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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 (3,187) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,642 57,156 33
Proteins 17,072 42,512 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 0.00000000000005013 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00000000000009436 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000000225 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000001764 Least Informative Direct
Biological Process (BP) biological regulation 0.000001585 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00003552 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1346 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8338 Least Informative Inherited
Biological Process (BP) single-organism cellular 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) regulation of cellular metabolic process 0.00000007244 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0001179 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0002182 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.3598 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.04218 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) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3625 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.9551 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.8534 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.09313 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2186 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.005526 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.03544 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.005795 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.9929 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.06789 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9669 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.2545 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.5471 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.279 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.7661 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) system development 0.09067 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) signaling 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01961 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.00000009503 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000001449 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000001952 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00006986 Informative Direct
Biological Process (BP) regulation of catabolic process 0.00008313 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0006141 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0008377 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.6838 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.838 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of transport 0.06987 Informative Inherited
Biological Process (BP) regulation of transmembrane transport 0.001266 Informative Inherited
Biological Process (BP) regulation of system process 0.01083 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.2187 Informative Inherited
Biological Process (BP) response to inorganic substance 0.4075 Informative Inherited
Biological Process (BP) response to radiation 0.2 Informative Inherited
Biological Process (BP) regulation of proteolysis 0.477 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.01082 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.05268 Informative Inherited
Biological Process (BP) regulation of ion transport 0.02501 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.359 Informative Inherited
Biological Process (BP) growth 0.001478 Informative Inherited
Biological Process (BP) generation of neurons 0.98 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.006166 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.01582 Informative Inherited
Biological Process (BP) single organism reproductive process 0.003655 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.6593 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.7483 Informative Inherited
Biological Process (BP) regulation of secretion 0.1746 Informative Inherited
Biological Process (BP) positive regulation of transport 0.0759 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) regulation of cell differentiation 0.3399 Informative Inherited
Biological Process (BP) behavior 0.006513 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.001441 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.5469 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.7184 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.1891 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.1161 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.001615 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.04262 Informative Inherited
Biological Process (BP) system process 0.3603 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.001311 Informative Inherited
Biological Process (BP) cell development 0.687 Informative Inherited
Biological Process (BP) nitrogen compound transport 0.004184 Informative Inherited
Biological Process (BP) epithelium development 0.001025 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.4862 Informative Inherited
Biological Process (BP) ncRNA processing 1 Informative Inherited
Biological Process (BP) regulation of RNA stability 0 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.00000000000009436 Highly Informative Direct
Biological Process (BP) mRNA metabolic process 0.00000000001456 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.000000001384 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.000000006558 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.000000008981 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000000009554 Highly Informative Direct
Biological Process (BP) negative regulation of ion transmembrane transport 0.00000003784 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.00000004252 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.00000005024 Highly Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.00000006673 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.00000007315 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.000000275 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.00001533 Highly Informative Direct
Biological Process (BP) response to UV 0.00002333 Highly Informative Direct
Biological Process (BP) regulation of transmembrane transporter activity 0.00005879 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.00007803 Highly Informative Direct
Biological Process (BP) regulation of binding 0.000154 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0001784 Highly Informative Direct
Biological Process (BP) regulation of cation transmembrane transport 0.0002491 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.000278 Highly Informative Direct
Biological Process (BP) appendage development 0.0007621 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0008001 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.0009815 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0.001832 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion by cell 0.003273 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.005008 Highly Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0.006961 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular component biogenesis 0.06196 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 1 Highly Informative Inherited
Biological Process (BP) regulation of response to wounding 0.01328 Highly Informative Inherited
Biological Process (BP) neuron development 0.2876 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.001217 Highly Informative Inherited
Biological Process (BP) chromosome organization 0.01638 Highly Informative Inherited
Biological Process (BP) sensory perception 0.7531 Highly Informative Inherited
Biological Process (BP) cell maturation 0.02649 Highly Informative Inherited
Biological Process (BP) muscle structure development 0.01149 Highly Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 0.05311 Highly Informative Inherited
Molecular Function (MF) binding 0.000000000000003237 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) transferase activity, transferring phosphorus-containing groups 0.3383 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3493 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.00000000003115 Informative Direct
Molecular Function (MF) nuclease activity 0.000007782 Informative Direct
Molecular Function (MF) protein dimerization activity 0.02414 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.2563 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) protein heterodimerization activity 0.000000002623 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.0000002748 Highly Informative Direct
Molecular Function (MF) mRNA binding 0.000001326 Highly Informative Direct
Molecular Function (MF) tubulin binding 0.0002071 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000001696 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.00006177 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0007314 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 0.00000000003564 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000002175 Moderately Informative Direct
Cellular Component (CC) cell projection 0.2322 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein granule 0.0000000009472 Informative Direct
Cellular Component (CC) neuron projection 0.000005886 Informative Direct
Cellular Component (CC) chromosome 0.0003748 Informative Direct
Cellular Component (CC) extrinsic component of membrane 0.0006126 Informative Direct
Cellular Component (CC) site of polarized growth 0.001386 Informative Inherited
Cellular Component (CC) synapse 0.00185 Informative Inherited
Cellular Component (CC) cell projection part 0.1688 Informative Inherited
Cellular Component (CC) cytoplasmic region 0.02377 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.168 Informative Inherited
Cellular Component (CC) pole plasm 0.00000001499 Highly Informative Direct
Cellular Component (CC) nucleolus 0.000001418 Highly Informative Direct
Cellular Component (CC) growth cone 0.00008039 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.0005625 Highly Informative Direct
Cellular Component (CC) neuronal cell body 0.0009816 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.01506 Highly Informative Inherited
Cellular Component (CC) dendrite 0.02137 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 variant0.03266Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1758Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.0004937InformativeDirect
Worm Phenotype (WP)dendrite development variant0.131Highly 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)embryo0.0007451Least InformativeDirect
Xenopus ANatomical entity (XAN)head0.007527Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.04101Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical cluster0.2338Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000001396InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.0005454InformativeDirect
Xenopus ANatomical entity (XAN)pharyngeal region0.0008327InformativeDirect
Xenopus ANatomical entity (XAN)trunk musculature0.0001868Highly 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)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
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 processDifferentiation0.0001981Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processRibosome biogenesis0.00001785InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processMyogenesis0.0000000027Highly InformativeDirect
Biological processRNA-mediated gene silencing0.0001042Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.000008408Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell junction0.4193Moderately InformativeInherited
Cellular componentSpliceosome0.00000002015InformativeDirect
Cellular componentChromosome0.03147InformativeInherited
Cellular componentSynapse0.25InformativeInherited
Cellular componentExosome0Highly InformativeDirect
Cellular componentSynaptosome0.000001528Highly InformativeDirect
Cellular componentTelomere0.00001328Highly InformativeDirect
DomainTransmembrane0.0000000004944Least InformativeDirect
DomainSH3-binding0.000000000000001551InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.2631Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000003968Moderately 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 ]