SUPERFAMILY 1.75 HMM library and genome assignments server


RNase III domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   RNase III domain-like [ 69064]
Superfamily:   RNase III domain-like [ 69065] (2)
Families:   RNase III catalytic domain-like [ 69066] (2)
  PF0609-like [ 140675]


Superfamily statistics
Genomes (3,003) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 7,024 12,364 10
Proteins 5,971 11,453 10


Functional annotation
General category Information
Detailed category RNA processing

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.096e-13 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 2.755e-13 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.683e-12 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.882e-12 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 8.982e-12 Least Informative Direct
Biological Process (BP) regulation of metabolic process 8.422e-11 Least Informative Direct
Biological Process (BP) response to stimulus 2.672e-10 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.613e-08 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.3698 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.5845 Least Informative Inherited
Biological Process (BP) localization 0.3126 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0 Moderately Informative Direct
Biological Process (BP) immune system process 4.823e-09 Moderately Informative Direct
Biological Process (BP) multi-organism process 9.338e-09 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.542e-05 Moderately Informative Direct
Biological Process (BP) macromolecule localization 2.027e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 2.664e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 6.208e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 7.263e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002762 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0004474 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.2306 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.6337 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6977 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.2414 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3518 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.01011 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.09807 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.6233 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.3351 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1756 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.03405 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.773 Moderately Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) immune effector process 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 1.931e-15 Informative Direct
Biological Process (BP) RNA processing 7.645e-14 Informative Direct
Biological Process (BP) ncRNA metabolic process 1.686e-13 Informative Direct
Biological Process (BP) defense response 2.815e-11 Informative Direct
Biological Process (BP) regulation of immune effector process 2.037e-10 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 1.241e-08 Informative Direct
Biological Process (BP) nitrogen compound transport 2.111e-08 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 1.597e-07 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 1.649e-07 Informative Direct
Biological Process (BP) regulation of defense response 2.031e-07 Informative Direct
Biological Process (BP) single-organism behavior 4.128e-07 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 4.438e-07 Informative Direct
Biological Process (BP) organophosphate catabolic process 4.954e-07 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 8.382e-07 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 1.288e-06 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.0005107 Informative Direct
Biological Process (BP) regulation of system process 0.0006159 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.302 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.5844 Informative Inherited
Biological Process (BP) chromosome organization 0.0216 Informative Inherited
Biological Process (BP) regulation of cell development 0.03794 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) mitochondrion organization 0.006449 Informative Inherited
Biological Process (BP) translation 0.06786 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.005004 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.002194 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.4905 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.6621 Informative Inherited
Biological Process (BP) response to virus 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 0 Highly Informative Direct
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 1.931e-15 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 7.333e-15 Highly Informative Direct
Biological Process (BP) regulation of response to biotic stimulus 3.516e-13 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 3.63e-12 Highly Informative Direct
Biological Process (BP) locomotory behavior 2.567e-10 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 1.781e-09 Highly Informative Direct
Biological Process (BP) ATP metabolic process 2.803e-09 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 4.731e-08 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 7.508e-08 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 8.714e-08 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 1.642e-07 Highly Informative Direct
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 2.181e-06 Highly Informative Direct
Biological Process (BP) stem cell development 0.0004622 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.6338 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.005429 Highly Informative Inherited
Biological Process (BP) cell division 0.01383 Highly Informative Inherited
Biological Process (BP) mRNA processing 1 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.1319 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 1.467e-08 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.771e-07 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.0006101 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.881e-06 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 1.686e-05 Informative Direct
Molecular Function (MF) endoribonuclease activity 2.702e-11 Highly Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 0.0003575 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04142 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.7893 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.08552 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.009145 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 1.3e-06 Informative Direct
Cellular Component (CC) mitochondrial matrix 7.237e-05 Informative Direct
Cellular Component (CC) mitochondrial ribosome 7.596e-08 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)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)vegetative growth0InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0Moderately InformativeDirect
Fly Phenotype (FP)neurophysiology defective0.0002734InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processRibosome biogenesis1.778e-07InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionManganese2.714e-12Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000999 SSF69065 Protein matches
Abstract

Prokaryotic ribonuclease III (gene rnc) [PubMed3903434] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related [PubMed9241229] to the fission yeast pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development; yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites; Caenorhabditis elegans hypothetical protein F26E4.13; Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R; Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346; fission yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain; and C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c.


InterPro database


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

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 4 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 RNase III domain-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 4 hidden Markov models representing the RNase III domain-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-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]