SUPERFAMILY 1.75 HMM library and genome assignments server

Preprotein translocase SecY subunit superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Preprotein translocase SecY subunit [ 103490]
Superfamily:   Preprotein translocase SecY subunit [ 103491]
Families:   Preprotein translocase SecY subunit [ 103492]


Superfamily statistics
Genomes (3,220) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,183 22,772 2
Proteins 4,143 22,759 2


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)localization0.0000000000037220.0000000005378Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.068490.2353Least InformativeInherited
Biological Process (BP)macromolecule localization0.000000000072710.0000000005288Moderately InformativeDirect
Biological Process (BP)cellular localization0.00000032520.000003291Moderately InformativeDirect
Biological Process (BP)organic substance transport00Moderately InformativeDirect
Biological Process (BP)protein transport0.000000012520.00000003249InformativeDirect
Biological Process (BP)cytoplasmic transport0.00018890.0001777InformativeDirect
Biological Process (BP)protein localization to organelle0.000094990.00005424InformativeDirect
Biological Process (BP)single-organism cellular localization0.00000000069140.000000006764InformativeDirect
Biological Process (BP)single-organism intracellular transport0.0000000040720.00000001245InformativeDirect
Molecular Function (MF)binding0.054380.2637Least InformativeInherited
Molecular Function (MF)ribonucleoprotein complex binding0.000000000000064350.000000000000291Highly InformativeDirect
Cellular Component (CC)membrane0.000000042410.000002395Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00000000040510.000000009425Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.000000000550.00000000007236Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0026120.01092Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum00Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle0.0000000000000014290.00000000000005851Moderately InformativeDirect
Cellular Component (CC)membrane region0.0000000007780.000000005143Moderately InformativeDirect
Cellular Component (CC)intrinsic component of membrane0.0026040.01794Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.0000000000000160.000000000000003071InformativeDirect
Cellular Component (CC)integral component of membrane0.0011460.00895InformativeInherited
Cellular Component (CC)integral component of organelle membrane00.000000000000003071Highly InformativeDirect

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) localization 0.0000000005378 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.2353 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.0000000005288 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000003291 Moderately Informative Direct
Biological Process (BP) organic substance transport 0 Moderately Informative Direct
Biological Process (BP) protein transport 0.00000003249 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0001777 Informative Direct
Biological Process (BP) protein localization to organelle 0.00005424 Informative Direct
Biological Process (BP) single-organism membrane organization 0.0001678 Informative Direct
Biological Process (BP) single-organism cellular localization 0.000000006764 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00000001245 Informative Direct
Molecular Function (MF) binding 0.2637 Least Informative Inherited
Molecular Function (MF) ribonucleoprotein complex binding 0.000000000000291 Highly Informative Direct
Cellular Component (CC) membrane 0.000002395 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000009425 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000007236 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.01092 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.00000000000005851 Moderately Informative Direct
Cellular Component (CC) membrane region 0.000000005143 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.01794 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.000000000000003071 Informative Direct
Cellular Component (CC) integral component of membrane 0.00895 Informative Inherited
Cellular Component (CC) integral component of organelle membrane 0.000000000000003071 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)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processTranslocation0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentPlastid0.000004374Moderately InformativeDirect
Cellular componentThylakoid0.0000000000004348InformativeDirect
DomainTransmembrane0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002208 SSF103491 Protein matches
Abstract

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. [PubMed2202721]. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) [PubMed2202721]. The chaperone protein SecB [PubMed11336818] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [PubMed10418149]. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains [PubMed12167867]. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.

The eubacterial secY protein [PubMed1406280] interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains 10 transmembrane (TM), 6 cytoplasmic and 5 periplasmic regions.

Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export [PubMed2110998]. Homologs of secY are found in archaebacteria [PubMed1764515]. SecY is also encoded in the chloroplast genome of some algae [PubMed1544427] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.


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-quality) · 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 1 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 Preprotein translocase SecY subunit 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 1 hidden Markov models representing the Preprotein translocase SecY subunit 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]