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The map label for this gene is rpoD [H]

Identifier: 226950364

GI number: 226950364

Start: 3362799

End: 3363884

Strand: Reverse

Name: rpoD [H]

Synonym: CLM_3332

Alternate gene names: 226950364

Gene position: 3363884-3362799 (Counterclockwise)

Preceding gene: 226950365

Following gene: 226950363

Centisome position: 80.95

GC content: 32.69

Gene sequence:

>1086_bases
ATGAAAGAAAAGAAGAATAATGCTAAAGATAAAAATGAAAAAATGAAGTTAGTTAGACGCTTAATAGATAAAGGTAAAAA
AAGTGGATCATTAAGTTATAAAGAAATTATGGATGAATTAGAAGAAATAGATTTAAGTCCAGAACAAATCGAAAAAATAT
ACGATGTATTAGAGTCTATGGGTGTGGAAGTTACAGGTGATATGAATGATATAGACGTAAAGGAAGAGGATATTGATTTA
TCAGTTCCGGAAGGTATTGCTATAGATGATCCTGTTAGAATGTATTTAAAAGAAATAGGGAAAGTAGCATTATTAACTTC
AGAAGAAGAAATAGAATTAGCACAAAGAATAGAAGCAGGAGATATGGTTGCTAAGAAGAAATTAGCAGAGGCTAATTTAA
GACTTGTTGTAAGCATTGCAAAGAGATATGTAGGAAGAGGAATGTTATTTTTAGATCTTATACAAGAAGGTAACCTAGGA
TTAATAAAAGCTGTAGAAAAATTTGACTATAGAAAAGGTTACAAATTTAGTACCTATGCTACTTGGTGGATAAGGCAGGC
CATTACAAGGGCTATAGCAGATCAAGCAAGAACCATAAGAATACCAGTTCACATGGTAGAAACTATAAATAAACTTATAA
GAGTATCAAGACAACTATTACAAGAACTAGGTAGGGAGCCACAGCCAGAGGAAGTGGCTAAGATTATGGAAATGCCTGTG
GATAAAGTAAGAGAAATAATGAAAATAGCTCAAGAACCTGTTTCTTTAGAAACTCCGATTGGTGAAGAGGAAGATAGTCA
TTTAGGAGACTTTATTCCAGATGATGAAGCACCGGCGCCGGCAGAAGCAGCAGCCTTTACAATGTTAAAAGAGCAACTTA
TTAATGTTTTAGATACATTAACACCAAGAGAAGAAAAGGTATTGAGATTAAGATTTGGTTTGGATGATGGAAGAGCCAGA
ACTTTAGAGGAAGTTGGAAAAGAATTTAATGTAACAAGAGAAAGAATAAGACAGATAGAAGCAAAAGCCCTAAGAAAATT
AAGACACCCAAGTAGAAGTAAAAAATTAAAAGATTATTTAGATTAA

Upstream 100 bases:

>100_bases
AGGAAAATTAGATGAAACTATAAAAATGAGCCAGGAACTCATCAAAGTAAAGAAAACCTTAGGGGCCATGAAATAATGGC
GAAAGGAGGCTACACTTATA

Downstream 100 bases:

>100_bases
TGCACCAATATAAGGTGCTTTTTTTTTTTTACTTATAATGATATAATGTTCATGTAATAAGGTAGGTGATAAACATGAAG
AAATTTAAGCCTATAAGTGG

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-A; Major vegetative sigma factor [H]

Number of amino acids: Translated: 361; Mature: 361

Protein sequence:

>361_residues
MKEKKNNAKDKNEKMKLVRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESMGVEVTGDMNDIDVKEEDIDL
SVPEGIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAGDMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLG
LIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEVAKIMEMPV
DKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRAR
TLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD

Sequences:

>Translated_361_residues
MKEKKNNAKDKNEKMKLVRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESMGVEVTGDMNDIDVKEEDIDL
SVPEGIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAGDMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLG
LIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEVAKIMEMPV
DKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRAR
TLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD
>Mature_361_residues
MKEKKNNAKDKNEKMKLVRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESMGVEVTGDMNDIDVKEEDIDL
SVPEGIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAGDMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLG
LIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEVAKIMEMPV
DKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDGRAR
TLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD

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 [H]

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 [H]

Homologues:

Organism=Escherichia coli, GI1789448, Length=269, Percent_Identity=64.3122676579926, Blast_Score=353, Evalue=1e-98,
Organism=Escherichia coli, GI1789098, Length=289, Percent_Identity=43.598615916955, Blast_Score=249, Evalue=3e-67,
Organism=Escherichia coli, GI1789871, Length=272, Percent_Identity=29.0441176470588, Blast_Score=106, Evalue=2e-24,
Organism=Escherichia coli, GI1788231, Length=199, Percent_Identity=27.1356783919598, Blast_Score=68, Evalue=9e-13,

Paralogues:

None

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

Swissprot (AC and ID): NA

Other databases:

- InterPro:   IPR014284
- InterPro:   IPR000943
- InterPro:   IPR009042
- InterPro:   IPR007627
- InterPro:   IPR007624
- InterPro:   IPR007630
- InterPro:   IPR007127
- InterPro:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991 [H]

Pfam domain/function: PF03979 Sigma70_r1_1; PF00140 Sigma70_r1_2; PF04542 Sigma70_r2; PF04539 Sigma70_r3; PF04545 Sigma70_r4 [H]

EC number: NA

Molecular weight: Translated: 41386; Mature: 41386

Theoretical pI: Translated: 5.14; Mature: 5.14

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.0 %Cys     (Translated Protein)
3.6 %Met     (Translated Protein)
3.6 %Cys+Met (Translated Protein)
0.0 %Cys     (Mature Protein)
3.6 %Met     (Mature Protein)
3.6 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MKEKKNNAKDKNEKMKLVRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESM
CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHC
GVEVTGDMNDIDVKEEDIDLSVPEGIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAG
CCEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEECCHHHHHHHHHHHHH
DMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYA
HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHH
TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEVAKIMEMPV
HHHHHHHHHHHHHHCCCEEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCH
DKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTL
HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
TPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYL
CCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC
D
C
>Mature Secondary Structure
MKEKKNNAKDKNEKMKLVRRLIDKGKKSGSLSYKEIMDELEEIDLSPEQIEKIYDVLESM
CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHC
GVEVTGDMNDIDVKEEDIDLSVPEGIAIDDPVRMYLKEIGKVALLTSEEEIELAQRIEAG
CCEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEECCHHHHHHHHHHHHH
DMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYA
HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHH
TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEVAKIMEMPV
HHHHHHHHHHHHHHCCCEEECHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCH
DKVREIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTL
HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC
TPREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYL
CCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC
D
C

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: 7961408; 11466286 [H]