SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,246) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,525 140,149 23
Proteins 26,333 139,936 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 process0.0000020660Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.0000080770Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000043530.000000002764Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000018910Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.0000000027450Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00026570.003651Least InformativeInherited
Biological Process (BP)gene expression0.000018250Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.00000031720.0000000001113Moderately InformativeDirect
Biological Process (BP)RNA processing0.00035720.000000000000007248InformativeDirect
Biological Process (BP)RNA modification00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.000000000000024410InformativeDirect
Biological Process (BP)ncRNA metabolic process0.00028530InformativeDirect
Biological Process (BP)tRNA modification0.85180.4036Highly InformativeInherited
Biological Process (BP)rRNA processing0.015240.0196Highly InformativeInherited
Molecular Function (MF)binding0.45051Least InformativeInherited
Molecular Function (MF)isomerase activity0.0000000031760Moderately InformativeDirect
Molecular Function (MF)lyase activity0.0011860.00000002085Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding0.00016140.004203Moderately InformativeInherited
Molecular Function (MF)RNA binding0.000013120.00000001863InformativeDirect
Molecular Function (MF)hydro-lyase activity0.00000030530InformativeDirect
Molecular Function (MF)intramolecular transferase activity0.000000000000001340Highly InformativeDirect
Molecular Function (MF)ribonucleoprotein complex binding0.000000042120.00000000001212Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.047440.5282Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.25010.4286Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.004220.03557Least InformativeInherited
Cellular Component (CC)nuclear part0.00031260.000166Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.00026110.00004568Moderately 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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000000002764 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 0.003651 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 0.0000000001113 Moderately Informative Direct
Biological Process (BP) RNA processing 0.000000000000007248 Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) tRNA modification 0.4036 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.0196 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0.00000002085 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.004203 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00000001863 Informative Direct
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 0.00000000001212 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.004522 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.03557 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.5282 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4286 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000166 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00004568 Moderately Informative Direct
Cellular Component (CC) chromosome 0.3845 Informative Inherited
Cellular Component (CC) chromatin 0.005918 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.09836 Highly 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)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.2705Least InformativeInherited
Yeast Phenotype (YP)RNA modification0.0000000000005021Highly InformativeDirect

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)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
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)guard cell0Least 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 ]