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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 (3,252) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 131,245 424,272 182
Proteins 127,420 407,374 182


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 process0.00000000000089880Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)response to stimulus0.72231Least InformativeInherited
Biological Process (BP)biological regulation0.31931Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process10.8707Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.00000000014950Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.000000000028860Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0000000095070.000000002188Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.0000029270.000001869Moderately InformativeDirect
Biological Process (BP)cell communication0.40921Moderately InformativeInherited
Biological Process (BP)signaling0.66391Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process0.000220.01012Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.77171Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process0.0000090.01846Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.000021960.01416Moderately InformativeInherited
Biological Process (BP)gene expression10.8017Moderately InformativeInherited
Biological Process (BP)response to stress0.00011770.001917Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.97290.00004169Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process11Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process10.1889Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.60010.00009437Moderately InformativeInherited
Biological Process (BP)organelle organization0.81310.6157Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.00000000000094310InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.000000041240InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.000069310InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.00000000000026460InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.000021010.00002007InformativeDirect
Biological Process (BP)positive regulation of nitrogen compound metabolic process0.27421InformativeInherited
Biological Process (BP)intracellular signal transduction0.014131InformativeInherited
Biological Process (BP)regulation of catabolic process0.0076930.01168InformativeInherited
Biological Process (BP)mitotic cell cycle0.0057340.5455InformativeInherited
Biological Process (BP)regulation of cell cycle0.082910.6632InformativeInherited
Biological Process (BP)cell cycle process0.1380.3198InformativeInherited
Biological Process (BP)ncRNA processing0.42080.6459InformativeInherited
Biological Process (BP)negative regulation of gene expression0.065530.00000000000001068InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.013510InformativeInherited
Biological Process (BP)regulation of cellular amide metabolic process0.015540InformativeInherited
Biological Process (BP)mitochondrion organization0.084120.0003027InformativeInherited
Biological Process (BP)DNA replication0.00000035930Highly InformativeDirect
Biological Process (BP)RNA catabolic process00Highly InformativeDirect
Biological Process (BP)positive regulation of catabolic process0.00000028360.0000005247Highly InformativeDirect
Biological Process (BP)gene silencing0.000000000055830Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process0.0000000042980.000334Highly InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.0010210.0000371Highly InformativeInherited
Biological Process (BP)negative regulation of mitotic cell cycle0.000012420.004776Highly InformativeInherited
Biological Process (BP)cell cycle checkpoint0.00010450.02115Highly InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle phase transition0.000088840.007689Highly InformativeInherited
Biological Process (BP)DNA recombination0.0053420.464Highly InformativeInherited
Biological Process (BP)DNA catabolic process0.10550.0000004657Highly InformativeInherited
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis0.024540.000000000001561Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)transferase activity10.4279Least InformativeInherited
Molecular Function (MF)binding10.0004404Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.00039680Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.69840Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.010960InformativeInherited
Molecular Function (MF)DNA binding0.75461InformativeInherited
Molecular Function (MF)single-stranded DNA binding0.000092840.00006625Highly InformativeDirect
Molecular Function (MF)DNA-directed DNA polymerase activity0.0000031150.000004077Highly InformativeDirect
Molecular Function (MF)endoribonuclease activity0.82910.6551Highly InformativeInherited
Molecular Function (MF)deoxyribonuclease activity0.71951Highly InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)protein complex0.1681Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.015970.00000001015Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.02843Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.03620.00005233Least InformativeInherited
Cellular Component (CC)transferase complex0.015750.1229Moderately InformativeInherited
Cellular Component (CC)nuclear part0.027960Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.14340.000004151Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein granule0.0000041590.00000000000001466InformativeDirect
Cellular Component (CC)nucleolus0.0000022020.00006464Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.00000024770Highly InformativeDirect
Cellular Component (CC)pole plasm0.00000015990Highly 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) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 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 0.8707 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00004169 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00009437 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000002188 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0002596 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000001869 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
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) signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8033 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) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.01012 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1889 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.02217 Moderately Informative Inherited
Biological Process (BP) response to stress 0.001917 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01416 Moderately Informative Inherited
Biological Process (BP) gene expression 0.8017 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.4254 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.03493 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6157 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.01846 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 1 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 0.0003027 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00000000000001068 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0003548 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.000000003754 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) symbiosis, encompassing mutualism through parasitism 0.0000000003868 Informative Direct
Biological Process (BP) single organism reproductive process 0.00008403 Informative Direct
Biological Process (BP) multi-organism cellular process 0.00000001354 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00002007 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of system process 0.9139 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.01168 Informative Inherited
Biological Process (BP) ion homeostasis 0.9683 Informative Inherited
Biological Process (BP) defense response to other organism 0.01961 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.004563 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) behavior 1 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.5455 Informative Inherited
Biological Process (BP) cell cycle process 0.3198 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.6632 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.00156 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.009044 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 1 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 protein modification process 1 Informative Inherited
Biological Process (BP) cell development 0.9344 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.0011 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.04469 Informative Inherited
Biological Process (BP) embryo development 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.04056 Informative Inherited
Biological Process (BP) ncRNA processing 0.6459 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0000004657 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) germ cell development 0.0008593 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0000005247 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0 Highly Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.0000371 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.00000002159 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000334 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.000000000002673 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.000000000001561 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) lipid homeostasis 0.00313 Highly Informative Inherited
Biological Process (BP) response to virus 0.002057 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.0587 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.897 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.7192 Highly Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.02115 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.004776 Highly Informative Inherited
Biological Process (BP) macromolecule methylation 0.9301 Highly Informative Inherited
Biological Process (BP) viral life cycle 0.005047 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 0.6971 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.7828 Highly Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.007689 Highly Informative Inherited
Biological Process (BP) mRNA metabolic process 0.002016 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.464 Highly Informative Inherited
Molecular Function (MF) binding 0.0004404 Least Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) transferase activity 0.4279 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) 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) macromolecular complex binding 0.00115 Informative Inherited
Molecular Function (MF) chromatin binding 0.00007138 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.00006625 Highly Informative Direct
Molecular Function (MF) DNA-directed DNA polymerase activity 0.000004077 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0.6551 Highly Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 1 Highly Informative Inherited
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00000001015 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00005233 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.02843 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000004151 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.1229 Moderately Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase complex 0.000001366 Informative Direct
Cellular Component (CC) chromosome 0.0000000006309 Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.00000000000001466 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) nuclear chromosome 0.00000005982 Highly Informative Direct
Cellular Component (CC) nucleolus 0.00006464 Highly Informative Direct
Cellular Component (CC) replisome 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) pole plasm 0 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.2414 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/homeostasis0.04234Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.05502Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.09034Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.6675Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.0561Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.3196Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.428Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.7433Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cell physiology0.02094InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the external nose0.1005InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lymphocytes0.1466InformativeInherited
Phenotypic Abnormality (PA)Increased antibody level in blood0.0004046Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.1618Highly 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 variant0.8781Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.000000001217InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00000009633InformativeDirect
Worm Phenotype (WP)RNAi response variant0.000000000002302Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.804Highly 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 organism0.000002051Least 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 H0.0000000003769Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000002982Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00001732Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters1Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use0.0004722Least InformativeDirect
Drugbank ATC_code (DB)sensory organs0.1504Least InformativeInherited
Drugbank ATC_code (DB)antiinfectives0.00251Moderately InformativeInherited
Drugbank ATC_code (DB)antivirals for systemic use0.000000003646InformativeDirect
Drugbank ATC_code (DB)antivirals0.0000007885Highly InformativeDirect

Document: DB 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 regulation0.000000000000002617InformativeDirect
Biological processmRNA processing0.00000009876InformativeDirect
Biological processMeiosis0.0000006477InformativeDirect
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 processIntron homing0.00001208Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.0008187Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.000722Least 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 termination0.000000000001714InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain0.000001834InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionLipid-binding0.000000000003357Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.9685InformativeInherited
Post-translational modificationProtein splicing0.0000000001929Highly 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]