SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,240) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,459 39,536 25
Proteins 10,435 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)biosynthetic process0.020030.000000000009662Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0089730.000000000000003692Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0055340.00000001268Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.0041280.000000000008004Least InformativeInherited
Biological Process (BP)primary metabolic process0.18240.0001975Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.42591Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.4291Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.50681Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.0083540.0000001682Least InformativeInherited
Biological Process (BP)peptide metabolic process0.000000044560Moderately InformativeDirect
Biological Process (BP)gene expression0.00000077890Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.0000041960Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.00000013630Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.089620.02376Moderately InformativeInherited
Biological Process (BP)organelle organization0.0023020.002195Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.39771Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.130.9944Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis0.00000009260.00000001589InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.00062270.001303InformativeInherited
Biological Process (BP)organelle assembly0.0012470.09956InformativeInherited
Biological Process (BP)rRNA metabolic process0.000015530.000009426Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex subunit organization0.00000099960.0006392Highly InformativeDirect
Molecular Function (MF)binding0.46940.4164Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000048050.0000000189Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.000000000078250Moderately InformativeDirect
Molecular Function (MF)RNA binding0.00000021148.405e-16InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.0000000000022150InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0000000015860Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0000079750.0000002469Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.0070030.00001322Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle10.9391Least InformativeInherited
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part0.0000000012460.0000000000003573Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.034090.0000003791Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0017690.0000000647Moderately InformativeInherited
Cellular Component (CC)mitochondrial ribosome0.00000012370InformativeDirect
Cellular Component (CC)organellar large ribosomal subunit0.019690.9713InformativeInherited

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 0.000000000009662 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000008004 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000001682 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0001975 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000001268 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000000000000003692 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.02376 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.9944 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.002195 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.00002733 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00000001589 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.001303 Informative Inherited
Biological Process (BP) organelle assembly 0.09956 Informative Inherited
Biological Process (BP) rRNA metabolic process 0.000009426 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.000000000005448 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 0.0006392 Highly Informative Direct
Molecular Function (MF) binding 0.4164 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000000189 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 8.405e-16 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.01711 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00001322 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000002469 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.9391 Least Informative Inherited
Cellular Component (CC) ribosome 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0000003791 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.0000000000003573 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000647 Moderately Informative Direct
Cellular Component (CC) mitochondrial ribosome 0 Informative Direct
Cellular Component (CC) small ribosomal subunit 0.02575 Informative Inherited
Cellular Component (CC) organellar large ribosomal subunit 0.9713 Informative Inherited
Cellular Component (CC) mitochondrial small ribosomal subunit 0.000000001854 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)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.007718Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.01903Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.02383Least InformativeInherited
Worm Phenotype (WP)cell development variant0.03907Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.0009215Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.001676Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.004164Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0053Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.04588Moderately InformativeInherited
Worm Phenotype (WP)pachytene progression during oogenesis variant0.00001137InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.00001261InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.00004603InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.00004716InformativeDirect
Worm Phenotype (WP)oocyte morphology variant0.0002063InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000007293Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00001304Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)head0Moderately InformativeDirect
Zebrafish Anatomy (ZA)trunk0Moderately InformativeDirect

Document: ZA 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)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.1082Moderately InformativeInherited
Xenopus ANatomical entity (XAN)kidney0InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0007381InformativeDirect

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)
Biological processGrowth regulation0.0003636Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationNuclease0.0000000001037Moderately 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) · Zebrafish Anatomy (ZA) · 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]