SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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 (3,254) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 45,160 219,448 51
Proteins 41,957 202,804 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 process0.000047430Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00038260Least InformativeDirect
Biological Process (BP)biosynthetic process0.0016010Least InformativeInherited
Biological Process (BP)gene expression0.000000035220Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000004120Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.0000000023560.00001803Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.000000000086120.00000000001531InformativeDirect
Cellular Component (CC)intracellular organelle part0.00040221Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0047630.000009301Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.000010410.03129Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.0000000068080Moderately InformativeDirect
Cellular Component (CC)cytosol0.03180.03211Moderately InformativeInherited
Cellular Component (CC)large ribosomal subunit00.000007964InformativeDirect
Cellular Component (CC)cytosolic ribosome0.089770.06877InformativeInherited

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 0.000000006803 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000002704 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000004154 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000009159 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000009681 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000728 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) localization 1 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) organic cyclic compound catabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound catabolic 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 0.00000000000001429 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00000000000117 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0000002881 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0007436 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 0.5411 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 0.6858 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 0.9145 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 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) ribonucleoprotein complex biogenesis 0.000000000000003741 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00000000000003287 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.000000004985 Informative Direct
Biological Process (BP) RNA modification 0.0000152 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001241 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.000203 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.000909 Informative Direct
Biological Process (BP) response to cytokine stimulus 0.2571 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.7576 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.9116 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.7774 Informative Inherited
Biological Process (BP) organelle assembly 0.7634 Informative Inherited
Biological Process (BP) central nervous system development 1 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) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) hair follicle development 0.00008229 Highly Informative Direct
Biological Process (BP) response to amino acid stimulus 0.0001385 Highly Informative Direct
Biological Process (BP) ER-nucleus signaling pathway 0.0009915 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.006867 Highly Informative Inherited
Biological Process (BP) neuromuscular process 0.001128 Highly Informative Inherited
Biological Process (BP) response to topologically incorrect protein 0.009139 Highly Informative Inherited
Biological Process (BP) response to endoplasmic reticulum stress 0.01183 Highly Informative Inherited
Biological Process (BP) mRNA catabolic process 0.006027 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.0000000001138 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.00001803 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000009355 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00001288 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) structural constituent of ribosome 0.00000000001531 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 0.0000000000004725 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0 Highly Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 0.0000000000006776 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.0000009647 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000009301 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9799 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.03129 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 0.03211 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.03396 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.2116 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.5579 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0.000007964 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.00006566 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0008843 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.06877 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0.0000004547 Highly Informative Direct

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 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 metabolism/homeostasis0.3494Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0006644Moderately 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 variant0.00002499Least 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 emb0.000006333InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00001068InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00001214InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00001556InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0000215InformativeDirect
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 variant0.00006563Highly InformativeDirect
Worm Phenotype (WP)organism oxidative stress response variant0.00006945Highly 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 organism0.03149Least InformativeInherited
Xenopus ANatomical entity (XAN)gonad0.1445Least InformativeInherited
Xenopus ANatomical entity (XAN)genital system0.3024Least InformativeInherited
Xenopus ANatomical entity (XAN)cell0.4061Least InformativeInherited
Xenopus ANatomical entity (XAN)ovary0.4566Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.04375Highly 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)Hydrolases0.000000004434Least 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)Nucleotidyltransferases0.0005287Moderately 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 functionZinc0.0000252Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0.000000005551Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide 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 ]