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 (3,239) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,454 39,536 25
Proteins 10,430 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 process0.00026880.0000001026Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.11740.004816Least InformativeInherited
Biological Process (BP)biosynthetic process0.010070.0000000001205Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.11870.8762Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.1830.843Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.11530.8394Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.16670.9629Least InformativeInherited
Biological Process (BP)protein metabolic process0.026340.00007321Least InformativeInherited
Biological Process (BP)gene expression0.000040420.000000000003875Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.000023590.0000000000001894Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.10560.004165Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.1480.5844Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0093370.1543Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis0.000087930.000005208InformativeDirect
Biological Process (BP)organelle assembly0.00016050.0007857InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.001410.003386InformativeInherited
Biological Process (BP)ncRNA metabolic process0.16090.221InformativeInherited
Biological Process (BP)ribonucleoprotein complex subunit organization0.0000019450.000148Highly InformativeDirect
Molecular Function (MF)binding0.3730.3891Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000098910.0000001378Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.0000000000024010Moderately InformativeDirect
Molecular Function (MF)RNA binding0.00000029520.00000000000000467InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.000000000000020640InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.000011150.00000002588Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.0000062310.000000001557Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0012220.002612Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribonucleoprotein complex0.0000000000045450Moderately InformativeDirect
Cellular Component (CC)cytosol0.030760.008756Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.13270.0002414Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.3280.09427Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.0012780.0000000203InformativeInherited
Cellular Component (CC)mitochondrial ribosome0.0000013760.0000000001071Highly 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 0.0000000001205 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00007321 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000001026 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.004816 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8762 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.843 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8394 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9629 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) gene expression 0.000000000003875 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.0000000000001894 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.004165 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5844 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1543 Moderately Informative Inherited
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000005208 Informative Direct
Biological Process (BP) organelle assembly 0.0007857 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.003386 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.221 Informative Inherited
Biological Process (BP) cellular component disassembly 0.0000000001001 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.000148 Highly Informative Direct
Molecular Function (MF) binding 0.3891 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000001378 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.00000000000000467 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.0151 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00000002588 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000001557 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.002612 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0002414 Moderately Informative Direct
Cellular Component (CC) cytosol 0.008756 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.09427 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.0000000203 Informative Direct
Cellular Component (CC) small ribosomal subunit 0.02105 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0.0000000001071 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 variant0.00001102InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.00001382InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00005071InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00005477InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00001432Highly 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 modificationNuclease0.0000000003126Moderately 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 ]