Click here to switch to the map view.

The map label for this gene is rpoD

Identifier: 16272477

GI number: 16272477

Start: 556243

End: 558132

Strand: Direct

Name: rpoD

Synonym: HI0533

Alternate gene names: 16272477

Gene position: 556243-558132 (Clockwise)

Preceding gene: 16272476

Following gene: 16272486

Centisome position: 30.39

GC content: 37.67

Gene sequence:

>1890_bases
ATGGAAAAAAATCAACAATCTACGGCTGAACAATATTCAGAACAAATTGAGCAATTGATGGAGCTAGGTCGTACACAAGG
GTATTTAACTTTTGCTGAAATCAATGACTTATTGCCCGAAGATGCTATTGATCCTGAATATTACGACAAATTGCTACAAA
CGTTGCAAAATGATGCTGGTATCCCTGTATTAGATGAAGCACCAGAAAGCGATGATATGATGTTGAGTGATACCATCCCT
GATGAAGATGCAGTGGAAGAAGCAACTCAAATTCTTTCAAATGTAGAATCTGAAATCGGTCGAACAACGGATCCCGTACG
CATGTATATGCGCGAAATGGGAACGGTGGATCTTCTTACTCGTGAAGATGAAATTAGCATTGCAAAACGTATTGAAGGAG
GGATTGATGAAGTTCAAACCTCTATCTCAGCCTATCCTGAAGCATTAAATGGATTACTAAAAAATTATGATGATGTAGAA
AAAGGTAATTTCCGTTTGACCGATTTAATTACGGGTTTTGTTGATCCAAATGCCGAAATAGAAGAACACAACGGACTTGA
TGAAGACTTTTCTGACGAAGATGATGAAGAAGAATCTAGTAATGCAGATGTGGAAGACAATGAAGATGAAGAAGACAATG
AATCAGAATCTACATCAGATTCAAGCGACTCTGATAACAGTATTGATCCTGAAGTTGCTCGCGAAAAATTTCAGCAATTA
AGAGAACAGCACTCTAAAACCCTTGCTGTTATTGAAAAACACGGTCGCTCTGGAAAACGTGCCCAAGATCAAATTGCACT
ACTTGGCGAAATTTTTAAACAATTCCGTTTAGTACCAAAACAATTTGATTTACTCGTTCTATCAATGAAAGAAATGATGA
AACGTGTGCGCTACCAAGAACGTCAGCTACAAAAAATATTAGTGGATATAGCAGGAATGCCAAAGGATGATTTTGAAAAA
ATTATTACCACTAATGGCAGTAACAGTGAATGGGTAGCAAAAGCATTAAAATCTAGCAAACCTTGGGCTAAACGTTTAAT
TAAATATGAAGATCGTATTTATGAAGCCTTAAACAATCTAGCGATAACAGAAGAAAATACTAAACTTACCATTACTCAAA
TGCGTGACATTTGCGATGCAGTCGCACGAGGCGAACAAAAAGCACGTCGAGCTAAAAAAGAAATGGTTGAAGCTAACTTG
CGTTTAGTAATTTCCATCGCGAAAAAATACACAAATCGAGGTTTACAATTCTTAGATTTAATTCAAGAAGGGAATATCGG
TTTAATGAAAGCGGTAGATAAATTTGAATATCGACGTGGCTACAAATTCTCTACATATGCTACTTGGTGGATTCGTCAAG
CAATCACTCGCTCTATTGCGGATCAAGCGCGTACAATCCGTATTCCTGTGCATATGATTGAAACAATCAATAAACTTAAT
CGTATTTCTCGCCAGTTGTTACAAGAAATGGGACGTGAAGCAACACCAGAAGAATTGGCAGAACGTATGGGAATGCCAGA
AGATAAAATCCGTAAAGTACTGAAAATTGCAAAAGAGCCGATTTCTATGGAAACACCTATTGGCGATGACGATGATTCGC
ATTTAGGGGATTTTATTGAAGATTCAACCTTAGAACTTCCTCTTGATTCTGCCACAGCACAAAGTTTAAAAGTTGCAACT
CACGAAGTGCTAGAAGGCTTGACGCCACGTGAAGCAAAAGTATTACGTATGCGTTTTGGCATTGATATGAATACCGACCA
TACACTTGAAGAAGTGGGTAAACAATTCGATGTAACACGCGAACGTATTCGTCAAATTGAAGCAAAAGCATTACGTAAAT
TACGTCATCCTAGCCGTTCTGAAACACTGAGAAGTTTTTTAGATGAATAG

Upstream 100 bases:

>100_bases
GCAGAAAAAACAGTTAGTGAATCCGCTATAACAATGGTAGAATCTCAAGTTCATAAAAAATCTTATCTTCTCAATCACAT
CAAGCAAAACGAGTATAAAA

Downstream 100 bases:

>100_bases
AGAGAAACATAAAAGAGGAAAATCGATCTAATCTTAAAAAATCAGATACATTTGTTTAAGGACTAAATTCTATAATCCGC
AGAATTTAGTCCTTTTACTT

Product: RNA polymerase sigma-70 factor

Products: NA

Alternate protein names: Sigma-70

Number of amino acids: Translated: 629; Mature: 629

Protein sequence:

>629_residues
MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLSDTIP
DEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVE
KGNFRLTDLITGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQL
REQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEK
IITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANL
RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN
RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVAT
HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDE

Sequences:

>Translated_629_residues
MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLSDTIP
DEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVE
KGNFRLTDLITGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQL
REQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEK
IITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANL
RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN
RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVAT
HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDE
>Mature_629_residues
MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPESDDMMLSDTIP
DEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLTREDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVE
KGNFRLTDLITGFVDPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQL
REQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQLQKILVDIAGMPKDDFEK
IITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANL
RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN
RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVAT
HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDE

Specific function: Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium

COG id: COG0568

COG function: function code K; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)

Gene ontology:

Cell location: Cytoplasm [C]

Metaboloic importance: Essential [C]

Operon status: Not Known

Operon components: None

Similarity: Belongs to the sigma-70 factor family

Homologues:

Organism=Escherichia coli, GI1789448, Length=629, Percent_Identity=67.0906200317965, Blast_Score=797, Evalue=0.0,
Organism=Escherichia coli, GI1789098, Length=241, Percent_Identity=41.9087136929461, Blast_Score=204, Evalue=2e-53,
Organism=Escherichia coli, GI1789871, Length=242, Percent_Identity=28.9256198347107, Blast_Score=91, Evalue=2e-19,
Organism=Escherichia coli, GI1788231, Length=212, Percent_Identity=30.188679245283, Blast_Score=74, Evalue=4e-14,

Paralogues:

None

Copy number: 700 (log & stationary phase) [C]

Swissprot (AC and ID): RPOD_HAEIN (P43766)

Other databases:

- EMBL:   L42023
- PIR:   B64075
- RefSeq:   NP_438691.1
- ProteinModelPortal:   P43766
- SMR:   P43766
- GeneID:   949596
- GenomeReviews:   L42023_GR
- KEGG:   hin:HI0533
- NMPDR:   fig|71421.1.peg.504
- TIGR:   HI_0533
- HOGENOM:   HBG745096
- OMA:   HPSRSET
- ProtClustDB:   CLSK808419
- BioCyc:   HINF71421:HI_0533-MONOMER
- InterPro:   IPR014284
- InterPro:   IPR000943
- InterPro:   IPR009042
- InterPro:   IPR007627
- InterPro:   IPR007624
- InterPro:   IPR007630
- InterPro:   IPR007631
- InterPro:   IPR007127
- InterPro:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991
- Gene3D:   G3DSA:1.10.10.10
- PRINTS:   PR00046
- TIGRFAMs:   TIGR02393
- TIGRFAMs:   TIGR02937

Pfam domain/function: PF04546 Sigma70_ner; PF03979 Sigma70_r1_1; PF00140 Sigma70_r1_2; PF04542 Sigma70_r2; PF04539 Sigma70_r3; PF04545 Sigma70_r4; SSF88946 Sigma_r2; SSF88659 Sigma_r3_r4

EC number: NA

Molecular weight: Translated: 72086; Mature: 72086

Theoretical pI: Translated: 4.42; Mature: 4.42

Prosite motif: PS00715 SIGMA70_1; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.2 %Cys     (Translated Protein)
3.3 %Met     (Translated Protein)
3.5 %Cys+Met (Translated Protein)
0.2 %Cys     (Mature Protein)
3.3 %Met     (Mature Protein)
3.5 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG
CCCCHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHHCCCCCCCHHHHHHHHHHHHCCCC
IPVLDEAPESDDMMLSDTIPDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT
CCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHEEC
REDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAEI
CCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEHHHHHHHHCCCCCCC
EEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQL
HHCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
REQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE
HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
RQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL
HHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL
EEECCCCEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN
HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHH
RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE
HHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHC
DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR
CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
ERIRQIEAKALRKLRHPSRSETLRSFLDE
HHHHHHHHHHHHHHHCCCHHHHHHHHHCC
>Mature Secondary Structure
MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG
CCCCHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHHCCCCCCCHHHHHHHHHHHHCCCC
IPVLDEAPESDDMMLSDTIPDEDAVEEATQILSNVESEIGRTTDPVRMYMREMGTVDLLT
CCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHEEC
REDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAEI
CCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEHHHHHHHHCCCCCCC
EEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQL
HHCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
REQHSKTLAVIEKHGRSGKRAQDQIALLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE
HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
RQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL
HHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL
EEECCCCEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN
HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHH
RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE
HHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHC
DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR
CCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
ERIRQIEAKALRKLRHPSRSETLRSFLDE
HHHHHHHHHHHHHHHCCCHHHHHHHHHCC

PDB accession: NA

Resolution: NA

Structure class: Alpha

Cofactors: NA

Metal ions: NA

Kcat value (1/min): NA

Specific activity: NA

Km value (mM): NA

Substrates: DNA [C]

Specific reaction: Protein + DNA = Protein-DNA [C]

General reaction: NA

Inhibitor: NA

Structure determination priority: 9.0

TargetDB status: NA

Availability: NA

References: 7542800