ID A0A220W4R2_9SPHN Unreviewed; 670 AA.
AC A0A220W4R2;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 27-MAR-2024, entry version 30.
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 ECO:0000313|EMBL:ASK87809.1};
GN ORFNames=SPHFLASMR4Y_01039 {ECO:0000313|EMBL:ASK87809.1};
OS Sphingorhabdus sp. SMR4y.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingorhabdus.
OX NCBI_TaxID=2584094 {ECO:0000313|EMBL:ASK87809.1, ECO:0000313|Proteomes:UP000198359};
RN [1] {ECO:0000313|EMBL:ASK87809.1, ECO:0000313|Proteomes:UP000198359}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SMR4y {ECO:0000313|EMBL:ASK87809.1,
RC ECO:0000313|Proteomes:UP000198359};
RA Topel M., Pinder M.I.M., Johansson O.N., Kourtchenko O., Godhe A.,
RA Clarke A.K.;
RT "Genome Sequence of Sphingorhabdus flavimaris Strain SMR4y Isolated from a
RT culture of the Diatom Skeletonema marinoi.";
RL Submitted (JUL-2017) to the EMBL/GenBank/DDBJ databases.
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; CP022336; ASK87809.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A220W4R2; -.
DR KEGG; sfla:SPHFLASMR4Y_01039; -.
DR OrthoDB; 9809557at2; -.
DR Proteomes; UP000198359; 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:SF47; RNA POLYMERASE SIGMA FACTOR SIGF, CHLOROPLASTIC; 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 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:UP000198359};
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 460..473
FT /note="RNA polymerase sigma-70"
FT /evidence="ECO:0000259|PROSITE:PS00715"
FT DOMAIN 629..655
FT /note="RNA polymerase sigma-70"
FT /evidence="ECO:0000259|PROSITE:PS00716"
FT DNA_BIND 630..649
FT /note="H-T-H motif"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 72..110
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 184..250
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 436..506
FT /note="Sigma-70 factor domain-2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 515..591
FT /note="Sigma-70 factor domain-3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 604..657
FT /note="Sigma-70 factor domain-4"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT MOTIF 460..463
FT /note="Interaction with polymerase core subunit RpoC"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT COMPBIAS 82..110
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 213..231
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 232..247
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 670 AA; 76144 MW; 225C3E45F37D56CC CRC64;
MASKAKNTKA EDEPLIDLND SAIKKLIAKA KKRGYLTIDE LNEALPQDQN EQIEDVMSAI
SEMGVRIVEN DEEAAEEMGG EEVESIDGKD KDKKSAAAAP KKASGDRTDD PVRMYLREMG
AVELLSREGE IAIAKRIEAG RDTMIWGLCE SPTTFNAIIE WSTALNDGEM QLREILDLDA
MLSKDPVPEN LEDAEDDDDG EISEKTAGPS FKDDDEVEDE ESADDEDDDE AGLTERRTKR
VVEEEEEDNT LSLAQMEEAL KPDALEKFAL ITSVFKKFSK LQTTRLESLA AGKDFPAASE
KKYHDLREEL TALVESVQFH ANKIEFLVDQ LYSFNRRLTT LGGQMLRLAE RHKVPRRAFL
DSYIGNELDD NWLASMAKVD KKWASFVEKE ADAVDRIRTE ISDIANATGT SLVEFRRIVN
MVQKGEREAR IAKKEMVEAN LRLVISIAKK YTNRGLQFLD LIQEGNIGLM KAVDKFEYRR
GYKFSTYATW WIRQAITRSI ADQARTIRIP VHMIETINKL VRTSRQFLHE QGREPTPEEM
AERLSMPLEK VRKVMKIAKE PISLETPIGD EEDSHLGDFI EDKNAIIPVD AAIQANLKET
VTRVLASLTP REERVLRMRF GIGMNTDHTL EEVGQQFSVT RERIRQIEAK ALRKLKHPSR
SRKMRSFLDQ
//
