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Entry version 125 (13 Nov 2019)
Sequence version 1 (01 Nov 1995)
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Protein

Uncharacterized outer membrane usher protein YhcD

Gene

yhcD

Organism
Escherichia coli (strain K12)
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

Involved in the export and assembly of a fimbrial subunit across the outer membrane.By similarity

<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 processFimbrium biogenesis, Transport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7670-MONOMER
ECOL316407:JW3183-MONOMER

Protein family/group databases

Transport Classification Database

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TCDBi
1.B.11.5.1 the outer membrane fimbrial usher porin (fup) 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:
Uncharacterized outer membrane usher protein YhcD
<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:yhcD
Ordered Locus Names:b3216, JW3183
<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 – 21Sequence analysisAdd BLAST21
<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_000000933322 – 793Uncharacterized outer membrane usher protein YhcDAdd BLAST772

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi769 ↔ 792Sequence analysis

Keywords - PTMi

Disulfide bond

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
P45420

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

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PaxDbi
P45420

PRoteomics IDEntifications database

More...
PRIDEi
P45420

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4261874, 172 interactors

Database of interacting proteins

More...
DIPi
DIP-12277N

STRING: functional protein association networks

More...
STRINGi
511145.b3216

<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
P45420

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 fimbrial export usher family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane beta strand

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105E6S Bacteria
ENOG410XPN5 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000260663

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P45420

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.60.40.2610, 1 hit
3.10.20.410, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR000015 Fimb_usher
IPR018030 Fimbrial_membr_usher_CS
IPR042186 FimD_plug_dom
IPR025949 PapC-like_C
IPR025885 PapC_N
IPR037224 PapC_N_sf

The PANTHER Classification System

More...
PANTHERi
PTHR30451 PTHR30451, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13953 PapC_C, 1 hit
PF13954 PapC_N, 1 hit
PF00577 Usher, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141729 SSF141729, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01151 FIMBRIAL_USHER, 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.

P45420-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLKKTLLAYT IGFAFSPPAN ADGIEIAAVD FDRETLKSLG VDPNISHYFS
60 70 80 90 100
RSARFLPGEY SLIVSVNGEK KGNIATRFDE NGDICLDQAF LQQAGLKIPS
110 120 130 140 150
EEKNGCYDYI LSYPGTTITP LPNQEALDII VSPQAIIPIG LDLTNAATGG
160 170 180 190 200
TAALLNYSLM SSRAEFSNGS SDYSQAALEG GININDWMLR SHQFLTQTNG
210 220 230 240 250
TFSNQNSSTY LQRTFTDLKT LMRAGEVNLN NSVLEGASIY GIEIAPDNAL
260 270 280 290 300
QTSGSGVQVT GIANTSQARV EIRQQGVLIH SILVPAGAFT IPDVPVRNGN
310 320 330 340 350
SDLNVTVVET DGSSHNYIVP STLFNQHVES FQGYRFAIGR VDDDYDESPW
360 370 380 390 400
VISASSGWNL TRWSAMNGGV IVAENYQAAS IRSSLVPLPD LTVSSQISTS
410 420 430 440 450
QDTKDSLQGQ KYRLDANYNL PFSLGLTTSL TRSDRHYREL SEAIDDDYTD
460 470 480 490 500
PTKSTYALGL NWSNSILGGF NISGYKTYSY DGDNDSSNLN INWNKAFKHA
510 520 530 540 550
TVSVNWQHQL SASENNEDDG DLFYVNISIP FGRSNTATLY TRHDDHKTHY
560 570 580 590 600
GTGVMGVVSD EMSYYVNAER DHDERETSLN GSISSNLHYT QVSLAAGASG
610 620 630 640 650
SDSRTYNGTM SGGIAVHDQG VTFSPWTIND TFAIAKMDNN IAGVRITSQA
660 670 680 690 700
GPVWTDFRGN AVIPSIQPWR TSGVEIDTAS LPKNVDIGNG TKMIKQGRGA
710 720 730 740 750
VGKVGFSAIT QRRALLNITL SDGKKLPRGV AIEDSEGNYL TTSVDDGVVF
760 770 780 790
LNNIKPDMVL DIKDEQQSCR IHLTFPEDAP KDVFYETATG ECQ
Length:793
Mass (Da):86,289
Last modified:November 1, 1995 - 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:i952CFAB835BB3681
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U18997 Genomic DNA Translation: AAA58018.1
U00096 Genomic DNA Translation: AAC76248.1
AP009048 Genomic DNA Translation: BAE77260.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B65113

NCBI Reference Sequences

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RefSeqi
NP_417683.1, NC_000913.3
WP_000914994.1, NZ_SSZK01000007.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76248; AAC76248; b3216
BAE77260; BAE77260; BAE77260

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947738

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3183
eco:b3216

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.3311

<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: AAA58018.1
U00096 Genomic DNA Translation: AAC76248.1
AP009048 Genomic DNA Translation: BAE77260.1
PIRiB65113
RefSeqiNP_417683.1, NC_000913.3
WP_000914994.1, NZ_SSZK01000007.1

3D structure databases

SMRiP45420
ModBaseiSearch...

Protein-protein interaction databases

BioGridi4261874, 172 interactors
DIPiDIP-12277N
STRINGi511145.b3216

Protein family/group databases

TCDBi1.B.11.5.1 the outer membrane fimbrial usher porin (fup) family

Proteomic databases

jPOSTiP45420
PaxDbiP45420
PRIDEiP45420

Genome annotation databases

EnsemblBacteriaiAAC76248; AAC76248; b3216
BAE77260; BAE77260; BAE77260
GeneIDi947738
KEGGiecj:JW3183
eco:b3216
PATRICifig|511145.12.peg.3311

Organism-specific databases

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

More...
EchoBASEi
EB2661

Phylogenomic databases

eggNOGiENOG4105E6S Bacteria
ENOG410XPN5 LUCA
HOGENOMiHOG000260663
PhylomeDBiP45420

Enzyme and pathway databases

BioCyciEcoCyc:G7670-MONOMER
ECOL316407:JW3183-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P45420

Family and domain databases

Gene3Di2.60.40.2610, 1 hit
3.10.20.410, 1 hit
InterProiView protein in InterPro
IPR000015 Fimb_usher
IPR018030 Fimbrial_membr_usher_CS
IPR042186 FimD_plug_dom
IPR025949 PapC-like_C
IPR025885 PapC_N
IPR037224 PapC_N_sf
PANTHERiPTHR30451 PTHR30451, 1 hit
PfamiView protein in Pfam
PF13953 PapC_C, 1 hit
PF13954 PapC_N, 1 hit
PF00577 Usher, 1 hit
SUPFAMiSSF141729 SSF141729, 1 hit
PROSITEiView protein in PROSITE
PS01151 FIMBRIAL_USHER, 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 nameiYHCD_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: P45420
Secondary accession number(s): Q2M8Z6
<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: November 1, 1995
Last modified: November 13, 2019
This is version 125 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

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
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