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 (3,186) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,609 57,156 33
Proteins 17,051 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 0.00000000000002922 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000006289 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000001323 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000001325 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00009851 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) developmental process 0.5817 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.6897 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.003775 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00001175 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.5094 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9389 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1044 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 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) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9453 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.03794 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.6636 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4519 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.3518 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.01618 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.007595 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.01786 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9829 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 0.0000000000001378 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.00000000298 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000293 Informative Direct
Biological Process (BP) sexual reproduction 0.0003507 Informative Direct
Biological Process (BP) single organism reproductive process 0.0008231 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.4416 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.1184 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.04573 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.8381 Informative Inherited
Biological Process (BP) growth 0.7414 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.09365 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.5339 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.6725 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.7604 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01546 Informative Inherited
Biological Process (BP) single-organism behavior 0.003149 Informative Inherited
Biological Process (BP) reproductive structure development 0.6018 Informative Inherited
Biological Process (BP) chromosome organization 0.3742 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.001728 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.5918 Informative Inherited
Biological Process (BP) ncRNA metabolic process 1 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.01179 Informative Inherited
Biological Process (BP) cell cycle process 0.4526 Informative Inherited
Biological Process (BP) regulation of mRNA processing 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) regulation of intrinsic apoptotic signaling pathway 0.0000000000003025 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.00000004539 Highly Informative Direct
Biological Process (BP) rRNA processing 0.00000075 Highly Informative Direct
Biological Process (BP) mRNA processing 0.000004056 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.00007308 Highly Informative Direct
Biological Process (BP) regulation of steroid biosynthetic process 0.0008538 Highly Informative Direct
Biological Process (BP) mRNA catabolic process 1 Highly Informative Inherited
Biological Process (BP) developmental growth 0.08499 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.01471 Highly Informative Inherited
Biological Process (BP) gonad development 0.003181 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000008525 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 8.141e-16 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 0.5404 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nuclease activity 0.00004446 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0004086 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.04255 Informative Inherited
Molecular Function (MF) protein complex binding 0.01342 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0.895 Informative Inherited
Molecular Function (MF) tubulin binding 0.000002441 Highly Informative Direct
Molecular Function (MF) mRNA binding 0.03263 Highly Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.001127 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00003493 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00008997 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1891 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 0.000002423 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000004255 Moderately Informative Direct
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.85 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 1 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.02718 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0 Highly Informative Direct
Cellular Component (CC) nuclear body 0.0000003938 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.0007521 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)embryo0.01649Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.02581Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.02013Moderately InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.4329Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0001133InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.09608InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.3588InformativeInherited
Xenopus ANatomical entity (XAN)trunk musculature0.00003062Highly InformativeDirect
Xenopus ANatomical entity (XAN)fused heart primordium0.0006006Highly 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 processDifferentiation0.0002603Moderately InformativeDirect
Biological processTranslation regulation4.711e-16InformativeDirect
Biological processRibosome biogenesis0.000005163InformativeDirect
Biological processmRNA splicing0.00005158InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processMyogenesis0.000000002073Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentNucleus0.00001525Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane6.436e-16Moderately InformativeDirect
Cellular componentSpliceosome0.00000001102InformativeDirect
Cellular componentChromosome0.6343InformativeInherited
Cellular componentTelomere0.00000005837Highly InformativeDirect
DomainTransmembrane0.000000000213Least InformativeDirect
DomainSH3-binding0.000000000000001826InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.164Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000005444Moderately 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 ]