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Database: UniProt
Entry: S5YCU8_PARAH
LinkDB: S5YCU8_PARAH
Original site: S5YCU8_PARAH 
ID   S5YCU8_PARAH            Unreviewed;       662 AA.
AC   S5YCU8;
DT   16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT   16-OCT-2013, sequence version 1.
DT   24-JAN-2024, entry version 57.
DE   RecName: Full=RNA polymerase sigma factor RpoD {ECO:0000256|HAMAP-Rule:MF_00963};
DE   AltName: Full=Sigma-70 {ECO:0000256|HAMAP-Rule:MF_00963};
GN   Name=rpoD {ECO:0000256|HAMAP-Rule:MF_00963};
GN   ORFNames=JCM7686_2204 {ECO:0000313|EMBL:AGT09283.1};
OS   Paracoccus aminophilus JCM 7686.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC   Paracoccaceae; Paracoccus.
OX   NCBI_TaxID=1367847 {ECO:0000313|EMBL:AGT09283.1, ECO:0000313|Proteomes:UP000015480};
RN   [1] {ECO:0000313|EMBL:AGT09283.1, ECO:0000313|Proteomes:UP000015480}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JCM 7686 {ECO:0000313|EMBL:AGT09283.1};
RX   PubMed=24517536; DOI=10.1186/1471-2164-15-124;
RA   Dziewit L., Czarnecki J., Wibberg D., Radlinska M., Mrozek P., Szymczak M.,
RA   Schluter A., Puhler A., Bartosik D.;
RT   "Architecture and functions of a multipartite genome of the methylotrophic
RT   bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary
RT   chromids.";
RL   BMC Genomics 15:124-124(2014).
CC   -!- FUNCTION: Sigma factors are initiation factors that promote the
CC       attachment of RNA polymerase to specific initiation sites and are then
CC       released. This sigma factor is the primary sigma factor during
CC       exponential growth. {ECO:0000256|HAMAP-Rule:MF_00963}.
CC   -!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic core.
CC       {ECO:0000256|HAMAP-Rule:MF_00963}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00963}.
CC   -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily.
CC       {ECO:0000256|HAMAP-Rule:MF_00963}.
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DR   EMBL; CP006650; AGT09283.1; -; Genomic_DNA.
DR   RefSeq; WP_020950921.1; NC_022041.1.
DR   AlphaFoldDB; S5YCU8; -.
DR   STRING; 1367847.JCM7686_2204; -.
DR   KEGG; pami:JCM7686_2204; -.
DR   PATRIC; fig|1367847.3.peg.2197; -.
DR   eggNOG; COG0568; Bacteria.
DR   HOGENOM; CLU_014793_7_2_5; -.
DR   OrthoDB; 9809557at2; -.
DR   Proteomes; UP000015480; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016987; F:sigma factor activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006352; P:DNA-templated transcription initiation; IEA:UniProtKB-UniRule.
DR   CDD; cd06171; Sigma70_r4; 1.
DR   Gene3D; 1.10.601.10; RNA Polymerase Primary Sigma Factor; 1.
DR   Gene3D; 1.10.220.120; Sigma-70 factor, region 1.1; 1.
DR   Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 2.
DR   HAMAP; MF_00963; Sigma70_RpoD_SigA; 1.
DR   InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR   InterPro; IPR000943; RNA_pol_sigma70.
DR   InterPro; IPR009042; RNA_pol_sigma70_r1_2.
DR   InterPro; IPR007627; RNA_pol_sigma70_r2.
DR   InterPro; IPR007624; RNA_pol_sigma70_r3.
DR   InterPro; IPR007630; RNA_pol_sigma70_r4.
DR   InterPro; IPR007631; RNA_pol_sigma_70_non-ess.
DR   InterPro; IPR007127; RNA_pol_sigma_70_r1_1.
DR   InterPro; IPR042189; RNA_pol_sigma_70_r1_1_sf.
DR   InterPro; IPR013325; RNA_pol_sigma_r2.
DR   InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
DR   InterPro; IPR012760; RNA_pol_sigma_RpoD_C.
DR   InterPro; IPR028630; Sigma70_RpoD.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   NCBIfam; TIGR02393; RpoD_Cterm; 1.
DR   NCBIfam; TIGR02937; sigma70-ECF; 1.
DR   PANTHER; PTHR30603; RNA POLYMERASE SIGMA FACTOR RPO; 1.
DR   PANTHER; PTHR30603:SF60; RNA POLYMERASE SIGMA FACTOR RPOD; 1.
DR   Pfam; PF04546; Sigma70_ner; 1.
DR   Pfam; PF03979; Sigma70_r1_1; 1.
DR   Pfam; PF00140; Sigma70_r1_2; 1.
DR   Pfam; PF04542; Sigma70_r2; 1.
DR   Pfam; PF04539; Sigma70_r3; 1.
DR   Pfam; PF04545; Sigma70_r4; 1.
DR   PRINTS; PR00046; SIGMA70FCT.
DR   SUPFAM; SSF88946; Sigma2 domain of RNA polymerase sigma factors; 1.
DR   SUPFAM; SSF88659; Sigma3 and sigma4 domains of RNA polymerase sigma factors; 2.
DR   PROSITE; PS00715; SIGMA70_1; 1.
DR   PROSITE; PS00716; SIGMA70_2; 1.
PE   3: Inferred from homology;
KW   Coiled coil {ECO:0000256|SAM:Coils};
KW   Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00963};
KW   DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW   Rule:MF_00963}; Reference proteome {ECO:0000313|Proteomes:UP000015480};
KW   Sigma factor {ECO:0000256|ARBA:ARBA00023082, ECO:0000256|HAMAP-
KW   Rule:MF_00963};
KW   Transcription {ECO:0000256|ARBA:ARBA00023163, ECO:0000256|HAMAP-
KW   Rule:MF_00963};
KW   Transcription regulation {ECO:0000256|ARBA:ARBA00023015, ECO:0000256|HAMAP-
KW   Rule:MF_00963}.
FT   DOMAIN          452..465
FT                   /note="RNA polymerase sigma-70"
FT                   /evidence="ECO:0000259|PROSITE:PS00715"
FT   DOMAIN          621..647
FT                   /note="RNA polymerase sigma-70"
FT                   /evidence="ECO:0000259|PROSITE:PS00716"
FT   DNA_BIND        622..641
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          1..26
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          74..110
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          194..239
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          428..498
FT                   /note="Sigma-70 factor domain-2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          507..583
FT                   /note="Sigma-70 factor domain-3"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          596..649
FT                   /note="Sigma-70 factor domain-4"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   COILED          407..434
FT                   /evidence="ECO:0000256|SAM:Coils"
FT   MOTIF           452..455
FT                   /note="Interaction with polymerase core subunit RpoC"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   COMPBIAS        1..23
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        85..101
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   662 AA;  75304 MW;  E0790F2D70D4D588 CRC64;
     MASKDDDDNK PDTKDDEHSL DMSQTAVKRM IAEGRERGFI TYDQLNAVLP PDQVSSDQIE
     DVMSMLSEMD IRVVESDEDS DDSETGGQLA TTGSGSREVA LATTETEKLD RTDDPVRMYL
     REMGSVELLS REGEIAIAKR IEAGRNTMIA GLCESPLTFK AITMWREELL DEDILLRDVI
     DLEATFGRVL DEEGEDTELE TAEPVVGAAP AQARTGDEEF DADGNPMRRE DEEDDEDGQS
     LSLAAMEASL KPKVLETLEQ IAHGYEELAH MQDSRMSATL NEDSTFSASD ELAYQRKRSE
     IVLLVNELHL HNNRIEALVD QIYGINRRIL TIDSGMVKLA DAARINRQEF IKAYRGCELD
     PTWVDRMSSG TSRGWQTLFD KSRDQVDRLR GDMADVGQYV GVDIEEFRRI VNQVQRGEKE
     ARQAKKEMVE ANLRLVISIA KKYTNRGLQF LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA
     TWWIRQAITR SIADQARTIR IPVHMIETIN KLVRTGRQML HEIGREPTPE ELAEKLQMPL
     EKVRKVMKIA KEPISLETPI GDEEDSQLGD FIEDKNAVLP LESAIQENLK ETTTRVLASL
     TPREERVLRM RFGIGMNTDH TLEEVGQQFS VTRERIRQIE AKALRKLKHP SRSRKLRSFL
     DQ
//
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