SUPERFAMILY 1.75 HMM library and genome assignments server


An anticodon-binding domain of class I aminoacyl-tRNA synthetases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   An anticodon-binding domain of class I aminoacyl-tRNA synthetases [ 48162]
Superfamily:   An anticodon-binding domain of class I aminoacyl-tRNA synthetases [ 48163] (2)
Families:   C-terminal domain of glutamyl-tRNA synthetase (GluRS) [ 48164]
  C-terminal domain of class I lysyl-tRNA synthetase [ 74759]


Superfamily statistics
Genomes (3,086) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,912 0 3
Proteins 3,902 0 3


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) cellular aromatic compound metabolic process 3.575e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001286 Least Informative Direct
Biological Process (BP) biosynthetic process 2.141e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 2.861e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0004263 Least Informative Direct
Biological Process (BP) single-organism metabolic process 9.007e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.135e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 6.185e-05 Least Informative Direct
Biological Process (BP) cellular amino acid metabolic process 4.364e-10 Moderately Informative Direct
Biological Process (BP) gene expression 1.287e-07 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 5.846e-08 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.624e-08 Moderately Informative Direct
Biological Process (BP) ncRNA metabolic process 4.759e-12 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01806 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.003563 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)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Glutamate--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc8.266e-07Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008925 SSF48163 Protein matches
Abstract

Structurally, an alpha-helix-bundle anticodon-binding domain characterises the class Ia synthetases, whereas the class Ib synthetases, GlnRS and GluRS have distinct anticodon-binding domains. The Rossmann-fold and anticodon-binding domains are connected by a beta-alpha-alpha-beta-alpha topology ('SC fold') domain that contains the class I specific KMSKS motif [PubMed10673435].


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) · 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 2 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 An anticodon-binding domain of class I aminoacyl-tRNA synthetases 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 2 hidden Markov models representing the An anticodon-binding domain of class I aminoacyl-tRNA synthetases 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]