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Ribosomal protein S5 domain 2-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ribosomal protein S5 domain 2-like [ 54210]
Superfamily:   Ribosomal protein S5 domain 2-like [ 54211] (12)
Families:   Translational machinery components [ 54212] (4)
  RNase P protein [ 54220]
  DNA gyrase/MutL, second domain [ 54224] (6)
  Hsp90 middle domain [ 102755]
  Ribonuclease PH domain 1-like [ 54229] (10)
  GHMP Kinase, N-terminal domain [ 54232] (6)
  Early switch protein XOL-1, N-terminal domain [ 89824]
  UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [ 89827]
  Imidazole glycerol phosphate dehydratase [ 102766]
  ATP-dependent protease Lon (La), catalytic domain [ 102769]
  YigZ N-terminal domain-like [ 102772] (2)
  Formaldehyde-activating enzyme, FAE [ 117795]


Superfamily statistics
Genomes (3,263) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 73,623 517,020 102
Proteins 66,750 464,960 93


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.03273Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)Aldehyde-lyases0.3584InformativeInherited
Enzyme Commission (EC)Endopeptidase La0Highly InformativeDirect
Enzyme Commission (EC)Homoserine kinase0Highly InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect
Enzyme Commission (EC)Histidinol-phosphatase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the digestive system0.05095Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1748Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.2268Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.242Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.3132Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.4947Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.596Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.6076Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.007577Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.05924Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.1405Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.1875Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.2148Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.2158Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.2202Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.3068Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.3293Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.3449Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.375Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.5778Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.6794Moderately InformativeInherited
Phenotypic Abnormality (PA)Internal hemorrhage0.002188InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the glial cells0.003605InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.004247InformativeInherited
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.01087InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.04544InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.04599InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the gastrointestinal tract0.06454InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.08063InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.1122InformativeInherited
Phenotypic Abnormality (PA)Functional abnormality of the gastrointestinal tract0.1913InformativeInherited
Phenotypic Abnormality (PA)Morphological abnormality of the gastrointestinal tract0.209InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.2582InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.3073InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.3469InformativeInherited
Phenotypic Abnormality (PA)Glioblastoma multiforme0.00000008672Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of creatine metabolism0.0000002803Highly InformativeDirect
Phenotypic Abnormality (PA)Agnosia0.0000007073Highly InformativeDirect
Phenotypic Abnormality (PA)Pancreatic adenocarcinoma0.0000009305Highly InformativeDirect
Phenotypic Abnormality (PA)Pituitary adenoma0.000001546Highly InformativeDirect
Phenotypic Abnormality (PA)Cardiac diverticulum0.00000698Highly InformativeDirect
Phenotypic Abnormality (PA)Neuroblastic tumors0.000008791Highly InformativeDirect
Phenotypic Abnormality (PA)Peripheral primitive neuroectodermal neoplasm0.000008791Highly InformativeDirect
Phenotypic Abnormality (PA)Amaurosis fugax0.000009226Highly InformativeDirect
Phenotypic Abnormality (PA)Colon cancer0.00001031Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the rectum0.00001171Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of intracranial pressure0.00002057Highly InformativeDirect
Phenotypic Abnormality (PA)Dysgraphia0.0000306Highly InformativeDirect
Phenotypic Abnormality (PA)Intestinal polyposis0.00003418Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatocellular carcinoma0.00004281Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the thyroid gland0.00005274Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.0000764Highly InformativeDirect
Phenotypic Abnormality (PA)Migraine0.00008859Highly InformativeDirect
Phenotypic Abnormality (PA)Dyskinesia0.00009234Highly InformativeDirect
Phenotypic Abnormality (PA)Ovarian neoplasm0.0001431Highly InformativeDirect
Phenotypic Abnormality (PA)Benign neoplasm of the central nervous system0.0001431Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skeletal system0.0003561Highly InformativeDirect
Phenotypic Abnormality (PA)Paresthesia0.0005426Highly InformativeDirect
Phenotypic Abnormality (PA)Hallucinations0.0005722Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0005722Highly InformativeDirect
Phenotypic Abnormality (PA)Gastrointestinal hemorrhage0.0006612Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.004138Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03136Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.09963Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.1163Least InformativeInherited
Worm Phenotype (WP)larval development variant0.2442Least InformativeInherited
Worm Phenotype (WP)cell development variant0.5552Least InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.03781Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.07312Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.1026Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.1372Moderately InformativeInherited
Worm Phenotype (WP)early larval arrest0.0000002331InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0004973InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0005096InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0005719InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0003895Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0Least 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 cell0.0002765Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.00001364Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0.0000001389Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.0000002178Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)In linear amides0InformativeDirect
Enzyme Commission (EC)Pentosyltransferases1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor1InformativeInherited
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.5228Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 86 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 Ribosomal protein S5 domain 2-like 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 86 hidden Markov models representing the Ribosomal protein S5 domain 2-like 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]