SUPERFAMILY 1.75 HMM library and genome assignments server

Cysteine-rich DNA binding domain, (DM domain) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Cysteine-rich DNA binding domain, (DM domain) [ 82926]
Superfamily:   Cysteine-rich DNA binding domain, (DM domain) [ 82927]
Families:   Cysteine-rich DNA binding domain, (DM domain) [ 82928]


Superfamily statistics
Genomes (134) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 805 1,371 1
Proteins 761 1,325 1


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0.000000000000005526 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0000000000008105 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8276 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1341 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.03386 Least Informative Inherited
Biological Process (BP) reproductive process 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0004283 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000667 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.05097 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.02939 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.0433 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.03317 Moderately Informative Inherited
Biological Process (BP) organ development 0.117 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.03393 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.004023 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2058 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.08181 Moderately Informative Inherited
Biological Process (BP) single organism reproductive process 0.00000003485 Informative Direct
Biological Process (BP) sexual reproduction 0.0000001081 Informative Direct
Biological Process (BP) reproductive structure development 0.000006496 Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.00004322 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0005646 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.000809 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.001366 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.001512 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.01043 Informative Inherited
Biological Process (BP) gonad development 0.000000000007103 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 0.000026 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.001862 Highly Informative Inherited
Molecular Function (MF) binding 0.0003501 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000000000001212 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.00000002184 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000007205 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.00004483 Highly Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal reproductive system morphology0.003206Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism segment morphology variant0.02969Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.00001966InformativeDirect
Worm Phenotype (WP)male tail morphology variant0.0000007122Highly InformativeDirect

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)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationActivator0.00000000001896Moderately InformativeDirect
Post-translational modificationRepressor0.00000000005203Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001275 SSF82927 Protein matches
Abstract This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans [PubMed9490411]. In D. melanogaste the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides [PubMed8978051]. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [PubMed1907913, PubMed3046751]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [PubMed8978051, PubMed9927589, PubMed10898790]. The NMR analysis of the DSX DM domain [PubMed10898790] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.

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-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 Cysteine-rich DNA binding domain, (DM 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 Cysteine-rich DNA binding domain, (DM 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-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]