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 (3,227) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,493 138,277 22
Proteins 22,652 136,690 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 process0.000042260.0002613Least InformativeDirect
Biological Process (BP)regulation of cellular process0.0038031Least InformativeInherited
Biological Process (BP)regulation of gene expression0.0000030180Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.0057590.000002147Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.0041110.0000003943Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.00000015980.05712Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity0.000000008240.000003607InformativeDirect

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 0.0002613 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000000157 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000000933 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000002131 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000003402 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000002331 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000004991 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001336 Least Informative Direct
Biological Process (BP) developmental process 0.00006068 Least Informative Direct
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.007734 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9784 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1796 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03484 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 0.0000003943 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000002147 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0000000000765 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000000001537 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000002575 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000004428 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0000008393 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.00000332 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.000007034 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000459 Moderately Informative Direct
Biological Process (BP) reproductive process 0.0005255 Moderately Informative Direct
Biological Process (BP) organ development 0.0006761 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.9187 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.5164 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.05712 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8888 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1691 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.0141 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.5555 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.005954 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.001009 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2993 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2759 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9079 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02471 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.03709 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.001223 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.001718 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4234 Moderately Informative Inherited
Biological Process (BP) sensory organ development 0.000000000000009016 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000000000001031 Informative Direct
Biological Process (BP) negative regulation of signaling 0.000000001939 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.00000006284 Informative Direct
Biological Process (BP) cell projection organization 0.00000009867 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0000006947 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.000001422 Informative Direct
Biological Process (BP) organ morphogenesis 0.000007224 Informative Direct
Biological Process (BP) DNA repair 0.000008201 Informative Direct
Biological Process (BP) central nervous system development 0.00003128 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.00006892 Informative Direct
Biological Process (BP) locomotion 0.0007364 Informative Direct
Biological Process (BP) positive regulation of intracellular signal transduction 0.01257 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.009865 Informative Inherited
Biological Process (BP) positive regulation of cell death 0.001612 Informative Inherited
Biological Process (BP) cellular component movement 0.001959 Informative Inherited
Biological Process (BP) muscle structure development 0.08618 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.09952 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.5915 Informative Inherited
Biological Process (BP) generation of neurons 0.4536 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01057 Informative Inherited
Biological Process (BP) tube development 0.1391 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.00534 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.009692 Informative Inherited
Biological Process (BP) epithelium development 0.001257 Informative Inherited
Biological Process (BP) response to light stimulus 0.00279 Informative Inherited
Biological Process (BP) cell cycle process 0.05638 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.1487 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.1478 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.02534 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001331 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.005049 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.5159 Informative Inherited
Biological Process (BP) regulation of cellular response to growth factor stimulus 0 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0.00000000004442 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.00000000006939 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.000000000244 Highly Informative Direct
Biological Process (BP) pattern specification process 0.0000000005232 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 0.0000000007366 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.00000002807 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.00000009608 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.0000001078 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.0000004242 Highly Informative Direct
Biological Process (BP) eye morphogenesis 0.000001023 Highly Informative Direct
Biological Process (BP) ensheathment of neurons 0.000003368 Highly Informative Direct
Biological Process (BP) response to UV 0.000004756 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00002796 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0001637 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0002299 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0002371 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0003075 Highly Informative Direct
Biological Process (BP) neural tube development 0.0006278 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.007342 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.0168 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.01496 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.04474 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.8505 Highly Informative Inherited
Biological Process (BP) glial cell differentiation 0.003404 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.001913 Highly Informative Inherited
Biological Process (BP) stem cell development 0.07555 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.001087 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.02073 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) epithelial tube formation 0.004118 Highly Informative Inherited
Biological Process (BP) in utero embryonic development 0.4964 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 0.007721 Highly Informative Inherited
Molecular Function (MF) binding 0.04281 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.01553 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.000003607 Informative Direct
Molecular Function (MF) chromatin binding 0.00000000001247 Informative Direct
Molecular Function (MF) ligase activity 0.00002616 Informative Direct
Molecular Function (MF) enzyme inhibitor activity 0.00005719 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.000000005033 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000001154 Least Informative Direct
Cellular Component (CC) protein complex 0.01182 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited

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 ]