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UniProtKB - P49988 (RP54_PSEAE)

Entry version 122 (02 Dec 2020)
Sequence version 2 (08 Dec 2000)
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Protein

RNA polymerase sigma-54 factor

Gene

rpoN

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score:

Annotation score:4 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

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (PubMed:9595661). Plays a role in the regulation of many virulence factors, motility, quorum sensing, mucoidy, a general mechanism for maintaining lytic phage in populations of bacteria, and biofilm formation (PubMed:2152909, PubMed:12644493, PubMed:10792721, PubMed:26633362, PubMed:29760208). Positively controls the T6 secretion system by directly binding to the promoter regions of hcpA and hcpB genes, leading to their expression (PubMed:29760208). Thereby, allows to colonize several hosts efficiently including mammals, insects, nematodes and plants (By similarity) (PubMed:2152909, PubMed:9595661, PubMed:12644493, PubMed:10792721, PubMed:26633362, PubMed:29760208).By similarity6 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi386 – 405H-T-H motifSequence analysisAdd BLAST20

<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 functionDNA-binding, Nucleotidyltransferase, Sigma factor, Transferase
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		PAER208964:G1FZ6-4551-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:
RNA polymerase sigma-54 factor
<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:rpoN
Ordered Locus Names:PA4462
<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>OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
<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 identifieri208964 [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 › Pseudomonadales › Pseudomonadaceae › Pseudomonas ›
<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
  • UP000002438 <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

Organism-specific databases

Pseudomonas genome database

More...PseudoCAPi		PA4462

<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

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

DNA-directed RNA polymerase

<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

Deletion mutants result in reduced production of pyocyanine, motility, and proteolytic activity. The motility defect is due to the inability of these mutants to synthesize flagellin (PubMed:2152909). Significantly decreased porin oprE expression under aerobic conditions (PubMed:9595661). Mutants also show defect in biofilm formation (PubMed:29760208).3 Publications

Miscellaneous databases

Pathogen-Host Interaction database

More...PHI-basei		PHI:7554

<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_00002055341 – 497RNA polymerase sigma-54 factorAdd BLAST497

Proteomic databases

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

More...PaxDbi		P49988

PRoteomics IDEntifications database

More...PRIDEi		P49988

<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

Gene expression databases

CollecTF database of bacterial transcription factor binding sites

More...CollecTFi		EXPREG_00000ad0

<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

Molecular INTeraction database

More...MINTi		P49988

<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		P49988

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

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi474 – 482RPON box9

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi11 – 35Gln-richAdd BLAST25

<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 sigma-54 factor family.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_020569_0_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P49988

Identification of Orthologs from Complete Genome Data

More...OMAi		VTTQKFM

Database for complete collections of gene phylogenies

More...PhylomeDBi		P49988

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.10.1330, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR000394, RNA_pol_sigma_54
IPR007046, RNA_pol_sigma_54_core-bd
IPR007634, RNA_pol_sigma_54_DNA-bd
IPR038709, RpoN_core-bd_sf

The PANTHER Classification System

More...PANTHERi		PTHR32248, PTHR32248, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00309, Sigma54_AID, 1 hit
PF04963, Sigma54_CBD, 1 hit
PF04552, Sigma54_DBD, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF000774, RpoN, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00045, SIGMA54FCT

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR02395, rpoN_sigma, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00717, SIGMA54_1, 1 hit
PS00718, SIGMA54_2, 1 hit
PS50044, SIGMA54_3, 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.

P49988-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKPSLVLKMG QQLTMTPQLQ QAIRLLQLST LDLQQEIQEA LESNPMLERQ 
        60         70         80         90        100
EDGDDFDNSD PLADGAEQAA SAPQESPLQE SATPSVESLD DDQWSERIPS 
       110        120        130        140        150
ELPVDTAWED IYQTSASSLP SNDDDEWDFT ARTSSGESLH SHLLWQVNLA 
       160        170        180        190        200
PMSDTDRMIA VTIIDSINND GYLEESLEEI LAAIDPELDV ELDEVEVVLR 
       210        220        230        240        250
RIQQLEPAGI GARNLRECLL LQLRQLPSTT PWLNEALRLV SDYLDLLGGR 
       260        270        280        290        300
DYSQLMRRMK LKEDELRQVI ELIQCLHPRP GSQIESSEAE YIVPDVIVRK 
       310        320        330        340        350
DNERWLVELN QEAMPRLRVN ATYAGMVRRA DSSADNTFMR NQLQEARWFI 
       360        370        380        390        400
KSLQSRNETL MKVATQIVEH QRGFLDYGEE AMKPLVLHDI AEAVGMHEST 
       410        420        430        440        450
ISRVTTQKYM HTPRGIFELK YFFSSHVSTA EGGECSSTAI RAIIKKLVAA 
       460        470        480        490 
ENAKKPLSDS KIAGLLEAQG IQVARRTVAK YRESLGIAPS SERKRLV
Length:497
Mass (Da):56,054
Last modified:December 8, 2000 - 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:iCE1994F03FD58405
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti352S → T in AAA19793 (PubMed:8113171).Curated1

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
L26916 Unassigned DNA Translation: AAA19793.1
AE004091 Genomic DNA Translation: AAG07850.1

Protein sequence database of the Protein Information Resource

More...PIRi		A53373
F83087

NCBI Reference Sequences

More...RefSeqi		NP_253152.1, NC_002516.2
WP_003094357.1, NZ_QZGE01000004.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAG07850; AAG07850; PA4462

Database of genes from NCBI RefSeq genomes

More...GeneIDi		45712433
881022

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		pae:PA4462

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|208964.12.peg.4672

<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
L26916 Unassigned DNA Translation: AAA19793.1
AE004091 Genomic DNA Translation: AAG07850.1
PIRiA53373
F83087
RefSeqiNP_253152.1, NC_002516.2
WP_003094357.1, NZ_QZGE01000004.1

3D structure databases

SMRiP49988
ModBaseiSearch...

Protein-protein interaction databases

MINTiP49988

Proteomic databases

PaxDbiP49988
PRIDEiP49988

Genome annotation databases

EnsemblBacteriaiAAG07850; AAG07850; PA4462
GeneIDi45712433
881022
KEGGipae:PA4462
PATRICifig|208964.12.peg.4672

Organism-specific databases

PseudoCAPiPA4462

Phylogenomic databases

HOGENOMiCLU_020569_0_1_6
InParanoidiP49988
OMAiVTTQKFM
PhylomeDBiP49988

Enzyme and pathway databases

BioCyciPAER208964:G1FZ6-4551-MONOMER

Miscellaneous databases

PHI-baseiPHI:7554

Gene expression databases

CollecTFiEXPREG_00000ad0

Family and domain databases

Gene3Di1.10.10.1330, 1 hit
InterProiView protein in InterPro
IPR000394, RNA_pol_sigma_54
IPR007046, RNA_pol_sigma_54_core-bd
IPR007634, RNA_pol_sigma_54_DNA-bd
IPR038709, RpoN_core-bd_sf
PANTHERiPTHR32248, PTHR32248, 1 hit
PfamiView protein in Pfam
PF00309, Sigma54_AID, 1 hit
PF04963, Sigma54_CBD, 1 hit
PF04552, Sigma54_DBD, 1 hit
PIRSFiPIRSF000774, RpoN, 1 hit
PRINTSiPR00045, SIGMA54FCT
TIGRFAMsiTIGR02395, rpoN_sigma, 1 hit
PROSITEiView protein in PROSITE
PS00717, SIGMA54_1, 1 hit
PS00718, SIGMA54_2, 1 hit
PS50044, SIGMA54_3, 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 nameiRP54_PSEAE
<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: P49988
<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: October 1, 1996
Last sequence update: December 8, 2000
Last modified: December 2, 2020
This is version 122 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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