SUPERFAMILY 1.75 HMM library and genome assignments server


Prokaryotic type KH domain (KH-domain type II) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Alpha-lytic protease prodomain-like [ 54805] (10)
Superfamily:   Prokaryotic type KH domain (KH-domain type II) [ 54814]
Families:   Prokaryotic type KH domain (KH-domain type II) [ 54815] (4)


Superfamily statistics
Genomes (3,235) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,344 72,975 20
Proteins 10,643 57,034 16


Functional annotation
General category Information
Detailed category Translation

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) single-organism cellular process 0.9228 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01544 Least Informative Inherited
Biological Process (BP) organelle organization 0.0005978 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 4.192e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 6.101e-06 Moderately Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 4.976e-09 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 5.338e-09 Informative Direct
Biological Process (BP) organelle assembly 3.359e-09 Informative Direct
Biological Process (BP) ribonucleoprotein complex subunit organization 6.33e-14 Highly Informative Direct
Molecular Function (MF) binding 0.1825 Least Informative Inherited
Molecular Function (MF) structural molecule activity 3.781e-05 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.173 Moderately Informative Inherited
Molecular Function (MF) RNA binding 1.613e-09 Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.501e-07 Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.2157 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.04456 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6646 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1116 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 2.753e-05 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 3.337e-05 Moderately Informative Direct
Cellular Component (CC) cytosol 0.1709 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.02566 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 4.906e-08 Informative Direct
Cellular Component (CC) small ribosomal subunit 1.376e-10 Informative Direct
Cellular Component (CC) cytosolic small ribosomal subunit 6.01e-12 Highly Informative Direct

Document: GO 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 structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation1Moderately InformativeInherited
Biological processRibosome biogenesis0InformativeDirect
Biological processTranscription termination0Highly InformativeDirect
Cellular componentMembrane3.186e-12Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCell inner membrane2.9e-08InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009019 SSF54814 Protein matches
Abstract

The K homology domain is a common RNA-binding motif present in one or multiple copies in both prokaryotic and eukaryotic regulatory proteins. The KH motifs may act cooperatively to bind RNA in the case of multiple motifs, or independently in the case of single KH motif proteins. Prokaryotic (pKH) and eukaryotic (eKH) KH domains share a KH-motif, but have different topologies. The pKH domain has been found in a number of proteins, including the N-terminal domain of the S3 ribosomal protein [PubMed11014182], the C-terminal domain of Era GTPase [PubMed10411886] and the two C-terminal domains of the NusA transcription factor [PubMed11430821]. The structure of the pKH domain consists of a two-layer alpha/beta fold in the arrangement alpha/beta(2)/alpha/beta.

More information about these proteins can be found at Protein of the Month: RNA Exosomes.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · 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 10 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 Prokaryotic type KH domain (KH-domain type II) 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 10 hidden Markov models representing the Prokaryotic type KH domain (KH-domain type II) 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]