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 (3,225) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,478 138,277 22
Proteins 22,637 136,690 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 process3.045e-050.0001032Least InformativeDirect
Biological Process (BP)regulation of cellular process0.0030791Least InformativeInherited
Biological Process (BP)regulation of gene expression6.093e-070Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.014851.319e-05Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process1.497e-070.113Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.012363.76e-06Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity8.305e-093.306e-06InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity7.124e-093.166e-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 0.0001032 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.086e-09 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 6.514e-09 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.538e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.443e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.159e-06 Least Informative Direct
Biological Process (BP) biosynthetic process 4.871e-06 Least Informative Direct
Biological Process (BP) multicellular organismal process 3.976e-05 Least Informative Direct
Biological Process (BP) developmental process 6.111e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03369 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1436 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.03176 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 3.76e-06 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1.319e-05 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 7.961e-11 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1.195e-09 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 1.841e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.954e-08 Moderately Informative Direct
Biological Process (BP) gene expression 2.077e-08 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 2.288e-06 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 3.08e-06 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 6.91e-06 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.0003463 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0007911 Moderately Informative Direct
Biological Process (BP) organ development 0.0008856 Moderately Informative Direct
Biological Process (BP) reproduction 0.0009148 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0009385 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.4589 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7512 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.113 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1661 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8792 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.04117 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2676 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.00137 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.003367 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2963 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.0116 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02245 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4246 Moderately Informative Inherited
Biological Process (BP) sensory organ development 3.741e-15 Informative Direct
Biological Process (BP) negative regulation of cell communication 3.189e-13 Informative Direct
Biological Process (BP) negative regulation of signaling 6.612e-10 Informative Direct
Biological Process (BP) negative regulation of gene expression 2.172e-09 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 1.976e-08 Informative Direct
Biological Process (BP) cell projection organization 7.872e-08 Informative Direct
Biological Process (BP) transcription, DNA-dependent 1.217e-06 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 1.39e-06 Informative Direct
Biological Process (BP) organ morphogenesis 7.492e-06 Informative Direct
Biological Process (BP) response to DNA damage stimulus 2.1e-05 Informative Direct
Biological Process (BP) central nervous system development 2.429e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 4.194e-05 Informative Direct
Biological Process (BP) epithelium development 0.0003426 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.0005618 Informative Direct
Biological Process (BP) locomotion 0.000748 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.6879 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.003042 Informative Inherited
Biological Process (BP) cellular component movement 0.001693 Informative Inherited
Biological Process (BP) tube development 0.05573 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.02354 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.1006 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001116 Informative Inherited
Biological Process (BP) generation of neurons 0.4432 Informative Inherited
Biological Process (BP) muscle structure development 0.1167 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.001681 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01906 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.005624 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.009367 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.1861 Informative Inherited
Biological Process (BP) muscle tissue development 0.02541 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.1712 Informative Inherited
Biological Process (BP) response to light stimulus 0.01135 Informative Inherited
Biological Process (BP) cell cycle process 0.04597 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.6027 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1315 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.005424 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.6338 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 4.323e-11 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 8.935e-11 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 2.066e-10 Highly Informative Direct
Biological Process (BP) pattern specification process 2.404e-10 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 4.529e-10 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 3.351e-08 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 1.432e-07 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 3.811e-07 Highly Informative Direct
Biological Process (BP) eye morphogenesis 9.555e-07 Highly Informative Direct
Biological Process (BP) muscle fiber development 2.066e-05 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 3.97e-05 Highly Informative Direct
Biological Process (BP) response to UV 4.953e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 7.059e-05 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0001515 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0.0002528 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0002781 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0003333 Highly Informative Direct
Biological Process (BP) neural tube development 0.0004931 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.006461 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.01604 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.01814 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.04332 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 1 Highly Informative Inherited
Biological Process (BP) glial cell differentiation 0.003572 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.001609 Highly Informative Inherited
Biological Process (BP) stem cell development 0.08431 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.08291 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 0.001132 Highly Informative Inherited
Biological Process (BP) epithelial tube formation 0.004085 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.001021 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.01377 Highly Informative Inherited
Molecular Function (MF) binding 0.03598 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.0375 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 3.306e-06 Informative Direct
Molecular Function (MF) chromatin binding 9.149e-12 Informative Direct
Molecular Function (MF) enzyme inhibitor activity 5.618e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 3.166e-06 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 8.225e-09 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 2.852e-06 Least Informative Direct
Cellular Component (CC) protein complex 0.01285 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 0.008798 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.8135 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.0006109 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)abnormal tumor incidence0.01223Moderately InformativeInherited
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0005092InformativeDirect
Mammalian Phenotype (MP)increased physiological sensitivity to xenobiotic0.0003889Highly 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 regulation2.554e-11Moderately InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseProto-oncogene0.0006504Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding2.339e-06Least InformativeDirect
Molecular functionZinc1Least InformativeInherited
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionDNA-binding0.0004201Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Molecular functionMercury4.929e-11Highly InformativeDirect
Molecular functionZinc transport2.547e-06Highly InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationActivator3.594e-08Moderately InformativeDirect
Post-translational modificationRepressor7.113e-07Moderately 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 ]