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 (2,472) 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 process1.148e-090Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.193e-080Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process3.964e-090Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.089e-090Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.942e-090Least InformativeDirect
Biological Process (BP)biosynthetic process3.021e-090.02031Least InformativeInherited
Biological Process (BP)RNA metabolic process1.253e-140.000268Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process5.798e-146.173e-05Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process1.967e-130.03401Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process8.224e-140.03063Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process1.668e-130.02722Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process6.519e-130.0804Moderately InformativeInherited
Biological Process (BP)gene expression1.263e-130.002115Moderately InformativeInherited
Biological Process (BP)transcription, DNA-dependent00.0004828InformativeDirect
Molecular Function (MF)transferase activity1.9e-100.328Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups1.872e-141.595e-08Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)protein complex1.37e-103.719e-13Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.39355.532e-07Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.031480.04986Least InformativeInherited
Cellular Component (CC)nuclear part0.0003832.501e-12Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.0003391.67e-10Moderately InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex2.481e-082.785e-07InformativeDirect
Cellular Component (CC)DNA polymerase complex03.874e-12Highly 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 0.5414 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9815 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.02631 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02031 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003762 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.8301 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.008616 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.000268 Moderately Informative Direct
Biological Process (BP) cellular response to stress 1.333e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.173e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.1109 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3858 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03683 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8736 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4042 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8116 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01604 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.04063 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03401 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.03063 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.02722 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.0804 Moderately Informative Inherited
Biological Process (BP) gene expression 0.002115 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2974 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.04975 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.223 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 2.591e-07 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0004828 Informative Direct
Biological Process (BP) response to DNA damage stimulus 4.701e-06 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0001574 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0006647 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.0001198 Informative Direct
Biological Process (BP) chromosome organization 1.508e-07 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001791 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.007798 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.001565 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1515 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.03012 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.1087 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.001154 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.2728 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.002234 Informative Inherited
Biological Process (BP) DNA catabolic process 0.0009898 Highly Informative Direct
Biological Process (BP) aging 2.459e-07 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 5.73e-05 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.0003601 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0004676 Highly Informative Direct
Biological Process (BP) purine ribonucleoside monophosphate metabolic process 0.0001172 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.0003417 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 0.0004831 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 1.06e-08 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 2.697e-06 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.000433 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 5.502e-06 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.04153 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0005199 Least Informative Direct
Molecular Function (MF) transferase activity 0.328 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1.595e-08 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3979 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 1.861e-11 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 2.888e-14 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.548e-06 Least Informative Direct
Cellular Component (CC) protein complex 3.719e-13 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.532e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.04986 Least Informative Inherited
Cellular Component (CC) nuclear part 2.501e-12 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.67e-10 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 2.785e-07 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1888 Informative Inherited
Cellular Component (CC) chromosome 0.06607 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 7.515e-06 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 3.874e-12 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 damage7.042e-05Moderately InformativeDirect
Biological processtRNA processing4.61e-14InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase1.439e-14Highly InformativeDirect
Molecular functionDNA-binding1.592e-09Least InformativeDirect
Molecular functionNucleotide-binding0.007872Least InformativeInherited
Molecular functionATP-binding0.0007284Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease1.763e-12Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase6.128e-13InformativeDirect

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 ]