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Signal peptide-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Signal peptide-binding domain [ 47445]
Superfamily:   Signal peptide-binding domain [ 47446]
Families:   Signal peptide-binding domain [ 47447] (2)


Superfamily statistics
Genomes (3,173) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,519 17,604 8
Proteins 3,499 17,574 8


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) macromolecule localization 0.00000001717 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0009004 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0000000121 Moderately Informative Direct
Biological Process (BP) nitrogen compound transport 0.000000001521 Moderately Informative Direct
Biological Process (BP) protein transport 0.00000000003616 Informative Direct
Biological Process (BP) intracellular transport 0.0001149 Informative Direct
Biological Process (BP) protein localization to organelle 0.01115 Informative Inherited
Biological Process (BP) protein targeting 0.00000000000002273 Highly Informative Direct
Biological Process (BP) establishment of protein localization to endoplasmic reticulum 0 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.0001591 Highly Informative Direct
Molecular Function (MF) binding 0.004618 Least Informative Inherited
Molecular Function (MF) amide binding 0.00000007999 Informative Direct
Molecular Function (MF) peptide binding 0.000000001597 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00006486 Least Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR004125 SSF47446 Protein matches
Abstract

This entry represents the M 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 5 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 Signal peptide-binding 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 5 hidden Markov models representing the Signal peptide-binding 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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]