SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,257) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 23,726 167,420 14
Proteins 23,281 164,437 14


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

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)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

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 the digestive system0.01123Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.01181Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.402Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0001099Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal muscle tone0.0006906Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.0007324Moderately InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0.1156Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.662Moderately InformativeInherited
Phenotypic Abnormality (PA)Acidosis0.00006272InformativeDirect
Phenotypic Abnormality (PA)Global developmental delay0.0001314InformativeDirect
Phenotypic Abnormality (PA)Hepatic steatosis0.0001334InformativeDirect
Phenotypic Abnormality (PA)Decreased liver function0.0006772Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.000006014Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.00006557Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0004054Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.004174Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01702Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.08005Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.0815Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00007662Moderately InformativeDirect
Worm Phenotype (WP)germ cell differentiation variant0.00009459Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport variant0.001368Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.001518Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.003427Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.01224Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.01322Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.0241Moderately InformativeInherited
Worm Phenotype (WP)cell cycle variant0.07255Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.1428Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2377Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.2419Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant1Moderately InformativeInherited
Worm Phenotype (WP)hypoxia response variant0.00000004248InformativeDirect
Worm Phenotype (WP)transgene expression increased0.000001443InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000787InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.000009834InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000415InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00004605InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00006461InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.0002902InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.0003968InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.001216InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.001258InformativeInherited
Worm Phenotype (WP)nuclear positioning variant0.01289InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.00000000003996Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.00000433Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000009323Highly InformativeDirect
Worm Phenotype (WP)protein expression reduced0.0004553Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.04283Highly 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)

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

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)urogenital system0Least 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)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.00003181InformativeDirect

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)Forming carbon-oxygen bonds0InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amine) ligases (amide synthases)1Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 17 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 17 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]