SUPERFAMILY 1.75 HMM library and genome assignments server

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HRDC-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   HRDC-like [ 47819] (4)
Families:   HRDC domain from helicases [ 47820] (2)
  RNA polymerase II subunit RBP4 (RpoF) [ 69044]
  RNase D C-terminal domains [ 140643]
  EXOSC10 HRDC domain-like [ 140646] (2)


Superfamily statistics
Genomes (2,472) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,294 28,899 14
Proteins 5,484 22,658 13


Functional annotation
General category Information
Detailed category DNA replication/repair

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)cellular aromatic compound metabolic process0.0000000010980Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.000000011490Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000000039260Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000000010420Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000000028370Least InformativeDirect
Biological Process (BP)biosynthetic process0.0000000029640.02016Least InformativeInherited
Biological Process (BP)RNA metabolic process0.000000000000014050.0002696Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000000000000059150.00006241Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00000000000016920.02709Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.000000000000067760.0243Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00000000000014110.02136Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000000057080.06758Moderately InformativeInherited
Biological Process (BP)gene expression0.00000000000012590.002114Moderately InformativeInherited
Biological Process (BP)transcription, DNA-dependent00.0004938InformativeDirect
Molecular Function (MF)transferase activity0.00000000018920.3284Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.000000000000018740.00000001646Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)protein complex0.00000000013810.0000000000003911Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.39220.0000005589Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.031290.04917Least InformativeInherited
Cellular Component (CC)nuclear part0.00038340.000000000002675Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.00034020.0000000001754Moderately InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex0.000000025090.0000002815InformativeDirect
Cellular Component (CC)DNA polymerase complex00.000000000003945Highly 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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.5408 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9802 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.0255 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02016 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003637 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.8262 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.008152 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.0002696 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000000001198 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00006241 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.1044 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.377 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.8076 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03652 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8712 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.00471 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4055 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8104 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01595 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.02709 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.0243 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.02136 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.06758 Moderately Informative Inherited
Biological Process (BP) gene expression 0.002114 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.2735 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2928 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.04968 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2185 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0000002684 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0004938 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.000005155 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.000166 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0006576 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.0001172 Informative Direct
Biological Process (BP) chromosome organization 0.0000001489 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001902 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.007076 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.001547 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1517 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.03015 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.1084 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.001145 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.1551 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.002281 Informative Inherited
Biological Process (BP) aging 0.0000002325 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00006084 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0004624 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0.0003375 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.00000001011 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000002817 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0.00007881 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.000428 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000005802 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.03966 Highly Informative Inherited
Biological Process (BP) DNA catabolic process 0.001049 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0005273 Least Informative Direct
Molecular Function (MF) transferase activity 0.3284 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000001646 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.0000000000001029 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.4043 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.00000000001871 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.00000000000002955 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000001607 Least Informative Direct
Cellular Component (CC) protein complex 0.0000000000003911 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000005589 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.04917 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000000002675 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000001754 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.0000002815 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1896 Informative Inherited
Cellular Component (CC) chromosome 0.06558 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.000007515 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.000000000003945 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)Acting on acid anhydrides0.0005332Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.001517Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)syndrome0Moderately InformativeDirect

Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.0004781Moderately InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0.00007051Moderately InformativeDirect
Biological processtRNA processing0.00000000000004277InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000000001466Highly InformativeDirect
Molecular functionNucleotide-binding0.007907Least InformativeInherited
Molecular functionDNA-binding0.0000000016Moderately InformativeDirect
Molecular functionATP-binding0.0007302Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.000000000001878Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000006241InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010997 SSF47819 Protein matches
Abstract

The HRDC (helicase and RNaseD C-terminal) domain is comprised of two orthogonally packed alpha-hairpin subdomains, and is involved in interactions with DNA and protein.

The HRDC (helicase and RNaseD C-terminal) domain is found at the C terminus of many RecQ helicases, including the human Werner and Bloom syndrome proteins [PubMed10647186]. RecQ helicases have been shown to unwind DNA in an ATP-dependent manner. The structure of the HRDC domain consists of a 4-5 helical bundle of two orthogonally packed alpha-hairpins, and as such it resembles auxiliary domains in bacterial DNA helicases and other proteins that interact with nucleic acids. A positively charged region on the surface of the HRDC domain is able to interact with DNA.

The HRDC domain is also present in eukaryotic and archaeal RNA polymerase II subunit RBP4, the N-terminal of which forms a heterodimerisation alpha-hairpin [PubMed15591044, PubMed11741548].


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) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 10 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 HRDC-like 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 10 hidden Markov models representing the HRDC-like 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) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]