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 (2,425) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 6,011 13,308 14
Proteins 5,200 10,542 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 process1.102e-090Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.124e-080Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process4.084e-090Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.02e-090Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.777e-090Least InformativeDirect
Biological Process (BP)biosynthetic process2.676e-090.01399Least InformativeInherited
Biological Process (BP)RNA metabolic process1.355e-140.0001915Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process5.139e-143.841e-05Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process1.459e-130.02303Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process6.097e-140.02108Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process1.13e-130.01733Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process5.168e-130.05969Moderately InformativeInherited
Biological Process (BP)gene expression1.077e-130.001278Moderately InformativeInherited
Biological Process (BP)transcription, DNA-dependent00.0006331InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups1.6e-149.672e-08Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Cellular Component (CC)protein complex1.342e-102.557e-13Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.36555.226e-07Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.025630.06583Least InformativeInherited
Cellular Component (CC)nuclear part0.00017622.259e-13Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.00015441.621e-11Moderately InformativeDirect
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex2.532e-088.849e-07InformativeDirect
Cellular Component (CC)DNA polymerase complex04.98e-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 0.3817 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.8553 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.05204 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.01399 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003102 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5595 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002878 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.0001915 Moderately Informative Direct
Biological Process (BP) cellular response to stress 1.19e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 3.841e-05 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0003333 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.09236 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3567 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7553 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03533 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.02303 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.02108 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.01733 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.05969 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001278 Moderately Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.006753 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02898 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.009722 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.07811 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2118 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 8.749e-07 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0006331 Informative Direct
Biological Process (BP) response to DNA damage stimulus 6.138e-06 Informative Direct
Biological Process (BP) chromosome organization 1.256e-07 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001843 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00625 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.001484 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.05341 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.001985 Informative Inherited
Biological Process (BP) cell cycle checkpoint 4.54e-06 Highly Informative Direct
Biological Process (BP) aging 2.331e-07 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 8.629e-09 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 2.662e-06 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 5.731e-06 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.03887 Highly Informative Inherited
Biological Process (BP) DNA catabolic process 0.001207 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0005425 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 9.672e-08 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.331 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 1.535e-11 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 3.943e-13 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 2.789e-07 Least Informative Direct
Cellular Component (CC) protein complex 2.557e-13 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.226e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.06583 Least Informative Inherited
Cellular Component (CC) nuclear part 2.259e-13 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.621e-11 Moderately Informative Direct
Cellular Component (CC) nucleolus 7.846e-10 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 8.849e-07 Informative Direct
Cellular Component (CC) nucleoplasm part 0.3843 Informative Inherited
Cellular Component (CC) chromosome 0.1101 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 6.289e-06 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 4.98e-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

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 anhydrides0.0004895Moderately 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 damage7.305e-05Moderately InformativeDirect
Biological processtRNA processing4.296e-14InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase1.608e-14Highly InformativeDirect
Molecular functionDNA-binding1.19e-09Least InformativeDirect
Molecular functionNucleotide-binding0.009009Least InformativeInherited
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease1.666e-12Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase5.837e-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 ]