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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 0 102
Proteins 66,750 0 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 system0.07171Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.2271Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.2283Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.2522Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.2695Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.309Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.473Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.5072Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.5156Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.003845Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.03065Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.1369Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.1556Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.1589Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.1861Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.2128Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.2764Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.286Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.3145Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.4059Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.4723Moderately InformativeInherited
Phenotypic Abnormality (PA)Internal hemorrhage0.001796InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.004447InformativeInherited
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.008153InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hypothalamus-pituitary axis0.01672InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.02059InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the gastrointestinal tract0.05538InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.08404InformativeInherited
Phenotypic Abnormality (PA)Abnormal intestine morphology0.1339InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.138InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.1907InformativeInherited
Phenotypic Abnormality (PA)Functional abnormality of the gastrointestinal tract0.2461InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.2602InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.2757InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.5724InformativeInherited
Phenotypic Abnormality (PA)Glioblastoma multiforme0.00000007139Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of creatine metabolism0.0000002313Highly InformativeDirect
Phenotypic Abnormality (PA)Agnosia0.0000004414Highly InformativeDirect
Phenotypic Abnormality (PA)Pancreatic adenocarcinoma0.000000772Highly InformativeDirect
Phenotypic Abnormality (PA)Pituitary adenoma0.000001285Highly InformativeDirect
Phenotypic Abnormality (PA)Neuroblastic tumors0.000007393Highly InformativeDirect
Phenotypic Abnormality (PA)Peripheral primitive neuroectodermal neoplasm0.000007393Highly InformativeDirect
Phenotypic Abnormality (PA)Dyskinesia0.000007827Highly InformativeDirect
Phenotypic Abnormality (PA)Colon cancer0.00000864Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the rectum0.000009577Highly InformativeDirect
Phenotypic Abnormality (PA)Cardiac diverticulum0.00001465Highly InformativeDirect
Phenotypic Abnormality (PA)Amaurosis fugax0.00001468Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of intracranial pressure0.00001686Highly InformativeDirect
Phenotypic Abnormality (PA)Intestinal polyposis0.00002878Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatocellular carcinoma0.00003604Highly InformativeDirect
Phenotypic Abnormality (PA)Migraine0.00004428Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the thyroid gland0.00004452Highly InformativeDirect
Phenotypic Abnormality (PA)Dysgraphia0.00005339Highly InformativeDirect
Phenotypic Abnormality (PA)Benign neoplasm of the central nervous system0.00009576Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.0001053Highly InformativeDirect
Phenotypic Abnormality (PA)Ovarian neoplasm0.0001128Highly InformativeDirect
Phenotypic Abnormality (PA)Gastrointestinal hemorrhage0.0001396Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skeletal system0.0002296Highly InformativeDirect
Phenotypic Abnormality (PA)Hallucinations0.0002886Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0003465Highly InformativeDirect
Phenotypic Abnormality (PA)Irritability0.0009474Highly 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 variant0.003993Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03099Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.0959Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.1135Least InformativeInherited
Worm Phenotype (WP)larval development variant0.2443Least InformativeInherited
Worm Phenotype (WP)cell development variant0.5331Least InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.03663Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.07643Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.1182Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.1389Moderately InformativeInherited
Worm Phenotype (WP)early larval arrest0.0000002168InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0004927InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0005059InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0005675InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0004001Highly 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)Hydrolases0.000004726Least 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 carbon-nitrogen bonds, other than peptide bonds0.00000005205Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0.000000203Moderately 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-lyases0.5258Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processDNA damage0Moderately InformativeDirect
Biological processLipid metabolism0.0000000000009499Moderately InformativeDirect
Biological processCarbohydrate metabolism0.003153Moderately InformativeInherited
Biological processStress response0InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processProtein biosynthesis0InformativeDirect
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processDNA repair0.000001301InformativeDirect
Biological processSteroid metabolism0.04631InformativeInherited
Biological processHistidine biosynthesis0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processSterol biosynthesis0.00000000001197Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00004199InformativeDirect
Cellular componentExosome0Highly InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationLyase0.00000000000293Moderately InformativeDirect
Post-translational modificationProtease0.00101Moderately InformativeInherited
Post-translational modificationIsomerase1Moderately InformativeInherited
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationElongation factor0Highly InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect

Document: KW 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) · 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 58 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 58 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) · UniProtKB KeyWords (KW) · Internal database links ]