SUPERFAMILY 1.75 HMM library and genome assignments server


Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47322]
Superfamily:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47323]
Families:   Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47324] (6)


Superfamily statistics
Genomes (3,207) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,303 49,434 14
Proteins 22,833 48,725 14


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

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GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.086e-14 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.298 Moderately Informative Inherited
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) mitochondrion organization 6.182e-06 Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.1952 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3072 Moderately Informative Inherited
Molecular Function (MF) RNA binding 6.077e-06 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.005201 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.006778 Informative Inherited
Molecular Function (MF) nucleotide binding 0.03355 Informative Inherited
Molecular Function (MF) ATP binding 0.0007592 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 4.697e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.3573 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.6156 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.8921 Moderately Informative Inherited
Cellular Component (CC) plastid 7.134e-06 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.0004683 Informative Direct
Cellular Component (CC) chloroplast stroma 3.896e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

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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)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Isoleucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Methionine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Leucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Arginine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0.9871Highly InformativeInherited

Document: EC 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)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0003118Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.02395Least InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.0009046Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0009756Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.001401Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.003584Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.005912Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.009232Moderately InformativeInherited
Worm Phenotype (WP)pachytene progression during oogenesis variant4.008e-06InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb6.875e-06InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant2.655e-05InformativeDirect
Worm Phenotype (WP)rachis morphology variant2.922e-05InformativeDirect
Worm Phenotype (WP)transgene expression increased3.307e-05InformativeDirect
Worm Phenotype (WP)germline nuclear positioning variant0.0001065InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.0001828InformativeDirect
Worm Phenotype (WP)oocyte number decreased5.552e-06Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.007363Highly InformativeInherited

Document: WP 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

Fly Anatomy (FA)

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FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

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ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)digestive system0Least InformativeDirect
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)eye0Moderately InformativeDirect
Zebrafish Anatomy (ZA)gut0Moderately InformativeDirect

Document: ZA 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)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage3.181e-05InformativeDirect

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
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0.9672Highly InformativeInherited

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
DomainCoiled coil0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding1Moderately InformativeInherited
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009080 SSF47323 Protein matches
Abstract

The twenty aminoacyl-tRNA synthetases catalyse the attachment of an amino acid to its cognate transfer RNA (tRNA) molecule in a highly specific two-step reaction. All of these proteins fall into one of two classes comprised of ten enzymes each: class 1 (Arg, Cys, Glu, Gln, Ile, Leu, Met, Tyr, Trp and Val) and class 2 (Ala, Asn, Gly, His, Lys, Phe, Pro, Ser, and Thr). Class 1 enzymes are mostly monomeric, and contain a characteristic Rossman binding fold that bind the tRNA acceptor stem from the minor groove side, using two highly conserved sequences. In contrast, class 2 enzymes share an anti-parallel beta-sheet formation that binds to the major groove side of the acceptor stem. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Class 1a (Arg, Cys, Ile, Leu, Met, Val) possess an RNA-binding domain with an alpha-helix-bundle fold; the binding of the anticodon of tRNA to the RNA-binding domain induces a conformation change in the catalytic domain of the enzyme [PubMed10993737].


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) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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 10 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 Anticodon-binding domain of a subclass 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 10 hidden Markov models representing the Anticodon-binding domain of a subclass 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]