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Ribonuclease H-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribonuclease H-like motif [ 53066] (7)
Superfamily:   Ribonuclease H-like [ 53098] (14)
Families:   Ribonuclease H [ 53099] (4)
  Retroviral integrase, catalytic domain [ 53107]
  mu transposase, core domain [ 53112]
  Transposase inhibitor (Tn5 transposase) [ 53115]
  DnaQ-like 3'-5' exonuclease [ 53118] (15)
  RuvC resolvase [ 53134]
  Mitochondrial resolvase ydc2 catalytic domain [ 69533]
  Putative Holliday junction resolvase RuvX [ 102485] (3)
  CAF1-like ribonuclease [ 102492] (2)
  PIWI domain [ 110640] (3)
  TM1739-like [ 142505]
  Hermes transposase-like [ 142508]
  Tex RuvX-like domain-like [ 159635]
  Prp8 beta-finger domain-like [ 159638]


Superfamily statistics
Genomes (3,259) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 132,337 626,221 182
Proteins 128,491 598,729 182


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.0000000008901InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000001817InformativeDirect
Enzyme Commission (EC)Ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III0.000005258Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.01284Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.01462Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.04745Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1181Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.123Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.0004589Moderately InformativeDirect
Phenotypic Abnormality (PA)Neoplasm0.0377Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.05591Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.3178Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.3376Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4671Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.4752Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the voice0.00009794InformativeDirect
Phenotypic Abnormality (PA)Lipodystrophy0.0002337InformativeDirect
Phenotypic Abnormality (PA)Abnormal breast morphology0.01719InformativeInherited
Phenotypic Abnormality (PA)Microcephaly0.01946InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.2266InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.3134InformativeInherited
Phenotypic Abnormality (PA)Breast carcinoma0.0008249Highly InformativeDirect
Phenotypic Abnormality (PA)Postnatal microcephaly0.04832Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal myelination0.2295Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.9459Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.00000000235InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.0000008178InformativeDirect
Worm Phenotype (WP)RNAi response variant0.00000000007849Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.6214Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0.0004568Least InformativeDirect
Xenopus ANatomical entity (XAN)urogenital system0.0007683Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0.02415Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00000225Moderately InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately 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)In phosphorus-containing anhydrides1InformativeInherited
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.000000003492Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000009848Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00002016Highly InformativeDirect
Enzyme Commission (EC)dUTP diphosphatase0.00003276Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters1Highly InformativeInherited

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR012337 SSF53098 Protein matches
Abstract

The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3-5 exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [PubMed15299518, PubMed8696976, PubMed12823554].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 88 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 88 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]