SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,197) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,991 19,573 25
Proteins 9,976 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 macromolecule metabolic process0.00052331.63e-06Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.07840.004175Least InformativeInherited
Biological Process (BP)single-organism cellular process0.55940.4962Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.063380.7038Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.10450.6571Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.060550.6606Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.094750.809Least InformativeInherited
Biological Process (BP)biosynthetic process0.017614.447e-09Least InformativeInherited
Biological Process (BP)protein metabolic process0.05260.0003647Least InformativeInherited
Biological Process (BP)gene expression7.881e-053.304e-11Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process9.259e-057.842e-12Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.15750.5382Moderately InformativeInherited
Biological Process (BP)organelle organization0.078850.1057Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.070355.302e-05Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0045060.08236Moderately InformativeInherited
Biological Process (BP)translation4.83e-060InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis7.149e-054.224e-06InformativeDirect
Biological Process (BP)organelle assembly9.017e-050.0003792InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.0010410.002374InformativeInherited
Biological Process (BP)ncRNA metabolic process0.15920.2091InformativeInherited
Biological Process (BP)ribonucleoprotein complex subunit organization1.507e-060.001007Highly InformativeInherited
Molecular Function (MF)binding0.41170.4583Least InformativeInherited
Molecular Function (MF)nucleic acid binding3.821e-054.105e-07Moderately InformativeDirect
Molecular Function (MF)structural molecule activity7.944e-130Moderately InformativeDirect
Molecular Function (MF)RNA binding1.311e-061.036e-14InformativeDirect
Molecular Function (MF)structural constituent of ribosome4.477e-150InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle8.008e-061.656e-08Least InformativeDirect
Cellular Component (CC)cytoplasmic part5.102e-069.647e-10Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.001930.003175Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex8.22e-110Moderately InformativeDirect
Cellular Component (CC)cytosol0.049620.01334Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.12580.0002882Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.16040.1121Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.0019211.26e-08InformativeInherited
Cellular Component (CC)mitochondrial ribosome1.082e-061.08e-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 4.447e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0003647 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.63e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4962 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004175 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7038 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.6571 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.6606 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.809 Least Informative Inherited
Biological Process (BP) gene expression 3.304e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 7.842e-12 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 5.302e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.5382 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1057 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.08236 Moderately Informative Inherited
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 4.224e-06 Informative Direct
Biological Process (BP) organelle assembly 0.0003792 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.002374 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.2091 Informative Inherited
Biological Process (BP) cellular component disassembly 7.585e-11 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.001007 Highly Informative Inherited
Molecular Function (MF) binding 0.4583 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 4.105e-07 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 1.036e-14 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.01973 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.656e-08 Least Informative Direct
Cellular Component (CC) cytoplasmic part 9.647e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.003175 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 0.0002882 Moderately Informative Direct
Cellular Component (CC) cytosol 0.01334 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1121 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 1.26e-08 Informative Direct
Cellular Component (CC) small ribosomal subunit 0.02569 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 1.08e-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

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP 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)male organism0Least 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
Xenopus ANatomical entity (XAN)mesonephric kidney0Highly InformativeDirect

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 modificationNuclease1.334e-09Moderately 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) · Fly Phenotype (FP) · 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) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]