SUPERFAMILY 1.75 HMM library and genome assignments server


Translation initiation factor IF3, C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   IF3-like [ 55199] (8)
Superfamily:   Translation initiation factor IF3, C-terminal domain [ 55200]
Families:   Translation initiation factor IF3, C-terminal domain [ 55201]


Superfamily statistics
Genomes (2,910) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,112 16,595 3
Proteins 3,109 16,594 3


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 0.0002798 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0003128 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.11 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.05916 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.04318 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01357 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.01169 Least Informative Inherited
Biological Process (BP) gene expression 5.347e-05 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0009764 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0004164 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.001287 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.003975 Moderately Informative Inherited
Biological Process (BP) cellular component disassembly 3.994e-10 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 3.956e-11 Highly Informative Direct
Molecular Function (MF) binding 0.08479 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0001136 Moderately Informative Direct
Molecular Function (MF) RNA binding 3.674e-07 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 5.537e-12 Highly Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 9.48e-14 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02093 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.004503 Least Informative Inherited

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001288 SSF55200 Protein matches
Abstract

Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit [PubMed8405963]. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 [PubMed8144528].


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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

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 3 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 initiation factor IF3, 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 3 hidden Markov models representing the Translation initiation factor IF3, 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]