SUPERFAMILY 1.75 HMM library and genome assignments server


Domain of the SRP/SRP receptor G-proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Four-helical up-and-down bundle [ 47161] (28)
Superfamily:   Domain of the SRP/SRP receptor G-proteins [ 47364]
Families:   Domain of the SRP/SRP receptor G-proteins [ 47365] (3)


Superfamily statistics
Genomes (3,089) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,188 18,045 21
Proteins 4,186 18,042 21


Functional annotation
General category Regulation
Detailed category Signal transduction

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) response to stimulus 0.2494 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003379 Least Informative Inherited
Biological Process (BP) localization 0.001859 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.000000227 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00005448 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0000001813 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.08276 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.002858 Moderately Informative Inherited
Biological Process (BP) protein transport 0.0000000004788 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0000000001078 Informative Direct
Biological Process (BP) protein localization to organelle 0.000000000009448 Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.00000000000001077 Highly Informative Direct
Molecular Function (MF) binding 0.0003614 Least Informative Direct
Molecular Function (MF) ribonucleoprotein complex binding 0.0000000002051 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000001266 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.3082 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01185 Least Informative Inherited
Cellular Component (CC) membrane 0.007369 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0000009299 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0000002139 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.000008197 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.000000009409 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)root system0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least 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)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten 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)
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane0.001271Least InformativeInherited
Cellular componentCell membrane0.00001855Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013822 SSF47364 Protein matches
Abstract

This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.

These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homolog of ftsY; and bacterial flagellar biosynthesis protein flhF.


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 8 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 Domain of the SRP/SRP receptor G-proteins 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 8 hidden Markov models representing the Domain of the SRP/SRP receptor G-proteins 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 ]