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Entry version 70 (31 Jul 2019)
Sequence version 1 (10 Jul 2007)
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Protein

RNA polymerase-associated protein RapA

Gene

rapA

Organism
Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
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

Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair.UniRule annotation

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi177 – 184ATPUniRule annotation8

<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

Molecular functionActivator, DNA-binding, Helicase, Hydrolase
Biological processTranscription, Transcription regulation
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
PPUT351746:G1G90-1235-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_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:
RNA polymerase-associated protein RapAUniRule annotation (EC:3.6.4.-UniRule annotation)
Alternative name(s):
ATP-dependent helicase HepAUniRule annotation
<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:rapAUniRule annotation
Ordered Locus Names:Pput_1179
<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>OrganismiPseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
<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 identifieri351746 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
<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
  • UP000006553 <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

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_10000883671 – 948RNA polymerase-associated protein RapAAdd BLAST948

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with the RNAP. Has a higher affinity for the core RNAP than for the holoenzyme. Its ATPase activity is stimulated by binding to RNAP.

UniRule annotation

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
351746.Pput_1179

<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_and_domains_section">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>Domaini164 – 332Helicase ATP-bindingUniRule annotationAdd BLAST169
Domaini473 – 627Helicase C-terminalUniRule annotationAdd BLAST155

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>Motifi278 – 281DEAH box4

<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 SNF2/RAD54 helicase family. RapA subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105BZK Bacteria
COG0553 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000218482

KEGG Orthology (KO)

More...
KOi
K03580

Identification of Orthologs from Complete Genome Data

More...
OMAi
MSILERD

Database of Orthologous Groups

More...
OrthoDBi
291634at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.10810, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01821 Helicase_RapA, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR023949 Helicase_RapA
IPR027417 P-loop_NTPase
IPR022737 RapA_C
IPR038718 SNF2-like_sf
IPR000330 SNF2_N
IPR040765 Tudor_1_RapA
IPR040766 Tudor_2_RapA

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00271 Helicase_C, 1 hit
PF12137 RapA_C, 1 hit
PF00176 SNF2_N, 1 hit
PF18339 Tudor_1_RapA, 1 hit
PF18337 Tudor_RapA, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52540 SSF52540, 2 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 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.

A5VZN0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQQYQPGQR WISDSEAELG LGTILAQDGR LLTVLYPATG DTRQYSLRNA
60 70 80 90 100
PLTRVRFSPG DQITHFEGWK LTVREVEDID GLMVYHGLDG QNQPRTLPET
110 120 130 140 150
QLSNFIQFRL ASDRLFAGQI DPLSWFSLRY NTLQHTSKQM QSALWGLGGC
160 170 180 190 200
RAQPIAHQLH IAREVADRSA PRVLLADEVG LGKTIEAGLV IHRQLLSGRA
210 220 230 240 250
SRVLILVPEN LQHQWLVEMR RRFNLQVALF DAERFIESDA SNPFEDAQLA
260 270 280 290 300
LVALEWLVDD EKAQDALFAA GWDLMVVDEA HHLVWHEDQV SAEYGLVEQL
310 320 330 340 350
AQVIPGVLLL TATPEQLGQD SHFARLRLLD PNRFHDLAAF RAESEHYRPV
360 370 380 390 400
AEAVQELLDE GRLSPKAHAT ILGFLGAEGE ALLAAVSDGD TQASARLIRE
410 420 430 440 450
LLDRHGTGRV LFRNTRAAIQ GFPERQLHPY PLATPEQYRN LPAGEHAELY
460 470 480 490 500
PEVAFQAQGE VADDERWWRF DPRVDWLIDT LKMLKRTKVL VICAHAETAM
510 520 530 540 550
DLEDALRVRS GIPASVFHEG MSILERDRAA AYFADEEFGA QVLICSEIGS
560 570 580 590 600
EGRNFQFAHH LVMFDLPAHP DLLEQRIGRL DRIGQKHTIQ LHIPYLQDSP
610 620 630 640 650
QERLFQWYHE GLNAFLNTCP TGNALQHQFG PRLLPLLEGG DHKAWDTLVA
660 670 680 690 700
DARSERERLE AELHTGRDRL LELNSGGAGE GQALVEAILE QDDQFALPIY
710 720 730 740 750
METLFDAFGI DSEDHSENAL ILKPSEKMLD ASFPLGDDEG VTITYDRGQA
760 770 780 790 800
LSREDMQFLT WEHPMVQGGM DLVLSGSMGN TAVALIKNKA LKPGTVLLEL
810 820 830 840 850
LFVSEVVAPR SLQLGRYLPP AALRCLLDAN GNDLASRVAF ETLNDQLESV
860 870 880 890 900
PRASANKFVQ AQRDVLAKRI SGGEEKILPA HNERVAEAQR RLTAEADEEL
910 920 930 940
ARLVALQAVN PSVRDSEIDA LRKRREDGLA MLEKAALRLE AIRVLVAG
Length:948
Mass (Da):106,025
Last modified:July 10, 2007 - 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:i0C7648B5CEE76D57
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
CP000712 Genomic DNA Translation: ABQ77340.1

NCBI Reference Sequences

More...
RefSeqi
WP_003254868.1, NC_009512.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABQ77340; ABQ77340; Pput_1179

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ppf:Pput_1179

<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
CP000712 Genomic DNA Translation: ABQ77340.1
RefSeqiWP_003254868.1, NC_009512.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi351746.Pput_1179

Genome annotation databases

EnsemblBacteriaiABQ77340; ABQ77340; Pput_1179
KEGGippf:Pput_1179

Phylogenomic databases

eggNOGiENOG4105BZK Bacteria
COG0553 LUCA
HOGENOMiHOG000218482
KOiK03580
OMAiMSILERD
OrthoDBi291634at2

Enzyme and pathway databases

BioCyciPPUT351746:G1G90-1235-MONOMER

Family and domain databases

Gene3Di3.40.50.10810, 1 hit
HAMAPiMF_01821 Helicase_RapA, 1 hit
InterProiView protein in InterPro
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR023949 Helicase_RapA
IPR027417 P-loop_NTPase
IPR022737 RapA_C
IPR038718 SNF2-like_sf
IPR000330 SNF2_N
IPR040765 Tudor_1_RapA
IPR040766 Tudor_2_RapA
PfamiView protein in Pfam
PF00271 Helicase_C, 1 hit
PF12137 RapA_C, 1 hit
PF00176 SNF2_N, 1 hit
PF18339 Tudor_1_RapA, 1 hit
PF18337 Tudor_RapA, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 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 nameiRAPA_PSEP1
<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: A5VZN0
<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: May 20, 2008
Last sequence update: July 10, 2007
Last modified: July 31, 2019
This is version 70 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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