SUPERFAMILY 1.75 HMM library and genome assignments server


EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Elongation factor/aminomethyltransferase common domain [ 50464] (2)
Superfamily:   EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [ 50465]
Families:   EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [ 50466] (6)


Superfamily statistics
Genomes (3,246) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,549 0 24
Proteins 10,537 0 24


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 6.65e-14 Least Informative Direct
Biological Process (BP) protein metabolic process 6.582e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001435 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) heterocycle metabolic process 0.9357 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9729 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3738 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) nucleobase-containing small molecule metabolic process 8.165e-10 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 8.344e-06 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0001188 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002487 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.0003931 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.3987 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0417 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.0181 Moderately Informative Inherited
Biological Process (BP) cellular component disassembly 3.722e-15 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 2.324e-12 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 8.652e-12 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 7.021e-11 Informative Direct
Biological Process (BP) organophosphate catabolic process 4.74e-10 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 2.188e-09 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0004646 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.2893 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.005995 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.5937 Informative Inherited
Biological Process (BP) guanosine-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 5.046e-14 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 1.075e-13 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 1.382e-13 Highly Informative Direct
Biological Process (BP) translational initiation 8.269e-10 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 1.933e-06 Highly Informative Direct
Molecular Function (MF) binding 3.193e-11 Least Informative Direct
Molecular Function (MF) hydrolase activity 0.0099 Least Informative Inherited
Molecular Function (MF) anion binding 1.249e-13 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.263 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 1.131e-09 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.001549 Least Informative Inherited
Cellular Component (CC) protein complex 0.3349 Least Informative Inherited
Cellular Component (CC) cytosol 9.243e-05 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Adenylyl-sulfate kinase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0Least InformativeDirect

Document: DO 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)organism environmental stimulus response variant0.0004611Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.009157Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant0.0002785Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.4226Moderately InformativeInherited
Worm Phenotype (WP)transgene expression increased0.0001343InformativeDirect
Worm Phenotype (WP)life span variant0.002292InformativeInherited
Worm Phenotype (WP)organism stress response variant0.0564InformativeInherited
Worm Phenotype (WP)organism oxidative stress response variant8.804e-06Highly InformativeDirect

Document: WP 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.155Least InformativeInherited
Xenopus ANatomical entity (XAN)ovary0.07887Moderately InformativeInherited
Xenopus ANatomical entity (XAN)germ cell0.1504Highly 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)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
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 processNonsense-mediated mRNA decay6.637e-05Highly InformativeDirect
Biological processNodulation0.0001119Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.2115Moderately InformativeInherited
UniPathway (UP)hydrogen sulfide biosynthesis0InformativeDirect
UniPathway (UP)protein biosynthesis4.444e-05InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009001 SSF50465 Protein matches
Abstract

A beta barrel of circularly permuted topology is found in the C-terminus of many translation elongation and initiation factors. This domain is found in the elongation factors EF1A (or EF-Tu) of both eukaryotes and prokaryotes, which functions to recognize and transport aminoacyl-tRNA to the acceptor (A) site of the ribosome during the elongation process [PubMed10715211, PubMed11106763]. This domain is also found in the initiation factor IF2 gamma subunit of eukaryotes [PubMed11927566], which functions to transport the initiator methionyl-tRNA to the ribosome. The C-terminal extension of mitochondrial EF1A (or EF-Tu) has structural similarities with DNA recognising zinc fingers, suggesting that the extension may be involved in recognition of RNA.

More information about EF1A proteins 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · 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 11 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 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 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 11 hidden Markov models representing the EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 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) · Disease Ontology (DO) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]