ID   F4GCJ4_ALIDK            Unreviewed;       802 AA.
AC   F4GCJ4;
DT   28-JUN-2011, integrated into UniProtKB/TrEMBL.
DT   28-JUN-2011, sequence version 1.
DT   27-MAR-2024, entry version 82.
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   OrderedLocusNames=Alide2_3600 {ECO:0000313|EMBL:AEB85926.1};
OS   Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601).
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Alicycliphilus.
OX   NCBI_TaxID=596154 {ECO:0000313|EMBL:AEB85926.1, ECO:0000313|Proteomes:UP000007938};
RN   [1] {ECO:0000313|EMBL:AEB85926.1, ECO:0000313|Proteomes:UP000007938}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 14773 / CIP 107495 / K601
RC   {ECO:0000313|Proteomes:UP000007938};
RX   PubMed=21742888; DOI=10.1128/JB.00365-11;
RA   Oosterkamp M.J., Veuskens T., Plugge C.M., Langenhoff A.A., Gerritse J.,
RA   van Berkel W.J., Pieper D.H., Junca H., Goodwin L.A., Daligault H.E.,
RA   Bruce D.C., Detter J.C., Tapia R., Han C.S., Land M.L., Hauser L.J.,
RA   Smidt H., Stams A.J.;
RT   "Genome Sequences of Alicycliphilus denitrificans Strains BC and K601T.";
RL   J. Bacteriol. 193:5028-5029(2011).
RN   [2] {ECO:0000313|EMBL:AEB85926.1, ECO:0000313|Proteomes:UP000007938}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 14773 / CIP 107495 / K601
RC   {ECO:0000313|Proteomes:UP000007938};
RG   US DOE Joint Genome Institute;
RA   Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA   Peters L., Zeytun A., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA   Kyrpides N., Ivanova N., Mikhailova N., Pagani I., Oosterkamp M.,
RA   Pieper D., van Berkel W., Langenhoff A., Smidt H., Stams A., Woyke T.;
RT   "Complete sequence of chromosome of Alicycliphilus denitrificans K601.";
RL   Submitted (APR-2011) 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; CP002657; AEB85926.1; -; Genomic_DNA.
DR   RefSeq; WP_013722798.1; NC_015422.1.
DR   AlphaFoldDB; F4GCJ4; -.
DR   STRING; 596154.Alide2_3600; -.
DR   KEGG; adk:Alide2_3600; -.
DR   eggNOG; COG0568; Bacteria.
DR   HOGENOM; CLU_014793_7_0_4; -.
DR   OrthoDB; 9809557at2; -.
DR   Proteomes; UP000007938; 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:UP000007938};
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          591..604
FT                   /note="RNA polymerase sigma-70"
FT                   /evidence="ECO:0000259|PROSITE:PS00715"
FT   DOMAIN          760..786
FT                   /note="RNA polymerase sigma-70"
FT                   /evidence="ECO:0000259|PROSITE:PS00716"
FT   DNA_BIND        761..780
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          1..137
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          567..637
FT                   /note="Sigma-70 factor domain-2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          646..722
FT                   /note="Sigma-70 factor domain-3"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   REGION          735..788
FT                   /note="Sigma-70 factor domain-4"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT   MOTIF           591..594
FT                   /note="Interaction with polymerase core subunit RpoC"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
SQ   SEQUENCE   802 AA;  89003 MW;  E02C9C576CE608A3 CRC64;
     MPVQKSAKSP KPASGTAAKA ASKAATPVKT AAKAPAKAAT AKAADAALQA ATKVKTVPTP
     KTTAELTKAA DELLKKKPAR APKAAAAQAE ASEDAPKKKP GRPAKAAGSA TAAAKAPAKR
     GRKPKAKEEG LEDDADLSDI EAELEGEPEA PEAEAEAATA EKAKPLRMKI SKAKERALMK
     EFGLDETVLS EEDMAKRRSQ LKKLITLGKT RGYLTQVEIS DHLPDKLVDA ETMEVVVAML
     GDMGVAVYEQ TPDAETLFQN NVAPTATTVE EAEEEAEAAL STVDSEFGRT TDPVRMYMRE
     MGTVELLTRE GEIEIAKRIE GGLMDMMEAI SASPATIAEI LNMGEEIREG KVVISTVVDG
     FSNPEEADDY VAEEDFDEYD EEDDDDGKGG SKAMTRLLEK LKTEALDRFD ELRSLFEKMH
     KIYDKEGYGS PAYMKVQHEI SAKLMTIRFT AKTIEKLCDM VRAQVDDVRK KERELRRIIV
     DKCGMPQETF IKEFPPNLLN LQWVEKQAAA GKPWSAVMQR NIPPIQELQQ HLIDLQSRVV
     VPLAELKAIN KRMNQGEANS RDAKKEMIEA NLRLVISIAK KYTNRGLQFL DLIQEGNIGL
     MKAVDKFEYR RGYKFSTYAT WWIRQAITRS IADQARTIRI PVHMIETINK MNRISRQHLQ
     EFGFEPDASI LAAKMEIPED KIRKIMKIAK EPISMETPIG DDDDSHLGDF IEDSNNTAPI
     DAAMQAGLRD VVKDILDGLT PREAKVLRMR FGIEMSTDHT LEEVGKQFDV TRERIRQIEA
     KALRKLKHPS RSDKLRSFID SL
//