Click here to switch to the map view.

The map label for this gene is rpoD [H]

Identifier: 78044024

GI number: 78044024

Start: 399269

End: 400381

Strand: Direct

Name: rpoD [H]

Synonym: CHY_0455

Alternate gene names: 78044024

Gene position: 399269-400381 (Clockwise)

Preceding gene: 78044503

Following gene: 78043325

Centisome position: 16.63

GC content: 44.12

Gene sequence:

>1113_bases
ATGAAGGAAATAATGCAAAATGAAAAGCTTATGGAAATTGTTGAAAAAGGTAAAAAGCGCGGCGTTTTAACCTATAATGA
TTTACTTGACAGCTTACAAAACGTCGATATAAATTCGGAACAAATCGATGAACTGTACGAATACTTGGCTAACCAGGGAA
TAGAAGTGGTACCGGAAATACCGGAGTTGGAGCTTGATTCTATTAATAGCTTAGATGACGACGTTGATTTTAAGCCTTCC
GACATTGACGAGGTCGATTTAGATTTAACCATTCCGGAAGGGATTGCTATCGATGATCCGGTCCGGATGTATTTAAAAGA
AATCGGCCGCGTTCCCTTGCTAACGCCGGAAGAAGAAATAGAGCTTGCCAAAAGGAAGGAAGAAGGCGATGAAGAAGCTA
AAAGGAAACTTGCCGAAGCCAACTTGCGCCTTGTGGTAAGCATTGCAAAACGGTATGTGGGCAGGGGCATGTTGTTTTTG
GATTTAATTCAGGAAGGCAATCTTGGTTTATTAAAAGCGGTGGAAAAGTTTGATTATCGTAAAGGTTACAAGTTTTCCAC
GTATGCTACCTGGTGGATAAGACAGGCCATAACCCGGGCTATAGCTGACCAGGCCCGGACCATTAGAATTCCGGTACACA
TGGTGGAAACGATAAACAAATTAATTCGCGTCTCGAGAAATCTTCTCCAGGAACTTGGGCGGGAACCTACCCCGGAAGAA
ATAGCCAAGGAAATGGGTATTTCTGAGGATAAAGTAAGGGAGATTATGAAAATTGCCCAAGAACCGGTGTCTTTGGAAAC
ACCGATTGGAGAGGAAGAAGATTCTCACCTCGGAGATTTTGTCGAAGATCCCGATGCCAAAGCTCCCGTAGAAGAAGCTT
CTTACACTTTACTGCGGGAACAGTTAGATGAGGTTTTAAAAACTTTAACCGAAAGGGAGCAAAAGGTCCTAAGACTTCGC
TTTGGCCTGGATGACGGTCGTGCCCGGACCTTAGAAGAGGTCGGGCAGATCTTTGGTGTTACCCGGGAGCGGATTCGCCA
AATTGAAGCCAAGGCTTTACGAAAACTTCGCCATCCAAGCCGGAGTAAAAAGCTGAAAGATTTTCTGGAATAG

Upstream 100 bases:

>100_bases
TTAGCGGAAAAAGAAGGAAACTGGGAAAAACTCCAGTTATTATTAAACAAACTGCAGGAACTTACCCAAAAAAACTAACG
AAGAAAGGGGGGAATGCGGC

Downstream 100 bases:

>100_bases
AAGTAAAAAATACCACAAAAATCTTTTAAAAAACTTCTTGACCAAATTAAAAATATCTCATATAATAAATCATGTCGCGG
TAACAAATGAAATTCGGGCC

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-43; Sigma-A [H]

Number of amino acids: Translated: 370; Mature: 370

Protein sequence:

>370_residues
MKEIMQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEIPELELDSINSLDDDVDFKPS
DIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEIELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFL
DLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEE
IAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVLRLR
FGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE

Sequences:

>Translated_370_residues
MKEIMQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEIPELELDSINSLDDDVDFKPS
DIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEIELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFL
DLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEE
IAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVLRLR
FGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE
>Mature_370_residues
MKEIMQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEIPELELDSINSLDDDVDFKPS
DIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEIELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFL
DLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEE
IAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVLRLR
FGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFLE

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=260, Percent_Identity=65, Blast_Score=350, Evalue=1e-97,
Organism=Escherichia coli, GI1789098, Length=294, Percent_Identity=42.8571428571429, Blast_Score=236, Evalue=1e-63,
Organism=Escherichia coli, GI1789871, Length=272, Percent_Identity=31.25, Blast_Score=120, Evalue=1e-28,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=30.1980198019802, Blast_Score=76, Evalue=3e-15,

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: 42623; Mature: 42623

Theoretical pI: Translated: 4.56; Mature: 4.56

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.0 %Cys     (Translated Protein)
2.2 %Met     (Translated Protein)
2.2 %Cys+Met (Translated Protein)
0.0 %Cys     (Mature Protein)
2.2 %Met     (Mature Protein)
2.2 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MKEIMQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEI
CCHHHHHHHHHHHHHHHHHCCCEEHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCEECCCC
PELELDSINSLDDDVDFKPSDIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEI
CCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCHHHH
ELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYR
HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
KGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEE
CCCCCHHHHHHHHHHHHHHHHHHCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
IAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLRE
HHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHH
QLDEVLKTLTEREQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPS
HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
RSKKLKDFLE
HHHHHHHHHC
>Mature Secondary Structure
MKEIMQNEKLMEIVEKGKKRGVLTYNDLLDSLQNVDINSEQIDELYEYLANQGIEVVPEI
CCHHHHHHHHHHHHHHHHHCCCEEHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCEECCCC
PELELDSINSLDDDVDFKPSDIDEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTPEEEI
CCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCHHHH
ELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYR
HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
KGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEE
CCCCCHHHHHHHHHHHHHHHHHHCCCEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
IAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLRE
HHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHHHHHH
QLDEVLKTLTEREQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPS
HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
RSKKLKDFLE
HHHHHHHHHC

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: 11058132 [H]