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 (3,209) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 125,241 222,727 182
Proteins 121,458 210,038 182


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 process1.787e-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 biogenesis0.83921Least InformativeInherited
Biological Process (BP)regulation of cellular process0.055161Least InformativeInherited
Biological Process (BP)single-organism cellular process0.3170.003217Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.0018650.01048Least InformativeInherited
Biological Process (BP)response to stimulus0.93581Least InformativeInherited
Biological Process (BP)biosynthetic process10.0009746Least InformativeInherited
Biological Process (BP)macromolecule catabolic process05.721e-14Moderately InformativeDirect
Biological Process (BP)negative regulation of metabolic process7.282e-100Moderately InformativeDirect
Biological Process (BP)RNA metabolic process1.222e-060Moderately InformativeDirect
Biological Process (BP)cellular response to stress2.591e-062.522e-11Moderately InformativeDirect
Biological Process (BP)cellular catabolic process8.736e-080.000179Moderately InformativeDirect
Biological Process (BP)organic cyclic compound catabolic process2.233e-082.48e-06Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.53420.4489Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.81471Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.23411Moderately InformativeInherited
Biological Process (BP)organelle organization0.63480.5658Moderately InformativeInherited
Biological Process (BP)gene expression0.95970.494Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.19660.2174Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process9.13e-050.02184Moderately InformativeInherited
Biological Process (BP)regulation of gene expression10.002202Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process10.8278Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process10.2467Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.45431Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.56840Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00040860.1716Moderately InformativeInherited
Biological Process (BP)DNA metabolic process2.267e-110InformativeDirect
Biological Process (BP)response to DNA damage stimulus1.768e-120InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis1.108e-062.1e-12InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00InformativeDirect
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.0018130.5089InformativeInherited
Biological Process (BP)positive regulation of nitrogen compound metabolic process0.13610.7073InformativeInherited
Biological Process (BP)regulation of cell cycle0.60470.5724InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)cellular macromolecular complex assembly0.062030.0001337InformativeInherited
Biological Process (BP)organelle assembly0.0050590.5213InformativeInherited
Biological Process (BP)RNA processing0.2340.4407InformativeInherited
Biological Process (BP)negative regulation of biosynthetic process10.04509InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.033840InformativeInherited
Biological Process (BP)negative regulation of protein metabolic process0.99950.0001565InformativeInherited
Biological Process (BP)negative regulation of gene expression0.46586.185e-09InformativeInherited
Biological Process (BP)cell cycle process0.70740.06041InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process3.681e-060.00313InformativeInherited
Biological Process (BP)mitochondrion organization0.040353.567e-07InformativeInherited
Biological Process (BP)DNA replication1.424e-050Highly InformativeDirect
Biological Process (BP)DNA catabolic process2.484e-060.0002085Highly InformativeDirect
Biological Process (BP)RNA catabolic process00Highly InformativeDirect
Biological Process (BP)response to ionizing radiation5.504e-050.0002554Highly InformativeDirect
Biological Process (BP)gene silencing8.237e-070Highly InformativeDirect
Biological Process (BP)positive regulation of cellular catabolic process1.215e-061.518e-08Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process1.061e-099.719e-08Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization4.543e-052.08e-09Highly InformativeDirect
Biological Process (BP)cell cycle checkpoint0.0052970.3731Highly InformativeInherited
Biological Process (BP)negative regulation of mitotic cell cycle phase transition0.0035040.002867Highly InformativeInherited
Biological Process (BP)regulation of translation0.0094460Highly InformativeInherited
Biological Process (BP)DNA recombination0.026531Highly InformativeInherited
Biological Process (BP)mRNA processing0.031760.02466Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)binding0.96270.002307Least InformativeInherited
Molecular Function (MF)nucleic acid binding1.848e-050Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.72780Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.0090510InformativeInherited
Molecular Function (MF)DNA polymerase activity7.73e-060Highly InformativeDirect
Molecular Function (MF)endoribonuclease activity11Highly InformativeInherited
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo0.010788.232e-06Highly InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.024712.408e-12Least InformativeInherited
Cellular Component (CC)protein complex0.2371Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.065830.5556Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.001623Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.0059890Moderately InformativeInherited
Cellular Component (CC)nuclear part0.16040Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.028878.323e-07Moderately InformativeInherited
Cellular Component (CC)nucleolus1.837e-053.512e-08InformativeDirect
Cellular Component (CC)cytoplasmic mRNA processing body1.284e-130Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex8.62e-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 0.0009746 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) 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 0.003217 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01048 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) macromolecule catabolic process 5.721e-14 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular response to stress 2.522e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000179 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 2.48e-06 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.9899 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) homeostatic process 0.8034 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) regulation of protein metabolic process 0.2467 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.002202 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.02184 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.8278 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2174 Moderately Informative Inherited
Biological Process (BP) gene expression 0.494 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 0.4489 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) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.2838 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.5658 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) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1716 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 3.567e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 6.185e-09 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 2.1e-12 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0001337 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0001565 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.665e-05 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.01233 Informative Inherited
Biological Process (BP) immune effector process 0.2707 Informative Inherited
Biological Process (BP) defense response 1 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.5089 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.01148 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.5724 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 0.5213 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.7073 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 0.01629 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.04509 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.7714 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.4436 Informative Inherited
Biological Process (BP) sexual reproduction 0.04761 Informative Inherited
Biological Process (BP) single organism reproductive process 0.0512 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.124 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) cell cycle process 0.06041 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) RNA processing 0.4407 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.00313 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.0002085 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.0002554 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 1.518e-08 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) stem cell development 5.695e-05 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 9.719e-08 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 2.8e-06 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 2.08e-09 Highly Informative Direct
Biological Process (BP) response to virus 0.01518 Highly Informative Inherited
Biological Process (BP) cell cycle phase 0.001525 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.1367 Highly Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.3731 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.002867 Highly Informative Inherited
Biological Process (BP) DNA modification 0.102 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.08316 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.005672 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3078 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.4555 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.3664 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) aging 0.001641 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.1184 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.02466 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.002307 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) DNA-directed RNA polymerase activity 5.492e-10 Highly Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 8.232e-06 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 2.408e-12 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.001623 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5556 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 8.323e-07 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0008823 Informative Direct
Cellular Component (CC) nucleolus 3.512e-08 Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) replisome 0 Highly Informative Direct
Cellular Component (CC) RNA cap binding complex 5.739e-09 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 2.142e-05 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.3357 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 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the abdomen0.2728Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.154Moderately InformativeInherited
Phenotypic Abnormality (PA)Elevated hepatic transaminases0.0004794Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal reproductive system morphology0.02212Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.0303Moderately InformativeInherited
Mammalian Phenotype (MP)endocrine/exocrine gland phenotype0.1145Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.0005241InformativeDirect
Mammalian Phenotype (MP)decreased germ cell number0.001161InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.001897InformativeInherited
Mammalian Phenotype (MP)abnormal male germ cell morphology0.002298InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.004135InformativeInherited
Mammalian Phenotype (MP)increased malignant tumor incidence0.2659InformativeInherited
Mammalian Phenotype (MP)small testis0.0001672Highly InformativeDirect
Mammalian Phenotype (MP)increased sarcoma incidence0.000449Highly 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 H3.716e-10Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H2.794e-09Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin1.885e-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 processHost gene expression shutoff by virus0InformativeDirect
Biological processTranslation regulation1.856e-15InformativeDirect
Biological processMeiosis7.605e-05InformativeDirect
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 nucleus2.365e-16Highly InformativeDirect
Biological processNonsense-mediated mRNA decay5.009e-07Highly InformativeDirect
Biological processIntron homing1.238e-05Highly 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 termination1.858e-12InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain1.495e-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 cleavage0.865InformativeInherited
Post-translational modificationProtein splicing1.739e-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

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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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]