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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 system0.02287Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.04349Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.06072Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.1085Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.4661Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.4807Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.6109Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.7993Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.01812Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1425Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.1428Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.2103Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.2768Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.4447Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4611Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.7098Moderately InformativeInherited
Phenotypic Abnormality (PA)Gonadal neoplasm0.001011InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the endocrine system0.002239InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the glial cells0.0104InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.01446InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pancreas0.04507InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.05087InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.07353InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.07531InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the gastrointestinal tract0.08784InformativeInherited
Phenotypic Abnormality (PA)Neurological speech impairment0.2263InformativeInherited
Phenotypic Abnormality (PA)Abnormal intestine morphology0.2342InformativeInherited
Phenotypic Abnormality (PA)Neoplasm by histology0.2378InformativeInherited
Phenotypic Abnormality (PA)Abnormality of vision0.5091InformativeInherited
Phenotypic Abnormality (PA)Agnosia0.000002119Highly InformativeDirect
Phenotypic Abnormality (PA)Pancreatic adenocarcinoma0.000003074Highly InformativeDirect
Phenotypic Abnormality (PA)Pituitary adenoma0.00000376Highly InformativeDirect
Phenotypic Abnormality (PA)Glioma0.0000124Highly InformativeDirect
Phenotypic Abnormality (PA)Cardiac diverticulum0.00001456Highly InformativeDirect
Phenotypic Abnormality (PA)Colon cancer0.00002147Highly InformativeDirect
Phenotypic Abnormality (PA)Neuroblastoma0.00002147Highly InformativeDirect
Phenotypic Abnormality (PA)Dysgraphia0.00002282Highly InformativeDirect
Phenotypic Abnormality (PA)Amaurosis fugax0.00002967Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of intracranial pressure0.00003596Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the rectum0.00003726Highly InformativeDirect
Phenotypic Abnormality (PA)Endometrial carcinoma0.00005388Highly InformativeDirect
Phenotypic Abnormality (PA)Intestinal polyposis0.00006671Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skin0.0001286Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatocellular carcinoma0.0001369Highly InformativeDirect
Phenotypic Abnormality (PA)Ovarian neoplasm0.0002302Highly InformativeDirect
Phenotypic Abnormality (PA)Benign neoplasm of the central nervous system0.0002638Highly InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the skeletal system0.0008627Highly InformativeDirect
Phenotypic Abnormality (PA)Headache0.01257Highly 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 spermatogenesis0.03943InformativeInherited
Mammalian Phenotype (MP)abnormal male meiosis0.0003305Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)blast cell physiology variant0.0006128Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0006162Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.01141Least InformativeInherited
Worm Phenotype (WP)larval development variant0.1081Least InformativeInherited
Worm Phenotype (WP)cell morphology variant0.1421Least InformativeInherited
Worm Phenotype (WP)larval growth variant0.1992Least InformativeInherited
Worm Phenotype (WP)cell development variant0.2481Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.002858Moderately InformativeInherited
Worm Phenotype (WP)germ cell development variant0.005117Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.01435Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.07867Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.2183Moderately InformativeInherited
Worm Phenotype (WP)early larval arrest0.0000001558InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0004286InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0004709InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0005053InformativeDirect

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)Lyases0.00000000000001138Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.000000000007177Least 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)0.00003338Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.001876Moderately 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-lyases0.5141Highly 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 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 Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]