SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,243) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,528 64,167 19
Proteins 15,513 64,144 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 0.00000000005468 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000000001135 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000002356 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000004667 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000001106 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00001297 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0004215 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9155 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.004298 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000000000001938 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0000000000001178 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2501 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3158 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.09249 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.1026 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1126 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2609 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1482 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.5294 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.7821 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.8464 Moderately Informative Inherited
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00000009324 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0000004836 Informative Direct
Biological Process (BP) mitochondrion organization 0.00001796 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.695 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.4494 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4566 Informative Inherited
Biological Process (BP) organelle assembly 0.03634 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.1225 Informative Inherited
Biological Process (BP) regulation of cellular response to insulin stimulus 0.000003397 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0007337 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0007337 Highly Informative Direct
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.7141 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.04553 Moderately Informative Inherited
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.000000001863 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0004739 Informative Direct
Molecular Function (MF) DNA polymerase activity 0.0000001828 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.5333 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.452 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1931 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9006 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.003271 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.025 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 nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect

Document: MP 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 defect0.000004793Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00009961Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001747Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.005901Moderately InformativeInherited
Worm Phenotype (WP)receptor mediated endocytosis defective0.000000345InformativeDirect
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)morphology0.02287Moderately InformativeInherited
Yeast Phenotype (YP)colony sectoring0.000668InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)developing material anatomical entity0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual 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)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.0000006415InformativeDirect

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)
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionATP-binding0Moderately 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)L-histidine biosynthesis0InformativeDirect

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]