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 (3,244) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 127,991 0 182
Proteins 124,306 0 182


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 process2.895e-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 biogenesis0.90341Least InformativeInherited
Biological Process (BP)regulation of cellular process0.048641Least InformativeInherited
Biological Process (BP)single-organism cellular process0.33540.006942Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.0029830.02817Least InformativeInherited
Biological Process (BP)response to stimulus0.95521Least InformativeInherited
Biological Process (BP)biosynthetic process10.0007029Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process2.474e-090Moderately InformativeDirect
Biological Process (BP)RNA metabolic process1.125e-060Moderately InformativeDirect
Biological Process (BP)cellular response to stress5.853e-061.913e-10Moderately InformativeDirect
Biological Process (BP)cellular catabolic process7.404e-080.0002544Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.59630.5842Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.86251Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.22831Moderately InformativeInherited
Biological Process (BP)organelle organization0.63780.51Moderately InformativeInherited
Biological Process (BP)gene expression0.97980.5584Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.23350.2541Moderately InformativeInherited
Biological Process (BP)regulation of gene expression10.001864Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process4.221e-050.0359Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.82011Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process10.2903Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.51611Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process8.35e-060.01034Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.60360Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00036270.2782Moderately InformativeInherited
Biological Process (BP)DNA metabolic process1.597e-110InformativeDirect
Biological Process (BP)response to DNA damage stimulus3.472e-120InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis1.622e-065.75e-12InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.38330.3379InformativeInherited
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.0020030.5536InformativeInherited
Biological Process (BP)positive regulation of nitrogen compound metabolic process0.14990.8299InformativeInherited
Biological Process (BP)regulation of mitotic cell cycle0.050530.1662InformativeInherited
Biological Process (BP)regulation of cell cycle process0.078980.4904InformativeInherited
Biological Process (BP)ncRNA metabolic process11InformativeInherited
Biological Process (BP)cellular macromolecular complex assembly0.07460.0002769InformativeInherited
Biological Process (BP)organelle assembly0.0059790.53InformativeInherited
Biological Process (BP)RNA processing0.21370.3725InformativeInherited
Biological Process (BP)negative regulation of biosynthetic process10.05494InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.031690InformativeInherited
Biological Process (BP)negative regulation of protein metabolic process10.0002289InformativeInherited
Biological Process (BP)cell cycle process0.68760.01941InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process2.838e-060.004691InformativeInherited
Biological Process (BP)mitochondrion organization0.045091.14e-07InformativeInherited
Biological Process (BP)DNA replication1.043e-050Highly InformativeDirect
Biological Process (BP)DNA catabolic process2.777e-060.000193Highly InformativeDirect
Biological Process (BP)positive regulation of catabolic process2.569e-061.355e-06Highly InformativeDirect
Biological Process (BP)response to ionizing radiation6.962e-050.000375Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process8.834e-101.164e-07Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization6.145e-054.507e-09Highly InformativeDirect
Biological Process (BP)negative regulation of mitotic cell cycle phase transition0.0045940.004418Highly InformativeInherited
Biological Process (BP)regulation of translation0.0091010Highly InformativeInherited
Biological Process (BP)DNA damage checkpoint0.30551Highly InformativeInherited
Biological Process (BP)DNA recombination0.030431Highly InformativeInherited
Biological Process (BP)mRNA processing0.030550.03051Highly InformativeInherited
Biological Process (BP)mRNA catabolic process0.0012682.624e-08Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)binding0.96080.02545Least InformativeInherited
Molecular Function (MF)nucleic acid binding3.864e-050Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.78230Moderately InformativeInherited
Molecular Function (MF)nuclease activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.01150InformativeInherited
Molecular Function (MF)DNA polymerase activity8.866e-060Highly InformativeDirect
Molecular Function (MF)endoribonuclease activity10.9929Highly InformativeInherited
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo0.0069511.617e-06Highly InformativeInherited
Cellular Component (CC)intracellular organelle part10.0006795Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0011845.379e-12Least InformativeInherited
Cellular Component (CC)protein complex0.23821Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.028790.3273Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.00031131.147e-06Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.0074560Moderately InformativeInherited
Cellular Component (CC)nuclear part0.022250Moderately InformativeInherited
Cellular Component (CC)cytoplasmic mRNA processing body3.448e-130Highly InformativeDirect
Cellular Component (CC)CCR4-NOT complex00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex9.22e-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 0.0007029 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 0.006942 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 0.02817 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
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 1.913e-10 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0002544 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 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) homeostatic process 0.9153 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 0.2903 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.001864 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0359 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2541 Moderately Informative Inherited
Biological Process (BP) gene expression 0.5584 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 0.5842 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 0.3899 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.51 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) organic substance catabolic process 0.01034 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2782 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 1.14e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 5.75e-12 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0002769 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0002289 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 5.311e-05 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.01974 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.3379 Informative Inherited
Biological Process (BP) immune effector process 0.3125 Informative Inherited
Biological Process (BP) defense response 1 Informative Inherited
Biological Process (BP) response to other organism 1 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.5536 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.0131 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0129 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1662 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.4904 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 0.53 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.8299 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 0.021 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.05494 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.8545 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.4914 Informative Inherited
Biological Process (BP) sexual reproduction 0.05096 Informative Inherited
Biological Process (BP) single organism reproductive process 0.05656 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.133 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) cell cycle process 0.01941 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) RNA processing 0.3725 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.004691 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.2526 Informative Inherited
Biological Process (BP) DNA replication 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.000193 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 2.624e-08 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 1.355e-06 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.000375 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) stem cell development 0.0001202 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 1.164e-07 Highly Informative Direct
Biological Process (BP) interphase 2.58e-05 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 4.507e-09 Highly Informative Direct
Biological Process (BP) response to virus 0.01997 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.004418 Highly Informative Inherited
Biological Process (BP) DNA modification 0.1159 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.09325 Highly Informative Inherited
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.006746 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3182 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.5361 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.4521 Highly Informative Inherited
Biological Process (BP) DNA damage checkpoint 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) aging 0.002149 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.1126 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.03051 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.02545 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 1.617e-06 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) endoribonuclease activity 0.9929 Highly Informative Inherited
Molecular Function (MF) RNA polymerase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 5.379e-12 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0006795 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3273 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 1.147e-06 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0006267 Informative Direct
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) CCR4-NOT complex 0 Highly Informative Direct
Cellular Component (CC) replisome 0 Highly Informative Direct
Cellular Component (CC) RNA cap binding complex 4.836e-09 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 1.957e-05 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.2644 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 abdomen0.2732Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1537Moderately InformativeInherited
Phenotypic Abnormality (PA)Elevated hepatic transaminases0.0004773Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal tumor incidence0.02525Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.02864Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.04665Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.0007532InformativeDirect
Mammalian Phenotype (MP)decreased germ cell number0.001601InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.002695InformativeInherited
Mammalian Phenotype (MP)abnormal male germ cell morphology0.003118InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.02035InformativeInherited
Mammalian Phenotype (MP)increased malignant tumor incidence0.2719InformativeInherited
Mammalian Phenotype (MP)small testis0.0002544Highly InformativeDirect
Mammalian Phenotype (MP)increased sarcoma incidence0.0005703Highly 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 H3.719e-10Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H2.648e-09Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin1.886e-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 regulation1.856e-15InformativeDirect
Biological processMeiosis0.0001114InformativeDirect
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 processIntron homing1.152e-05Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.0007565Highly 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 termination1.772e-12InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain1.506e-06InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionDNA-binding0Moderately 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 cleavage0.8675InformativeInherited
Post-translational modificationProtein splicing1.747e-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 ]