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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 (3,254) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 26,620 137,133 23
Proteins 26,429 136,613 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 process0.00000029260Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.00000030310Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000097860Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.0000012090Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.000004430.000000000003134Least InformativeDirect
Biological Process (BP)primary metabolic process0.0011020.000000001177Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.016920.01368Least InformativeInherited
Biological Process (BP)RNA metabolic process0.000000000000096610Moderately InformativeDirect
Biological Process (BP)gene expression0.00072650Moderately InformativeDirect
Biological Process (BP)RNA modification00InformativeDirect
Biological Process (BP)ncRNA processing0.0000000000008240InformativeDirect
Biological Process (BP)ribosome biogenesis0.000000086980InformativeDirect
Biological Process (BP)tRNA metabolic process0.57610.3337InformativeInherited
Biological Process (BP)tRNA modification0.76180.3691Highly InformativeInherited
Molecular Function (MF)isomerase activity0.00000000051130Moderately InformativeDirect
Molecular Function (MF)intramolecular transferase activity0.0000000000000053890Highly InformativeDirect

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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000000003134 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000000001177 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.01368 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ncRNA processing 0 Informative Direct
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) tRNA metabolic process 0.3337 Informative Inherited
Biological Process (BP) tRNA modification 0.3691 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.003721 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.1025 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3182 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0.000008468 Informative Direct
Molecular Function (MF) RNA binding 0.0008451 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.792 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1942 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4101 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1616 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2208 Moderately Informative Inherited
Cellular Component (CC) nucleolar part 0.000007759 Highly Informative Direct

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

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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]