SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,473) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,297 28,899 14
Proteins 5,487 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)heterocycle metabolic process0.0000000012830Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.0000000013540Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000000034020Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000000040220Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.000000013590Least InformativeDirect
Biological Process (BP)biosynthetic process0.0000000029560.01733Least InformativeInherited
Biological Process (BP)RNA metabolic process0.000000000000012480.000288Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000000000000059230.00006111Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00000000000017850.02564Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.000000000000088850.0296Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.00000000000020910.03283Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000000068860.07804Moderately InformativeInherited
Biological Process (BP)gene expression0.00000000000019840.003335Moderately InformativeInherited
Biological Process (BP)transcription, DNA-templated00.0003271InformativeDirect
Molecular Function (MF)transferase activity0.00000000031540.5379Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.000000000000018830.00000001642Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)protein complex0.00000000013220.0000000000003143Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.39320.0000004018Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.028310.02686Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.00030010.00000000001367Moderately InformativeDirect
Cellular Component (CC)nuclear part0.00033980.000000000000228Moderately InformativeDirect
Cellular Component (CC)transferase complex00.002733Moderately InformativeInherited
Cellular Component (CC)DNA-directed RNA polymerase complex0.000000026460InformativeDirect
Cellular Component (CC)DNA polymerase complex00.00000000000461Highly 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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.004846 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2631 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9299 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.5406 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.03581 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.01733 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003764 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.000288 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00006111 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000000001529 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.1297 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3458 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2833 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.02564 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03732 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01504 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8329 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.9024 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.4574 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.03908 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.2794 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.0296 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03283 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.07804 Moderately Informative Inherited
Biological Process (BP) gene expression 0.003335 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4567 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.002317 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2327 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.0003271 Informative Direct
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.000000006088 Informative Direct
Biological Process (BP) chromosome organization 0.000003532 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001766 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0002872 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.0007495 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.001702 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00261 Informative Inherited
Biological Process (BP) cell cycle process 0.006926 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1421 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.001033 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.02644 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.002424 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.257 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.002245 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.1006 Informative Inherited
Biological Process (BP) response to ionizing radiation 0.00000001138 Highly Informative Direct
Biological Process (BP) aging 0.0000002552 Highly Informative Direct
Biological Process (BP) DNA integrity checkpoint 0.0000005443 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000001667 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000007025 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00005689 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.0003394 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.0003575 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0004301 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0004646 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0009641 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.04203 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000512 Least Informative Direct
Molecular Function (MF) transferase activity 0.5379 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000001642 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.4129 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.00000000000002882 Informative Direct
Molecular Function (MF) nuclease activity 0.00000000002827 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) protein complex 0.0000000000003143 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000004018 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000001768 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02686 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00000000001367 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000000000228 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.002733 Moderately Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.02161 Informative Inherited
Cellular Component (CC) chromosome 0.05333 Informative Inherited
Cellular Component (CC) DNA polymerase complex 0.00000000000461 Highly Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00006014 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 anhydrides0.0004691Moderately 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 damage0.00007042Moderately InformativeDirect
Biological processtRNA processing0.0000000000000461InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000000001439Highly InformativeDirect
Molecular functionDNA-binding0.000000001592Least InformativeDirect
Molecular functionNucleotide-binding0.007872Least InformativeInherited
Molecular functionATP-binding0.0007284Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.000000000001763Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000006128InformativeDirect

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 ]