SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,104) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,211 19,468 21
Proteins 4,208 19,463 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) nitrogen compound transport 0.0000000002674 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.00000000268 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.000000003946 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0003551 Moderately Informative Direct
Biological Process (BP) protein transport 0.000000000004154 Informative Direct
Biological Process (BP) intracellular transport 0.00003468 Informative Direct
Biological Process (BP) protein localization to organelle 0.005575 Informative Inherited
Biological Process (BP) establishment of protein localization to endoplasmic reticulum 0 Highly Informative Direct
Biological Process (BP) protein targeting 0 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.0008579 Highly Informative Direct
Molecular Function (MF) binding 0.00008453 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.8029 Moderately Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.000005487 Informative Direct
Molecular Function (MF) RNA binding 0.00003535 Informative Direct
Cellular Component (CC) cytoplasmic part 0.000002216 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.2049 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3649 Least Informative Inherited
Cellular Component (CC) membrane 0.002083 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0002884 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.000000005661 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane0.00198Least InformativeInherited
Cellular componentCell membrane0.00003728Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]