SUPERFAMILY 1.75 HMM library and genome assignments server


Zn-binding ribosomal proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Zn-binding ribosomal proteins [ 57829] (8)
Families:   Ribosomal protein L37ae [ 57830]
  Ribosomal protein L37e [ 57833]
  Ribosomal protein L44e [ 57836]
  Ribosomal protein S27e [ 90217]
  Ribosomal protein L32p [ 144200]
  Ribosomal protein L33p [ 144203]
  Ribosomal protein L40e [ 161181]
  Ribosomal protein S27a [ 161184]


Superfamily statistics
Genomes (3,169) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 11,703 23,941 32
Proteins 11,696 23,933 32


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 process4.98e-102.302e-09Least InformativeDirect
Biological Process (BP)protein metabolic process1.878e-082.379e-08Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.61e-152.408e-10Least InformativeDirect
Biological Process (BP)localization0.37370.6023Least InformativeInherited
Biological Process (BP)gene expression3.893e-122.582e-09Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process06.366e-14Moderately InformativeDirect
Biological Process (BP)translation00InformativeDirect
Biological Process (BP)vesicle-mediated transport0.025970.03309InformativeInherited
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome00InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle3.334e-106.319e-14Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.000265.651e-09Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.00023122.407e-06Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytosol1.248e-059.341e-08Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.46740.03339Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.75720.9663Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.0019211.137e-05InformativeInherited
Cellular Component (CC)large ribosomal subunit0.12860.577InformativeInherited
Cellular Component (CC)mitochondrial ribosome3.478e-067.157e-08Highly 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 2.302e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 2.379e-08 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.408e-10 Least Informative Direct
Biological Process (BP) localization 0.6023 Least Informative Inherited
Biological Process (BP) gene expression 2.582e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.366e-14 Moderately Informative Direct
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.03309 Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 6.319e-14 Least Informative Direct
Cellular Component (CC) cytoplasmic part 5.651e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 2.407e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytosol 9.341e-08 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.9663 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.03339 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 1.137e-05 Informative Direct
Cellular Component (CC) cytosolic ribosome 1.927e-05 Informative Direct
Cellular Component (CC) small ribosomal subunit 0.7361 Informative Inherited
Cellular Component (CC) large ribosomal subunit 0.577 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 7.157e-08 Highly Informative Direct
Cellular Component (CC) cytosolic small ribosomal subunit 0.0001728 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)early embryonic lethal3.351e-08Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.0002488Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0007298Moderately InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb4.325e-14InformativeDirect
Worm Phenotype (WP)body width variant5.88e-05InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

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)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.1958Least InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.6101Least InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.01003Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.0004212InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.001396InformativeInherited
Xenopus ANatomical entity (XAN)pancreas5.212e-07Highly InformativeDirect
Xenopus ANatomical entity (XAN)bone tissue0.0006956Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAntibiotic resistance0.0004067InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationIsopeptide bond5.294e-15Moderately InformativeDirect
Post-translational modificationUbl conjugation1.982e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011332 SSF57829 Protein matches
Abstract

This entry represents a rubredoxin-like metal-binding fold found in ribosomal proteins L37ae, L37e, L44e and S27e. This domain contains two CX(n)C motifs (where n is usually two) [PubMed15184028, PubMed15096641].


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) · 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 14 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 Zn-binding ribosomal proteins 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 14 hidden Markov models representing the Zn-binding ribosomal proteins 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]