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.


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 (3,212) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,198 51,188 32
Proteins 12,188 51,178 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 process0.0000000000052150.000000000001695Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.0000000000012250.0000000001607Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.000000000013690.00000000002502Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000015820.0000003248Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00000000040.0000000000001739Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.82331Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.82751Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.92091Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.00075580.01027Least InformativeInherited
Biological Process (BP)peptide metabolic process00Moderately InformativeDirect
Biological Process (BP)gene expression0.00000000000030570.000000000001404Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000000000025530.00000000000003068Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.39390.9329Moderately InformativeInherited
Biological Process (BP)ribonucleoprotein complex biogenesis0.000000044230.00000001428InformativeDirect
Biological Process (BP)ncRNA processing0.00000033590.0000002806InformativeDirect
Biological Process (BP)rRNA metabolic process0.0000000025770.000000001179Highly InformativeDirect
Molecular Function (MF)structural molecule activity00Moderately InformativeDirect
Molecular Function (MF)structural constituent of ribosome00InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.000072970.0000001364Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.000000016790.0000000006818Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)ribosome00Moderately InformativeDirect
Cellular Component (CC)cytosolic part00Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0460.00008868Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.030810.009533Moderately InformativeInherited
Cellular Component (CC)mitochondrial ribosome0.00000000000010750InformativeDirect
Cellular Component (CC)organellar large ribosomal subunit0.099780.1602InformativeInherited

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 0.000000000001695 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000000001607 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000002502 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000003248 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000000001739 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) cellular component organization or biogenesis 0.01027 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000423 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000001404 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.00000000000003068 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.9329 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.000002462 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00000001428 Informative Direct
Biological Process (BP) ncRNA processing 0.0000002806 Informative Direct
Biological Process (BP) rRNA metabolic process 0.000000001179 Highly Informative Direct
Molecular Function (MF) structural molecule activity 0 Moderately 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 0.0000001364 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000000006818 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) ribosome 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.00008868 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.009533 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.4623 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.4363 Moderately Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0 Informative Direct
Cellular Component (CC) organellar large ribosomal subunit 0.1602 Informative Inherited

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)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.002657Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.004369Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.005829Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1289Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00000003093Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.0000006637Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0002131Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.0006234Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0009323Moderately InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000000003279InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00000003978InformativeDirect
Worm Phenotype (WP)body width variant0.000154InformativeDirect
Worm Phenotype (WP)RNA expression variant0.0009577InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.02356InformativeInherited
Worm Phenotype (WP)nonsense mRNA accumulation0.00000135Highly InformativeDirect
Worm Phenotype (WP)RNA processing variant0.000001996Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00001807Highly InformativeDirect

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)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)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0.3858Least InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.005182Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.1082Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endomesoderm0InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0000002064InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.0001519InformativeDirect
Xenopus ANatomical entity (XAN)skeletal system0.0007151InformativeDirect
Xenopus ANatomical entity (XAN)connective tissue0.002626InformativeInherited
Xenopus ANatomical entity (XAN)solid compound organ0.01226InformativeInherited
Xenopus ANatomical entity (XAN)stomach0.0005333Highly 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 resistance0.0003675InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationIsopeptide bond0.0000000503Moderately 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 ]