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Ribonuclease H-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribonuclease H-like motif [ 53066] (7)
Superfamily:   Ribonuclease H-like [ 53098] (14)
Families:   Ribonuclease H [ 53099] (4)
  Retroviral integrase, catalytic domain [ 53107]
  mu transposase, core domain [ 53112]
  Transposase inhibitor (Tn5 transposase) [ 53115]
  DnaQ-like 3'-5' exonuclease [ 53118] (15)
  RuvC resolvase [ 53134]
  Mitochondrial resolvase ydc2 catalytic domain [ 69533]
  Putative Holliday junction resolvase RuvX [ 102485] (3)
  CAF1-like ribonuclease [ 102492] (2)
  PIWI domain [ 110640] (3)
  TM1739-like [ 142505]
  Hermes transposase-like [ 142508]
  Tex RuvX-like domain-like [ 159635]
  Prp8 beta-finger domain-like [ 159638]


Superfamily statistics
Genomes (3,257) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 131,920 500,497 182
Proteins 128,086 475,209 182


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

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 process00Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.000000000012760Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)response to stimulus0.72681Least InformativeInherited
Biological Process (BP)biological regulation0.081731Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process00Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.0000000000039960Moderately InformativeDirect
Biological Process (BP)cellular response to stress0.00000000060640.00000000001267Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.000000011640.000000003489Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.00000084220.0000001091Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process10.6441Moderately InformativeInherited
Biological Process (BP)cell communication0.60251Moderately InformativeInherited
Biological Process (BP)single organism signaling0.46671Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.98231Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.99961Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.0036390.001267Moderately InformativeInherited
Biological Process (BP)gene expression10.6639Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.80680.000006912Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process10.8088Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.57530.001733Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000030240.162Moderately InformativeInherited
Biological Process (BP)organelle organization0.91240.3157Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.00000000000079650InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.000000027570InformativeDirect
Biological Process (BP)negative regulation of gene expression0.00023260InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.00000000000001620InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)negative regulation of macromolecule biosynthetic process0.65060.1073InformativeInherited
Biological Process (BP)negative regulation of cellular biosynthetic process0.13150.00000004709InformativeInherited
Biological Process (BP)intracellular signal transduction0.018061InformativeInherited
Biological Process (BP)regulation of catabolic process0.14070.4464InformativeInherited
Biological Process (BP)positive regulation of nucleobase-containing compound metabolic process0.11930.8013InformativeInherited
Biological Process (BP)mitotic cell cycle0.0013420.4627InformativeInherited
Biological Process (BP)cell cycle process0.047750.3384InformativeInherited
Biological Process (BP)ncRNA processing0.44980.6303InformativeInherited
Biological Process (BP)regulation of cell cycle0.087450.7876InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.084360InformativeInherited
Biological Process (BP)regulation of cellular amide metabolic process0.011070InformativeInherited
Biological Process (BP)mitochondrion organization0.043110.000001485InformativeInherited
Biological Process (BP)DNA replication0.000000048520Highly InformativeDirect
Biological Process (BP)RNA catabolic process00Highly InformativeDirect
Biological Process (BP)positive regulation of catabolic process0.0000032610.00006883Highly InformativeDirect
Biological Process (BP)gene silencing0.000000000069940Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process0.000000027810.00009249Highly InformativeDirect
Biological Process (BP)negative regulation of cell cycle phase transition0.0000079480.0003929Highly InformativeDirect
Biological Process (BP)negative regulation of mitotic cell cycle0.000034680.008074Highly InformativeInherited
Biological Process (BP)cell cycle checkpoint0.00010480.01822Highly InformativeInherited
Biological Process (BP)DNA recombination0.0063150.48Highly InformativeInherited
Biological Process (BP)DNA catabolic process0.11220.0000001089Highly InformativeInherited
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis0.048720.000000000005784Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)transferase activity10.7153Least InformativeInherited
Molecular Function (MF)binding10.0006467Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.73170Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding0.0015140Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.011760InformativeInherited
Molecular Function (MF)DNA binding0.84231InformativeInherited
Molecular Function (MF)single-stranded DNA binding0.0001140.00006086Highly InformativeDirect
Molecular Function (MF)DNA-directed DNA polymerase activity0.0000032710.00000571Highly InformativeDirect
Molecular Function (MF)deoxyribonuclease activity0.62261Highly InformativeInherited
Molecular Function (MF)endoribonuclease activity0.88460.2587Highly InformativeInherited
Cellular Component (CC)macromolecular complex0.0013340.0000000000004114Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0046010.000000006525Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.026270.00005597Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.01625Least InformativeInherited
Cellular Component (CC)transferase complex0.01860.05626Moderately InformativeInherited
Cellular Component (CC)nuclear part0.0085240Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.058470.0000008666Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein granule0.000022470.00000000000005959InformativeDirect
Cellular Component (CC)transferase complex, transferring phosphorus-containing groups0.00023640InformativeDirect
Cellular Component (CC)CCR4-NOT complex00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.00000030190Highly InformativeDirect
Cellular Component (CC)pole plasm0.00000017010Highly 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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary 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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000006912 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000000001267 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000003489 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0003367 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001091 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9726 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001267 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.001733 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.6441 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.162 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8088 Moderately Informative Inherited
Biological Process (BP) gene expression 0.6639 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1351 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.6632 Moderately Informative Inherited
Biological Process (BP) reproduction 0.0115 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.5983 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3157 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.000001485 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0004587 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.00000004709 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) single organism reproductive process 0.00003584 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0000000001042 Informative Direct
Biological Process (BP) response to nitrogen compound 0.005934 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.4464 Informative Inherited
Biological Process (BP) regulation of system process 0.9393 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) ion homeostasis 1 Informative Inherited
Biological Process (BP) immune effector process 0.0172 Informative Inherited
Biological Process (BP) defense response to other organism 0.02095 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) behavior 1 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.7876 Informative Inherited
Biological Process (BP) cell cycle process 0.3384 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.4627 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.005729 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.1073 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.7979 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.8013 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 1 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.01865 Informative Inherited
Biological Process (BP) ncRNA processing 0.6303 Informative Inherited
Biological Process (BP) ribosome biogenesis 1 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) cell development 0.9267 Informative Inherited
Biological Process (BP) interspecies interaction between organisms 0.002154 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.001166 Informative Inherited
Biological Process (BP) embryo development 0.9852 Informative Inherited
Biological Process (BP) cell activation 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.01941 Informative Inherited
Biological Process (BP) chromosome organization 0.003898 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0000001089 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) germ cell development 0.0002031 Highly Informative Direct
Biological Process (BP) response to virus 0.000006792 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00006883 Highly Informative Direct
Biological Process (BP) viral process 0.00000628 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.0007353 Highly Informative Direct
Biological Process (BP) negative regulation of cellular amide metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.000000003569 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00009249 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.000000000005784 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle phase transition 0.0003929 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 1 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.7675 Highly Informative Inherited
Biological Process (BP) neurological system process 1 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.008074 Highly Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.01822 Highly Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 1 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.07021 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.7066 Highly Informative Inherited
Biological Process (BP) fertilization 0.05337 Highly Informative Inherited
Biological Process (BP) cell maturation 0.2912 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.8118 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.48 Highly Informative Inherited
Biological Process (BP) macromolecule methylation 0.8761 Highly Informative Inherited
Biological Process (BP) double-strand break repair 0.8996 Highly Informative Inherited
Molecular Function (MF) binding 0.0006467 Least Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) transferase activity 0.7153 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 1 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 1 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00004454 Informative Direct
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) chromatin binding 0.000001453 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.00006086 Highly Informative Direct
Molecular Function (MF) DNA-directed DNA polymerase activity 0.00000571 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0.2587 Highly Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 1 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0.0000000000004114 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000000006525 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00005597 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01625 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000008666 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.05626 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00009567 Informative Direct
Cellular Component (CC) protein-DNA complex 0.000000000008325 Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.00000000000005959 Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) CCR4-NOT complex 0 Highly Informative Direct
Cellular Component (CC) replisome 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0004301 Highly Informative Direct
Cellular Component (CC) pole plasm 0 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.2312 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.0000000008901InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000001817InformativeDirect
Enzyme Commission (EC)Ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III0.000005258Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.0416Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.05559Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.09098Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.5067Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.05694Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.3207Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.422Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.7421Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the external nose0.1018InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lymphocytes0.1495InformativeInherited
Phenotypic Abnormality (PA)Increased antibody level in blood0.0003921Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.1626Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.9075Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.000000002696InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00000009291InformativeDirect
Worm Phenotype (WP)RNAi response variant0.000000000002663Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7921Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0.000002094Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)1Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.0000000007078Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000002954Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00002171Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processRibosome biogenesis0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processTranslation regulation0.000000000000004741InformativeDirect
Biological processMeiosis0.00000005598InformativeDirect
Biological processmRNA processing0.0000001237InformativeDirect
Biological processViral immunoevasion1InformativeInherited
Biological processDNA integration0Highly InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0Highly InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.000005908Highly InformativeDirect
Biological processIntron homing0.00001392Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentVirion0Moderately InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0.000000000001924InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain0.000001866InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionLipid-binding0.00000000003335Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.9709InformativeInherited
Post-translational modificationProtein splicing0.0000000001918Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR012337 SSF53098 Protein matches
Abstract

The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3-5 exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [PubMed15299518, PubMed8696976, PubMed12823554].


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

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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 58 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 Ribonuclease H-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 58 hidden Markov models representing the Ribonuclease H-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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]