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Class II aaRS ABD-related superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Anticodon-binding domain-like [ 52953] (6)
Superfamily:   Class II aaRS ABD-related [ 52954] (2)
Families:   Anticodon-binding domain of Class II aaRS [ 52955] (6)
  Brix domain [ 142420]

 Superfamily statistics
Genomes (2,480) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,728 29,628 19
Proteins 12,716 29,616 19

 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 2.143e-11 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 6.151e-11 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.079e-09 Least Informative Direct
Biological Process (BP) biosynthetic process 4.646e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.464e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001126 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.9819 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.002365 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.007052 Least Informative Inherited
Biological Process (BP) RNA metabolic process 5.966e-15 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 5.966e-15 Moderately Informative Direct
Biological Process (BP) gene expression 7.835e-15 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 4.431e-12 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.1546 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2233 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.4622 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4779 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.5196 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.7352 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.04163 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.2039 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.5421 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.7734 Moderately Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 3.495e-08 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 5.385e-07 Informative Direct
Biological Process (BP) mitochondrion organization 1.126e-05 Informative Direct
Biological Process (BP) tRNA metabolic process 1.505e-05 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.08717 Informative Inherited
Biological Process (BP) organelle assembly 0.0002526 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.000581 Highly Informative Direct
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.002484 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.6102 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) RNA binding 1.176e-09 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0004281 Informative Direct
Molecular Function (MF) DNA polymerase activity 2.775e-07 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.516 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2919 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2249 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8517 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.003062 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.03931 Moderately 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)Threonine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Proline--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Histidine--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the central nervous system0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.001274Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.009157Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect4.793e-06Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal9.961e-05Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001747Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.005901Moderately InformativeInherited
Worm Phenotype (WP)receptor mediated endocytosis defective3.45e-07InformativeDirect
Worm Phenotype (WP)sick0.0008683InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.01846Moderately InformativeInherited
Yeast Phenotype (YP)colony sectoring0.0007419InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately 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)root0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage7.261e-07InformativeDirect

Document: AP 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)
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)histidine metabolism0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR004154 SSF52954 Protein matches
Abstract tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [PubMed10447505] it is probably the anticodon binding domain [PubMed9115984].

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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 Class II aaRS ABD-related 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 Class II aaRS ABD-related 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.