SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,179) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 30,234 57,156 33
Proteins 16,367 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) regulation of metabolic process 0.00000002986 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000007152 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000001513 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000001554 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001066 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.3193 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.5615 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.00627 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) reproduction 0.0004641 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.3394 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.6496 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.08345 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.5159 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6539 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4761 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.4198 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.71 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.4625 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.0106 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2239 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9697 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 0.0000000000003911 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000000005158 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0000003098 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000004495 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0001314 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.1332 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.06189 Informative Inherited
Biological Process (BP) regulation of response to stress 0.007182 Informative Inherited
Biological Process (BP) muscle structure development 0.002077 Informative Inherited
Biological Process (BP) muscle tissue development 0.009994 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.8426 Informative Inherited
Biological Process (BP) cell-cell signaling 0.7703 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.752 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.8522 Informative Inherited
Biological Process (BP) single-organism behavior 0.2633 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01621 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8975 Informative Inherited
Biological Process (BP) growth 0.002243 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.006655 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) chromosome organization 0.416 Informative Inherited
Biological Process (BP) DNA metabolic process 0.8622 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.07895 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.1654 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) reproductive system development 0.569 Informative Inherited
Biological Process (BP) sexual reproduction 0.0921 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.398 Informative Inherited
Biological Process (BP) cell cycle process 0.2354 Informative Inherited
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 0.00000000000007603 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000006377 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.000000721 Highly Informative Direct
Biological Process (BP) rRNA processing 0.000001093 Highly Informative Direct
Biological Process (BP) developmental growth 0.000001294 Highly Informative Direct
Biological Process (BP) mRNA processing 0.000002508 Highly Informative Direct
Biological Process (BP) muscle organ development 0.00002491 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.00007514 Highly Informative Direct
Biological Process (BP) chromatin assembly 0.0003643 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 1 Highly Informative Inherited
Biological Process (BP) gonad development 0.002187 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.01479 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.09038 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000005363 Least Informative Direct
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 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.5619 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 0.00003955 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0004845 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.07755 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.9495 Informative Inherited
Molecular Function (MF) tubulin binding 0.000003598 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.001185 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.9458 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000002431 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00009224 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.05524 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000009442 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000001296 Moderately Informative Direct
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.9372 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 1 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.02862 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) chromosome 0.9812 Informative Inherited
Cellular Component (CC) nuclear body 0.00000000000001492 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 0.00004787 Highly Informative Direct
Cellular Component (CC) lipid particle 0.0001582 Highly Informative Direct
Cellular Component (CC) chromatin 0.0003182 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.01237 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)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.1143Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.006071Moderately InformativeInherited
Worm Phenotype (WP)receptor mediated endocytosis defective0.0004743InformativeDirect

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)trunk0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.01577Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.02523Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.01809Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.4311Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001132InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.0897InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.3592InformativeInherited
Xenopus ANatomical entity (XAN)trunk musculature0.00002641Highly InformativeDirect
Xenopus ANatomical entity (XAN)fused heart primordium0.0005854Highly 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)seed0.0003722Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0.001616Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.03701Least 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 phosphorous-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 processDifferentiation0.0002421Moderately InformativeDirect
Biological processTranslation regulation4.701e-16InformativeDirect
Biological processRibosome biogenesis0.000005189InformativeDirect
Biological processmRNA splicing0.00005018InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.00001496Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane3.235e-16Moderately InformativeDirect
Cellular componentSpliceosome0.00000001139InformativeDirect
Cellular componentChromosome0.6347InformativeInherited
Cellular componentTelomere0.00000005971Highly InformativeDirect
DomainTransmembrane0.0000000001875Least InformativeDirect
DomainSH3-binding0.000000000000001825InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.1513Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000005822Moderately 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) · 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]