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UniProtKB - Q9KVL2 (CDPA_VIBCH)

Entry version 94 (25 May 2022)
Sequence version 1 (01 Oct 2000)
Previous versions | rss
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Protein

Cyclic di-GMP phosphodiesterase CdpA

Gene

cdpA

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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 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

Phosphodiesterase (PDE) that catalyzes the hydrolysis of cyclic diguanylate (c-di-GMP). Is involved in the modulation of intracellular c-di-GMP levels. Cyclic-di-GMP is a second messenger which positively regulates biofilm formation and negatively regulates virulence in V.cholerae, and is proposed to play an important role in the transition from persistence in the environment to survival in the host. CdpA functions as a repressor of biofilm formation but has no effect on colonization of the infant mouse small intestine. Does not possess diguanylate cyclase (DGC) activity, due to its inactive degenerate GGDEF domain.

1 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>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+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

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, Magnesium

<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:
Cyclic di-GMP phosphodiesterase CdpA (EC:3.1.4.52)
Short name:
c-di-GMP PDE
<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:cdpA
Ordered Locus Names:VC_0130
<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>OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
<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 identifieri243277 [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 › Vibrionales › Vibrionaceae › Vibrio ›
<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
  • UP000000584 <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 1

<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 have a level of c-di-GMP almost four-fold higher than that of the respective parent strain. Disruption of this gene also results in increased biofilm formation.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi493 – 496GVGE → AVGA: Reduction in PDE activity. 1 Publication4

<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_00004259601 – 829Cyclic di-GMP phosphodiesterase CdpAAdd BLAST829

<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

Is up-regulated during biofilm formation, and is also induced during a late stage of infection of the host. However, cdpA expression is not regulated by c-di-GMP concentration.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

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		243277.VC_0130

<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

AlphaFold Protein Structure Database

More...AlphaFoldDBi		Q9KVL2

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

More...SMRi		Q9KVL2

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>Domaini593 – 829EALPROSITE-ProRule annotationAdd BLAST237

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>Regioni419 – 480Degenerate GGDEF domainAdd BLAST62

<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 EAL domain is required for c-di-GMP PDE activity, and the degenerate GGDEF domain is required for full PDE activity of the EAL domain (PubMed:18227161). The GG(D/E)EF motif in CdpA is degenerate, having the sequence GVGEW.1 Publication

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2199, Bacteria
COG2200, Bacteria
COG3287, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_000445_75_2_6

Identification of Orthologs from Complete Genome Data

More...OMAi		FEHNTDI

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
3.30.70.270, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR019494, FIST_C
IPR013702, FIST_domain_N
IPR000160, GGDEF_dom
IPR029787, Nucleotide_cyclase
IPR043128, Rev_trsase/Diguanyl_cyclase

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00563, EAL, 1 hit
PF08495, FIST, 1 hit
PF10442, FIST_C, 1 hit
PF00990, GGDEF, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00052, EAL, 1 hit
SM00897, FIST, 1 hit
SM01204, FIST_C, 1 hit
SM00267, GGDEF, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF141868, SSF141868, 1 hit
SSF55073, SSF55073, 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.

Q9KVL2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MFTVSRLIPD LASANQVLET MDLPHGQSIL VQIFSPLSRE HVVQLARLIR 
        60         70         80         90        100
SRHPQACLLG CSTEEVIFQG EVHHQVTLLQ ITVFEQTYLS RAVVDYSDDE 
       110        120        130        140        150
AADAERLARQ LELTSMSRAV VCFSWQMDTL QVARFALRDT QGAPVPVAGG 
       160        170        180        190        200
AAKQTPSGRW VLLDEACYQN ASVAIALHGE ALYVETGGYT EWQPVGRTYR 
       210        220        230        240        250
VTAVEGDRVL RLDDEPIEAI YQRNLGAQAD LPHDWLISFP LMKGECRHQD 
       260        270        280        290        300
LYLPLGLAEE GGLRFNRPLA LQDEVRFCFD HPSLTLERVY LTAQQLQAKQ 
       310        320        330        340        350
CQQVWVFNCA LRLNFMHENH ELQPLQAVAP TDGCYCWGEL LYEHGQQQVM 
       360        370        380        390        400
HHSMTFLALR EGAVRDDLVP IPLPSYPEGM TSPLFNLIRH AFHDLDAMTD 
       410        420        430        440        450
NLAQQIRAQT SLLTASYRRD RRTGLPNRVV LRERLANFAA NEHLIALKVT 
       460        470        480        490        500
NFNQINEKYG YPVGDKLLRD LSEQFQVFLD QKLAGQSGLY AIGVGEWATV 
       510        520        530        540        550
FRAKLDGKSI HSHFYQFVEQ LEHVNFEPYG LPNVDYLSIS LCAGLVSQGD 
       560        570        580        590        600
FAEHSPDELL LRAIEARRYA FNNNHHFCNA ARLKVQESVR QERLNWLSRV 
       610        620        630        640        650
SRAVVRDDVV VYAQPICQAR SHIVASYECL VRIEDEGEII LPGNFLPIIT 
       660        670        680        690        700
DTHLYTRLSR QMITHTFNMM RHRPEAFSIN LSPQDLMSER TLQHLEAAIK 
       710        720        730        740        750
SVADPARVGL EVLESEQIKD YGRMIEVCNH FRTLGATIIV DDFGSGYSNI 
       760        770        780        790        800
DEIVKLEPQV IKLDGSLIRN IDQDVKQRRI AEQLVKLCQV LNAKTVAEFV 
       810        820 
HNQTVCRISE DMGVDYLQGY FLGRPSRLG
Length:829
Mass (Da):94,055
Last modified:October 1, 2000 - 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:iF3A6FCC77AD5BE3B
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
AE003852 Genomic DNA Translation: AAF93307.1

Protein sequence database of the Protein Information Resource

More...PIRi		C82361

NCBI Reference Sequences

More...RefSeqi		NP_229788.1, NC_002505.1
WP_000495585.1, NZ_LT906614.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAF93307; AAF93307; VC_0130

Database of genes from NCBI RefSeq genomes

More...GeneIDi		57741373

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		vch:VC_0130

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|243277.26.peg.121

<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
AE003852 Genomic DNA Translation: AAF93307.1
PIRiC82361
RefSeqiNP_229788.1, NC_002505.1
WP_000495585.1, NZ_LT906614.1

3D structure databases

AlphaFoldDBiQ9KVL2
SMRiQ9KVL2
ModBaseiSearch...

Protein-protein interaction databases

STRINGi243277.VC_0130

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		2614885

Genome annotation databases

EnsemblBacteriaiAAF93307; AAF93307; VC_0130
GeneIDi57741373
KEGGivch:VC_0130
PATRICifig|243277.26.peg.121

Phylogenomic databases

eggNOGiCOG2199, Bacteria
COG2200, Bacteria
COG3287, Bacteria
HOGENOMiCLU_000445_75_2_6
OMAiFEHNTDI

Family and domain databases

CDDicd01948, EAL, 1 hit
Gene3Di3.20.20.450, 1 hit
3.30.70.270, 1 hit
InterProiView protein in InterPro
IPR001633, EAL_dom
IPR035919, EAL_sf
IPR019494, FIST_C
IPR013702, FIST_domain_N
IPR000160, GGDEF_dom
IPR029787, Nucleotide_cyclase
IPR043128, Rev_trsase/Diguanyl_cyclase
PfamiView protein in Pfam
PF00563, EAL, 1 hit
PF08495, FIST, 1 hit
PF10442, FIST_C, 1 hit
PF00990, GGDEF, 1 hit
SMARTiView protein in SMART
SM00052, EAL, 1 hit
SM00897, FIST, 1 hit
SM01204, FIST_C, 1 hit
SM00267, GGDEF, 1 hit
SUPFAMiSSF141868, SSF141868, 1 hit
SSF55073, SSF55073, 1 hit
PROSITEiView protein in PROSITE
PS50883, EAL, 1 hit

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 nameiCDPA_VIBCH
<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: Q9KVL2
<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: March 19, 2014
Last sequence update: October 1, 2000
Last modified: May 25, 2022
This is version 94 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
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