Nucleic acid-binding proteins superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	All beta proteins [ 48724] (174)
Fold:	OB-fold [ 50198] (16)
Superfamily:	Nucleic acid-binding proteins [ 50249] (16)
Families:	Anticodon-binding domain [ 50250] (2)
	RecG "wedge" domain [ 69259]
	DNA helicase RuvA subunit, N-terminal domain [ 50259]
	Single strand DNA-binding domain, SSB [ 50263] (12)
	Myf domain [ 50277] (6)
	Cold shock DNA-binding domain-like [ 50282] (30)
	TRAM domain [ 101768] (3)
	Hypothetical protein MTH1 (MT0001), insert domain [ 74955]
	DNA ligase/mRNA capping enzyme postcatalytic domain [ 50307] (5)
	Phage ssDNA-binding proteins [ 50315] (3)
	DNA replication initiator (cdc21/cdc54) N-terminal domain [ 89332]
	RNA polymerase subunit RBP8 [ 50321]
	RecO N-terminal domain-like [ 117204]
	TIP49 domain [ 141315]
	SSO2064-like [ 159109]
	RNB domain-like [ 159112] (3)

Superfamily statistics

	Genomes (2,490)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	117,033	313,595	241
Proteins	90,408	245,559	208

Functional annotation

General category	Information
Detailed category	DNA replication/repair

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)

	GO term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	biosynthetic process	5.044e-07	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	1.149e-09	0	Least Informative	Direct
Biological Process (BP)	cellular component organization or biogenesis	0.0001245	6.316e-05	Least Informative	Direct
Biological Process (BP)	developmental process	1	1	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	0.09218	0.03304	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	0.9765	1	Least Informative	Inherited
Biological Process (BP)	response to stimulus	0.9877	1	Least Informative	Inherited
Biological Process (BP)	protein metabolic process	0.004457	1	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	0.03764	1	Least Informative	Inherited
Biological Process (BP)	localization	0.2378	1	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	0.007864	0	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	0.1212	0	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	0.02344	0	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	0.006247	0	Least Informative	Inherited
Biological Process (BP)	gene expression	9.05e-15	0	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	0	0	Moderately Informative	Direct
Biological Process (BP)	anatomical structure morphogenesis	0.898	1	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	1	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	0.002743	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.1761	0.2682	Moderately Informative	Inherited
Biological Process (BP)	regulation of biosynthetic process	0.05158	0.8976	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular component organization	0.7182	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of nitrogen compound metabolic process	0.3165	0.9929	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.04005	0.02527	Moderately Informative	Inherited
Biological Process (BP)	cellular localization	0.02423	1	Moderately Informative	Inherited
Biological Process (BP)	macromolecule localization	0.0005798	0.7253	Moderately Informative	Inherited
Biological Process (BP)	organic substance transport	0.04259	1	Moderately Informative	Inherited
Biological Process (BP)	cellular component biogenesis	0.04714	0.1583	Moderately Informative	Inherited
Biological Process (BP)	organelle organization	0.006193	2.15e-11	Moderately Informative	Inherited
Biological Process (BP)	homeostatic process	0.6714	0.08141	Moderately Informative	Inherited
Biological Process (BP)	ribonucleoprotein complex biogenesis	1.162e-10	9.823e-12	Informative	Direct
Biological Process (BP)	mitochondrion organization	0.0218	2.487e-05	Informative	Inherited
Biological Process (BP)	cellular component morphogenesis	0.448	1	Informative	Inherited
Biological Process (BP)	cytoplasmic transport	2.149e-07	0.06855	Informative	Inherited
Biological Process (BP)	posttranscriptional regulation of gene expression	0.01512	4.395e-10	Informative	Inherited
Biological Process (BP)	nucleocytoplasmic transport	5.218e-12	0.001535	Informative	Inherited
Biological Process (BP)	nitrogen compound transport	8.085e-05	0.1745	Informative	Inherited
Biological Process (BP)	chromosome organization	0.3242	1.494e-07	Informative	Inherited
Biological Process (BP)	DNA metabolic process	0.2935	0	Informative	Inherited
Biological Process (BP)	anatomical structure homeostasis	0.00986	0	Informative	Inherited
Biological Process (BP)	translational initiation	2.461e-07	1.704e-08	Highly Informative	Direct
Biological Process (BP)	response to cold	1.322e-08	0.0009288	Highly Informative	Direct
Biological Process (BP)	regulation of protein complex disassembly	0.0004635	0.01226	Highly Informative	Inherited
Biological Process (BP)	RNA export from nucleus	0.0353	0.1737	Highly Informative	Inherited
Molecular Function (MF)	transferase activity	1	1	Least Informative	Inherited
Molecular Function (MF)	binding	0.009033	2.178e-07	Least Informative	Inherited
Molecular Function (MF)	structural molecule activity	0	1.206e-10	Moderately Informative	Direct
Molecular Function (MF)	organic cyclic compound binding	6.629e-11	0	Moderately Informative	Direct
Molecular Function (MF)	heterocyclic compound binding	1.453e-11	0	Moderately Informative	Direct
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	0.4757	0.9564	Moderately Informative	Inherited
Molecular Function (MF)	structural constituent of ribosome	0	0	Informative	Direct
Molecular Function (MF)	DNA binding	0.1549	0.9537	Informative	Inherited
Molecular Function (MF)	nucleotidyltransferase activity	0.003229	6.599e-13	Informative	Inherited
Molecular Function (MF)	chromatin binding	3.393e-07	1.2e-10	Highly Informative	Direct
Molecular Function (MF)	RNA polymerase activity	1.989e-05	6.33e-06	Highly Informative	Direct
Molecular Function (MF)	structure-specific DNA binding	2.525e-09	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0	0	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	8.892e-07	3.971e-11	Least Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	1	1	Least Informative	Inherited
Cellular Component (CC)	protein complex	1	1	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.04297	1	Least Informative	Inherited
Cellular Component (CC)	ribonucleoprotein complex	0	0	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	9.986e-05	4.175e-09	Moderately Informative	Direct
Cellular Component (CC)	cytosol	0.009253	0.0002734	Moderately Informative	Inherited
Cellular Component (CC)	mitochondrial part	0.02197	0.03904	Moderately Informative	Inherited
Cellular Component (CC)	nuclear part	0.3279	2.347e-11	Moderately Informative	Inherited
Cellular Component (CC)	DNA-directed RNA polymerase complex	2.567e-07	6.149e-15	Informative	Direct
Cellular Component (CC)	small ribosomal subunit	0	0.000147	Informative	Direct
Cellular Component (CC)	chromosome	0.978	2.213e-14	Informative	Inherited
Cellular Component (CC)	cytosolic ribosome	0.09551	0.0004167	Informative	Inherited
Cellular Component (CC)	nucleoplasm part	0.07351	1	Informative	Inherited
Cellular Component (CC)	DNA-directed RNA polymerase II, core complex	4.708e-10	1.584e-11	Highly Informative	Direct
Cellular Component (CC)	cytosolic small ribosomal subunit	5.641e-08	2.503e-10	Highly Informative	Direct
Cellular Component (CC)	replisome	0.0001149	1.149e-07	Highly Informative	Direct
Cellular Component (CC)	nuclear chromosome part	0.008314	0	Highly Informative	Inherited

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)	cellular macromolecule metabolic process	0	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	0	Least Informative	Direct
Biological Process (BP)	cellular component organization or biogenesis	6.316e-05	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	0	Least Informative	Direct
Biological Process (BP)	regulation of metabolic process	0.03304	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1	Least Informative	Inherited
Biological Process (BP)	protein metabolic process	1	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	1	Least Informative	Inherited
Biological Process (BP)	multicellular organismal process	1	Least Informative	Inherited
Biological Process (BP)	developmental process	1	Least Informative	Inherited
Biological Process (BP)	single-organism metabolic process	1	Least Informative	Inherited
Biological Process (BP)	localization	1	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	1	Least Informative	Inherited
Biological Process (BP)	organelle organization	2.15e-11	Moderately Informative	Direct
Biological Process (BP)	gene expression	0	Moderately Informative	Direct
Biological Process (BP)	RNA metabolic process	1.093e-07	Moderately Informative	Direct
Biological Process (BP)	cellular response to stress	0	Moderately Informative	Direct
Biological Process (BP)	cellular macromolecule biosynthetic process	0	Moderately Informative	Direct
Biological Process (BP)	anatomical structure morphogenesis	1	Moderately Informative	Inherited
Biological Process (BP)	macromolecular complex subunit organization	0.416	Moderately Informative	Inherited
Biological Process (BP)	homeostatic process	0.08141	Moderately Informative	Inherited
Biological Process (BP)	regulation of developmental process	0.8996	Moderately Informative	Inherited
Biological Process (BP)	regulation of molecular function	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of nitrogen compound metabolic process	0.9929	Moderately Informative	Inherited
Biological Process (BP)	negative regulation of cellular process	0.03938	Moderately Informative	Inherited
Biological Process (BP)	regulation of biosynthetic process	0.8976	Moderately Informative	Inherited
Biological Process (BP)	regulation of protein metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	positive regulation of metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	positive regulation of cellular process	1	Moderately Informative	Inherited
Biological Process (BP)	reproduction	0.001725	Moderately Informative	Inherited
Biological Process (BP)	cellular response to chemical stimulus	1	Moderately Informative	Inherited
Biological Process (BP)	negative regulation of metabolic process	0.1562	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	1	Moderately Informative	Inherited
Biological Process (BP)	response to organic substance	1	Moderately Informative	Inherited
Biological Process (BP)	cellular protein modification process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular component organization	1	Moderately Informative	Inherited
Biological Process (BP)	cellular catabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of multicellular organismal process	1	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.02527	Moderately Informative	Inherited
Biological Process (BP)	carbohydrate derivative metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	nucleobase-containing small molecule metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	organophosphate metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	single-organism developmental process	1	Moderately Informative	Inherited
Biological Process (BP)	cell differentiation	1	Moderately Informative	Inherited
Biological Process (BP)	cellular amino acid metabolic process	0.099	Moderately Informative	Inherited
Biological Process (BP)	cellular component biogenesis	0.1583	Moderately Informative	Inherited
Biological Process (BP)	cellular localization	1	Moderately Informative	Inherited
Biological Process (BP)	macromolecule localization	0.7253	Moderately Informative	Inherited
Biological Process (BP)	organic substance transport	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.2682	Moderately Informative	Inherited
Biological Process (BP)	immune system process	1	Moderately Informative	Inherited
Biological Process (BP)	DNA metabolic process	0	Informative	Direct
Biological Process (BP)	response to DNA damage stimulus	0	Informative	Direct
Biological Process (BP)	mitochondrion organization	2.487e-05	Informative	Direct
Biological Process (BP)	posttranscriptional regulation of gene expression	4.395e-10	Informative	Direct
Biological Process (BP)	cell cycle process	3.446e-12	Informative	Direct
Biological Process (BP)	ribonucleoprotein complex biogenesis	9.823e-12	Informative	Direct
Biological Process (BP)	single organism reproductive process	0.0001719	Informative	Direct
Biological Process (BP)	multicellular organismal reproductive process	2.166e-05	Informative	Direct
Biological Process (BP)	chromosome organization	1.494e-07	Informative	Direct
Biological Process (BP)	anatomical structure homeostasis	0	Informative	Direct
Biological Process (BP)	regulation of cell cycle process	0.03928	Informative	Inherited
Biological Process (BP)	cellular response to nitrogen compound	0.1804	Informative	Inherited
Biological Process (BP)	cellular component morphogenesis	1	Informative	Inherited
Biological Process (BP)	cellular macromolecular complex assembly	0.005603	Informative	Inherited
Biological Process (BP)	cytoplasmic transport	0.06855	Informative	Inherited
Biological Process (BP)	negative regulation of developmental process	0.1177	Informative	Inherited
Biological Process (BP)	regulation of hydrolase activity	1	Informative	Inherited
Biological Process (BP)	negative regulation of cellular metabolic process	0.7044	Informative	Inherited
Biological Process (BP)	negative regulation of nitrogen compound metabolic process	0.6998	Informative	Inherited
Biological Process (BP)	positive regulation of macromolecule biosynthetic process	1	Informative	Inherited
Biological Process (BP)	positive regulation of cellular biosynthetic process	1	Informative	Inherited
Biological Process (BP)	positive regulation of protein metabolic process	1	Informative	Inherited
Biological Process (BP)	cellular macromolecule catabolic process	0.4409	Informative	Inherited
Biological Process (BP)	response to organic cyclic compound	1	Informative	Inherited
Biological Process (BP)	regulation of reproductive process	0.315	Informative	Inherited
Biological Process (BP)	cellular membrane organization	1	Informative	Inherited
Biological Process (BP)	ribose phosphate metabolic process	0.005581	Informative	Inherited
Biological Process (BP)	purine nucleotide metabolic process	0.522	Informative	Inherited
Biological Process (BP)	carbohydrate derivative catabolic process	0.02824	Informative	Inherited
Biological Process (BP)	nucleobase-containing compound catabolic process	0.743	Informative	Inherited
Biological Process (BP)	organophosphate catabolic process	0.01776	Informative	Inherited
Biological Process (BP)	developmental process involved in reproduction	0.03874	Informative	Inherited
Biological Process (BP)	cellular process involved in reproduction	0.01689	Informative	Inherited
Biological Process (BP)	sexual reproduction	0.001066	Informative	Inherited
Biological Process (BP)	tRNA metabolic process	0.004054	Informative	Inherited
Biological Process (BP)	nucleocytoplasmic transport	0.001535	Informative	Inherited
Biological Process (BP)	nitrogen compound transport	0.1745	Informative	Inherited
Biological Process (BP)	purine nucleoside metabolic process	0.00514	Informative	Inherited
Biological Process (BP)	ribonucleoside metabolic process	0.01073	Informative	Inherited
Biological Process (BP)	nucleoside triphosphate metabolic process	0.03642	Informative	Inherited
Biological Process (BP)	organonitrogen compound catabolic process	1	Informative	Inherited
Biological Process (BP)	cell activation	1	Informative	Inherited
Biological Process (BP)	immune effector process	0.7568	Informative	Inherited
Biological Process (BP)	immune response	1	Informative	Inherited
Biological Process (BP)	ncRNA processing	0.9285	Informative	Inherited
Biological Process (BP)	DNA replication	0	Highly Informative	Direct
Biological Process (BP)	DNA repair	0.0004481	Highly Informative	Direct
Biological Process (BP)	DNA recombination	5.923e-05	Highly Informative	Direct
Biological Process (BP)	translational initiation	1.704e-08	Highly Informative	Direct
Biological Process (BP)	regulation of translation	1.752e-07	Highly Informative	Direct
Biological Process (BP)	germ cell development	0.0001205	Highly Informative	Direct
Biological Process (BP)	nucleoside triphosphate catabolic process	0.0001318	Highly Informative	Direct
Biological Process (BP)	purine ribonucleoside triphosphate metabolic process	0.0003853	Highly Informative	Direct
Biological Process (BP)	response to cold	0.0009288	Highly Informative	Direct
Biological Process (BP)	response to ionizing radiation	0	Highly Informative	Direct
Biological Process (BP)	regulation of gene expression, epigenetic	4.725e-08	Highly Informative	Direct
Biological Process (BP)	purine ribonucleoside catabolic process	0.0002109	Highly Informative	Direct
Biological Process (BP)	regulation of DNA metabolic process	0	Highly Informative	Direct
Biological Process (BP)	negative regulation of cell cycle	0.5203	Highly Informative	Inherited
Biological Process (BP)	cellular response to organic cyclic compound	0.1288	Highly Informative	Inherited
Biological Process (BP)	organelle localization	0.4988	Highly Informative	Inherited
Biological Process (BP)	cell cycle phase	0.007863	Highly Informative	Inherited
Biological Process (BP)	leukocyte activation involved in immune response	0.04436	Highly Informative	Inherited
Biological Process (BP)	B cell activation	0.0957	Highly Informative	Inherited
Biological Process (BP)	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	0.0092	Highly Informative	Inherited
Biological Process (BP)	negative regulation of gene expression	0.5425	Highly Informative	Inherited
Biological Process (BP)	protein methylation	0.1268	Highly Informative	Inherited
Biological Process (BP)	histone modification	0.3553	Highly Informative	Inherited
Biological Process (BP)	regulation of protein complex disassembly	0.01226	Highly Informative	Inherited
Biological Process (BP)	nucleotide catabolic process	0.0343	Highly Informative	Inherited
Biological Process (BP)	RNA export from nucleus	0.1737	Highly Informative	Inherited
Biological Process (BP)	leukocyte mediated immunity	0.2832	Highly Informative	Inherited
Biological Process (BP)	cell division	0.577	Highly Informative	Inherited
Biological Process (BP)	rRNA processing	0.4662	Highly Informative	Inherited
Biological Process (BP)	mitotic cell cycle	0.2409	Highly Informative	Inherited
Molecular Function (MF)	binding	2.178e-07	Least Informative	Direct
Molecular Function (MF)	hydrolase activity	0.0001357	Least Informative	Direct
Molecular Function (MF)	transferase activity	1	Least Informative	Inherited
Molecular Function (MF)	structural molecule activity	1.206e-10	Moderately Informative	Direct
Molecular Function (MF)	organic cyclic compound binding	0	Moderately Informative	Direct
Molecular Function (MF)	heterocyclic compound binding	0	Moderately Informative	Direct
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	0.9564	Moderately Informative	Inherited
Molecular Function (MF)	hydrolase activity, acting on ester bonds	0.2111	Moderately Informative	Inherited
Molecular Function (MF)	structural constituent of ribosome	0	Informative	Direct
Molecular Function (MF)	nuclease activity	0	Informative	Direct
Molecular Function (MF)	nucleotidyltransferase activity	6.599e-13	Informative	Direct
Molecular Function (MF)	nucleoside-triphosphatase activity	0	Informative	Direct
Molecular Function (MF)	DNA binding	0.9537	Informative	Inherited
Molecular Function (MF)	RNA binding	0.003087	Informative	Inherited
Molecular Function (MF)	chromatin binding	1.2e-10	Highly Informative	Direct
Molecular Function (MF)	RNA polymerase activity	6.33e-06	Highly Informative	Direct
Molecular Function (MF)	structure-specific DNA binding	0	Highly Informative	Direct
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	3.971e-11	Least Informative	Direct
Cellular Component (CC)	protein complex	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	1	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	1	Least Informative	Inherited
Cellular Component (CC)	cytosol	0.0002734	Moderately Informative	Direct
Cellular Component (CC)	ribonucleoprotein complex	0	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	2.347e-11	Moderately Informative	Direct
Cellular Component (CC)	intracellular organelle lumen	4.175e-09	Moderately Informative	Direct
Cellular Component (CC)	mitochondrial part	0.03904	Moderately Informative	Inherited
Cellular Component (CC)	DNA-directed RNA polymerase complex	6.149e-15	Informative	Direct
Cellular Component (CC)	chromosome	2.213e-14	Informative	Direct
Cellular Component (CC)	small ribosomal subunit	0.000147	Informative	Direct
Cellular Component (CC)	cytosolic ribosome	0.0004167	Informative	Direct
Cellular Component (CC)	nucleoplasm part	1	Informative	Inherited
Cellular Component (CC)	DNA-directed RNA polymerase II, core complex	1.584e-11	Highly Informative	Direct
Cellular Component (CC)	cytosolic small ribosomal subunit	2.503e-10	Highly Informative	Direct
Cellular Component (CC)	replisome	1.149e-07	Highly Informative	Direct
Cellular Component (CC)	nuclear chromosome part	0	Highly Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Nucleotidyltransferases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	0	Least Informative	Direct
Enzyme Commission (EC)	Ligases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on ester bonds	1	Least Informative	Inherited
Enzyme Commission (EC)	Transferring one-carbon groups	1	Least Informative	Inherited
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	0	Moderately Informative	Direct
Enzyme Commission (EC)	Ligases forming aminoacyl-tRNA and related compoun	0	Moderately Informative	Direct
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Methyltransferases	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Phenylalanine--tRNA ligase	0	Informative	Direct
Enzyme Commission (EC)	Ligases that form phosphoric-ester bonds	1	Informative	Inherited
Enzyme Commission (EC)	Aminoacyltransferases	0.1092	Informative	Inherited
Enzyme Commission (EC)	Methionine--tRNA ligase	0	Highly Informative	Direct
Enzyme Commission (EC)	Aspartate--tRNA ligase	0	Highly Informative	Direct
Enzyme Commission (EC)	Polyribonucleotide nucleotidyltransferase	0	Highly Informative	Direct
Enzyme Commission (EC)	DNA ligase (NAD(+))	6.306e-13	Highly Informative	Direct
Enzyme Commission (EC)	mRNA guanylyltransferase	3.114e-09	Highly Informative	Direct

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	cellular phenotype	0.004238	Least Informative	Inherited
Mammalian Phenotype (MP)	hematopoietic system phenotype	0.05888	Least Informative	Inherited
Mammalian Phenotype (MP)	tumorigenesis	0.001494	Moderately Informative	Inherited
Mammalian Phenotype (MP)	embryogenesis phenotype	0.1103	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal cell proliferation	0.01184	Informative	Inherited
Mammalian Phenotype (MP)	abnormal embryonic tissue morphology	0.6529	Informative	Inherited
Mammalian Phenotype (MP)	chromosomal instability	0	Highly Informative	Direct
Mammalian Phenotype (MP)	abnormal erythropoiesis	0.001409	Highly Informative	Inherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	cell physiology variant	1.849e-11	Least Informative	Direct
Worm Phenotype (WP)	organism environmental stimulus response variant	0.7785	Least Informative	Inherited
Worm Phenotype (WP)	growth variant	1	Least Informative	Inherited
Worm Phenotype (WP)	early embryonic lethal	1.125e-09	Moderately Informative	Direct
Worm Phenotype (WP)	endocytic transport defect	2.739e-05	Moderately Informative	Direct
Worm Phenotype (WP)	reproductive system morphology variant	0.009473	Moderately Informative	Inherited
Worm Phenotype (WP)	gametogenesis variant	0.02999	Moderately Informative	Inherited
Worm Phenotype (WP)	cell organization biogenesis variant	0.0449	Moderately Informative	Inherited
Worm Phenotype (WP)	cell homeostasis metabolism variant	0.05699	Moderately Informative	Inherited
Worm Phenotype (WP)	germ cell morphology variant	0.6343	Moderately Informative	Inherited
Worm Phenotype (WP)	chemical response variant	0.8606	Moderately Informative	Inherited
Worm Phenotype (WP)	sick	5.096e-09	Informative	Direct
Worm Phenotype (WP)	pleiotropic defects severe early emb	3.473e-08	Informative	Direct
Worm Phenotype (WP)	pachytene progression during oogenesis variant	2.454e-07	Informative	Direct
Worm Phenotype (WP)	germ cell compartment expansion variant	1.103e-05	Informative	Direct
Worm Phenotype (WP)	embryonic cell organization biogenesis variant	0.0002954	Informative	Direct
Worm Phenotype (WP)	germline nuclear positioning variant	0.0006507	Informative	Direct
Worm Phenotype (WP)	chromosome segregation variant	0.06895	Informative	Inherited
Worm Phenotype (WP)	cell division variant	0.1339	Informative	Inherited
Worm Phenotype (WP)	oocyte number decreased	4.784e-07	Highly Informative	Direct
Worm Phenotype (WP)	nuclear number variant	9.87e-05	Highly Informative	Direct
Worm Phenotype (WP)	excessive blebbing early emb	0.0001555	Highly Informative	Direct
Worm Phenotype (WP)	embryonic cell morphology variant	0.0002173	Highly Informative	Direct
Worm Phenotype (WP)	cell cycle variant	0.002204	Highly Informative	Inherited
Worm Phenotype (WP)	cleavage furrow defective early emb	0.8074	Highly Informative	Inherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)

	YP term	FDR (all)	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	chromosome/plasmid maintenance	2.007e-06	Informative	Direct
Yeast Phenotype (YP)	heat sensitivity	1.529e-05	Informative	Direct
Yeast Phenotype (YP)	cell cycle progression	0.0007657	Informative	Direct

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

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	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	embryo	1.341e-05	Least Informative	Direct
Xenopus ANatomical entity (XAN)	portion of tissue	0.001148	Least Informative	Inherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	seed	0.0004745	Least Informative	Direct
Plant ANatomical entity (PAN)	pedicel	0.0006621	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0.0004168	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

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	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0.116	Least Informative	Inherited
Enzyme Commission (EC)	Oxidoreductases	1	Least Informative	Inherited
Enzyme Commission (EC)	Hydrolases	1	Least Informative	Inherited
Enzyme Commission (EC)	Nucleotidyltransferases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	0	Moderately Informative	Direct
Enzyme Commission (EC)	Ligases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Transferring one-carbon groups	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Acyltransferases	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Exoribonucleases producing 5'-phosphomonoesters	0	Informative	Direct
Enzyme Commission (EC)	DNA helicase	0	Informative	Direct
Enzyme Commission (EC)	Ligases forming aminoacyl-tRNA and related compounds	0	Informative	Direct
Enzyme Commission (EC)	Acting on CH or CH(2) groups	1	Informative	Inherited
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	1	Informative	Inherited
Enzyme Commission (EC)	Polyribonucleotide nucleotidyltransferase	0	Highly Informative	Direct
Enzyme Commission (EC)	Phenylalanine--tRNA ligase	0	Highly Informative	Direct
Enzyme Commission (EC)	mRNA guanylyltransferase	2.54e-09	Highly Informative	Direct
Enzyme Commission (EC)	Aminoacyltransferases	0.1001	Highly Informative	Inherited
Enzyme Commission (EC)	With NAD(+) or NADP(+) as acceptor	1	Highly Informative	Inherited
Enzyme Commission (EC)	Ligases that form phosphoric-ester bonds	1	Highly Informative	Inherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

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	DB term	FDR (all)	SDDB level	Annotation (direct or inherited)
Drugbank ATC_code (DB)	blood and blood forming organs	0	Least Informative	Direct

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	DNA damage	0	Moderately Informative	Direct
Biological process	Transcription regulation	1	Moderately Informative	Inherited
Biological process	DNA recombination	0	Informative	Direct
Biological process	DNA replication	0	Informative	Direct
Biological process	Initiation factor	0	Informative	Direct
Biological process	Transcription termination	9.209e-16	Highly Informative	Direct
Biological process	Elongation factor	2.064e-14	Highly Informative	Direct
Cellular component	Cytoplasm	0	Least Informative	Direct
Cellular component	Plastid	0.0009649	Moderately Informative	Direct
Cellular component	Mitochondrion	1	Moderately Informative	Inherited
Cellular component	Chromosome	1	Informative	Inherited
Cellular component	Primosome	0	Highly Informative	Direct
Cellular component	Telomere	3.685e-09	Highly Informative	Direct
Molecular function	Zinc	0	Least Informative	Direct
Molecular function	Nucleotide-binding	2.482e-10	Least Informative	Direct
Molecular function	DNA-binding	0	Moderately Informative	Direct
Molecular function	Magnesium	0	Moderately Informative	Direct
Molecular function	Manganese	0	Moderately Informative	Direct
Molecular function	NAD	0	Moderately Informative	Direct
Molecular function	RNA-binding	0	Moderately Informative	Direct
Molecular function	Helicase	0	Informative	Direct
Molecular function	tRNA-binding	0	Informative	Direct
Post-translational modification	Hydrolase	1	Least Informative	Inherited
Post-translational modification	Transferase	1	Least Informative	Inherited
Post-translational modification	Ligase	0	Moderately Informative	Direct
Post-translational modification	Nucleotidyltransferase	0	Moderately Informative	Direct
Post-translational modification	Ribonucleoprotein	0	Moderately Informative	Direct
Post-translational modification	Nuclease	0.2562	Moderately Informative	Inherited
Post-translational modification	Aminoacyl-tRNA synthetase	0	Informative	Direct
Post-translational modification	Exonuclease	0	Informative	Direct
Post-translational modification	Ribosomal protein	0	Informative	Direct
Post-translational modification	Hydroxylation	0	Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	biopolymer metabolism	0	Least Informative	Direct
UniPathway (UP)	biopolymer biosynthesis	0	Moderately Informative	Direct
UniPathway (UP)	protein biosynthesis	0	Highly Informative	Direct

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 131 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 Nucleic acid-binding proteins 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 131 hidden Markov models representing the Nucleic acid-binding proteins superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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Nucleic acid-binding proteins superfamily