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 (3,144) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 28,504 30,948 33
Proteins 15,575 20,431 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 4.511e-09 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.016e-08 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.195e-07 Least Informative Direct
Biological Process (BP) regulation of metabolic process 2.499e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.178e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0009033 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.3454 Least Informative Inherited
Biological Process (BP) developmental process 0.1779 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 component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 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 programmed cell death 0.08526 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.1299 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.4498 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.02302 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) macromolecule catabolic process 0.06079 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9912 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.2918 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.3536 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) macromolecule localization 0.2779 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.9639 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7055 Moderately Informative Inherited
Biological Process (BP) organ development 0.9997 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5185 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.006075 Moderately Informative Inherited
Biological Process (BP) reproduction 0.005364 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0823 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.5488 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8512 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.9786 Moderately Informative Inherited
Biological Process (BP) RNA processing 1.409e-12 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 7.195e-10 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 1.697e-08 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 1.146e-07 Informative Direct
Biological Process (BP) single organism reproductive process 4.117e-05 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 8.48e-05 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.05593 Informative Inherited
Biological Process (BP) muscle tissue development 0.01517 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.7609 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.8575 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.9538 Informative Inherited
Biological Process (BP) single-organism behavior 0.5401 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01556 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8771 Informative Inherited
Biological Process (BP) growth 0.002386 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.002757 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) DNA metabolic process 0.8474 Informative Inherited
Biological Process (BP) chromosome organization 0.3019 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.04392 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.1051 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) reproductive structure development 0.5508 Informative Inherited
Biological Process (BP) muscle structure development 0.003753 Informative Inherited
Biological Process (BP) sexual reproduction 0.01995 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1251 Informative Inherited
Biological Process (BP) cell cycle process 0.1697 Informative Inherited
Biological Process (BP) regulation of cell cycle 1 Informative Inherited
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) spermatogenesis 8.581e-08 Highly Informative Direct
Biological Process (BP) rRNA processing 5.478e-07 Highly Informative Direct
Biological Process (BP) developmental growth 1.377e-06 Highly Informative Direct
Biological Process (BP) cell fate commitment 1.688e-06 Highly Informative Direct
Biological Process (BP) mRNA processing 4.39e-06 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 6.012e-06 Highly Informative Direct
Biological Process (BP) muscle organ development 3.739e-05 Highly Informative Direct
Biological Process (BP) development of primary male sexual characteristics 6.614e-05 Highly Informative Direct
Biological Process (BP) chromatin assembly 0.0002539 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.0003683 Highly Informative Direct
Biological Process (BP) regulation of steroid biosynthetic process 0.000996 Highly Informative Direct
Biological Process (BP) gonad development 0.001246 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.02405 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.0862 Highly Informative Inherited
Molecular Function (MF) binding 2.786e-13 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 0.4459 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 1.797e-05 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0002506 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.06527 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.9629 Informative Inherited
Molecular Function (MF) tubulin binding 1.422e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.00253 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.9598 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.076e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.04939 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.001026 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 1.731e-06 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 2.951e-05 Moderately Informative Direct
Cellular Component (CC) cell projection 0.9697 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.8602 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 1 Moderately Informative Inherited
Cellular Component (CC) nucleolus 2.504e-05 Informative Direct
Cellular Component (CC) neuron projection 0.01351 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.9969 Informative Inherited
Cellular Component (CC) chromosome 0.8657 Informative Inherited
Cellular Component (CC) nuclear body 1.284e-14 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 2.827e-05 Highly Informative Direct
Cellular Component (CC) lipid particle 7.613e-05 Highly Informative Direct
Cellular Component (CC) chromatin 0.0002559 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 0.01326 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)embryo0.01534Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.02462Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.01597Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.429Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001121InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.3569InformativeInherited
Xenopus ANatomical entity (XAN)trunk musculature2.092e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)fused heart primordium0.0005686Highly 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 processDifferentiation0.0002169Moderately InformativeDirect
Biological processTranslation regulation4.701e-16InformativeDirect
Biological processRibosome biogenesis5.429e-06InformativeDirect
Biological processmRNA splicing1.476e-05InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus1.18e-05Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane3.21e-16Moderately InformativeDirect
Cellular componentSpliceosome6.017e-09InformativeDirect
Cellular componentChromosome0.6228InformativeInherited
Cellular componentTelomere3.699e-08Highly InformativeDirect
DomainTransmembrane2.352e-10Least InformativeDirect
DomainSH3-binding2.138e-15InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.1471Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein5.717e-06Moderately 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 ]