SUPERFAMILY 1.75 HMM library and genome assignments server

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Translation proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Reductase/isomerase/elongation factor common domain [ 50412] (4)
Superfamily:   Translation proteins [ 50447] (6)
Families:   Elongation factors [ 50448] (10)
  Ribosomal protein L3 [ 50461]
  Ribosomal protein L35ae [ 117220]
  RimM N-terminal domain-like [ 141338]
  Gar1-like SnoRNP [ 141341]
  AlaX-M N-terminal domain-like [ 159161]


Superfamily statistics
Genomes (3,263) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 45,742 331,508 51
Proteins 42,527 307,803 50


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)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.0004224Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Acting on GTP; involved in cellular and subcellula0Highly InformativeDirect
Enzyme Commission (EC)Alanine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Adenylyl-sulfate kinase0.0000000008141Highly 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 metabolism/homeostasis0.4743Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.01162Moderately InformativeInherited
Phenotypic Abnormality (PA)Increased serum lactate0.000316Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.000002178Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0001846Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.00136Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.06612Least InformativeInherited
Worm Phenotype (WP)cell development variant0.1129Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.0003195Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0006471Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0008715Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.00322Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.009467Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.01214Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1808Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.6726Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.9316Moderately InformativeInherited
Worm Phenotype (WP)germ cell compartment expansion variant0.00000232InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.000002486InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00000297InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000003438InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00001348InformativeDirect
Worm Phenotype (WP)sick0.0009803InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.001353InformativeInherited
Worm Phenotype (WP)protein modification variant0.001662InformativeInherited
Worm Phenotype (WP)oocyte physiology variant0.03546InformativeInherited
Worm Phenotype (WP)RNA expression variant0.063InformativeInherited
Worm Phenotype (WP)mRNA levels increased0.00004071Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0002447Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.0009372Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least 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 system0.04356Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.05716Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.7206Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.00333Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ line cell0.3257Moderately InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.000000001573Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.0001514Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009000 SSF50447 Protein matches
Abstract

A beta barrel of circularly permuted topology is found in many transcription proteins, including initiation and elongation factors, and also some ribosomal proteins, although in these cases the fold is elaborated with additional structures. The beta barrel domain is represented by domain 2 of the elongation factors EF-Tu [PubMed10715211] and eEF1A [PubMed11106763], both of which function to recognize and transport aminoacyl-tRNA to the acceptor (A) site of the ribosome during the elongation process, and of EF-G [PubMed11054294], which functions in translocating the peptidyl tRNA from the A site to the peptidyl (P) site. This domain is also present in initiation factors, in domain 2 of eIF2 gamma subunit [PubMed11927566], and domains 2 and 4 of IF2/eIF5B [PubMed11114334], both of which function to transport the initiator methionyl-tRNA to the ribosome. This beta barrel domain may be involved in interactions with the switch 2 region to stabilise the relative orientations of the domains, which undergo functionally important conformational changes between GTP- and GDP-bound states.

More information about translation elongation factors can be found at Protein of the Month: Elongation Factors.


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) · 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 27 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 Translation proteins 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 27 hidden Markov models representing the Translation proteins 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) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]