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Entry version 115 (11 Dec 2019)
Sequence version 1 (01 Nov 1998)
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Protein

Protein translocase subunit SecD

Gene

secD

Organism
Treponema pallidum (strain Nichols)
Status
Reviewed-Annotation score:

Annotation score:2 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>
-Protein inferred from homologyi <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

Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA.UniRule annotation

<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, Translocation, 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:
Protein translocase subunit SecDUniRule annotation
<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:secDUniRule annotation
Ordered Locus Names:TP_0410
<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>OrganismiTreponema pallidum (strain Nichols)
<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 identifieri243276 [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 lineageiBacteriaSpirochaetesSpirochaetalesSpirochaetaceaeTreponema
<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
  • UP000000811 <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

<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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei7 – 27HelicalUniRule annotationAdd BLAST21
Transmembranei419 – 439HelicalUniRule annotationAdd BLAST21
Transmembranei446 – 468HelicalUniRule annotationAdd BLAST23
Transmembranei469 – 489HelicalUniRule annotationAdd BLAST21
Transmembranei511 – 531HelicalUniRule annotationAdd BLAST21
Transmembranei538 – 558HelicalUniRule annotationAdd BLAST21

GO - Cellular componenti

Keywords - Cellular componenti

Cell inner membrane, Cell 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 describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000959731 – 583Protein translocase subunit SecDAdd BLAST583

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
O83425

<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 complex with SecF. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.

UniRule annotation

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
O83425, 9 interactors

STRING: functional protein association networks

More...
STRINGi
243276.TPANIC_0410

<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

3D structure databases

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

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SMRi
O83425

Database of comparative protein structure models

More...
ModBasei
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

<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

Belongs to the SecD/SecF family. SecD subfamily.UniRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG4107QN8 Bacteria
COG0342 LUCA

KEGG Orthology (KO)

More...
KOi
K03072

Identification of Orthologs from Complete Genome Data

More...
OMAi
APMEIIE

Database of Orthologous Groups

More...
OrthoDBi
121331at2

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01463_B SecD_B, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR005791 SecD
IPR022813 SecD/SecF_arch_bac
IPR022645 SecD/SecF_bac

The PANTHER Classification System

More...
PANTHERi
PTHR30081 PTHR30081, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02355 SecD_SecF, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00916 2A0604s01, 1 hit
TIGR01129 secD, 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.

O83425-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSKKARFGVV LVVLAACSGF LFPTLQWYFL TDAQTRQRAL SSREQIKEYA
60 70 80 90 100
VQSAERDLAD LTRLARAGSD EDISARYAPL VAAARQNLSY SGRPAPSRWT
110 120 130 140 150
AAALVSAFPV KSEQGFVLYA RPLMEQTYRE AVLKMKRRQA QAVKLGLDLS
160 170 180 190 200
GGTSVVIKAD LSEVTKGVPD AERAAIRSEA MALVLSTLEN RINRFGLSEP
210 220 230 240 250
VIRRQGEDRV YVEIPGLTDR DRVHSIVMGR GVLAFHLVDD DATQKLLDHY
260 270 280 290 300
RNNPQGTFDA AHQLHDLSLV PEHTSVLGVY RKDSYGLDVR DGFLVVKKEP
310 320 330 340 350
ALEGRHIRDA TVSSGRANEP LVLFDLDHEG ARIFSELTTK EIGRRLAIVS
360 370 380 390 400
DGKIRSAPAI REPITAGSGS ISGFSAEEAQ NLKTALRSAW LNVALEIENQ
410 420 430 440 450
QVVGASMGEE SIRQGTRALV WGLCAVLLFM LVWYQEAGVN ACVAQLLNLY
460 470 480 490 500
IMFGVLSAFN LTLTLSSIAG MILTIGMAVD ANVVVFERIR EELALGKSRG
510 520 530 540 550
AAVCSGFERA FWAIMDSNVT TFIAALFLSV LGTGPIKGFA YSLAIGVVSS
560 570 580
VFTALFVSRL MFDYGTEVLH KKTVRIGWRI ARV
Length:583
Mass (Da):63,861
Last modified:November 1, 1998 - v1
<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:i9A787E64C4CFE1A1
GO

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
AE000520 Genomic DNA Translation: AAC65398.1

Protein sequence database of the Protein Information Resource

More...
PIRi
H71326

NCBI Reference Sequences

More...
RefSeqi
WP_010881858.1, NC_021490.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC65398; AAC65398; TP_0410

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
34331877

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
tpa:TP_0410

<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
AE000520 Genomic DNA Translation: AAC65398.1
PIRiH71326
RefSeqiWP_010881858.1, NC_021490.2

3D structure databases

SMRiO83425
ModBaseiSearch...

Protein-protein interaction databases

IntActiO83425, 9 interactors
STRINGi243276.TPANIC_0410

Proteomic databases

PRIDEiO83425

Genome annotation databases

EnsemblBacteriaiAAC65398; AAC65398; TP_0410
GeneIDi34331877
KEGGitpa:TP_0410

Phylogenomic databases

eggNOGiENOG4107QN8 Bacteria
COG0342 LUCA
KOiK03072
OMAiAPMEIIE
OrthoDBi121331at2

Family and domain databases

HAMAPiMF_01463_B SecD_B, 1 hit
InterProiView protein in InterPro
IPR005791 SecD
IPR022813 SecD/SecF_arch_bac
IPR022645 SecD/SecF_bac
PANTHERiPTHR30081 PTHR30081, 1 hit
PfamiView protein in Pfam
PF02355 SecD_SecF, 1 hit
TIGRFAMsiTIGR00916 2A0604s01, 1 hit
TIGR01129 secD, 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 nameiSECD_TREPA
<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: O83425
<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: December 15, 1998
Last sequence update: November 1, 1998
Last modified: December 11, 2019
This is version 115 of the entry and version 1 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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