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Eukaryotic type KH-domain (KH-domain type I) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Eukaryotic type KH-domain (KH-domain type I) [ 54790]
Superfamily:   Eukaryotic type KH-domain (KH-domain type I) [ 54791]
Families:   Eukaryotic type KH-domain (KH-domain type I) [ 54792] (16)


Superfamily statistics
Genomes (3,194) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 32,340 91,615 33
Proteins 17,403 56,849 31


Functional annotation
General category Information
Detailed category RNA processing

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 0.000000009779 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000011 Least Informative Direct
Biological Process (BP) primary metabolic process 0.01137 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) cellular component organization or biogenesis 0.4528 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.002138 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) regulation of gene expression 0.0002388 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01498 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2912 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8351 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9952 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.75 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1607 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1446 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.9506 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.03928 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.828 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.07707 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.7882 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3734 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.9369 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.517 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.898 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.1721 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8955 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7325 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4703 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03321 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.02973 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3974 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular amide metabolic process 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.00000002898 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00005625 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00006993 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.000613 Informative Direct
Biological Process (BP) response to temperature stimulus 0.0006731 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.0007429 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.02997 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.005126 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.8894 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.003105 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.1691 Informative Inherited
Biological Process (BP) regulation of ion transport 0.04241 Informative Inherited
Biological Process (BP) regulation of system process 0.02194 Informative Inherited
Biological Process (BP) cellular response to inorganic substance 0.006249 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.2393 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.006736 Informative Inherited
Biological Process (BP) regulation of proteolysis 0.5841 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.003489 Informative Inherited
Biological Process (BP) negative regulation of transport 0.1665 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.6275 Informative Inherited
Biological Process (BP) regulation of secretion 0.2416 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.8601 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.05553 Informative Inherited
Biological Process (BP) generation of neurons 0.2495 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1303 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.00134 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.006991 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 gene expression 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.001053 Informative Inherited
Biological Process (BP) behavior 0.006335 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.7847 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.9739 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.6906 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.08234 Informative Inherited
Biological Process (BP) chromosome organization 0.5416 Informative Inherited
Biological Process (BP) epithelium development 0.00892 Informative Inherited
Biological Process (BP) cell development 0.3892 Informative Inherited
Biological Process (BP) embryo development 0.7331 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.2233 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.1798 Informative Inherited
Biological Process (BP) response to radiation 0.2736 Informative Inherited
Biological Process (BP) growth 0.006292 Informative Inherited
Biological Process (BP) single organism reproductive process 0.001034 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.01441 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.6645 Informative Inherited
Biological Process (BP) ribonucleoprotein complex subunit organization 0.001256 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) ribosome biogenesis 1 Informative Inherited
Biological Process (BP) regulation of RNA stability 0 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.0000000000003881 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.0000000006655 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0.000000001573 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000000008729 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.00000001009 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.00000001742 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.00000004094 Highly Informative Direct
Biological Process (BP) negative regulation of ion transmembrane transport 0.0000001514 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.0000002923 Highly Informative Direct
Biological Process (BP) mRNA processing 0.000003319 Highly Informative Direct
Biological Process (BP) response to UV 0.0000145 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.00001514 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.00003771 Highly Informative Direct
Biological Process (BP) regulation of transmembrane transporter activity 0.0001531 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.0001863 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0003258 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0003277 Highly Informative Direct
Biological Process (BP) anatomical structure maturation 0.0004121 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0004606 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0005211 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0007854 Highly Informative Direct
Biological Process (BP) chromatin assembly or disassembly 0.0008025 Highly Informative Direct
Biological Process (BP) regulation of cation transmembrane transport 0.0008226 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0008271 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.01582 Highly Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.002718 Highly Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0.01126 Highly Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 0.06401 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.009586 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular component biogenesis 0.1301 Highly Informative Inherited
Biological Process (BP) regulation of response to wounding 0.02048 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.002322 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion by cell 0.003656 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 1 Highly Informative Inherited
Biological Process (BP) cell maturation 0.0358 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.003047 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.3728 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) neuron development 0.09295 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.00464 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.475 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2888 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.000000000002425 Informative Direct
Molecular Function (MF) nuclease activity 0.00001842 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.6339 Informative Inherited
Molecular Function (MF) protein dimerization activity 0.04283 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.3169 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) protein heterodimerization activity 0.0000000332 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.0000007666 Highly Informative Direct
Molecular Function (MF) tubulin binding 0.000409 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000001839 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000235 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0007593 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000000001783 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000001086 Moderately Informative Direct
Cellular Component (CC) cell projection 0.3554 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000001279 Informative Direct
Cellular Component (CC) neuron projection 0.00004194 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.2084 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.8248 Informative Inherited
Cellular Component (CC) cytoplasmic region 0.06446 Informative Inherited
Cellular Component (CC) extrinsic component of membrane 0.001665 Informative Inherited
Cellular Component (CC) chromosome 0.1517 Informative Inherited
Cellular Component (CC) nuclear body 0.00000000000001166 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.00000006002 Highly Informative Direct
Cellular Component (CC) pole plasm 0.000000311 Highly Informative Direct
Cellular Component (CC) growth cone 0.000003247 Highly Informative Direct
Cellular Component (CC) dendrite 0.03869 Highly Informative Inherited
Cellular Component (CC) presynapse 0.1324 Highly Informative Inherited
Cellular Component (CC) neuronal cell body 0.005131 Highly Informative Inherited
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.01927 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Polyribonucleotide nucleotidyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDifferentiation0.0001063Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processRibosome biogenesis0.0003483InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processMyogenesis0.000000003697Highly InformativeDirect
Biological processRNA-mediated gene silencing0.00001748Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.000005581Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane6.573e-16Moderately InformativeDirect
Cellular componentCell junction0.4456Moderately InformativeInherited
Cellular componentSpliceosome0.000000003366InformativeDirect
Cellular componentChromosome0.03887InformativeInherited
Cellular componentSynapse0.2528InformativeInherited
Cellular componentExosome0Highly InformativeDirect
Cellular componentSynaptosome0.000001659Highly InformativeDirect
Cellular componentTelomere0.00001159Highly InformativeDirect
DomainTransmembrane0.0000000004327Least InformativeDirect
DomainSH3-binding0.00000000000000185InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.9947Least InformativeInherited
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00006012Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationIsopeptide bond0.00001092Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00001125Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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 29 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 Eukaryotic type KH-domain (KH-domain type I) 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 29 hidden Markov models representing the Eukaryotic type KH-domain (KH-domain type I) 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]