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 (3,237) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,445 39,536 25
Proteins 10,421 39,522 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 process0.00026419.534e-08Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.11120.003288Least InformativeInherited
Biological Process (BP)single-organism cellular process0.6660.6236Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.11120.8719Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.17770.8424Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.10820.8353Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.16230.9577Least InformativeInherited
Biological Process (BP)biosynthetic process0.010141.178e-10Least InformativeInherited
Biological Process (BP)protein metabolic process0.026466.725e-05Least InformativeInherited
Biological Process (BP)gene expression2.935e-051.588e-12Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process2.433e-051.972e-13Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.068850.0001176Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.15370.6106Moderately InformativeInherited
Biological Process (BP)organelle organization0.099980.06295Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0096120.1506Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis8.908e-054.75e-06InformativeDirect
Biological Process (BP)organelle assembly0.00014580.0007545InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.0013490.002766InformativeInherited
Biological Process (BP)ncRNA metabolic process0.16220.2268InformativeInherited
Biological Process (BP)ribonucleoprotein complex subunit organization1.86e-060.0009267Highly InformativeDirect
Molecular Function (MF)binding0.36370.4544Least InformativeInherited
Molecular Function (MF)nucleic acid binding5.78e-061.95e-07Moderately InformativeDirect
Molecular Function (MF)structural molecule activity2.43e-120Moderately InformativeDirect
Molecular Function (MF)RNA binding1.056e-071.557e-15InformativeDirect
Molecular Function (MF)structural constituent of ribosome2.116e-140InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle1.052e-052.308e-08Least InformativeDirect
Cellular Component (CC)cytoplasmic part6.719e-061.358e-09Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.001190.003205Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex4.51e-120Moderately InformativeDirect
Cellular Component (CC)cytosol0.030180.008222Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.13120.0002226Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.36490.1782Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.0011879.032e-09InformativeInherited
Cellular Component (CC)mitochondrial ribosome1.396e-061.085e-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 1.178e-10 Least Informative Direct
Biological Process (BP) protein metabolic process 6.725e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 9.534e-08 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.6236 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003288 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8719 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.8424 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8353 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9577 Least Informative Inherited
Biological Process (BP) gene expression 1.588e-12 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 1.972e-13 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0001176 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.6106 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06295 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1506 Moderately Informative Inherited
Biological Process (BP) ribonucleoprotein complex biogenesis 4.75e-06 Informative Direct
Biological Process (BP) organelle assembly 0.0007545 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.002766 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.2268 Informative Inherited
Biological Process (BP) cellular component disassembly 1.041e-10 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0009267 Highly Informative Direct
Molecular Function (MF) binding 0.4544 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 1.95e-07 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 1.557e-15 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.02898 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 2.308e-08 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1.358e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.003205 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 0.0002226 Moderately Informative Direct
Cellular Component (CC) cytosol 0.008222 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1782 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 9.032e-09 Informative Direct
Cellular Component (CC) small ribosomal subunit 0.02104 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 1.085e-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 modificationNuclease3.085e-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) · 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 ]