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Translational machinery components superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribonuclease H-like motif [ 53066] (7)
Superfamily:   Translational machinery components [ 53137] (2)
Families:   Ribosomal protein L18 and S11 [ 53138] (2)
  ERF1/Dom34 middle domain-like [ 53143] (3)

Superfamily statistics
Genomes (2,485) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,427 19,573 25
Proteins 8,412 19,564 25

 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)cellular component organization or biogenesis0.10730.002568Least InformativeInherited
Biological Process (BP)single-organism cellular process0.80470.6933Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0010661.04e-06Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.056580.7407Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.1190.7544Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.052410.6831Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.082840.8341Least InformativeInherited
Biological Process (BP)biosynthetic process0.024921.873e-09Least InformativeInherited
Biological Process (BP)protein metabolic process0.060850.001306Least InformativeInherited
Biological Process (BP)gene expression6.114e-055.619e-11Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process9.573e-058.968e-12Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.13050.4423Moderately InformativeInherited
Biological Process (BP)organelle organization0.089310.06286Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.058363.835e-05Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0035190.09248Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis0.00010227.193e-06InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.00066520.001462InformativeInherited
Biological Process (BP)organelle assembly1.057e-051.601e-06Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization1.226e-060.001149Highly InformativeInherited
Molecular Function (MF)binding0.64860.6957Least InformativeInherited
Molecular Function (MF)structural molecule activity5.033e-120Moderately InformativeDirect
Molecular Function (MF)organic cyclic compound binding0.0050732.418e-05Moderately InformativeInherited
Molecular Function (MF)heterocyclic compound binding0.0039241.875e-05Moderately InformativeInherited
Molecular Function (MF)RNA binding2.139e-063.82e-15InformativeDirect
Molecular Function (MF)structural constituent of ribosome3.148e-140InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle7.752e-051.007e-06Least InformativeDirect
Cellular Component (CC)cytoplasmic part9.948e-058.888e-10Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0045890.008869Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex6.483e-100Moderately InformativeDirect
Cellular Component (CC)cytosol0.08420.01914Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.11330.0001983Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.1730.198Moderately InformativeInherited
Cellular Component (CC)mitochondrial ribosome1.308e-061.012e-10Highly InformativeDirect

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) biosynthetic process 1.873e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.04e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.6933 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002568 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7407 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7544 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.6831 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.8341 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.001306 Least Informative Inherited
Biological Process (BP) gene expression 5.619e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 8.968e-12 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 3.835e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.4423 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06286 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.09248 Moderately Informative Inherited
Biological Process (BP) cellular component disassembly 4.903e-11 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 7.193e-06 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.001462 Informative Inherited
Biological Process (BP) cellular protein complex disassembly 5.898e-12 Highly Informative Direct
Biological Process (BP) organelle assembly 1.601e-06 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.001149 Highly Informative Inherited
Molecular Function (MF) binding 0.6957 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 2.418e-05 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 1.875e-05 Moderately Informative Direct
Molecular Function (MF) RNA binding 3.82e-15 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.02417 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.007e-06 Least Informative Direct
Cellular Component (CC) cytoplasmic part 8.888e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.008869 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0001983 Moderately Informative Direct
Cellular Component (CC) cytosol 0.01914 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.198 Moderately Informative Inherited
Cellular Component (CC) small ribosomal subunit 0.04446 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 1.012e-10 Highly Informative Direct

Document: GO 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)early embryonic lethal0.0009456Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0009657Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.00286Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.004375Moderately InformativeInherited
Worm Phenotype (WP)pachytene progression during oogenesis variant1.102e-05InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant1.382e-05InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant5.071e-05InformativeDirect
Worm Phenotype (WP)rachis morphology variant5.477e-05InformativeDirect
Worm Phenotype (WP)oocyte number decreased1.432e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)kidney0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentPlastid0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationNuclease5.089e-10Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 10 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 Translational machinery components 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 10 hidden Markov models representing the Translational machinery components 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.