SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,248) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 44,823 0 51
Proteins 41,626 0 50


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)protein metabolic process8.719e-050Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00064980Least InformativeDirect
Biological Process (BP)biosynthetic process0.0022360Least InformativeInherited
Biological Process (BP)gene expression6.398e-080Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process4.438e-060Moderately InformativeDirect
Molecular Function (MF)structural molecule activity3.886e-092.833e-05Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome1.417e-102.981e-11InformativeDirect
Cellular Component (CC)intracellular organelle part0.00041431Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0044521.165e-05Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle1.044e-050.01786Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex6.988e-090Moderately InformativeDirect
Cellular Component (CC)cytosol0.028820.0663Moderately InformativeInherited
Cellular Component (CC)cytosolic large ribosomal subunit0.0002190.000825InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 9.315e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 3.408e-07 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 7.99e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 5.277e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 8.171e-06 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.00509 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 1.098e-12 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.312e-12 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 2.53e-11 Moderately Informative Direct
Biological Process (BP) organelle organization 2.472e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.6229 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.6801 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.001297 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 0 Informative Direct
Biological Process (BP) mitochondrion organization 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) cellular component disassembly 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 1.422e-14 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 7.449e-14 Informative Direct
Biological Process (BP) ncRNA metabolic process 7.952e-09 Informative Direct
Biological Process (BP) RNA modification 1.626e-05 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001895 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0003218 Informative Direct
Biological Process (BP) response to cytokine stimulus 0.2781 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.7777 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.8131 Informative Inherited
Biological Process (BP) organelle assembly 0.7313 Informative Inherited
Biological Process (BP) central nervous system development 1 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.00155 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 1 Informative Inherited
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) translational initiation 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) guanosine-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) cellular protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) hair follicle development 9.804e-05 Highly Informative Direct
Biological Process (BP) response to acid 0.0003647 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.005437 Highly Informative Inherited
Biological Process (BP) neuromuscular process 0.001217 Highly Informative Inherited
Biological Process (BP) response to topologically incorrect protein 0.01131 Highly Informative Inherited
Biological Process (BP) ER-nucleus signaling pathway 0.001265 Highly Informative Inherited
Biological Process (BP) response to endoplasmic reticulum stress 0.01428 Highly Informative Inherited
Biological Process (BP) mRNA catabolic process 0.01242 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 3.969e-09 Least Informative Direct
Molecular Function (MF) structural molecule activity 2.833e-05 Moderately Informative Direct
Molecular Function (MF) anion binding 5.192e-08 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1.172e-05 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) structural constituent of ribosome 2.981e-11 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 1.322e-13 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0 Highly Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 7.958e-13 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 1.194e-06 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1.165e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.01786 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) cytosol 0.0663 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.06783 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.1959 Moderately Informative Inherited
Cellular Component (CC) cytosolic large ribosomal subunit 0.000825 Informative Direct
Cellular Component (CC) mitochondrial matrix 5.588e-05 Informative Direct
Cellular Component (CC) external encapsulating structure 0.02692 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 4.73e-07 Highly Informative Direct
Cellular Component (CC) cell wall 0.001389 Highly 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)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 kinase8.141e-10Highly 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 metabolism/homeostasis0.3551Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0006499Moderately 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 variant2.499e-05Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0007682Least InformativeDirect
Worm Phenotype (WP)growth variant0.04488Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.0895Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant0.0007465Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.001247Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.00129Moderately InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.002063Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.002845Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.006728Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.4534Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb6.333e-06InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant1.068e-05InformativeDirect
Worm Phenotype (WP)rachis morphology variant1.214e-05InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant1.556e-05InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant2.15e-05InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.0001433InformativeDirect
Worm Phenotype (WP)sick0.0002291InformativeDirect
Worm Phenotype (WP)protein metabolism variant0.005181InformativeInherited
Worm Phenotype (WP)organism stress response variant0.02137InformativeInherited
Worm Phenotype (WP)life span variant0.0299InformativeInherited
Worm Phenotype (WP)RNA expression variant0.1049InformativeInherited
Worm Phenotype (WP)protein expression variant0.6114InformativeInherited
Worm Phenotype (WP)protein phosphorylation variant6.563e-05Highly InformativeDirect
Worm Phenotype (WP)organism oxidative stress response variant6.945e-05Highly InformativeDirect
Worm Phenotype (WP)mRNA expression variant0.000576Highly InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.001835Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

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

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0.03148Least InformativeInherited
Xenopus ANatomical entity (XAN)gonad0.1448Least InformativeInherited
Xenopus ANatomical entity (XAN)genital system0.3024Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.4049Least InformativeInherited
Xenopus ANatomical entity (XAN)ovary0.4562Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.04356Highly 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)Hydrolases2.603e-09Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.0007999Moderately 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Biological processRibosome biogenesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc2.488e-05Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein6.68e-09Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationAutocatalytic cleavage1InformativeInherited
Post-translational modificationProtein splicing0.0009875Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide biosynthesis0InformativeDirect
UniPathway (UP)protein biosynthesis0InformativeDirect

Document: UP 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · 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 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]