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Entry version 30 (18 Sep 2019)
Sequence version 1 (16 Apr 2014)
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Protein

ESX-1 secretion system protein EccD1

Gene

eccD1

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
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

Part of the ESX-1 specialized secretion system, which delivers several virulence factors to host cells during infection, including the key virulence factors EsxA (ESAT-6) and EsxB (CFP-10).1 Publication2 Publications

Miscellaneous

The structure in 4KV3 was determined for a fusion protein with E.coli maltose-binding protein.1 Publication

<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 - 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 processTransport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MTBH37RV:G185E-8175-MONOMER

<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:
ESX-1 secretion system protein EccD1Curated
Alternative name(s):
ESX conserved component D11 Publication
Snm4 secretory protein1 Publication
Type VII secretion system protein EccD1Curated
Short name:
T7SS protein EccD1Curated
<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:eccD11 Publication
Synonyms:snm41 Publication
Ordered Locus Names:Rv3877
<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>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
<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 identifieri83332 [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 lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
<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
  • UP000001584 <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

Organism-specific databases

Mycobacterium tuberculosis strain H37Rv genome database

More...
TubercuListi
Rv3877

<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 subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini2 – 143Cytoplasmic1 PublicationAdd BLAST142
<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>Transmembranei144 – 164HelicalSequence analysisAdd BLAST21
Topological domaini165 – 170PeriplasmicCurated6
Transmembranei171 – 191HelicalSequence analysisAdd BLAST21
Topological domaini192 – 202CytoplasmicCuratedAdd BLAST11
Transmembranei203 – 223HelicalSequence analysisAdd BLAST21
Topological domaini224 – 227PeriplasmicCurated4
Transmembranei228 – 248HelicalSequence analysisAdd BLAST21
Topological domaini249 – 257CytoplasmicCurated9
Transmembranei258 – 278HelicalSequence analysisAdd BLAST21
Topological domaini279 – 285PeriplasmicCurated7
Transmembranei286 – 306HelicalSequence analysisAdd BLAST21
Topological domaini307 – 367CytoplasmicCuratedAdd BLAST61
Transmembranei368 – 388HelicalSequence analysisAdd BLAST21
Transmembranei389 – 409HelicalSequence analysisAdd BLAST21
Topological domaini410 – 420CytoplasmicCuratedAdd BLAST11
Transmembranei421 – 441HelicalSequence analysisAdd BLAST21
Topological domaini442 – 444PeriplasmicCurated3
Transmembranei445 – 465HelicalSequence analysisAdd BLAST21
Topological domaini466 – 482CytoplasmicCuratedAdd BLAST17
Transmembranei483 – 503HelicalSequence analysisAdd BLAST21
Topological domaini504 – 511PeriplasmicCurated8

GO - Cellular componenti

Keywords - Cellular componenti

Cell inner membrane, Cell 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

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Double espI-eccD1 mutants abolish EsxA and EsxB secretion, but not their expression (PubMed:14557547). Disruption abolishes EsxA and EsxB secretion, but not their expression (PubMed:14557536). Results in a lack of antigen specific immunogenicity and leads to attenuated virulence (PubMed:16368961). Mutants exhibit defects in bacterial growth during the acute phase of C57BL/6 mouse infection, but survive for 140 days despite a wild-type bacterial load in the lungs at 100 days post-infection, suggesting the pathway is required for virulence (PubMed:14557536). Nearly wild-type levels of IL-12 p40 (IL12B) and TNF-alpha are produced by infected murine macrophages, while the nitric oxide response is about 50% reduced (PubMed:14557536). Mouse macrophages do not induce cGAMP production, and thus do not sense bacterial DNA correctly to induce the innate immune response (PubMed:26048137).4 Publications

<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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedCombined sources
<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_00003932332 – 511ESX-1 secretion system protein EccD1Add BLAST510

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylserineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

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

More...
PaxDbi
P9WNQ7

PRoteomics IDEntifications database

More...
PRIDEi
P9WNQ7

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P9WNQ7

<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

Possibly a homodimer (PubMed:26922638). Part of the ESX-1 / type VII secretion system (T7SS), which is composed of cytosolic and membrane components. The ESX-1 membrane complex is composed of EccB1, EccCa1, EccCb1, EccD1 and EccE1.

2 Publications2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
83332.Rv3877

<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

More...
SMRi
P9WNQ7

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

<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 EccD/Snm4 family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

Identification of Orthologs from Complete Genome Data

More...
OMAi
VVQGHFF

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR006707 T7SS_EccD
IPR024962 YukD-like

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF08817 YukD, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF017804 Secretion_EccD1, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03920 T7SS_EccD, 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.

P9WNQ7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSAPAVAAGP TAAGATAARP ATTRVTILTG RRMTDLVLPA AVPMETYIDD
60 70 80 90 100
TVAVLSEVLE DTPADVLGGF DFTAQGVWAF ARPGSPPLKL DQSLDDAGVV
110 120 130 140 150
DGSLLTLVSV SRTERYRPLV EDVIDAIAVL DESPEFDRTA LNRFVGAAIP
160 170 180 190 200
LLTAPVIGMA MRAWWETGRS LWWPLAIGIL GIAVLVGSFV ANRFYQSGHL
210 220 230 240 250
AECLLVTTYL LIATAAALAV PLPRGVNSLG APQVAGAATA VLFLTLMTRG
260 270 280 290 300
GPRKRHELAS FAVITAIAVI AAAAAFGYGY QDWVPAGGIA FGLFIVTNAA
310 320 330 340 350
KLTVAVARIA LPPIPVPGET VDNEELLDPV ATPEATSEET PTWQAIIASV
360 370 380 390 400
PASAVRLTER SKLAKQLLIG YVTSGTLILA AGAIAVVVRG HFFVHSLVVA
410 420 430 440 450
GLITTVCGFR SRLYAERWCA WALLAATVAI PTGLTAKLII WYPHYAWLLL
460 470 480 490 500
SVYLTVALVA LVVVGSMAHV RRVSPVVKRT LELIDGAMIA AIIPMLLWIT
510
GVYDTVRNIR F
Length:511
Mass (Da):53,999
Last modified:April 16, 2014 - 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:i32B7C158E6E7C6FF
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
AL123456 Genomic DNA Translation: CCP46706.1

Protein sequence database of the Protein Information Resource

More...
PIRi
C70803

NCBI Reference Sequences

More...
RefSeqi
NP_218394.1, NC_000962.3
WP_003399976.1, NZ_NVQJ01000086.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CCP46706; CCP46706; Rv3877

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
886207

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mtu:Rv3877
mtv:RVBD_3877

<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
AL123456 Genomic DNA Translation: CCP46706.1
PIRiC70803
RefSeqiNP_218394.1, NC_000962.3
WP_003399976.1, NZ_NVQJ01000086.1

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
4KV2X-ray1.88A/B21-109[»]
4KV3X-ray2.20A/B21-109[»]
SMRiP9WNQ7
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv3877

PTM databases

iPTMnetiP9WNQ7

Proteomic databases

PaxDbiP9WNQ7
PRIDEiP9WNQ7

Genome annotation databases

EnsemblBacteriaiCCP46706; CCP46706; Rv3877
GeneIDi886207
KEGGimtu:Rv3877
mtv:RVBD_3877

Organism-specific databases

TubercuListiRv3877

Phylogenomic databases

OMAiVVQGHFF

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-8175-MONOMER

Family and domain databases

InterProiView protein in InterPro
IPR006707 T7SS_EccD
IPR024962 YukD-like
PfamiView protein in Pfam
PF08817 YukD, 1 hit
PIRSFiPIRSF017804 Secretion_EccD1, 1 hit
TIGRFAMsiTIGR03920 T7SS_EccD, 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 nameiECCD1_MYCTU
<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: P9WNQ7
Secondary accession number(s): L0TGV6, O69741, Q7D4P2
<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: April 16, 2014
Last sequence update: April 16, 2014
Last modified: September 18, 2019
This is version 30 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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