SUPERFAMILY 1.75 HMM library and genome assignments server


PRC-barrel domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   PRC-barrel domain [ 50345]
Superfamily:   PRC-barrel domain [ 50346] (4)
Families:   MTH1895 [ 101773]
  Photosynthetic reaction centre, H-chain, cytoplasmic domain [ 50347]
  RIKEN cDNA 2310057j16 protein (KIAA1543) [ 110202]
  RimM C-terminal domain-like [ 141326]


Superfamily statistics
Genomes (2,669) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,696 12,123 10
Proteins 5,241 11,399 10


Functional annotation
General category Metabolism
Detailed category Photosynthesis

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of cellular process 0.4742 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.8213 Least Informative Inherited
Biological Process (BP) developmental process 0.6959 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2912 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.00262 Least Informative Inherited
Biological Process (BP) organelle organization 4.619e-05 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 3.869e-07 Moderately Informative Direct
Biological Process (BP) nervous system development 0.02356 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1302 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.4726 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 0.000145 Informative Direct
Biological Process (BP) microtubule-based process 2.564e-05 Informative Direct
Biological Process (BP) cell projection organization 0.0006883 Informative Direct
Biological Process (BP) regulation of organelle organization 6.869e-06 Informative Direct
Biological Process (BP) generation of neurons 0.003835 Informative Inherited
Biological Process (BP) neuron projection development 0.0001467 Highly Informative Direct
Molecular Function (MF) binding 0.7557 Least Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 1.021e-11 Informative Direct
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.05917 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001794 Least Informative Inherited
Cellular Component (CC) protein complex 0.06971 Least Informative Inherited
Cellular Component (CC) cytoskeleton 5.142e-06 Moderately Informative Direct
Cellular Component (CC) microtubule cytoskeleton 4.748e-08 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processRibosome biogenesis0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011033 SSF50346 Protein matches
Abstract

The PRC-barrel is a partly opened all-beta barrel domain of approximately 80 residues long, which is found in several bacterial, archaeal and plant proteins.

The PRC-barrel domain is found in subunit H of the photosynthetic reaction centre (PRC) in purple bacteria. PRC is an integral membrane pigment-protein complex that carries out light-driven electron transfer reactions during photosynthesis. At the core of the reaction centre is a collection of light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H polypeptide subunits [PubMed11005826]. The H subunit has a single transmembrane helix and a large cytoplasmic domain [PubMed10611277]. The core of the cytoplasmic domain contains the PRC-barrel.

A PRC-barrel domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [PubMed12429060].


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

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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 6 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 PRC-barrel domain 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 6 hidden Markov models representing the PRC-barrel domain 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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]