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Entry version 103 (13 Nov 2019)
Sequence version 2 (01 Dec 2000)
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Protein

Secretin GspD

Gene

epsD

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins. Required for secretion of cholera toxin through the outer membrane. This subunit forms the outer membrane channel.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei477May serve as a pivot that allows opening of the central gate for substrate egress1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processProtein transport, Transport

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Secretin GspD1 Publication
Alternative name(s):
Cholera toxin secretion protein EpsD
General secretion pathway protein D
Short name:
GspD
Type II secretion system protein D
Short name:
T2SS protein D
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:epsD
Ordered Locus Names:VC_2733
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri243277 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000584 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cell outer membrane, Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi395 – 417Missing : Complex resembles E.coli. 1 PublicationAdd BLAST23
Mutagenesisi477G → A: Decreased complex assembly; complex is partially open. 1 Publication1
Mutagenesisi505G → A: No complex assembly. 1 Publication1
Mutagenesisi508L → D: No complex assembly. 1 Publication1
Mutagenesisi510V → D: No complex assembly. 1 Publication1
Mutagenesisi522L → D: No complex assembly. 1 Publication1
Mutagenesisi524I → E: No complex assembly. 1 Publication1
Mutagenesisi605I → E: No complex assembly. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 24Sequence analysisAdd BLAST24
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000001310525 – 674Secretin GspDAdd BLAST650

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
P45779

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Forms a cylindrical channel with 15 subunits; unlike E.coli no 16-subunit channels are seen. The closed pentadeacameric channels are 195 Angstroms long and 145 Angstroms in diameter. Each subunit turns in a clock-wise manner around the channel.

1 Publication

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
itself17EBI-6449570,EBI-6449570

GO - Molecular functioni

Protein-protein interaction databases

Database of interacting proteins

More...
DIPi
DIP-59035N

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1674
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P45779

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni25 – 121N01 PublicationAdd BLAST97
Regioni123 – 187N11 PublicationAdd BLAST65
Regioni188 – 261N21 PublicationAdd BLAST74
Regioni264 – 338N31 PublicationAdd BLAST75
Regioni343 – 612Secretin1 PublicationAdd BLAST270
Regioni395 – 417Cap gate1 PublicationAdd BLAST23
Regioni614 – 674S domain1 PublicationAdd BLAST61

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N0, N1, N2 and N3 domains are periplasmic, while the secretin and S domains form a channel that is partially inserted in the outer membrane. The cap gate extends out on the extracellular side of the channel partially closing the channel. The secretin domain forms a double beta-barrel structure; the outer barrel has an outer diameter of about 110 Angstroms while the inner barrel forms the central gate with a small pore in the closed state.1 Publication

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

Signal, Transmembrane, Transmembrane beta strand

Phylogenomic databases

Identification of Orthologs from Complete Genome Data

More...
OMAi
YAVVEMD

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.1370.120, 3 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001775 GspD/PilQ
IPR005644 NolW-like
IPR038591 NolW-like_sf
IPR004846 T2SS/T3SS
IPR013356 T2SS_GspD
IPR004845 T2SS_GspD_CS

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00263 Secretin, 1 hit
PF03958 Secretin_N, 3 hits

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00811 BCTERIALGSPD

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02517 type_II_gspD, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00875 T2SP_D, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P45779-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKYWLKKSSW LLAGSLLSTP LAMANEFSAS FKGTDIQEFI NIVGRNLEKT
60 70 80 90 100
IIVDPSVRGK VDVRSFDTLN EEQYYSFFLS VLEVYGFAVV EMDNGVLKVI
110 120 130 140 150
KSKDAKTSAI PVLSGEERAN GDEVITQVVA VKNVSVRELS PLLRQLIDNA
160 170 180 190 200
GAGNVVHYDP ANIILITGRA AVVNRLAEII RRVDQAGDKE IEVVELNNAS
210 220 230 240 250
AAEMVRIVEA LNKTTDAQNT PEFLKPKFVA DERTNSILIS GDPKVRERLK
260 270 280 290 300
RLIKQLDVEM AAKGNNRVVY LKYAKAEDLV EVLKGVSENL QAEKGTGQPT
310 320 330 340 350
TSKRNEVMIA AHADTNSLVL TAPQDIMNAM LEVIGQLDIR RAQVLIEALI
360 370 380 390 400
VEMAEGDGIN LGVQWGSLES GSVIQYGNTG ASIGNVMIGL EEAKDTTQTK
410 420 430 440 450
AVYDTNNNFL RNETTTTKGD YTKLASALSS IQGAAVSIAM GDWTALINAV
460 470 480 490 500
SNDSSSNILS SPSITVMDNG EASFIVGEEV PVITGSTAGS NNDNPFQTVD
510 520 530 540 550
RKEVGIKLKV VPQINEGNSV QLNIEQEVSN VLGANGAVDV RFAKRQLNTS
560 570 580 590 600
VMVQDGQMLV LGGLIDERAL ESESKVPLLG DIPLLGQLFR STSSQVEKKN
610 620 630 640 650
LMVFIKPTII RDGVTADGIT QRKYNYIRAE QLFRAEKGLR LLDDASVPVL
660 670
PKFGDDRRHS PEIQAFIEQM EAKQ
Length:674
Mass (Da):73,470
Last modified:December 1, 2000 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i3D77B891A59E6223
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AE003852 differs from that shown. Reason: Frameshift. This may be a natural frameshift.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti89V → A in AAA58785 (Ref. 1) Curated1
Sequence conflicti144R → P in AAA58785 (Ref. 1) Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
L33796 Genomic DNA Translation: AAA58785.1
AE003852 Genomic DNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
WP_000878557.1, NZ_LT906614.1

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L33796 Genomic DNA Translation: AAA58785.1
AE003852 Genomic DNA No translation available.
RefSeqiWP_000878557.1, NZ_LT906614.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5WQ8electron microscopy3.26A/B/C/D/E/F/G/H/I/J/K/L/M/N/O25-674[»]
5WQ9electron microscopy4.22A/B/C/D/E/F/G/H/I/J/K/L/M/N/O25-674[»]
SMRiP45779
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

DIPiDIP-59035N

Proteomic databases

PRIDEiP45779

Phylogenomic databases

OMAiYAVVEMD

Family and domain databases

Gene3Di3.30.1370.120, 3 hits
InterProiView protein in InterPro
IPR001775 GspD/PilQ
IPR005644 NolW-like
IPR038591 NolW-like_sf
IPR004846 T2SS/T3SS
IPR013356 T2SS_GspD
IPR004845 T2SS_GspD_CS
PfamiView protein in Pfam
PF00263 Secretin, 1 hit
PF03958 Secretin_N, 3 hits
PRINTSiPR00811 BCTERIALGSPD
TIGRFAMsiTIGR02517 type_II_gspD, 1 hit
PROSITEiView protein in PROSITE
PS00875 T2SP_D, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiGSPD_VIBCH
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P45779
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 1, 2000
Last modified: November 13, 2019
This is version 103 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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