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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 system0.05231Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.123Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.1938Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.244Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.3657Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.454Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.4941Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.6835Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.008231Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.05159Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.1724Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.194Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.2011Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.3354Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.3812Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.3826Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral nervous system morphology0.3953Moderately InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.5708Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.6001Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the glial cells0.004242InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.006972InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.0106InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.03302InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.05199InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the gastrointestinal tract0.05991InformativeInherited
Phenotypic Abnormality (PA)Abnormal intestine morphology0.08626InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.08663InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.107InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.2584InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.349InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.4236InformativeInherited
Phenotypic Abnormality (PA)Agnosia0.0000006508Highly InformativeDirect
Phenotypic Abnormality (PA)Pituitary adenoma0.00000141Highly InformativeDirect
Phenotypic Abnormality (PA)Glioma0.000002714Highly InformativeDirect
Phenotypic Abnormality (PA)Cardiac diverticulum0.000006158Highly InformativeDirect
Phenotypic Abnormality (PA)Amaurosis fugax0.000009231Highly InformativeDirect
Phenotypic Abnormality (PA)Neuroblastoma0.00001091Highly InformativeDirect
Phenotypic Abnormality (PA)Colon cancer0.00001452Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of intracranial pressure0.00001827Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the rectum0.00002215Highly InformativeDirect
Phenotypic Abnormality (PA)Dysgraphia0.00002452Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatocellular carcinoma0.00004352Highly InformativeDirect
Phenotypic Abnormality (PA)Intestinal polyposis0.00005367Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the thyroid gland0.0000593Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.00008566Highly InformativeDirect
Phenotypic Abnormality (PA)Migraine0.0001305Highly InformativeDirect
Phenotypic Abnormality (PA)Benign neoplasm of the central nervous system0.0001313Highly InformativeDirect
Phenotypic Abnormality (PA)Ovarian neoplasm0.0002063Highly InformativeDirect
Phenotypic Abnormality (PA)Dyskinesia0.000243Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skeletal system0.0004864Highly InformativeDirect
Phenotypic Abnormality (PA)Paresthesia0.0005309Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0006837Highly InformativeDirect
Phenotypic Abnormality (PA)Hallucinations0.0008349Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the pancreas0.00432Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.004004Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.0134Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.102Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.2095Least InformativeInherited
Worm Phenotype (WP)larval development variant0.2452Least InformativeInherited
Worm Phenotype (WP)cell development variant0.5404Least InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.03464Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.06441Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.09291Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.1335Moderately InformativeInherited
Worm Phenotype (WP)early larval arrest0.0000001678InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0004812InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0004923InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0005526InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0003815Highly 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 cell0.0002784Least 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)Lyases0.00000000000001035Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.00000000002684Least 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)0.00002405Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.001396Moderately InformativeInherited
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)Isomerases altering macromolecular conformation0InformativeDirect
Enzyme Commission (EC)Pentosyltransferases1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor1InformativeInherited
Enzyme Commission (EC)Carboxy-lyases1InformativeInherited
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.5165Highly 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 ]