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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 nervous system morphology0.04945Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.0499Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.08888Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.0895Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.1211Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.4601Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.5669Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.6957Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.8628Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.006328Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.02353Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.02657Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1457Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1513Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.2209Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.3377Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skeletal muscle morphology0.4122Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.5044Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5271Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.6588Moderately InformativeInherited
Phenotypic Abnormality (PA)Flexion contracture0.0008605InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the endocrine system0.002118InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.00902InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the glial cells0.01313InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiac ventricle morphology0.01417InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.01856InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.04272InformativeInherited
Phenotypic Abnormality (PA)Anorectal anomaly0.04845InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.06178InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.07738InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the gastrointestinal tract0.08841InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.1711InformativeInherited
Phenotypic Abnormality (PA)Abnormal intestine morphology0.2289InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.2355InformativeInherited
Phenotypic Abnormality (PA)Agnosia0.000003507Highly InformativeDirect
Phenotypic Abnormality (PA)Pancreatic adenocarcinoma0.000004031Highly InformativeDirect
Phenotypic Abnormality (PA)Pituitary adenoma0.000004917Highly InformativeDirect
Phenotypic Abnormality (PA)Cardiac diverticulum0.00001254Highly InformativeDirect
Phenotypic Abnormality (PA)Glioma0.00001597Highly InformativeDirect
Phenotypic Abnormality (PA)Neuroblastoma0.00002438Highly InformativeDirect
Phenotypic Abnormality (PA)Colon cancer0.00002767Highly InformativeDirect
Phenotypic Abnormality (PA)Amaurosis fugax0.00002767Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of intracranial pressure0.00004975Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the rectum0.00005033Highly InformativeDirect
Phenotypic Abnormality (PA)Dysgraphia0.00006187Highly InformativeDirect
Phenotypic Abnormality (PA)Endometrial carcinoma0.00006601Highly InformativeDirect
Phenotypic Abnormality (PA)Intestinal polyposis0.00008519Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.0001363Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatocellular carcinoma0.0001726Highly InformativeDirect
Phenotypic Abnormality (PA)Ovarian neoplasm0.0002891Highly InformativeDirect
Phenotypic Abnormality (PA)Benign neoplasm of the central nervous system0.000356Highly InformativeDirect
Phenotypic Abnormality (PA)Headache0.01782Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal reproductive system morphology0.2551Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal spermatogenesis0.03942InformativeInherited
Mammalian Phenotype (MP)abnormal male meiosis0.0003306Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.004588Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.08104Least InformativeInherited
Worm Phenotype (WP)larval development variant0.124Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.2149Least InformativeInherited
Worm Phenotype (WP)cell development variant0.5393Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.009515Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.02993Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.04212Moderately InformativeInherited
Worm Phenotype (WP)cell cycle variant0.1101Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.1256Moderately InformativeInherited
Worm Phenotype (WP)early larval arrest0.0000001757InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000433InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0004749InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0005089InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.0003417Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect

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)Lyases0.00000000000001193Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.000000000003233Least 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)0.00004417Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.002197Moderately 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-lyases0.5129Highly InformativeInherited

Document: EC annotation of SCOP domains

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