SUPERFAMILY 1.75 HMM library and genome assignments server

Ribonuclease Rh-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ribonuclease Rh-like [ 55894]
Superfamily:   Ribonuclease Rh-like [ 55895]
Families:   Ribonuclease Rh-like [ 55896] (8)


Superfamily statistics
Genomes (895) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,880 7,981 12
Proteins 1,847 7,970 12


Functional annotation
General category Information
Detailed category RNA processing

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 process0.000048910.00001031Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00025270.00007106Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00010690.0003477Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000047070.000008455Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000095010.00002344Least InformativeDirect
Biological Process (BP)RNA metabolic process0.000000010390.0000000004065Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0003280.00000004696Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.00075680.0000001828Moderately InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.00068520.0000000512InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.0000042510.00000000002069InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis0.00011080.00000000006571InformativeDirect
Molecular Function (MF)hydrolase activity0.00038730.000002666Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds0.000001570.00000000002061Moderately InformativeDirect
Molecular Function (MF)nuclease activity0.000000000078150InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.094741Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.099520.7707Least InformativeInherited

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 0.00001031 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00007106 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0003477 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000008455 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00002344 Least Informative Direct
Biological Process (BP) RNA metabolic process 0.0000000004065 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000004696 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001828 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000000512 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000000002069 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.00000000006571 Informative Direct
Molecular Function (MF) hydrolase activity 0.000002666 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.00000000002061 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7707 Least Informative Inherited

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)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.8302Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.05259Least InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0.00001407Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0.00004815Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.0004788Moderately InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphatase0.0000000001751InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0.00000001353InformativeDirect
Enzyme Commission (EC)Pestivirus NS3 polyprotein peptidase0Highly InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing other than 5'-phosphom0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)C globular 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)Transferring phosphorous-containing groups0.8074Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.05917Moderately InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.8373Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)RNA-directed RNA polymerase0.00000001272InformativeDirect
Enzyme Commission (EC)RNA helicase0.000003745InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.00001255InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0.00004855InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0.0000000001766Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0.00001061Moderately InformativeDirect
Biological processViral RNA replication0.0000000006876InformativeDirect
Biological processViral immunoevasion0.000000007681InformativeDirect
Biological processVirus entry into host cell0.0000001916InformativeDirect
Biological processInhibition of host IRF3 by virus0.00000000000001182Highly InformativeDirect
Biological processActivation of host autophagy by virus0.000000000000566Highly InformativeDirect
Biological processFusion of virus membrane with host endosomal membrane0.0000000001198Highly InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentSecreted0.0000000001967Moderately InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentLysosome0.000000006981InformativeDirect
Cellular componentHost membrane0.0000004706InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.004902Moderately InformativeInherited
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationThiol protease0.0000001558InformativeDirect
Post-translational modificationIon channel0.000001354InformativeDirect
Post-translational modificationSerine protease0.000002874InformativeDirect
Post-translational modificationViral ion channel0.00000000000004448Highly InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0.0000000004645Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.0000000000003883Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001568 SSF55895 Protein matches
Abstract

The fungal ribonucleases T2 from Aspergillus oryzae, M from Aspergillus saitoi and Rh from Rhizopus niveus are structurally and functionally related 30 Kd glycoproteins [PubMed2229029] that cleave the 3'-5' internucleotide linkage of RNA via a nucleotide 2',3'-cyclic phosphate intermediate .

Two histidines residues have been shown [PubMed2298207, PubMed1633875] to be involved in the catalytic mechanism of RNase T2 and Rh. These residues and the region around them are highly conserved in a number of other RNAses that have been found to be evolutionary related to these fungal enzymes.


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 8 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 Rh-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 8 hidden Markov models representing the Ribonuclease Rh-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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]