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PRTase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   PRTase-like [ 53270]
Superfamily:   PRTase-like [ 53271] (2)
Families:   Phosphoribosyltransferases (PRTases) [ 53272] (15)
  Phosphoribosylpyrophosphate synthetase-like [ 53296] (2)

Superfamily statistics
Genomes (2,443) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 24,316 70,586 56
Proteins 22,847 68,047 54

 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 process00Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process7.195e-100Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.012050.4017Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.00083011Least InformativeInherited
Biological Process (BP)regulation of cellular process0.11771Least InformativeInherited
Biological Process (BP)response to stimulus0.049761Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process1.195e-140Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process00Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process3.322e-110Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process00Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process00Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00027620.01653Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.0027350.1414Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process1.359e-080.2426Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process5.535e-070.9655Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process6.094e-051Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process2.621e-050.9725Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.27330.6009Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.50350.6896Moderately InformativeInherited
Biological Process (BP)ribonucleoside metabolic process00InformativeDirect
Biological Process (BP)nucleotide biosynthetic process3.176e-081.982e-11InformativeDirect
Biological Process (BP)ribose phosphate metabolic process1.91e-090InformativeDirect
Biological Process (BP)pigment metabolic process00InformativeDirect
Biological Process (BP)cellular metabolic compound salvage00InformativeDirect
Biological Process (BP)protein oligomerization1.442e-107.246e-09InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process00InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00036661.53e-14InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process00InformativeDirect
Biological Process (BP)purine nucleotide metabolic process0.49610.8448InformativeInherited
Biological Process (BP)carbohydrate derivative catabolic process0.0059750.1612InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.2891InformativeInherited
Biological Process (BP)positive regulation of nitrogen compound metabolic process4.041e-120.02315InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process0.49730.8345InformativeInherited
Biological Process (BP)organophosphate catabolic process0.00011840.09125InformativeInherited
Biological Process (BP)purine nucleoside metabolic process0.39581InformativeInherited
Biological Process (BP)nucleobase metabolic process00Highly InformativeDirect
Biological Process (BP)nucleoside monophosphate metabolic process00Highly InformativeDirect
Biological Process (BP)regulation of cellular amine metabolic process00Highly InformativeDirect
Biological Process (BP)pigment biosynthetic process00Highly InformativeDirect
Biological Process (BP)protein homooligomerization1.747e-119.312e-11Highly InformativeDirect
Biological Process (BP)protein tetramerization9.82e-134.136e-05Highly InformativeDirect
Biological Process (BP)nucleotide catabolic process0.60651Highly InformativeInherited
Biological Process (BP)purine ribonucleoside catabolic process11Highly InformativeInherited
Biological Process (BP)guanosine-containing compound metabolic process0.90890.1678Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.00065790.8856Least InformativeInherited
Molecular Function (MF)protein binding0.0048970.205Moderately InformativeInherited
Molecular Function (MF)cation binding9.4e-110.02877Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring glycosyl groups00InformativeDirect
Molecular Function (MF)protein dimerization activity2.668e-051.165e-09InformativeDirect
Molecular Function (MF)magnesium ion binding00Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring pentosyl groups00Highly 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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism 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 component organization or biogenesis 0.4017 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.01653 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1414 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.2426 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.9655 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8804 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9725 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6009 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6896 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.6765 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0.0008453 Informative Direct
Biological Process (BP) ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 1.982e-11 Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0 Informative Direct
Biological Process (BP) pigment metabolic process 0 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0 Informative Direct
Biological Process (BP) protein oligomerization 7.246e-09 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 1.53e-14 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 1 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.8448 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1612 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.02315 Informative Inherited
Biological Process (BP) amine biosynthetic process 0.2341 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8345 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.09125 Informative Inherited
Biological Process (BP) purine nucleoside metabolic process 1 Informative Inherited
Biological Process (BP) hexose metabolic process 0.001874 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.03717 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 0.0006351 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.0005181 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of cellular amine metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 2.916e-05 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0.0005847 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0001359 Highly Informative Direct
Biological Process (BP) protein homooligomerization 9.312e-11 Highly Informative Direct
Biological Process (BP) protein tetramerization 4.136e-05 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 1.249e-08 Highly Informative Direct
Biological Process (BP) pyrimidine nucleoside metabolic process 0.002223 Highly Informative Inherited
Biological Process (BP) nucleotide catabolic process 1 Highly Informative Inherited
Biological Process (BP) purine ribonucleoside catabolic process 1 Highly Informative Inherited
Biological Process (BP) guanosine-containing compound metabolic process 0.1678 Highly Informative Inherited
Biological Process (BP) response to drug 0.03269 Highly Informative Inherited
Biological Process (BP) indole-containing compound biosynthetic process 0.0641 Highly Informative Inherited
Biological Process (BP) aromatic amino acid family biosynthetic process 0.03352 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.8856 Least Informative Inherited
Molecular Function (MF) protein binding 0.205 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.7168 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.6853 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.2046 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.02877 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring glycosyl groups 0 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 8.469e-06 Informative Direct
Molecular Function (MF) protein dimerization activity 1.165e-09 Informative Direct
Molecular Function (MF) nucleotide binding 0.7805 Informative Inherited
Molecular Function (MF) magnesium ion binding 0 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring pentosyl groups 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 2.114e-07 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.8924 Least Informative Inherited
Cellular Component (CC) cytosol 9.153e-05 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Diphosphotransferases0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)bone disease0Moderately InformativeDirect
Disease Ontology (DO)arthritis0InformativeDirect
Disease Ontology (DO)gout0Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the urinary system0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of renal physiology0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0InformativeDirect
Phenotypic Abnormality (PA)Renal insufficiency0Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.01393Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.001416Moderately InformativeInherited
Worm Phenotype (WP)drug resistant5.341e-05InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Pentosyltransferases0InformativeDirect
Enzyme Commission (EC)Diphosphotransferases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation3.118e-06Moderately InformativeDirect
Biological processNucleotide biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainGlutamine amidotransferase1.768e-05Highly InformativeDirect
Molecular functionNucleotide-binding1.467e-13Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0Moderately InformativeDirect
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)purine biosynthesis via salvage pathway0InformativeDirect
UniPathway (UP)nucleotide biosynthesis1InformativeInherited
UniPathway (UP)5-phospho-alpha-D-ribose 1-diphosphate biosynthesis0Highly InformativeDirect
UniPathway (UP)pyrimidine salvage0Highly InformativeDirect
UniPathway (UP)AMP biosynthesis0Highly InformativeDirect
UniPathway (UP)XMP biosynthesis0Highly InformativeDirect
UniPathway (UP)CTP biosynthesis1Highly InformativeInherited

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 39 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 PRTase-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 39 hidden Markov models representing the PRTase-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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · 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.