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UniProtKB - Q5JFI4 (PDAD_THEKO)

Entry version 89 (23 Feb 2022)
Sequence version 1 (15 Feb 2005)
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Protein

Pyruvoyl-dependent arginine decarboxylase

Gene

pdaD

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
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

<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

pyruvateUniRule annotationNote: Binds 1 pyruvoyl group covalently per subunit.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

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 functionDecarboxylase, Lyase
LigandPyruvate

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		4.1.1.19, 5246

<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:
Pyruvoyl-dependent arginine decarboxylaseUniRule annotation (EC:4.1.1.19UniRule annotation)
Short name:
PvlArgDCUniRule annotation
Cleaved into the following 2 chains:
Pyruvoyl-dependent arginine decarboxylase subunit betaUniRule annotation
Pyruvoyl-dependent arginine decarboxylase subunit alphaUniRule annotation
<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:pdaDUniRule annotation
Ordered Locus Names:TK0149
<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>OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
<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 identifieri69014 [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 lineageiArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›
<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
  • UP000000536 <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

<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_00000233341 – 43Pyruvoyl-dependent arginine decarboxylase subunit betaUniRule annotationAdd BLAST43
ChainiPRO_000002333544 – 157Pyruvoyl-dependent arginine decarboxylase subunit alphaUniRule annotationAdd BLAST114

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 residuei44Pyruvic acid (Ser)UniRule annotation1

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei43 – 44Cleavage (non-hydrolytic)UniRule annotation2

<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

Protein interaction database and analysis system

More...IntActi		Q5JFI4, 1 interactor

Molecular INTeraction database

More...MINTi		Q5JFI4

STRING: functional protein association networks

More...STRINGi		69014.TK0149

<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		Q5JFI4

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 PdaD family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		arCOG04490, Archaea

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_114389_2_0_2

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q5JFI4

Identification of Orthologs from Complete Genome Data

More...OMAi		AAALWYK

Database of Orthologous Groups

More...OrthoDBi		98606at2157

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q5JFI4

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.50.20.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01404, PvlArgDC, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR016104, Pyr-dep_his/arg-deCO2ase
IPR016105, Pyr-dep_his/arg-deCO2ase_sand
IPR002724, Pyruvoyl-dep_arg_deCO2ase

The PANTHER Classification System

More...PANTHERi		PTHR40438, PTHR40438, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01862, PvlArgDC, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF005216, Pyruvoyl-dep_arg_deCO2ase, 1 hit

Structure-Function Linkage Database

More...SFLDi		SFLDG01170, Pyruvoyl-dependent_arginine_de, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF56271, SSF56271, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00286, TIGR00286, 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.

<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 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.

Q5JFI4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSWTTPKRAF IGAATAEGGT KLNAFDNALL KLGIGNVNLV KLSSVIPAHI 
        60         70         80         90        100
EWMEKVHDVP IGMLLPTVYA HIESDEPGMT ISAALGVGIS KNNEGGLIYE 
       110        120        130        140        150
YSGYCTKEEA EEMVRKMVEE GFRQRGWELG EFKVASAEIT VKDKPAAAIA 

VVVMFPY
Length:157
Mass (Da):17,062
Last modified:February 15, 2005 - 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:i9D91137305B1126E
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
AP006878 Genomic DNA Translation: BAD84338.1

NCBI Reference Sequences

More...RefSeqi		WP_011249104.1, NC_006624.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		BAD84338; BAD84338; TK0149

Database of genes from NCBI RefSeq genomes

More...GeneIDi		3234595

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		tko:TK0149

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|69014.16.peg.149

<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
AP006878 Genomic DNA Translation: BAD84338.1
RefSeqiWP_011249104.1, NC_006624.1

3D structure databases

SMRiQ5JFI4
ModBaseiSearch...

Protein-protein interaction databases

IntActiQ5JFI4, 1 interactor
MINTiQ5JFI4
STRINGi69014.TK0149

Genome annotation databases

EnsemblBacteriaiBAD84338; BAD84338; TK0149
GeneIDi3234595
KEGGitko:TK0149
PATRICifig|69014.16.peg.149

Phylogenomic databases

eggNOGiarCOG04490, Archaea
HOGENOMiCLU_114389_2_0_2
InParanoidiQ5JFI4
OMAiAAALWYK
OrthoDBi98606at2157
PhylomeDBiQ5JFI4

Enzyme and pathway databases

BRENDAi4.1.1.19, 5246

Family and domain databases

Gene3Di3.50.20.10, 1 hit
HAMAPiMF_01404, PvlArgDC, 1 hit
InterProiView protein in InterPro
IPR016104, Pyr-dep_his/arg-deCO2ase
IPR016105, Pyr-dep_his/arg-deCO2ase_sand
IPR002724, Pyruvoyl-dep_arg_deCO2ase
PANTHERiPTHR40438, PTHR40438, 1 hit
PfamiView protein in Pfam
PF01862, PvlArgDC, 1 hit
PIRSFiPIRSF005216, Pyruvoyl-dep_arg_deCO2ase, 1 hit
SFLDiSFLDG01170, Pyruvoyl-dependent_arginine_de, 1 hit
SUPFAMiSSF56271, SSF56271, 1 hit
TIGRFAMsiTIGR00286, TIGR00286, 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 nameiPDAD_THEKO
<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: Q5JFI4
<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 29, 2005
Last sequence update: February 15, 2005
Last modified: February 23, 2022
This is version 89 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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