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 (3,254) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,764 100,252 46
Proteins 23,599 100,109 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 process0.000030180Least InformativeDirect
Biological Process (BP)protein metabolic process0.000043480.0000000000588Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00000000000010670Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.77251Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.89961Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.76361Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.87381Least InformativeInherited
Biological Process (BP)gene expression0.00000034360Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.00000000074620Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.16460.3836Moderately InformativeInherited
Biological Process (BP)RNA modification0.000020020.001769InformativeInherited
Biological Process (BP)RNA methylation0.000000003910.0000009194Highly InformativeDirect
Molecular Function (MF)binding0.56911Least InformativeInherited
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.00012630.002638Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0000065320.000000003208InformativeDirect
Molecular Function (MF)structural constituent of ribosome00InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.000000000010260Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.00000064240.0000000000009498Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.0015060.00000000008905Least InformativeInherited
Cellular Component (CC)cytosol0.00000000018480.0000003396Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)large ribosomal subunit00.000000000006082InformativeDirect
Cellular Component (CC)cytosolic ribosome0.00020650.0000534InformativeDirect

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 0.0000000000588 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) localization 0.7077 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) single-organism 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) cellular component organization or biogenesis 0.06569 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
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) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0006519 Moderately Informative Direct
Biological Process (BP) cellular localization 0.6185 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.9308 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.7504 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.8021 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 0.8863 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.01176 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.9711 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.9546 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2083 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2454 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.5416 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3836 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism cellular localization 0.04815 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.004793 Informative Inherited
Biological Process (BP) protein localization to organelle 0.005956 Informative Inherited
Biological Process (BP) mitochondrion organization 0.01058 Informative Inherited
Biological Process (BP) microtubule-based process 0.001685 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.3692 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.02459 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.06069 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.1919 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.02919 Informative Inherited
Biological Process (BP) protein transport 0.05092 Informative Inherited
Biological Process (BP) RNA modification 0.001769 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.6159 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.9704 Informative Inherited
Biological Process (BP) cell cycle process 0.06207 Informative Inherited
Biological Process (BP) RNA methylation 0.0000009194 Highly Informative Direct
Biological Process (BP) translational initiation 0.0000001947 Highly Informative Direct
Biological Process (BP) spindle organization 0.0000009535 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.000003122 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0009747 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.001822 Highly Informative Inherited
Biological Process (BP) protein localization to membrane 0.004001 Highly Informative Inherited
Biological Process (BP) mRNA catabolic process 0.005836 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 0.002638 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.000000003208 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000008905 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000000000009498 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 0.0000003396 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.7861 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.01202 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2959 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.000004042 Informative Direct
Cellular Component (CC) large ribosomal subunit 0.000000000006082 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.0000534 Informative Direct
Cellular Component (CC) nucleoplasm part 0.02859 Informative Inherited
Cellular Component (CC) plastid 0.001411 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0 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 variant0.00001162Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00002169Least InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0000008869Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.00000117Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.00001821Moderately 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 emb0.0000000000002135InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000006838InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.00000001019InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000001014InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.0000001161InformativeDirect
Worm Phenotype (WP)pigmentation variant0.001134InformativeInherited
Worm Phenotype (WP)gonad vesiculated0.000000001188Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.00000001087Highly 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

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)heat sensitivity0.0007415InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP 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 system0.04905Least 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 system0.0002257Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.0000009752InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0.000008356InformativeDirect
Xenopus ANatomical entity (XAN)limb0.0004195InformativeDirect
Xenopus ANatomical entity (XAN)spleen0.0006029InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.000003688Highly 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 componentPlastid6.436e-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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]