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UniProtKB - P76261 (PDED_ECOLI)

Entry version 128 (02 Dec 2020)
Sequence version 2 (27 Apr 2001)
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Protein

Probable cyclic di-GMP phosphodiesterase PdeD

Gene

pdeD

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

Annotation score:3 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 transcript 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

Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic-di-GMP (c-di-GMP) to 5'-pGpG (By similarity). May serve as a negative regulator of cellulose synthesis (as has been suggested for S.typhimurium); overexpression inhibits cell aggregation in strains able to produce adhesive curli fimbriae. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria (PubMed:16513732).By similarity1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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

Molecular functionHydrolase
Ligandc-di-GMP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G6996-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%5Fand%5Ftaxonomy%5Fsection">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:
Probable cyclic di-GMP phosphodiesterase PdeDCurated (EC:3.1.4.52By similarity)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:pdeD1 Publication
Synonyms:adrB, yoaD
Ordered Locus Names:b1815, JW1804
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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>Transmembranei16 – 36HelicalSequence analysisAdd BLAST21
Transmembranei245 – 265HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

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

Cells lacking this gene show increased aggregation, increased cellulose production but no increase in surface attachment.1 Publication

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001690331 – 532Probable cyclic di-GMP phosphodiesterase PdeDAdd BLAST532

Proteomic databases

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

More...PaxDbi		P76261

PRoteomics IDEntifications database

More...PRIDEi		P76261

<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

Expressed at 28 degrees Celsius in late stationary phase, constitutively expressed at low levels at 37 degrees Celsius, more highly expressed on plates than in liquid medium. Expression is RpoS- and CsgD-dependent.2 Publications

<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		4260346, 6 interactors

Protein interaction database and analysis system

More...IntActi		P76261, 1 interactor

STRING: functional protein association networks

More...STRINGi		511145.b1815

<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		P76261

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini266 – 515EALPROSITE-ProRule annotationAdd BLAST250

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2200, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_000445_131_2_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P76261

Database for complete collections of gene phylogenies

More...PhylomeDBi		P76261

Family and domain databases

Conserved Domains Database

More...CDDi		cd01948, EAL, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.450, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR024744, CSS-motif_dom
IPR001633, EAL_dom
IPR035919, EAL_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF12792, CSS-motif, 1 hit
PF00563, EAL, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00052, EAL, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF141868, SSF141868, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50883, EAL, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P76261-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQKAQRIIKT YRRNRMIVCT ICALVTLAST LSVRFISQRN LNQQRVVQFA 
        60         70         80         90        100
NHAVEELDKV LLPLQAGSEV LLPLIGLPCS VAHLPLRKQA AKLQTVRSIG 
       110        120        130        140        150
LVQDGTLYCS SIFGYRNVPV VDILAELPAP QPLLRLTIDR ALIKGSPVLI 
       160        170        180        190        200
QWTPAAGSSN AGVMEMINID LLTAMLLEPQ LPQISSASLT VDKRHLLYGN 
       210        220        230        240        250
GLVDSLPQPE DNENYQVSSQ RFPFTINVNG PGATALAWHY LPTQLPLAVL 
       260        270        280        290        300
LSLLVGYIAW LATAYRMSFS REINLGLAQH EFELFCQPLL NARSQQCIGV 
       310        320        330        340        350
EILLRWNNPR QGWISPDVFI PIAEEHHLIV PLTRYVMAET IRQRHVFPMS 
       360        370        380        390        400
SQFHVGINVA PSHFRRGVLI KDLNQYWFSA HPIQQLILEI TERDALLDVD 
       410        420        430        440        450
YRIARELHRK NVKLAIDDFG TGNSSFSWLE TLRPDVLKID KSFTAAIGSD 
       460        470        480        490        500
AVNSTVTDII IALGQRLNIE LVAEGVETQE QAKYLRRHGV HILQGYLYAQ 
       510        520        530 
PMPLRDFPKW LAGSQPPPAR HNGHITPIMP LR
Length:532
Mass (Da):59,711
Last modified:April 27, 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:i977155A7D56C18C7
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
U00096 Genomic DNA Translation: AAC74885.2
AP009048 Genomic DNA Translation: BAA15622.1

Protein sequence database of the Protein Information Resource

More...PIRi		G64942

NCBI Reference Sequences

More...RefSeqi		NP_416329.4, NC_000913.3
WP_001295494.1, NZ_SSUW01000012.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74885; AAC74885; b1815
BAA15622; BAA15622; BAA15622

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946336

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1804
eco:b1815

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.1892

<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
U00096 Genomic DNA Translation: AAC74885.2
AP009048 Genomic DNA Translation: BAA15622.1
PIRiG64942
RefSeqiNP_416329.4, NC_000913.3
WP_001295494.1, NZ_SSUW01000012.1

3D structure databases

SMRiP76261
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4260346, 6 interactors
IntActiP76261, 1 interactor
STRINGi511145.b1815

Proteomic databases

PaxDbiP76261
PRIDEiP76261

Genome annotation databases

EnsemblBacteriaiAAC74885; AAC74885; b1815
BAA15622; BAA15622; BAA15622
GeneIDi946336
KEGGiecj:JW1804
eco:b1815
PATRICifig|511145.12.peg.1892

Organism-specific databases

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

More...EchoBASEi		EB3289

Phylogenomic databases

eggNOGiCOG2200, Bacteria
HOGENOMiCLU_000445_131_2_6
InParanoidiP76261
PhylomeDBiP76261

Enzyme and pathway databases

BioCyciEcoCyc:G6996-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P76261

Family and domain databases

CDDicd01948, EAL, 1 hit
Gene3Di3.20.20.450, 1 hit
InterProiView protein in InterPro
IPR024744, CSS-motif_dom
IPR001633, EAL_dom
IPR035919, EAL_sf
PfamiView protein in Pfam
PF12792, CSS-motif, 1 hit
PF00563, EAL, 1 hit
SMARTiView protein in SMART
SM00052, EAL, 1 hit
SUPFAMiSSF141868, SSF141868, 1 hit
PROSITEiView protein in PROSITE
PS50883, EAL, 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 nameiPDED_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: P76261
Secondary accession number(s): P97188, P97189
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: April 27, 2001
Last modified: December 2, 2020
This is version 128 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

Reference proteome
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