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The map label for this gene is rpoD [H]

Identifier: 108562514

GI number: 108562514

Start: 90398

End: 92476

Strand: Reverse

Name: rpoD [H]

Synonym: HPAG1_0089

Alternate gene names: 108562514

Gene position: 92476-90398 (Counterclockwise)

Preceding gene: 108562515

Following gene: 108562513

Centisome position: 5.79

GC content: 38.72

Gene sequence:

>2079_bases
TTGAAAGCATGGGTTCTTTATTTTATGGAGTGTCCAATGAAAAAGAAAGCTAACGAAGAAAAAGCCCCCAAAAGAGCTAA
AACAGAAGCCAAAGCAGAAGCCACACAAGAAATTAGACAAGAAAACAAAGCTAAAGAAAGCAATAAAGCCAAAGAGAGCA
AAATCAAAGAAAATAAAGCCAAAGAAAACAAAATCAAAGAAGCTAAAGCGAAAGAACTTGTTCCTGTTAAAAAGCTTAGT
TTTAATGAAGCGTTAGAAGAATTGTTCGCTAATTCCTTAAGCGATTGCGTTTCTTATGAGTCTATCATTCAAATCAGCGC
GAAAGTCCCCACTCTAGCCCAAGTCAAAAAAATCAAAGAATTGTGCCAAAAATACCAAAAGAAATTAGTCAGCTCTTCAG
AATACGCTAAAAAACTCAATGCGATTGACAAGATTAAAAAAACCGAAGAAAAGCAAAAAGTTTTAGATGAAGAATTAGAA
GATGGCTATGACTTTTTGAAAGAAAAGGATTTTTTAGAGTGGAGCAGAAGCGATAGCCCAGTACGCATGTATTTGCGCGA
AATGGGGGATATAAAACTTTTAAGCAAAGATGAAGAGATTGAATTGAGCAAGCAAATCCGCTTGGGTGAAGACATTATTT
TAGACGCGATTTGCTCGGTGCCGTATTTGATTGATTTTATCTATGCGTATAAAGACGCTTTAATCAATCGTGAAAGAAGG
GTTAAAGAGCTTTTCAGGAGCTTTGATGATGACGATGAAAATAGCGTGAGCGATTCTAAAAAAGATGATGACAGCGAAGA
AGATGAAGAAAACAAAGAAAGGAAAAAAGTCGTTTCTGAAAAAGACAAGAAGCGTGTAGAAAAGGTTCAAGAAAGCTTTA
AAGCCCTAGACAAGGCTAAAAAAGAATGGCTTAAAGCCCTTGAAGCCCCTGTAGATGAAAAAGAAGATGAATTGGTGCGT
TTATTGACTCTAGCTTACAAACGCCAAACGCTCAAAGACAGACTCTATGACTTAGAGCCTACCAGCAAACTGATTAATGA
ATTAGTCAAAACGATGGAAACCACTTTAAAAAGCGGCGATGGGTTTGAAAAAGAGTTGAAACGCTTGGAATACAAACTGC
CCTTATTCAATGACACTCTCATCGCTAACCATAAAAAAATCCTTGCCAATATCACTCACATGACTAAAGAAGATATTATC
GCTCAAGTGCCAGAAGCGACTATGGTGAGCGTGTATATGGATCTTAAAAAGCTTTTTTTGACTAAAGAAGCGAGCGAAGA
AGGCTTTGATCTAGACCCCAACAAGTTAAAAGAAATTTTAGAGCAAATCAAGAGAGGGAAATTGATTTCCGATCGCGCTA
AAAACAAAATGGCTCAATCCAATTTAAGGTTGGTGGTGAGCATCGCTAAACGATTCACAAGTAGAGGCTTACCCTTCTTG
GATTTGATTCAAGAGGGCAATATTGGCTTGATGAAAGCAGTGGATAAGTTTGAGCATGAAAAGGGCTTCAAGTTTTCTAC
CTATGCGACCTGGTGGATCAAGCAAGCCATCAGCAGAGCCATAGCCGATCAAGCCCGCACTATCCGCATCCCCATTCACA
TGATTGACACCATTAATCGCATCAATAAAGTCATGCGCAAACACATTCAAGAAACCGGCAAAGAGCCTGATTTAGAAGTG
GTGGCTGAAGAAGTGGGGCTTTCGTTAGATAAAGTGAAGAATGTGATTAAGGTTACTAAAGAGCCTATCAGTTTGGAAAC
CCCAGTCGGCAATGATGATGACGGCAAATTTGGGGATTTCGTGGAAGATAAAAATATCGTTAGCTCCATTGATCACATCA
TGCGAGAAGATTTAAAAGCACAAATTGAAAGCGTTTTGGATCAGTTGAATGAGCGAGAAAAAGCGGTGATTCGCATGCGT
TTTGGGCTTTTGGACGATGAAAGCGATCGAACTTTAGAAGAAATTGGTAAGGAATTGAATGTTACTAGAGAAAGGGTGCG
CCAGATTGAAAGCTCTGCGATTAAAAAATTGAGAAGCCCGCAATACGGGCGCATTTTAAGAAATTATTTGCGCATTTGA

Upstream 100 bases:

>100_bases
AGTGGGGAAAAATTCCAATGATATAATTAGAATTTAAGCTATTTTTTAGTAAAATGGCAAAGGATTAGGTGTATCTTAAT
CTTATGGACCTAGCTTTTGA

Downstream 100 bases:

>100_bases
TGTTAAGGTTTCTCTAAAACATGCGTTATTTTCTTGTCGTTTTCTTGTTTTTGTTTGTGGGTTGCATGAAAAAGGATTTC
ACACTCAAAGATTTATCCTT

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70 [H]

Number of amino acids: Translated: 692; Mature: 692

Protein sequence:

>692_residues
MKAWVLYFMECPMKKKANEEKAPKRAKTEAKAEATQEIRQENKAKESNKAKESKIKENKAKENKIKEAKAKELVPVKKLS
FNEALEELFANSLSDCVSYESIIQISAKVPTLAQVKKIKELCQKYQKKLVSSSEYAKKLNAIDKIKKTEEKQKVLDEELE
DGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALINRERR
VKELFRSFDDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAPVDEKEDELVR
LLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITHMTKEDII
AQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFL
DLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEV
VAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMR
FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYLRI

Sequences:

>Translated_692_residues
MKAWVLYFMECPMKKKANEEKAPKRAKTEAKAEATQEIRQENKAKESNKAKESKIKENKAKENKIKEAKAKELVPVKKLS
FNEALEELFANSLSDCVSYESIIQISAKVPTLAQVKKIKELCQKYQKKLVSSSEYAKKLNAIDKIKKTEEKQKVLDEELE
DGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALINRERR
VKELFRSFDDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAPVDEKEDELVR
LLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITHMTKEDII
AQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFL
DLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEV
VAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMR
FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYLRI
>Mature_692_residues
MKAWVLYFMECPMKKKANEEKAPKRAKTEAKAEATQEIRQENKAKESNKAKESKIKENKAKENKIKEAKAKELVPVKKLS
FNEALEELFANSLSDCVSYESIIQISAKVPTLAQVKKIKELCQKYQKKLVSSSEYAKKLNAIDKIKKTEEKQKVLDEELE
DGYDFLKEKDFLEWSRSDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALINRERR
VKELFRSFDDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESFKALDKAKKEWLKALEAPVDEKEDELVR
LLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGDGFEKELKRLEYKLPLFNDTLIANHKKILANITHMTKEDII
AQVPEATMVSVYMDLKKLFLTKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFL
DLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINRINKVMRKHIQETGKEPDLEV
VAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMR
FGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLRSPQYGRILRNYLRI

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=265, Percent_Identity=54.7169811320755, Blast_Score=309, Evalue=4e-85,
Organism=Escherichia coli, GI1789098, Length=234, Percent_Identity=43.1623931623932, Blast_Score=199, Evalue=5e-52,
Organism=Escherichia coli, GI1789871, Length=237, Percent_Identity=32.0675105485232, Blast_Score=106, Evalue=6e-24,
Organism=Escherichia coli, GI1788231, Length=232, Percent_Identity=26.7241379310345, Blast_Score=67, Evalue=4e-12,

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:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991 [H]

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

EC number: NA

Molecular weight: Translated: 80258; Mature: 80258

Theoretical pI: Translated: 8.45; Mature: 8.45

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.6 %Cys     (Translated Protein)
2.2 %Met     (Translated Protein)
2.7 %Cys+Met (Translated Protein)
0.6 %Cys     (Mature Protein)
2.2 %Met     (Mature Protein)
2.7 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MKAWVLYFMECPMKKKANEEKAPKRAKTEAKAEATQEIRQENKAKESNKAKESKIKENKA
CCHHEEHHHHCCCHHCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
KENKIKEAKAKELVPVKKLSFNEALEELFANSLSDCVSYESIIQISAKVPTLAQVKKIKE
HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
LCQKYQKKLVSSSEYAKKLNAIDKIKKTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSP
HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
VRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALINRERR
HHHHHHHHCCEEEECCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
VKELFRSFDDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESFKALDKAK
HHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
KEWLKALEAPVDEKEDELVRLLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGD
HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC
GFEKELKRLEYKLPLFNDTLIANHKKILANITHMTKEDIIAQVPEATMVSVYMDLKKLFL
CHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
TKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFL
HHHCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH
DLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINR
HHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEHHHHHHHHHH
INKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDF
HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCH
VEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELN
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
VTRERVRQIESSAIKKLRSPQYGRILRNYLRI
HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC
>Mature Secondary Structure
MKAWVLYFMECPMKKKANEEKAPKRAKTEAKAEATQEIRQENKAKESNKAKESKIKENKA
CCHHEEHHHHCCCHHCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
KENKIKEAKAKELVPVKKLSFNEALEELFANSLSDCVSYESIIQISAKVPTLAQVKKIKE
HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
LCQKYQKKLVSSSEYAKKLNAIDKIKKTEEKQKVLDEELEDGYDFLKEKDFLEWSRSDSP
HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
VRMYLREMGDIKLLSKDEEIELSKQIRLGEDIILDAICSVPYLIDFIYAYKDALINRERR
HHHHHHHHCCEEEECCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
VKELFRSFDDDDENSVSDSKKDDDSEEDEENKERKKVVSEKDKKRVEKVQESFKALDKAK
HHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
KEWLKALEAPVDEKEDELVRLLTLAYKRQTLKDRLYDLEPTSKLINELVKTMETTLKSGD
HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC
GFEKELKRLEYKLPLFNDTLIANHKKILANITHMTKEDIIAQVPEATMVSVYMDLKKLFL
CHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
TKEASEEGFDLDPNKLKEILEQIKRGKLISDRAKNKMAQSNLRLVVSIAKRFTSRGLPFL
HHHCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH
DLIQEGNIGLMKAVDKFEHEKGFKFSTYATWWIKQAISRAIADQARTIRIPIHMIDTINR
HHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEHHHHHHHHHH
INKVMRKHIQETGKEPDLEVVAEEVGLSLDKVKNVIKVTKEPISLETPVGNDDDGKFGDF
HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCH
VEDKNIVSSIDHIMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELN
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
VTRERVRQIESSAIKKLRSPQYGRILRNYLRI
HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC

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: 9923682 [H]