SUPERFAMILY 1.75 HMM library and genome assignments server


Translation proteins SH3-like domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   Translation proteins SH3-like domain [ 50104] (7)
Families:   Ribosomal proteins L24p and L21e [ 50105] (2)
  eIF5a N-terminal domain-like [ 50110] (3)
  C-terminal domain of ribosomal protein L2 [ 50114]
  N-utilization substance G protein NusG, C-terminal domain [ 82072]
  SPT5 KOW domain-like [ 141242]
  Ribosomal protein L19 [ 141245]
  Ribosomal protein L14e [ 159031]


Superfamily statistics
Genomes (3,212) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,245 47,924 46
Proteins 23,115 47,838 46


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 process0.0001480Least InformativeDirect
Biological Process (BP)protein metabolic process0.00021632.334e-09Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process3.712e-130Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.6141Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.76820.9763Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.60011Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.73811Least InformativeInherited
Biological Process (BP)gene expression1.241e-060Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process1.208e-080Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.1040.1563Moderately InformativeInherited
Biological Process (BP)translation00InformativeDirect
Biological Process (BP)RNA modification2.064e-050.001793InformativeInherited
Biological Process (BP)RNA methylation1.72e-095.437e-07Highly InformativeDirect
Molecular Function (MF)binding0.54991Least InformativeInherited
Molecular Function (MF)structural molecule activity1.119e-140Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.00036970.004733Moderately InformativeInherited
Molecular Function (MF)RNA binding2.318e-058.893e-09InformativeDirect
Molecular Function (MF)structural constituent of ribosome00InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle2.368e-110Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00061545.638e-12Least InformativeDirect
Cellular Component (CC)intracellular organelle part3.918e-051.969e-12Least InformativeDirect
Cellular Component (CC)cytosol1.232e-092.093e-07Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit02.17e-11InformativeDirect
Cellular Component (CC)cytosolic ribosome0.00018180.0001843InformativeDirect

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 Least Informative Direct
Biological Process (BP) protein metabolic process 2.334e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) localization 0.3623 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.008576 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.9763 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.154e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.119 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.322 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.4681 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.6673 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.7609 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.03154 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.8117 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.7937 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.7533 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9875 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1563 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.005918 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.4429 Moderately Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.8716 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.2272 Moderately Informative Inherited
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) microtubule-based process 0.0008023 Informative Direct
Biological Process (BP) protein localization to organelle 0.0008637 Informative Direct
Biological Process (BP) cytoskeleton organization 0.4191 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.004626 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.03906 Informative Inherited
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00439 Informative Inherited
Biological Process (BP) cell cycle process 0.04157 Informative Inherited
Biological Process (BP) protein transport 0.01219 Informative Inherited
Biological Process (BP) RNA modification 0.001793 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.4257 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.6828 Informative Inherited
Biological Process (BP) microtubule cytoskeleton organization 9.065e-05 Highly Informative Direct
Biological Process (BP) RNA methylation 5.437e-07 Highly Informative Direct
Biological Process (BP) translational initiation 7.872e-08 Highly Informative Direct
Biological Process (BP) cellular component disassembly 1.424e-07 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 5.385e-05 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.002602 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.004733 Moderately Informative Inherited
Molecular Function (MF) RNA binding 8.893e-09 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.01024 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 5.638e-12 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1.969e-12 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytosol 2.093e-07 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.9563 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4072 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.009961 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 1.62e-06 Informative Direct
Cellular Component (CC) plastid 0.0004416 Informative Direct
Cellular Component (CC) large ribosomal subunit 2.17e-11 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.0001843 Informative Direct
Cellular Component (CC) nucleoplasm part 0.145 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 5.839e-15 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant1.162e-05Least InformativeDirect
Worm Phenotype (WP)cell physiology variant2.169e-05Least InformativeDirect
Worm Phenotype (WP)early embryonic lethal8.869e-07Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant1.17e-06Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant1.821e-05Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.0007656Moderately InformativeDirect
Worm Phenotype (WP)cell death variant0.1557Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2008Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.6126Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb2.135e-13InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant6.838e-09InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant1.019e-08InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant1.014e-07InformativeDirect
Worm Phenotype (WP)rachis morphology variant1.161e-07InformativeDirect
Worm Phenotype (WP)pigmentation variant0.001134InformativeInherited
Worm Phenotype (WP)gonad vesiculated1.188e-09Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased1.087e-08Highly InformativeDirect
Worm Phenotype (WP)cell membrane organization biogenesis variant0.0004757Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0004773Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.04876Least InformativeInherited
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.0002204Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle9.478e-07InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system8.178e-06InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0004157InformativeDirect
Xenopus ANatomical entity (XAN)spleen0.0006022InformativeDirect
Xenopus ANatomical entity (XAN)pancreas3.561e-06Highly 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)
Biological processTransport1Least InformativeInherited
Biological processProtein transport1Moderately InformativeInherited
Biological processTranscription regulation1Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Biological processTranslocation1Highly InformativeInherited
Cellular componentPlastid6.373e-16Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationInitiation factor0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)protein biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008991 SSF50104 Protein matches
Abstract

The fundamental activity of the ribosome is two-fold: to decode the message of the mRNA in the small subunit, and to form a peptide bond between peptidyl-tRNA and aminoacyl-tRNA by a peptidyl transferase activity in the large subunit. Several prokaryotic and eukaryotic proteins that are involved in the translation process contain an SH3-like domain. The structure of the translation protein SH3-like domain is a partly opened beta barrel, where the last strand is interrupted by a 3-10 helical turn. The structure of the RNA-binding C-terminal domain of the Bacillus stearothermophilus ribosomal protein L2 has been shown to adopt the SH3-like barrel topology [PubMed10075918]. The L2 protein is located near the peptidyl transferase centre in the large ribosomal subunit where it may contribute to peptidyl transferase activity, and is involved in the assembly of the 23SrRNA. Likewise, the N-terminal domain of the ubiquitous eukaryotic initiation translation factor 5a (IF-5A) protein adopts the SH3-like barrel topology [PubMed9724718, PubMed9753699]. IF-5A is involved in the initial step of peptide bond formation in translation and in cell-cycle regulation. IF-5A acts as a cofactor of the Rev protein in HIV-1-infected cells and of the Rex protein in T-cell leukaemia virus 1-infected cells.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 23 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 Translation proteins SH3-like domain 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 23 hidden Markov models representing the Translation proteins SH3-like domain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]