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Entry version 138 (13 Nov 2019)
Sequence version 2 (11 Jul 2001)
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Protein

Putative secretin GspD

Gene

gspD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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 folded proteins across the outer membrane. This subunit would form the outer membrane channel.By similarity

Miscellaneous

Part of a cryptic operon that encodes proteins involved in type II secretion machinery in other organisms, but is not expressed in strain K12.

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>Sitei461May serve as a pivot that allows opening of the central gate for substrate egressBy similarity1

<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

  • identical protein binding Source: IntAct

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7703-MONOMER
ECOL316407:JW5707-MONOMER
MetaCyc:G7703-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
1.B.22.1.3 the outer bacterial membrane secretin (secretin) family

<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:
Putative secretin GspD1 Publication
Alternative name(s):
Putative general secretion pathway protein D
Putative 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:gspD
Synonyms:yheF
Ordered Locus Names:b3325, JW5707
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<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 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 – 23Sequence analysisAdd BLAST23
<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_000001309924 – 650Putative secretin GspDAdd BLAST627

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P45758

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P45758

PRoteomics IDEntifications database

More...
PRIDEi
P45758

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Silenced by the DNA-binding protein H-NS under standard growth conditions.1 Publication

<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; approximately 25% of the particles have 16-subunit channels. Closed pentadeacameric channels are 180 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
itself3EBI-21225187,EBI-21225187

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4261297, 269 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3325

<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

1650
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
P45758

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>Regioni24 – 122N01 PublicationAdd BLAST99
Regioni124 – 188N11 PublicationAdd BLAST65
Regioni189 – 263N21 PublicationAdd BLAST75
Regioni266 – 342N31 PublicationAdd BLAST77
Regioni345 – 596Secretin1 PublicationAdd BLAST252
Regioni598 – 650S domain1 PublicationAdd BLAST53

<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 N1, N2 and N3 domains each form a periplasmic ring; the N0 domain was present but not resolved by electron microscopy. The secretin domain forms a double beta-barrel structure; the outer barrel has a 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

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105GVR Bacteria
COG1450 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000253751

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P45758

KEGG Orthology (KO)

More...
KOi
K02453

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P45758

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.

P45758-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKGLNKITCC LLAALLMPCA GHAENEQYGA NFNNADIRQF VEIVGQHLGK
60 70 80 90 100
TILIDPSVQG TISVRSNDTF SQQEYYQFFL SILDLYGYSV ITLDNGFLKV
110 120 130 140 150
VRSANVKTSP GMIADSSRPG VGDELVTRIV PLENVPARDL APLLRQMMDA
160 170 180 190 200
GSVGNVVHYE PSNVLILTGR ASTINKLIEV IKRVDVIGTE KQQIIHLEYA
210 220 230 240 250
SAEDLAEILN QLISESHGKS QMPALLSAKI VADKRTNSLI ISGPEKARQR
260 270 280 290 300
ITSLLKSLDV EESEEGNTRV YYLKYAKATN LVEVLTGVSE KLKDEKGNAR
310 320 330 340 350
KPSSSGAMDN VAITADEQTN SLVITADQSV QEKLATVIAR LDIRRAQVLV
360 370 380 390 400
EAIIVEVQDG NGLNLGVQWA NKNVGAQQFT NTGLPIFNAA QGVADYKKNG
410 420 430 440 450
GITSANPAWD MFSAYNGMAA GFFNGDWGVL LTALASNNKN DILATPSIVT
460 470 480 490 500
LDNKLASFNV GQDVPVLSGS QTTSGDNVFN TVERKTVGTK LKVTPQVNEG
510 520 530 540 550
DAVLLEIEQE VSSVDSSSNS TLGPTFNTRT IQNAVLVKTG ETVVLGGLLD
560 570 580 590 600
DFSKEQVSKV PLLGDIPLVG QLFRYTSTER AKRNLMVFIR PTIIRDDDVY
610 620 630 640 650
RSLSKEKYTR YRQEQQQRID GKSKALVGSE DLPVLDENTF NSHAPAPSSR
Length:650
Mass (Da):70,698
Last modified:July 11, 2001 - 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:i973259A12A7237B2
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 AAA58122 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated

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
U18997 Genomic DNA Translation: AAA58122.1 Different initiation.
U00096 Genomic DNA Translation: AAC76350.2
AP009048 Genomic DNA Translation: BAE77966.1

Protein sequence database of the Protein Information Resource

More...
PIRi
H65125

NCBI Reference Sequences

More...
RefSeqi
NP_417784.4, NC_000913.3
WP_001326512.1, NZ_SSZK01000040.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76350; AAC76350; b3325
BAE77966; BAE77966; BAE77966

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947822

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW5707
eco:b3325

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3406

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<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
U18997 Genomic DNA Translation: AAA58122.1 Different initiation.
U00096 Genomic DNA Translation: AAC76350.2
AP009048 Genomic DNA Translation: BAE77966.1
PIRiH65125
RefSeqiNP_417784.4, NC_000913.3
WP_001326512.1, NZ_SSZK01000040.1

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
5WQ7electron microscopy3.04A/B/C/D/E/F/G/H/I/J/K/L/M/N/O24-650[»]
SMRiP45758
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261297, 269 interactors
STRINGi511145.b3325

Protein family/group databases

TCDBi1.B.22.1.3 the outer bacterial membrane secretin (secretin) family

Proteomic databases

jPOSTiP45758
PaxDbiP45758
PRIDEiP45758

Genome annotation databases

EnsemblBacteriaiAAC76350; AAC76350; b3325
BAE77966; BAE77966; BAE77966
GeneIDi947822
KEGGiecj:JW5707
eco:b3325
PATRICifig|1411691.4.peg.3406

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB2727

Phylogenomic databases

eggNOGiENOG4105GVR Bacteria
COG1450 LUCA
HOGENOMiHOG000253751
InParanoidiP45758
KOiK02453
PhylomeDBiP45758

Enzyme and pathway databases

BioCyciEcoCyc:G7703-MONOMER
ECOL316407:JW5707-MONOMER
MetaCyc:G7703-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P45758

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_ECOLI
<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: P45758
Secondary accession number(s): Q2M6Z0
<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: July 11, 2001
Last modified: November 13, 2019
This is version 138 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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