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PAP/OAS1 substrate-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PAP/OAS1 substrate-binding domain [ 81632]
Superfamily:   PAP/OAS1 substrate-binding domain [ 81631] (5)
Families:   Poly(A) polymerase, PAP, middle domain [ 81630]
  2'-5'-oligoadenylate synthetase 1, OAS1, second domain [ 101271]
  Archaeal tRNA CCA-adding enzyme substrate-binding domain [ 101274]
  RNA editing terminal uridyl transferase 2, RET2, domain 2 [ 140679]
  AadK C-terminal domain-like [ 158607]

 Superfamily statistics
Genomes (729) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,988 5,123 11
Proteins 4,720 4,839 11

 Functional annotation
General category Information
Detailed category RNA processing

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.046361.394e-08Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)heterocyclic compound binding3.405e-050Moderately InformativeDirect
Molecular Function (MF)organic cyclic compound binding4.179e-050Moderately InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)RNA binding1.428e-070InformativeDirect
Molecular Function (MF)adenylyltransferase activity00Highly 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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 7.265e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.06734 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4693 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9651 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 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) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 4.26e-08 Moderately Informative Direct
Biological Process (BP) immune system process 5.636e-05 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 7.284e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0005822 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.224 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.7077 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.221 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.1035 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.01979 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.004911 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.004464 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.08027 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.003908 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3904 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4087 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.458 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6802 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) regulation of reproductive process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) purine nucleotide metabolic process 1.711e-13 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 3.916e-10 Informative Direct
Biological Process (BP) immune effector process 6.476e-10 Informative Direct
Biological Process (BP) response to other organism 2.201e-09 Informative Direct
Biological Process (BP) defense response 1.836e-07 Informative Direct
Biological Process (BP) response to cytokine stimulus 2.116e-07 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.001425 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.0213 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) regulation of multi-organism process 0 Highly Informative Direct
Biological Process (BP) response to virus 0 Highly Informative Direct
Biological Process (BP) RNA 3'-end processing 0 Highly Informative Direct
Biological Process (BP) negative regulation of reproductive process 0 Highly Informative Direct
Biological Process (BP) chromosome segregation 1.901e-05 Highly Informative Direct
Biological Process (BP) protein glycosylation 0.0001577 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.0008067 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 0.5051 Highly Informative Inherited
Biological Process (BP) mRNA processing 0.2644 Highly Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.05941 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1.394e-08 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.07029 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1478 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 1.205e-07 Informative Direct
Molecular Function (MF) adenylyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) ATP binding 4.036e-11 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.7575 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1119 Least Informative Inherited
Cellular Component (CC) protein complex 0.4359 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02279 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 4.228e-05 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0004212 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0.2234 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.0001462 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0002255 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)CCA tRNA nucleotidyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant5.657e-07Least InformativeDirect
Worm Phenotype (WP)RNA expression variant2.283e-11InformativeDirect
Worm Phenotype (WP)miRNA expression variant0Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)RNA accumulation0Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately 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)root0Least InformativeDirect
Plant ANatomical entity (PAN)radicle4.842e-09Highly InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.000783Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.0005067InformativeDirect

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 groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.0008954Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processMitosis6.649e-13InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum2.804e-07Moderately InformativeDirect
Cellular componentMitochondrion0.0006081Moderately InformativeDirect
Cellular componentMicrosome2.682e-06Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.0002777Least InformativeDirect
Post-translational modificationAcetylation8.593e-06Moderately 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 Anatomy (FA) · 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 6 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 PAP/OAS1 substrate-binding domain 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 6 hidden Markov models representing the PAP/OAS1 substrate-binding domain 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 Anatomy (FA) · 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.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.