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Pseudouridine synthase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Pseudouridine synthase [ 100877]
Superfamily:   Pseudouridine synthase [ 55120] (4)
Families:   Pseudouridine synthase I TruA [ 55121]
  Pseudouridine synthase II TruB [ 69746]
  Pseudouridine synthase RsuA/RluD [ 75459] (3)
  tRNA pseudouridine synthase TruD [ 103021]

 Superfamily statistics
Genomes (2,483) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 20,770 62,050 23
Proteins 20,621 61,926 23

 Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process1.232e-060Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process7.677e-060Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process7.808e-066.159e-11Least InformativeDirect
Biological Process (BP)heterocycle metabolic process9.967e-070Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.253e-090Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00036390.001844Least InformativeInherited
Biological Process (BP)gene expression6.872e-060Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis3.223e-075.317e-12Moderately InformativeDirect
Biological Process (BP)RNA modification00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis6.227e-140InformativeDirect
Biological Process (BP)ncRNA processing00InformativeDirect
Biological Process (BP)tRNA metabolic process0.84580.5724InformativeInherited
Biological Process (BP)tRNA modification0.890.5201Highly InformativeInherited
Biological Process (BP)rRNA processing0.019710.02654Highly InformativeInherited
Molecular Function (MF)binding0.47371Least InformativeInherited
Molecular Function (MF)lyase activity0.00087835.292e-05Moderately InformativeDirect
Molecular Function (MF)isomerase activity9.891e-090Moderately InformativeDirect
Molecular Function (MF)carbon-oxygen lyase activity1.884e-063.503e-12InformativeDirect
Molecular Function (MF)intramolecular transferase activity2.587e-150Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.54850.6669Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.020890.07729Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.15620.8355Least InformativeInherited
Cellular Component (CC)nuclear part0.0030120.003125Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0025980.001414Moderately InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 6.159e-11 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.001844 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 5.317e-12 Moderately Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) ncRNA processing 0 Informative Direct
Biological Process (BP) tRNA metabolic process 0.5724 Informative Inherited
Biological Process (BP) tRNA modification 0.5201 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.02654 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 5.292e-05 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity 3.503e-12 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.005934 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6669 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8355 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.07729 Least Informative Inherited
Cellular Component (CC) nuclear part 0.003125 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.001414 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring other groups0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least 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)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 11 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 Pseudouridine synthase 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 11 hidden Markov models representing the Pseudouridine synthase 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.