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 (3,251) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 131,130 424,272 182
Proteins 127,299 407,374 182


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 process0.000000000000076360Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)positive regulation of biological process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.92491Least InformativeInherited
Biological Process (BP)regulation of cellular process0.073651Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.0047210.01656Least InformativeInherited
Biological Process (BP)response to stimulus0.90521Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process10.000234Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.00000033830.000000000004439Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.0000012880Moderately InformativeDirect
Biological Process (BP)cellular response to stress0.0000017640.0000000001171Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.000000065290.0002308Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.7610.7243Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000037120.1959Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.00010640.0858Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.25460.2485Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.95081Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.66881Moderately InformativeInherited
Biological Process (BP)gene expression10.775Moderately InformativeInherited
Biological Process (BP)regulation of gene expression10.003719Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.54961Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.58070Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.0000073280.01057Moderately InformativeInherited
Biological Process (BP)DNA repair0.00000010530InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.0000014630.0000000000002375InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00InformativeDirect
Biological Process (BP)positive regulation of RNA metabolic process0.000079790.341InformativeInherited
Biological Process (BP)positive regulation of catabolic process0.0015390.0924InformativeInherited
Biological Process (BP)regulation of cellular catabolic process0.33750.4467InformativeInherited
Biological Process (BP)positive regulation of gene expression0.0051661InformativeInherited
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.0016440.6741InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle0.061090.2229InformativeInherited
Biological Process (BP)regulation of cell cycle process0.077480.4512InformativeInherited
Biological Process (BP)cell cycle process0.38560.2294InformativeInherited
Biological Process (BP)mitotic cell cycle0.16890.3136InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)cellular macromolecular complex assembly0.076760.0002862InformativeInherited
Biological Process (BP)organelle assembly0.0086210.6984InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process0.000002190.002617InformativeInherited
Biological Process (BP)RNA processing0.1530.3218InformativeInherited
Biological Process (BP)mitochondrion organization0.040820.0000001898InformativeInherited
Biological Process (BP)DNA replication0.0000031360Highly InformativeDirect
Biological Process (BP)DNA catabolic process0.0000010120.00009535Highly InformativeDirect
Biological Process (BP)response to ionizing radiation0.000071110.0001024Highly InformativeDirect
Biological Process (BP)gene silencing0.00000013710Highly InformativeDirect
Biological Process (BP)regulation of mRNA processing0.000000094370.0000001149Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process0.00000000084770.0000004704Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.000055270.000000000174Highly InformativeDirect
Biological Process (BP)negative regulation of mitotic cell cycle phase transition0.0045860.005953Highly InformativeInherited
Biological Process (BP)DNA integrity checkpoint0.00074150.002937Highly InformativeInherited
Biological Process (BP)mRNA processing0.025360.02624Highly InformativeInherited
Biological Process (BP)DNA recombination0.036211Highly InformativeInherited
Biological Process (BP)mRNA catabolic process0.0014470.00000001995Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)transferase activity10.5636Least InformativeInherited
Molecular Function (MF)binding0.98840.01079Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.00010250Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.79430Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.012210InformativeInherited
Molecular Function (MF)DNA polymerase activity0.0000087090Highly InformativeDirect
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo0.0023970.00000005441Highly InformativeInherited
Molecular Function (MF)endoribonuclease activity0.94410.8115Highly InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0012740.000000000002352Least InformativeInherited
Cellular Component (CC)protein complex0.24161Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.0008777Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0120.001369Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0002030.000000004832Moderately InformativeDirect
Cellular Component (CC)transferase complex0.072910.00001612Moderately InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.0082690Moderately InformativeInherited
Cellular Component (CC)nuclear part0.015250Moderately InformativeInherited
Cellular Component (CC)cytoplasmic ribonucleoprotein granule0.000000000073380Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.000010010Highly 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 0.000234 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) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01656 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.000000000004439 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0007166 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0000000001171 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0002308 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0003998 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9932 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1959 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) defense response 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.775 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.7823 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.003719 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.02781 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2485 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0858 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.7243 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.4067 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.2161 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01057 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.001084 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 1 Moderately Informative Inherited
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.0000001898 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0000000000002375 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000001455 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0002862 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0008647 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.00002211 Informative Direct
Biological Process (BP) positive regulation of RNA metabolic process 0.341 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.4467 Informative Inherited
Biological Process (BP) regulation of system process 0.8024 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.01305 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.0924 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) immune effector process 0.3068 Informative Inherited
Biological Process (BP) defense response to other organism 0.4803 Informative Inherited
Biological Process (BP) cell proliferation 0.1184 Informative Inherited
Biological Process (BP) single-organism behavior 1 Informative Inherited
Biological Process (BP) neurological system process 1 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.6741 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.2229 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.4512 Informative Inherited
Biological Process (BP) cell cycle process 0.2294 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.3136 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.08757 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) organelle assembly 0.6984 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) chromosome organization 0.02892 Informative Inherited
Biological Process (BP) RNA processing 0.3218 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.8862 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.6074 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.04673 Informative Inherited
Biological Process (BP) sexual reproduction 0.04703 Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.003165 Informative Inherited
Biological Process (BP) single organism reproductive process 0.02959 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.002617 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.00009535 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 0.00000001995 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) aging 0.0009267 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.0001024 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) regulation of neurological system process 0.0008324 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) stem cell development 0.0001294 Highly Informative Direct
Biological Process (BP) regulation of mRNA processing 0.0000001149 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000004704 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.000000000174 Highly Informative Direct
Biological Process (BP) response to virus 0.01918 Highly Informative Inherited
Biological Process (BP) learning or memory 0.2398 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.005953 Highly Informative Inherited
Biological Process (BP) DNA integrity checkpoint 0.002937 Highly Informative Inherited
Biological Process (BP) DNA modification 0.1056 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 1 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.02624 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.1448 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3316 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.5195 Highly Informative Inherited
Biological Process (BP) germ cell development 0.002355 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) cell fate commitment 0.4209 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.1456 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) transferase activity 0.5636 Least Informative Inherited
Molecular Function (MF) binding 0.01079 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 0.00000005441 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0.8115 Highly Informative Inherited
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.000000000002352 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0008777 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.001369 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 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 0.000000004832 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.00001612 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000499 Informative Direct
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.00009961 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 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

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 variant0.0000000000001675InformativeDirect
Worm Phenotype (WP)RNAi response variant0.00000000001803Highly 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 H0.0000000003725Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000002953Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.0000189Highly 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 use0.001006Least InformativeInherited
Drugbank ATC_code (DB)sensory organs0.1006Least InformativeInherited
Drugbank ATC_code (DB)antiinfectives0.001356Moderately InformativeInherited
Drugbank ATC_code (DB)antivirals for systemic use0.00000004193InformativeDirect
Drugbank ATC_code (DB)antivirals0.0000004216InformativeDirect

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 processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processTranslation regulation0.000000000000001859InformativeDirect
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 homing0.00001227Highly 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 termination0.000000000001581InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain0.000001466InformativeDirect
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 splicing0.0000000001933Highly 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]