(data stored in SCRATCH zone)

SWISSPROT: Q3IIB9_PSEHT

ID   Q3IIB9_PSEHT            Unreviewed;       615 AA.
AC   Q3IIB9;
DT   08-NOV-2005, integrated into UniProtKB/TrEMBL.
DT   08-NOV-2005, sequence version 1.
DT   05-JUL-2017, entry version 89.
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:CAI85447.1};
GN   OrderedLocusNames=PSHAa0349 {ECO:0000313|EMBL:CAI85447.1};
OS   Pseudoalteromonas haloplanktis (strain TAC 125).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Pseudoalteromonadaceae; Pseudoalteromonas.
OX   NCBI_TaxID=326442 {ECO:0000313|EMBL:CAI85447.1, ECO:0000313|Proteomes:UP000006843};
RN   [1] {ECO:0000313|EMBL:CAI85447.1, ECO:0000313|Proteomes:UP000006843}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=TAC 125 {ECO:0000313|Proteomes:UP000006843};
RX   PubMed=16169927; DOI=10.1101/gr.4126905;
RA   Medigue C., Krin E., Pascal G., Barbe V., Bernsel A., Bertin P.,
RA   Cheung F., Cruveiller S., Damico S., Duilio A., Fang G., Feller G.,
RA   Mangenot S., Marino G., Nilsson J., Parilli E., Rocha E., Rouy Z.,
RA   Sekowska A., Tutino M.L., Vallenet D., von Heijne G., Danchin A.;
RT   "Coping with cold: the genome of the versatile marine Antarctica
RT   bacterium Pseudoalteromonas haloplanktis TAC125.";
RL   Genome Res. 15:1325-1335(2005).
CC   -!- FUNCTION: Sigma factors are initiation factors that promote the
CC       attachment of RNA polymerase to specific initiation sites and are
CC       then released. This sigma factor is the primary sigma factor
CC       during exponential growth. {ECO:0000256|SAAS:SAAS00535554}.
CC   -!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic
CC       core. {ECO:0000256|HAMAP-Rule:MF_00963,
CC       ECO:0000256|SAAS:SAAS00003340}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00963,
CC       ECO:0000256|SAAS:SAAS00003349}.
CC   -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA
CC       subfamily. {ECO:0000256|SAAS:SAAS00535555}.
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DR   EMBL; CR954246; CAI85447.1; -; Genomic_DNA.
DR   RefSeq; WP_011327061.1; NC_007481.1.
DR   ProteinModelPortal; Q3IIB9; -.
DR   STRING; 326442.PSHAa0349; -.
DR   EnsemblBacteria; CAI85447; CAI85447; PSHAa0349.
DR   GeneID; 32565882; -.
DR   KEGG; pha:PSHAa0349; -.
DR   eggNOG; ENOG4105DG1; Bacteria.
DR   eggNOG; COG0568; LUCA.
DR   HOGENOM; HOG000270272; -.
DR   KO; K03086; -.
DR   OMA; AICSVPY; -.
DR   OrthoDB; POG091H0012; -.
DR   Proteomes; UP000006843; Chromosome I.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0016987; F:sigma factor activity; IEA:UniProtKB-HAMAP.
DR   GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; IEA:InterPro.
DR   GO; GO:0001123; P:transcription initiation from bacterial-type RNA polymerase promoter; IEA:UniProtKB-HAMAP.
DR   Gene3D; 1.10.10.10; -; 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; IPR013325; RNA_pol_sigma_r2.
DR   InterPro; IPR013324; RNA_pol_sigma_r3_r4.
DR   InterPro; IPR012760; RNA_pol_sigma_RpoD_C.
DR   InterPro; IPR028630; Sigma70_RpoD.
DR   InterPro; IPR011991; WHTH_DNA-bd_dom.
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; SSF88659; SSF88659; 2.
DR   SUPFAM; SSF88946; SSF88946; 1.
DR   TIGRFAMs; TIGR02393; RpoD_Cterm; 1.
DR   TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR   PROSITE; PS00715; SIGMA70_1; 1.
DR   PROSITE; PS00716; SIGMA70_2; 1.
PE   3: Inferred from homology;
DR   PRODOM; Q3IIB9.
DR   SWISS-2DPAGE; Q3IIB9.
KW   Complete proteome {ECO:0000313|Proteomes:UP000006843};
KW   Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00963,
KW   ECO:0000256|SAAS:SAAS00051776};
KW   DNA-binding {ECO:0000256|HAMAP-Rule:MF_00963,
KW   ECO:0000256|SAAS:SAAS00611263};
KW   Reference proteome {ECO:0000313|Proteomes:UP000006843};
KW   Sigma factor {ECO:0000256|HAMAP-Rule:MF_00963,
KW   ECO:0000256|SAAS:SAAS00611278};
KW   Transcription {ECO:0000256|HAMAP-Rule:MF_00963,
KW   ECO:0000256|SAAS:SAAS00611290};
KW   Transcription regulation {ECO:0000256|HAMAP-Rule:MF_00963,
KW   ECO:0000256|SAAS:SAAS00611294}.
FT   DOMAIN      404    417       RNA_pol_sigma70. {ECO:0000259|PROSITE:
FT                                PS00715}.
FT   DOMAIN      573    599       RNA_pol_sigma70. {ECO:0000259|PROSITE:
FT                                PS00716}.
FT   DNA_BIND    574    593       H-T-H motif. {ECO:0000256|HAMAP-Rule:
FT                                MF_00963}.
FT   REGION      380    450       Sigma-70 factor domain-2.
FT                                {ECO:0000256|HAMAP-Rule:MF_00963}.
FT   REGION      459    535       Sigma-70 factor domain-3.
FT                                {ECO:0000256|HAMAP-Rule:MF_00963}.
FT   REGION      548    601       Sigma-70 factor domain-4.
FT                                {ECO:0000256|HAMAP-Rule:MF_00963}.
FT   MOTIF       404    407       Interaction with polymerase core subunit
FT                                RpoC. {ECO:0000256|HAMAP-Rule:MF_00963}.
SQ   SEQUENCE   615 AA;  70358 MW;  A177F6AAB6C5637F CRC64;
     MDPTPQSQLK LLILKGKEQG YLTFAEVNDH LPQDIIDSDQ VEDIISMIND MGIKVSENAP
     DADELMMQET TTDEDAAEAA AAALATVEKE IGRTTDPVRM YMREMGTVEL LTREGEIVIA
     KRIEEGINQV QISVAEYPEA ITYLLEQWDK FEAEEMRLSD IIVGFIDPNE DTAPISATNI
     GSELSAKQLN DDDKDDDDSD EDDEDEEEVD TGPDPEEARV HFENLRDLYN KARETFEAKG
     RSHPDSLAAI FEIGELFKTF KLIPKQFDRM VNNMREMMDR VRVQERLIMK QAVQIAKLPK
     KTFVKHFANN ETDATWVDLE IAANEKYSAK LEEVKPEIIR SLNKLRVIES STGLNIERIK
     DINRRMSIGE AKARRAKKEM VEANLRLVIS IAKKYTNRGL QFLDLIQEGN IGLMKAVDKF
     EYRRGYKFST YATWWIRQAI TRSIADQART IRIPVHMIET INKLNRISRQ MLQEMGREPN
     PEELAERMMM PEDKVRKVLK IAKEPISMET PIGDDEDSHL GDFIEDTTID SPIDSATMES
     LRGATNDVLA GLTAREAKVL RMRFGIDMNT DHTLEEVGKQ FDVTRERIRQ IEAKALRKLR
     HPSRSDLLKS FLDAK
//

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