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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 (3,192) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 32,073 91,615 33
Proteins 17,278 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) 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 0.00000000000003802 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000000000003269 Least Informative Direct
Biological Process (BP) biological regulation 0.000000000285 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00001786 Least Informative Direct
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 0.6441 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.09185 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00006683 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0005743 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.3712 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.5667 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1096 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.8958 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system development 0.04592 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03492 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2629 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.4809 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8546 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.01934 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2982 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8345 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02357 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8598 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01341 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.973 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.05795 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7788 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.148 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) regulation of cellular amide metabolic process 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000006165 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000634 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.00006697 Informative Direct
Biological Process (BP) single organism reproductive process 0.0003826 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0004731 Informative Direct
Biological Process (BP) regulation of organelle organization 0.6437 Informative Inherited
Biological Process (BP) regulation of secretion 0.1906 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.07417 Informative Inherited
Biological Process (BP) regulation of ion transport 0.03285 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of transport 0.1489 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.1441 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.983 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.5885 Informative Inherited
Biological Process (BP) cellular response to inorganic substance 0.00419 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.1622 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.2158 Informative Inherited
Biological Process (BP) regulation of proteolysis 0.5122 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.003952 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.009996 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.003235 Informative Inherited
Biological Process (BP) generation of neurons 0.3126 Informative Inherited
Biological Process (BP) regulation of system process 0.01576 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.8182 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.002792 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.03922 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.007375 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1233 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 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) response to temperature stimulus 0.00136 Informative Inherited
Biological Process (BP) behavior 0.006651 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.6 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.9004 Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.002231 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.07962 Informative Inherited
Biological Process (BP) chromosome organization 0.4467 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.8229 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.001842 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.09122 Informative Inherited
Biological Process (BP) cell development 0.4291 Informative Inherited
Biological Process (BP) response to radiation 0.2111 Informative Inherited
Biological Process (BP) growth 0.001642 Informative Inherited
Biological Process (BP) tissue development 0.6783 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.5473 Informative Inherited
Biological Process (BP) cell cycle process 0.2395 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.9257 Informative Inherited
Biological Process (BP) ribosome biogenesis 0.1121 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.02219 Informative Inherited
Biological Process (BP) negative regulation of cellular amide metabolic process 0.0000000000006128 Highly Informative Direct
Biological Process (BP) regulation of proteolysis involved in cellular protein catabolic process 0.000000002799 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000000002847 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.000000004876 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.000000006605 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00000003629 Highly Informative Direct
Biological Process (BP) negative regulation of ion transmembrane transport 0.0000001008 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.0000001805 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.0000001918 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.0000001924 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.000001329 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000001583 Highly Informative Direct
Biological Process (BP) response to UV 0.00002744 Highly Informative Direct
Biological Process (BP) regulation of transmembrane transporter activity 0.0001012 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.0001241 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0002278 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0003355 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0003723 Highly Informative Direct
Biological Process (BP) regulation of cation transmembrane transport 0.0005638 Highly Informative Direct
Biological Process (BP) chromatin assembly or disassembly 0.0006857 Highly Informative Direct
Biological Process (BP) regulation of cytoplasmic translation 0.05628 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion by cell 0.002584 Highly Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 0.05369 Highly Informative Inherited
Biological Process (BP) regulation of chromosome organization 0.01119 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.01076 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.001698 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 1 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular component biogenesis 0.1162 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.001566 Highly Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.00389 Highly Informative Inherited
Biological Process (BP) neuron development 0.1734 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.001078 Highly Informative Inherited
Biological Process (BP) cell maturation 0.02553 Highly Informative Inherited
Biological Process (BP) muscle structure development 0.005142 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.004793 Highly Informative Inherited
Molecular Function (MF) binding 0.000000000000001646 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2065 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3923 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000000000005882 Informative Direct
Molecular Function (MF) nuclease activity 0.00001329 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.5491 Informative Inherited
Molecular Function (MF) protein dimerization activity 0.02454 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.2714 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) protein heterodimerization activity 0.000000006191 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.0000004811 Highly Informative Direct
Molecular Function (MF) tubulin binding 0.0002548 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.00000000000469 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000004207 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0000154 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0005025 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000000002298 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000001744 Moderately Informative Direct
Cellular Component (CC) cell projection 0.3229 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000393 Informative Direct
Cellular Component (CC) neuron projection 0.00006998 Informative Direct
Cellular Component (CC) extrinsic component of membrane 0.000994 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.3666 Informative Inherited
Cellular Component (CC) cytoplasmic region 0.03446 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.5586 Informative Inherited
Cellular Component (CC) synapse 0.003512 Informative Inherited
Cellular Component (CC) chromosome 0.1751 Informative Inherited
Cellular Component (CC) nuclear body 0.000000000000001616 Highly Informative Direct
Cellular Component (CC) pole plasm 0.000001866 Highly Informative Direct
Cellular Component (CC) growth cone 0.00008798 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.0006166 Highly Informative Direct
Cellular Component (CC) dendrite 0.01068 Highly Informative Inherited
Cellular Component (CC) neuronal cell body 0.001051 Highly Informative Inherited
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.01416 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

Human Phenotype (HP)

(show details) Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.0332Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.2078Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0006192InformativeDirect
Worm Phenotype (WP)dendrite development variant0.1416Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.0008424Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0.2316Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.01584Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000001351InformativeDirect
Xenopus ANatomical entity (XAN)trunk musculature0.0002762Highly InformativeDirect
Xenopus ANatomical entity (XAN)blastopore lip0.00127Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0.0003728Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0.001629Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.03719Least InformativeInherited
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processDifferentiation0.0001024Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processRibosome biogenesis0.0003333InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processMyogenesis0.000000003562Highly InformativeDirect
Biological processRNA-mediated gene silencing0.00001747Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.000006688Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell junction0.44Moderately InformativeInherited
Cellular componentSpliceosome0.00000001956InformativeDirect
Cellular componentChromosome0.03847InformativeInherited
Cellular componentSynapse0.2544InformativeInherited
Cellular componentExosome0Highly InformativeDirect
Cellular componentSynaptosome0.000001717Highly InformativeDirect
Cellular componentTelomere0.00001196Highly InformativeDirect
DomainTransmembrane0.0000000003725Least InformativeDirect
DomainSH3-binding0.000000000000001855InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.9963Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00005899Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · 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 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]