SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,250) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 130,286 424,272 182
Proteins 126,470 407,374 182


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)nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.441e-130Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.91491Least InformativeInherited
Biological Process (BP)regulation of cellular process0.041081Least InformativeInherited
Biological Process (BP)single-organism cellular process0.2910.03447Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.0026260.006888Least InformativeInherited
Biological Process (BP)response to stimulus0.91011Least InformativeInherited
Biological Process (BP)biosynthetic process10.0004464Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process2.65e-091.938e-15Moderately InformativeDirect
Biological Process (BP)RNA metabolic process1.343e-060Moderately InformativeDirect
Biological Process (BP)cellular response to stress1.772e-061.075e-10Moderately InformativeDirect
Biological Process (BP)cellular catabolic process7.781e-080.000298Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.60210.4142Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.2421Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.88021Moderately InformativeInherited
Biological Process (BP)organelle organization0.66380.578Moderately InformativeInherited
Biological Process (BP)gene expression0.98530.5979Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.25620.1844Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process4.302e-050.04683Moderately InformativeInherited
Biological Process (BP)regulation of gene expression10.0008846Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process10.6833Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process10.4331Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.54851Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process9.423e-060.01202Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.580Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00032310.1654Moderately InformativeInherited
Biological Process (BP)DNA metabolic process9.371e-120InformativeDirect
Biological Process (BP)response to DNA damage stimulus3.951e-130InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis1.48e-062.328e-13InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00InformativeDirect
Biological Process (BP)positive regulation of nucleobase-containing compound metabolic process0.14850.5464InformativeInherited
Biological Process (BP)regulation of cellular catabolic process0.35480.4017InformativeInherited
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.0022980.6766InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle0.050760.176InformativeInherited
Biological Process (BP)regulation of cell cycle process0.079220.492InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)cellular macromolecular complex assembly0.073774.469e-05InformativeInherited
Biological Process (BP)organelle assembly0.0082870.6439InformativeInherited
Biological Process (BP)RNA processing0.21640.3939InformativeInherited
Biological Process (BP)negative regulation of biosynthetic process10.08343InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.032470InformativeInherited
Biological Process (BP)negative regulation of protein metabolic process0.9940.0001576InformativeInherited
Biological Process (BP)negative regulation of gene expression0.46272.151e-07InformativeInherited
Biological Process (BP)cell cycle process0.70220.4206InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process3.938e-060.004105InformativeInherited
Biological Process (BP)mitochondrion organization0.044241.054e-07InformativeInherited
Biological Process (BP)DNA replication2.276e-060Highly InformativeDirect
Biological Process (BP)DNA catabolic process1.076e-060.0001035Highly InformativeDirect
Biological Process (BP)positive regulation of catabolic process3.868e-063.619e-06Highly InformativeDirect
Biological Process (BP)response to ionizing radiation7.185e-059.205e-05Highly InformativeDirect
Biological Process (BP)gene silencing1.009e-060Highly InformativeDirect
Biological Process (BP)regulation of mRNA processing2.656e-071.779e-07Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process6.784e-102.531e-07Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization5.245e-051.389e-10Highly InformativeDirect
Biological Process (BP)negative regulation of mitotic cell cycle phase transition0.0045060.004694Highly InformativeInherited
Biological Process (BP)regulation of translation0.010560Highly InformativeInherited
Biological Process (BP)DNA damage checkpoint0.33411Highly InformativeInherited
Biological Process (BP)DNA recombination0.037271Highly InformativeInherited
Biological Process (BP)mRNA processing0.025450.02587Highly InformativeInherited
Biological Process (BP)mRNA catabolic process0.0015252.212e-08Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)transferase activity10.1105Least InformativeInherited
Molecular Function (MF)binding0.98180.01088Least InformativeInherited
Molecular Function (MF)nucleic acid binding4.41e-050Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.78990Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.012180InformativeInherited
Molecular Function (MF)DNA polymerase activity8.659e-060Highly InformativeDirect
Molecular Function (MF)endoribonuclease activity0.99230.9671Highly InformativeInherited
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo0.0052775.743e-07Highly InformativeInherited
Cellular Component (CC)intracellular organelle part10.0005362Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0011381.387e-12Least InformativeInherited
Cellular Component (CC)protein complex0.24591Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.025750.01495Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.00029582.122e-07Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.0080590Moderately InformativeInherited
Cellular Component (CC)nuclear part0.020970Moderately InformativeInherited
Cellular Component (CC)cytoplasmic mRNA processing body3.154e-130Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex9.317e-060Highly 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) biosynthetic process 0.0004464 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.03447 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.006888 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1.938e-15 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0008846 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0008232 Moderately Informative Direct
Biological Process (BP) cellular response to stress 1.075e-10 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000298 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0005118 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.9869 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 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) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4331 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.04683 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.6833 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1844 Moderately Informative Inherited
Biological Process (BP) gene expression 0.5979 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.4142 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.3307 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.578 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.00125 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03068 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01202 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1654 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 1.054e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 2.151e-07 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 2.328e-13 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 4.469e-05 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0001576 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.157e-05 Informative Direct
Biological Process (BP) regulation of system process 1 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.01229 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.4017 Informative Inherited
Biological Process (BP) immune effector process 0.3021 Informative Inherited
Biological Process (BP) defense response 1 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.6766 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.01598 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.008407 Informative Inherited
Biological Process (BP) single-organism behavior 1 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.176 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.492 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) organelle assembly 0.6439 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.5464 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) chromosome organization 0.0202 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.08343 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.8849 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.4952 Informative Inherited
Biological Process (BP) sexual reproduction 0.07014 Informative Inherited
Biological Process (BP) single organism reproductive process 0.07473 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1711 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) cell cycle process 0.4206 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) RNA processing 0.3939 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.004105 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0001035 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 2.212e-08 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) aging 0.0008671 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 3.619e-06 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 9.205e-05 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) stem cell development 0.000139 Highly Informative Direct
Biological Process (BP) regulation of mRNA processing 1.779e-07 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 2.531e-07 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 1.389e-10 Highly Informative Direct
Biological Process (BP) regulation of behavior 0.06883 Highly Informative Inherited
Biological Process (BP) response to virus 0.01845 Highly Informative Inherited
Biological Process (BP) learning or memory 0.2298 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.004694 Highly Informative Inherited
Biological Process (BP) DNA modification 0.1275 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.09196 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.008164 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3341 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.5134 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.4213 Highly Informative Inherited
Biological Process (BP) DNA damage checkpoint 1 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 1 Highly Informative Inherited
Biological Process (BP) DNA recombination 1 Highly Informative Inherited
Biological Process (BP) double-strand break repair 1 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.1476 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.02587 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.01088 Least Informative Inherited
Molecular Function (MF) transferase activity 0.1105 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) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 5.743e-07 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0.9671 Highly Informative Inherited
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.387e-12 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0005362 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01495 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 2.122e-07 Moderately Informative Direct
Cellular Component (CC) chromosome 0.00115 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 3.781e-05 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)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 H8.901e-10InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H1.817e-09InformativeDirect
Enzyme Commission (EC)Ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III5.258e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal reproductive system morphology0.02806Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.03929Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.04639Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.0007169InformativeDirect
Mammalian Phenotype (MP)decreased germ cell number0.001529InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.002559InformativeInherited
Mammalian Phenotype (MP)abnormal male germ cell morphology0.003049InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.01918InformativeInherited
Mammalian Phenotype (MP)increased malignant tumor incidence0.2788InformativeInherited
Mammalian Phenotype (MP)small testis0.0002509Highly InformativeDirect
Mammalian Phenotype (MP)increased sarcoma incidence0.0005579Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.1156Least InformativeInherited
Worm Phenotype (WP)RNA expression variant1.675e-13InformativeDirect
Worm Phenotype (WP)RNAi response variant1.803e-11Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.84Highly InformativeInherited

Document: WP 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

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)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 H3.725e-10Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H2.953e-09Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin1.89e-05Highly 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 processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processTranslation regulation1.859e-15InformativeDirect
Biological processMeiosis0.000113InformativeDirect
Biological processViral immunoevasion1InformativeInherited
Biological processDNA integration0Highly InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processViral penetration into host nucleus2.372e-16Highly InformativeDirect
Biological processIntron homing1.227e-05Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.0007489Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination1.581e-12InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain1.466e-06InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately 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 cleavage0.8686InformativeInherited
Post-translational modificationProtein splicing1.933e-10Highly 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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]