SUPERFAMILY 1.75 HMM library and genome assignments server


tRNA-intron endonuclease catalytic domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Restriction endonuclease-like [ 52979] (4)
Superfamily:   tRNA-intron endonuclease catalytic domain-like [ 53032]
Families:   tRNA-intron endonuclease catalytic domain-like [ 53033] (3)


Superfamily statistics
Genomes (640) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,553 1,990 6
Proteins 1,488 1,832 4


Functional annotation
General category Information
Detailed category Translation

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) heterocycle metabolic process 0.01575 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.1044 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01747 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02657 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.04558 Least Informative Inherited
Biological Process (BP) RNA metabolic process 7.549e-05 Moderately Informative Direct
Biological Process (BP) gene expression 0.0009613 Moderately Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 1.618e-06 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0004981 Informative Direct
Biological Process (BP) RNA processing 0.003116 Informative Inherited
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 9.035e-11 Highly Informative Direct
Biological Process (BP) RNA splicing 1.688e-08 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.01236 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 2.192e-05 Moderately Informative Direct
Molecular Function (MF) nuclease activity 1.062e-09 Informative Direct
Molecular Function (MF) endoribonuclease activity 1.567e-11 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 other than 5'-phosphom0Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processtRNA processing0InformativeDirect
Cellular componentNucleus4.753e-05Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006677 SSF53032 Protein matches
Abstract

tRNA-intron endonucleases cleave pre-tRNA producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron [PubMed9200602]. This entry is for C-terminal domain of tRNA-intron endonuclease.


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) · Xenopus Anatomy (XA) · 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 tRNA-intron endonuclease catalytic 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 tRNA-intron endonuclease catalytic 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) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]