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 (2,465) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,237 28,899 14
Proteins 5,426 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 process0.000000031190Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000029360Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00000011930Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000029150Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000007640Least InformativeDirect
Biological Process (BP)biosynthetic process0.000000077930.01434Least InformativeInherited
Biological Process (BP)RNA metabolic process0.00000000000048160.0001666Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000000000021340.00004498Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000000000052670.02166Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.0000000000022020.0195Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000000000041690.01669Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.000000000017540.05572Moderately InformativeInherited
Biological Process (BP)gene expression0.0000000000043830.001424Moderately InformativeInherited
Biological Process (BP)transcription, DNA-dependent00.0005018InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.00000000000063650.00000003495Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA polymerase activity00Highly InformativeDirect
Cellular Component (CC)protein complex0.0000000047820.000000000002067Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.39280.0000006599Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.068930.05607Least InformativeInherited
Cellular Component (CC)nuclear part0.00083770.000000000003576Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.00074250.0000000002219Moderately InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex0.000000059690.0000002575InformativeDirect
Cellular Component (CC)DNA polymerase complex00.000000000004058Highly 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 0.5435 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9814 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.02648 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.01434 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003522 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.76 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.007926 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.0001666 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000000001253 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00004498 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0005729 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.1282 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3682 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.8062 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03535 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.02166 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.0195 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.01669 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.05572 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001424 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02772 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.06407 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.04913 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2628 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0000008013 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0005018 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.000005406 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.0001553 Informative Direct
Biological Process (BP) chromosome organization 0.0000002567 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001848 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.008987 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.05281 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.00184 Informative Inherited
Biological Process (BP) aging 0.000000325 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.0000000134 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000002488 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000005759 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.03883 Highly Informative Inherited
Biological Process (BP) DNA catabolic process 0.00108 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0009591 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000003495 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3262 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.00000000002924 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.000000000001185 Informative Direct
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000001551 Least Informative Direct
Cellular Component (CC) protein complex 0.000000000002067 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000006599 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.05607 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000000003576 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000002219 Moderately Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 0.0000002575 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1774 Informative Inherited
Cellular Component (CC) chromosome 0.06176 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.000007176 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.000000000004058 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 anhydrides0.0005056Moderately 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 damage0.00007024Moderately InformativeDirect
Biological processtRNA processing0.00000000000004339InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000000001495Highly InformativeDirect
Molecular functionNucleotide-binding0.007927Least InformativeInherited
Molecular functionDNA-binding0.000000001582Moderately InformativeDirect
Molecular functionATP-binding0.0007306Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0.000000000001713Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0.0000000000006255InformativeDirect

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 ]