projection organization 0.00000007883 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.000001182 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.000001432 Informative Direct
Biological Process (BP) organ morphogenesis 0.000007569 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.0000215 Informative Direct
Biological Process (BP) central nervous system development 0.00002556 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.00004087 Informative Direct
Biological Process (BP) epithelium development 0.0003515 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.0005891 Informative Direct
Biological Process (BP) locomotion 0.00074 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.6858 Informative Inherited
Biological Process (BP) regulation of apoptotic signaling pathway 0.002636 Informative Inherited
Biological Process (BP) cellular component movement 0.001644 Informative Inherited
Biological Process (BP) tube development 0.05552 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.02459 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.1014 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001346 Informative Inherited
Biological Process (BP) generation of neurons 0.4494 Informative Inherited
Biological Process (BP) muscle structure development 0.1182 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.001755 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01908 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.005902 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.00891 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.1846 Informative Inherited
Biological Process (BP) muscle tissue development 0.02608 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.169 Informative Inherited
Biological Process (BP) response to light stimulus 0.01151 Informative Inherited
Biological Process (BP) cell cycle process 0.04568 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.6003 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1303 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.005301 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.5036 Informative Inherited
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0.0000000000419 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.00000000009135 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.0000000002046 Highly Informative Direct
Biological Process (BP) pattern specification process 0.00000000023 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 0.0000000005661 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.00000003296 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.0000001523 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.0000003866 Highly Informative Direct
Biological Process (BP) eye morphogenesis 0.000001025 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.00002135 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00003598 Highly Informative Direct
Biological Process (BP) response to UV 0.00004954 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00007572 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0001493 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0.0002459 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0002553 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0003103 Highly Informative Direct
Biological Process (BP) neural tube development 0.0004878 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.006726 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.01615 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.01769 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.04338 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 1 Highly Informative Inherited
Biological Process (BP) glial cell differentiation 0.003529 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.001696 Highly Informative Inherited
Biological Process (BP) stem cell development 0.08362 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.08515 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.001096 Highly Informative Inherited
Biological Process (BP) epithelial tube formation 0.004076 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.001014 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.01329 Highly Informative Inherited
Molecular Function (MF) binding 0.03802 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.03772 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.000003403 Informative Direct
Molecular Function (MF) chromatin binding 0.00000000001167 Informative Direct
Molecular Function (MF) enzyme inhibitor activity 0.00005609 Informative Direct
Molecular Function (MF) ligase activity 0.001471 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.000003263 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.000000005075 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000003063 Least Informative Direct
Cellular Component (CC) protein complex 0.01261 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.008723 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.8087 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.0006063 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Phenylalanine--tRNA ligase0InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)tumorigenesis0.01673Moderately InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0005192InformativeDirect
Mammalian Phenotype (MP)increased physiological sensitivity to xenobiotic0.0003966Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)adult segment0Moderately InformativeDirect

Document: FA 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)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Phenylalanine--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.00000000002801Moderately InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseProto-oncogene0.0006481Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.000004871Least InformativeDirect
Molecular functionDNA-binding0.0003904Least InformativeDirect
Molecular functionZinc1Least InformativeInherited
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Molecular functionMercury0.0000000000483Highly InformativeDirect
Molecular functionZinc transport0.000002534Highly InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationActivator0.00000003588Moderately InformativeDirect
Post-translational modificationRepressor0.0000008798Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009061 SSF46955 Protein matches
Abstract

A putative DNA-binding domain with a conserved structure is found in several different protein families. The core structure of the domain consists of a three-helical fold that is architecturally similar to that of the "winged-helix" fold, but is topologically distinct. Representatives of this domain can be found in domains B1 and B5 from the beta subunit of phenylalanine-tRNA synthetases [PubMed11679717], the C-terminal region of the DNA/RPA-binding domain of the DNA excision repair factor XPA [PubMed10563794], the N-terminal domain of the transcriptional activators BmrR and MtaN [PubMed11201751], the most conserved domain of the retinal development protein Dachshund [PubMed12057194], and the DNA-binding domain of the gpNU1 subunit from the bacteriophage lambda viral packing protein terminase [PubMed12049735].


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) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · 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 14 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 Putative DNA-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 14 hidden Markov models representing the Putative DNA-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]