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 (3,184) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,398 57,156 33
Proteins 16,902 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 1.054e-08 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 6.44e-08 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.369e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.427e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001004 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.1922 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.3293 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 0.004878 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) reproduction 0.0002089 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.3157 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.5785 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.08527 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 0.5109 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6661 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) response to abiotic stimulus 0.4481 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.3913 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7075 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 0.459 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.01613 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2015 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.5418 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9464 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 9.568e-13 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 6.654e-10 Informative Direct
Biological Process (BP) single organism reproductive process 2.933e-07 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 3.055e-07 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.0002939 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.1236 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.04787 Informative Inherited
Biological Process (BP) muscle structure development 0.00223 Informative Inherited
Biological Process (BP) muscle tissue development 0.009133 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.8506 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.7603 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.8602 Informative Inherited
Biological Process (BP) single-organism behavior 0.27 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01408 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8631 Informative Inherited
Biological Process (BP) growth 0.006173 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.005172 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) DNA metabolic process 0.8362 Informative Inherited
Biological Process (BP) chromosome organization 0.3855 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.08564 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.1713 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) reproductive system development 0.5843 Informative Inherited
Biological Process (BP) sexual reproduction 0.09036 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.397 Informative Inherited
Biological Process (BP) cell cycle process 0.2052 Informative Inherited
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 7.829e-14 Highly Informative Direct
Biological Process (BP) spermatogenesis 4.543e-08 Highly Informative Direct
Biological Process (BP) cell fate commitment 6.332e-07 Highly Informative Direct
Biological Process (BP) rRNA processing 8.729e-07 Highly Informative Direct
Biological Process (BP) developmental growth 1.116e-06 Highly Informative Direct
Biological Process (BP) mRNA processing 3.295e-06 Highly Informative Direct
Biological Process (BP) muscle organ development 2.125e-05 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 7.967e-05 Highly Informative Direct
Biological Process (BP) regulation of steroid biosynthetic process 0.00085 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 1 Highly Informative Inherited
Biological Process (BP) gonad development 0.002006 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.01323 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.08458 Highly Informative Inherited
Molecular Function (MF) binding 8.389e-11 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 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.5362 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 3.442e-05 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.000442 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.07968 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.9043 Informative Inherited
Molecular Function (MF) tubulin binding 2.887e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.001089 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.9002 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 3.057e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 5.647e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.04821 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 8.092e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1.215e-06 Moderately Informative Direct
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.9397 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 1 Moderately Informative Inherited
Cellular Component (CC) nucleolus 4.536e-05 Informative Direct
Cellular Component (CC) neuron projection 0.02571 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) chromosome 0.9904 Informative Inherited
Cellular Component (CC) nuclear body 1.628e-14 Highly Informative Direct
Cellular Component (CC) chromatin 0.0003158 Highly Informative Direct

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)embryo0.01612Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.02548Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.01956Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.431Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001134InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.09141InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.3588InformativeInherited
Xenopus ANatomical entity (XAN)trunk musculature3.059e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)fused heart primordium0.0005814Highly 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 processDifferentiation0.0002388Moderately InformativeDirect
Biological processTranslation regulation4.713e-16InformativeDirect
Biological processRibosome biogenesis5.034e-06InformativeDirect
Biological processmRNA splicing5.027e-05InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus1.415e-05Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane3.239e-16Moderately InformativeDirect
Cellular componentSpliceosome1.121e-08InformativeDirect
Cellular componentChromosome0.6335InformativeInherited
Cellular componentTelomere5.877e-08Highly InformativeDirect
DomainTransmembrane2.117e-10Least InformativeDirect
DomainSH3-binding1.83e-15InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.1537Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein5.636e-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 ]