Click here to switch to the map view.

The map label for this gene is rpoD [H]

Identifier: 189183187

GI number: 189183187

Start: 282103

End: 283950

Strand: Direct

Name: rpoD [H]

Synonym: OTT_0280

Alternate gene names: 189183187

Gene position: 282103-283950 (Clockwise)

Preceding gene: 189183186

Following gene: 189183188

Centisome position: 14.04

GC content: 31.28

Gene sequence:

>1848_bases
ATGGCAAGTCTGCGTAATAAAAATAATAAAATTATTATCTGCAATAAAAAAACTAAAAAAAATACAAATGTAGAAGAGTT
AGCTAGCAATTTCGTTGATGAATCAGAAAAATTATCATCAAAAATTTCTGATTCTGACATTAACTTAGATAAAGATTTTG
ATTATACTAAATTGGGAGTATGTCCTGATAAAATCGAAGAAGAAGAAGTAGTATTAGCTTCTAATGCTACTGAAGGAGAA
TTTGAAGAAGATTTAGATGATAATATATACTCTACGGATATTGTTAGAGCATATCTAAAAGATATGAGCAACACCACTTT
ACTTTCGAGAGAGGGAGAAATTGAACTTGCTAAGCAAATGGAAGAAGGAAAAAAAACAGTGATACACTTCATTTGTCATC
TTCCATATGTTATGAAACTCTTAATACAGTGGTATGAAGACTTAGTTCATAGTAGAATATTAGTAAGGAATCTTATTGAG
CTAGAAAGTAACATTTATGATCAGCCTGAAGATGATAACCAACATGACTATGATTCTGATGGTGATTGTGAAGAATTACA
AAATGAACCTTTAACCAAGGTAGAATCAGAAATTTTGCCTAAAATTCTTGATAAGATGCAAGTTGTTTCTGACTTAGCAA
CTCAGCTTTTTGAAGTTGCAGCTCATGATTTTAAATTGCATAAATCTAGCTGTAATTATCAGGAAAGTAAAAAATTTACT
GAGTTATCAAAAGAACTAATTGCTGCAGTTAGTAATATTCACTTTAACAAGCAGTCTATTAAAAATATTTTAAACAAATT
ATATAGTGTTAATAAAGATATAATTAGTAAAGAAATTAATTTGCTTAAAGCTGCGGAAAAATATAAAATAAGCCGCCATG
ATTTCTTATTTCAATATAATAGCGGTAGTAATTGGTTACAGAAAGTAAAGTTATTACATCAAGATGAGTGGAATAAATTT
TTAAGCAAGGAAAAAGACCTTATTAAGTCTACCATTGATTATTTCAGCGAAATTGAACAAGCAATGTTATTGCCTTTAAA
AAGGTTTAAGGAAATTATTCAAGCTATTCAAAATGGCGAACGGAAGGTTAGAGTAGCAAAAAAGAAAATGGTTGAATCTA
ATACACGTTTGGTAGTACATGTTGCTAAACCATATGTTAATCGTGGATTACCATTTTTAGACTTAATTCAGGAAGGTAAC
ATCGGGCTTATGAAGGCTGTAGATAAATACAATTATCTTCTTGGATATAAATTTTCCACTTGTGCTACTTGGTGGGTTAG
GCAATCAATTAGCCGCGCTGTTGCAGATCAAGCTCGAACTATTCGTATACCAGTTCATATGGCTGATACCATCAGCAAGA
TTGTTAGAGTTAGCAAGCAAATGCATAACGAATTAGGTTATGAACCTACTGCCTCTGAAATCGCTGAGAAGTTGTCAATG
CCAATAGATAAGGTTAAAAAAGTAATGAGAATTGCTAAAGAGCCAGTTAGTTTAGAAAACCCTATCGGTGAAGAAGATGG
AAGTTGCTTATCAGACTTCATTGAGGATAAAAACGCTATATTACCAATAGAAGAAGCTATCAAATTTAGTTTACGTGAGA
CTACTACGCGCGCTCTATCAACTCTTACAGCTAGAGAAGAAAGAGTATTAAGGCTAAGATTTGGTATTGGGTTACCTACT
GATTATACACTTGAAGAAGTTGGTGGCGAATTTAAAGTAACAAGAGAAAGAGTTAGGCAAATTGAAGCTAAGGCTCTAAG
AAAACTTAAACATCCTGTTAGATCAAAAAAATTAAAGAGTTTTTTAAGTAGTAAAAATAAAACTTTAAGTAATAACGAGA
ATGATTAA

Upstream 100 bases:

>100_bases
AATAGTGTTGACAATGCGAGTCTATATCAGCAAGAAATTTTTAAAATTGAACATGAAATTGACCTTTTAAATGAAGCTTT
ACACTTAGAACAAGAAGAAC

Downstream 100 bases:

>100_bases
TGTATTCTACTTTTTTGTTCAGGAATAGCTATAAAAAAAGAAATATGTTATGCTGCTCTCATAATTATAGAAGTGGTAAA
TGAAAGCAAGAAAGACAATA

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70 [H]

Number of amino acids: Translated: 615; Mature: 614

Protein sequence:

>615_residues
MASLRNKNNKIIICNKKTKKNTNVEELASNFVDESEKLSSKISDSDINLDKDFDYTKLGVCPDKIEEEEVVLASNATEGE
FEEDLDDNIYSTDIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIE
LESNIYDQPEDDNQHDYDSDGDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCNYQESKKFT
ELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYNSGSNWLQKVKLLHQDEWNKF
LSKEKDLIKSTIDYFSEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGN
IGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSM
PIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDKNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPT
DYTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKSFLSSKNKTLSNNEND

Sequences:

>Translated_615_residues
MASLRNKNNKIIICNKKTKKNTNVEELASNFVDESEKLSSKISDSDINLDKDFDYTKLGVCPDKIEEEEVVLASNATEGE
FEEDLDDNIYSTDIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIE
LESNIYDQPEDDNQHDYDSDGDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCNYQESKKFT
ELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYNSGSNWLQKVKLLHQDEWNKF
LSKEKDLIKSTIDYFSEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGN
IGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSM
PIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDKNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPT
DYTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKSFLSSKNKTLSNNEND
>Mature_614_residues
ASLRNKNNKIIICNKKTKKNTNVEELASNFVDESEKLSSKISDSDINLDKDFDYTKLGVCPDKIEEEEVVLASNATEGEF
EEDLDDNIYSTDIVRAYLKDMSNTTLLSREGEIELAKQMEEGKKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIEL
ESNIYDQPEDDNQHDYDSDGDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCNYQESKKFTE
LSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYNSGSNWLQKVKLLHQDEWNKFL
SKEKDLIKSTIDYFSEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNI
GLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSMP
IDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDKNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTD
YTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKSFLSSKNKTLSNNEND

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=319, Percent_Identity=54.2319749216301, Blast_Score=350, Evalue=2e-97,
Organism=Escherichia coli, GI1789098, Length=272, Percent_Identity=37.1323529411765, Blast_Score=201, Evalue=8e-53,
Organism=Escherichia coli, GI1789871, Length=247, Percent_Identity=28.7449392712551, Blast_Score=91, Evalue=2e-19,
Organism=Escherichia coli, GI1788231, Length=199, Percent_Identity=28.1407035175879, Blast_Score=78, Evalue=2e-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:   IPR007631
- InterPro:   IPR007127
- InterPro:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991 [H]

Pfam domain/function: PF04546 Sigma70_ner; PF03979 Sigma70_r1_1; PF00140 Sigma70_r1_2; PF04542 Sigma70_r2; PF04539 Sigma70_r3; PF04545 Sigma70_r4 [H]

EC number: NA

Molecular weight: Translated: 70853; Mature: 70722

Theoretical pI: Translated: 6.85; Mature: 6.85

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

1.1 %Cys     (Translated Protein)
2.0 %Met     (Translated Protein)
3.1 %Cys+Met (Translated Protein)
1.1 %Cys     (Mature Protein)
1.8 %Met     (Mature Protein)
2.9 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MASLRNKNNKIIICNKKTKKNTNVEELASNFVDESEKLSSKISDSDINLDKDFDYTKLGV
CCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCCCCCCCC
CPDKIEEEEVVLASNATEGEFEEDLDDNIYSTDIVRAYLKDMSNTTLLSREGEIELAKQM
CCCCCCCCCEEEECCCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCEEECCCCCHHHHHHH
EEGKKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIELESNIYDQPEDDNQHDYDSD
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
GDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCNYQESKKFT
CCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
ELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYN
HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC
SGSNWLQKVKLLHQDEWNKFLSKEKDLIKSTIDYFSEIEQAMLLPLKRFKEIIQAIQNGE
CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
RKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNIGLMKAVDKYNYLLGYKFST
HHHHHHHHHHHCCCCEEEEEECCHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHCCCHHH
CATWWVRQSISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSM
HHHHHHHHHHHHHHHHCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCC
PIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDKNAILPIEEAIKFSLRETTTRALS
CHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
TLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKS
HHHHHHHHHHHHHCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
FLSSKNKTLSNNEND
HHHHCCCCCCCCCCC
>Mature Secondary Structure 
ASLRNKNNKIIICNKKTKKNTNVEELASNFVDESEKLSSKISDSDINLDKDFDYTKLGV
CCCCCCCCEEEEECCCCCCCCCHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCCCCCCCC
CPDKIEEEEVVLASNATEGEFEEDLDDNIYSTDIVRAYLKDMSNTTLLSREGEIELAKQM
CCCCCCCCCEEEECCCCCCCCHHHHCCCHHHHHHHHHHHHHCCCCEEECCCCCHHHHHHH
EEGKKTVIHFICHLPYVMKLLIQWYEDLVHSRILVRNLIELESNIYDQPEDDNQHDYDSD
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
GDCEELQNEPLTKVESEILPKILDKMQVVSDLATQLFEVAAHDFKLHKSSCNYQESKKFT
CCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
ELSKELIAAVSNIHFNKQSIKNILNKLYSVNKDIISKEINLLKAAEKYKISRHDFLFQYN
HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEC
SGSNWLQKVKLLHQDEWNKFLSKEKDLIKSTIDYFSEIEQAMLLPLKRFKEIIQAIQNGE
CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
RKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNIGLMKAVDKYNYLLGYKFST
HHHHHHHHHHHCCCCEEEEEECCHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHCCCHHH
CATWWVRQSISRAVADQARTIRIPVHMADTISKIVRVSKQMHNELGYEPTASEIAEKLSM
HHHHHHHHHHHHHHHHCCCEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCC
PIDKVKKVMRIAKEPVSLENPIGEEDGSCLSDFIEDKNAILPIEEAIKFSLRETTTRALS
CHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
TLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRERVRQIEAKALRKLKHPVRSKKLKS
HHHHHHHHHHHHHCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
FLSSKNKTLSNNEND
HHHHCCCCCCCCCCC

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: NA