SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,470) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 17,921 62,426 22
Proteins 17,183 61,435 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 process6.039e-056.14e-05Least InformativeDirect
Biological Process (BP)regulation of cellular process0.005111Least InformativeInherited
Biological Process (BP)regulation of gene expression3.777e-060Moderately InformativeDirect
Biological Process (BP)regulation of nitrogen compound metabolic process0.0077670.1531Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process8.156e-060.07782Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.0056190.08056Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity9.782e-091.515e-06InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity8.661e-091.291e-06Highly 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 6.14e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 8.212e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 4.93e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 9.399e-07 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.098e-05 Least Informative Direct
Biological Process (BP) developmental process 2.396e-05 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.113e-05 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0002087 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0004474 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.02137 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01311 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) cellular component organization or biogenesis 0.8111 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.872e-10 Moderately Informative Direct
Biological Process (BP) cell differentiation 3.875e-09 Moderately Informative Direct
Biological Process (BP) gene expression 6.431e-08 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 2.399e-07 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 7.873e-07 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 1.148e-06 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1.701e-06 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1.822e-05 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 9.89e-05 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0003266 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0004721 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0004822 Moderately Informative Direct
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1729 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8443 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.02224 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.07782 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.1531 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0666 Moderately Informative Inherited
Biological Process (BP) reproduction 0.001394 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.1871 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.08056 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.002377 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001784 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.005922 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.359 Moderately Informative Inherited
Biological Process (BP) organ development 0.00367 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.0487 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4134 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.001103 Moderately Informative Inherited
Biological Process (BP) negative regulation of cell communication 0 Informative Direct
Biological Process (BP) sensory organ development 6.802e-14 Informative Direct
Biological Process (BP) negative regulation of signaling 1.417e-13 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 1.995e-11 Informative Direct
Biological Process (BP) transcription, DNA-dependent 1.326e-07 Informative Direct
Biological Process (BP) chordate embryonic development 1.114e-06 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 4.132e-06 Informative Direct
Biological Process (BP) regulation of apoptotic process 8.517e-06 Informative Direct
Biological Process (BP) organ morphogenesis 3.545e-05 Informative Direct
Biological Process (BP) tRNA metabolic process 4.29e-05 Informative Direct
Biological Process (BP) central nervous system development 5.312e-05 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.0002184 Informative Direct
Biological Process (BP) epithelium development 0.0003561 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.0006601 Informative Direct
Biological Process (BP) locomotion 0.0009899 Informative Direct
Biological Process (BP) tube development 0.1108 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.04367 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.1206 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00373 Informative Inherited
Biological Process (BP) response to external stimulus 0.05963 Informative Inherited
Biological Process (BP) muscle structure development 0.1493 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.002009 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01251 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.00487 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.01669 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.02057 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.2663 Informative Inherited
Biological Process (BP) generation of neurons 0.3465 Informative Inherited
Biological Process (BP) muscle tissue development 0.03099 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.228 Informative Inherited
Biological Process (BP) cell projection organization 0.001055 Informative Inherited
Biological Process (BP) cell cycle process 0.08857 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1349 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.03892 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3189 Informative Inherited
Biological Process (BP) negative regulation of signal transduction 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 1.575e-10 Highly Informative Direct
Biological Process (BP) pattern specification process 9.856e-10 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 7.019e-09 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 7.933e-08 Highly Informative Direct
Biological Process (BP) photoreceptor cell differentiation 3.104e-07 Highly Informative Direct
Biological Process (BP) axonogenesis 3.402e-07 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 6.261e-07 Highly Informative Direct
Biological Process (BP) eye morphogenesis 1.039e-06 Highly Informative Direct
Biological Process (BP) muscle fiber development 3.235e-05 Highly Informative Direct
Biological Process (BP) DNA repair 0.0001203 Highly Informative Direct
Biological Process (BP) epithelial tube morphogenesis 0.0001338 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0002303 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0.0004669 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0005587 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.0006177 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0007987 Highly Informative Direct
Biological Process (BP) tube formation 0.0009187 Highly Informative Direct
Biological Process (BP) skeletal system development 0.01901 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.02969 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.001081 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 1 Highly Informative Inherited
Biological Process (BP) glial cell differentiation 0.003999 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.002043 Highly Informative Inherited
Biological Process (BP) stem cell development 0.1126 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.08926 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.001241 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.008264 Highly Informative Inherited
Molecular Function (MF) binding 0.2911 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.06403 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.008394 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 1.515e-06 Informative Direct
Molecular Function (MF) enzyme inhibitor activity 0.0001817 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 1.291e-06 Highly Informative Direct
Molecular Function (MF) chromatin binding 1.636e-12 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 1.306e-08 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1.219e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1631 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01144 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.7921 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.001416 Informative Inherited
Cellular Component (CC) transcription factor complex 5.6e-08 Highly 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)tumorigenesis0.01742Moderately InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.000534InformativeDirect
Mammalian Phenotype (MP)increased physiological sensitivity to xenobiotic0.0004759Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP 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 regulation1.034e-10Moderately InformativeDirect
Biological processInitiation factor0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseProto-oncogene0.0006368Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding1.07e-07Least InformativeDirect
Molecular functionZinc1Least InformativeInherited
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionDNA-binding0.0009366Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Molecular functionMercury5.739e-11Highly InformativeDirect
Molecular functionZinc transport2.597e-06Highly InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationActivator8.349e-10Moderately InformativeDirect
Post-translational modificationRepressor7.629e-07Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

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) · 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) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]