SUPERFAMILY 1.75 HMM library and genome assignments server


Ribonuclease PH domain 2-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ribonuclease PH domain 2-like [ 55665]
Superfamily:   Ribonuclease PH domain 2-like [ 55666]
Families:   Ribonuclease PH domain 2-like [ 55667] (10)


Superfamily statistics
Genomes (3,030) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,062 43,979 21
Proteins 7,338 28,379 20


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

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 aromatic compound metabolic process 0.00000000009134 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000000124 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000009847 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000000544 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000000007681 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.2092 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) gene expression 0.000003849 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0008979 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000004612 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000003698 Moderately Informative Direct
Biological Process (BP) organelle organization 0.5831 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.198 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.00007977 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000001107 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000002255 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000000000000007281 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.000000000000007281 Informative Direct
Biological Process (BP) RNA processing 0.002087 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.1024 Informative Inherited
Biological Process (BP) mRNA catabolic process 0.00005242 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.000002757 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00000862 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.00000000000000897 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.01239 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.06204 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0000932 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000000005979 Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1293 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05816 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1156 Least Informative Inherited
Cellular Component (CC) nuclear part 0.001289 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.002234 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.05339 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.01371 Moderately Informative Inherited
Cellular Component (CC) mitochondrial intermembrane space 0.0000009893 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)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)larval development variant0.748Least InformativeInherited
Worm Phenotype (WP)growth variant0.8212Least InformativeInherited
Worm Phenotype (WP)early larval arrest0.00000013Highly InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately 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)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.04 four 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)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processtRNA processing0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0.01062Moderately InformativeInherited
Post-translational modificationExonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015847 SSF55666 Protein matches
Abstract

This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes. [PubMed9390555].

More information about these proteins can be found at Protein of the Month: RNA Exosomes.


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) · Worm Phenotype (WP) · 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 15 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 PH domain 2-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 15 hidden Markov models representing the Ribonuclease PH domain 2-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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]