Click here to switch to the map view.

The map label for this gene is rpoD [H]

Identifier: 83594214

GI number: 83594214

Start: 3322342

End: 3324432

Strand: Reverse

Name: rpoD [H]

Synonym: Rru_A2882

Alternate gene names: 83594214

Gene position: 3324432-3322342 (Counterclockwise)

Preceding gene: 83594215

Following gene: 83594211

Centisome position: 76.37

GC content: 64.18

Gene sequence:

>2091_bases
ATGGCGACCAAGGCGACCAACACGGCGGAAGCGGTGAACACCCAGGAAGAGGGCGGCGATAGCCCCTTGCTTGATTCGAT
GAACGCCGCCGTCAAGAAATTGGTCAACCGGGGCAAAGACCGGGGTTACATCACCTACGACGAACTCAATAACGCTCTGC
CCCCAGACGATGTGTCCTCCGAGCAGATCGAGGACACCATGGCCATGCTTTCCGATATGGGAATCAACGTCGTCGAGGAC
GAGGAAGAGGGCGAGGCCAGCGCCGCCCCCCCGGCCGAGGCCGGCGAGGAGGAACCCGGCCGCGAAGTCGCCGCGACCGG
CAATGTCAGTGAAGACGATATCGGCCGGACCGACGATCCGGTGCGCATGTATCTGCGCGAGATGGGCTCGGTCGAACTGC
TGTCGCGCGAGGGCGAAATCGCCATCGCCAAGCGGATCGAAGCCGGCCGCGAGATGATGATCGGCGGCATCTGCGAAAGC
CCGCTGACCATCCGCGCCCTGCTGCAATGGCACGACGCCCTGGTCGATGGCCGCATGCTGCTGCGCGACATCATCGATCT
CGACGCCACCTATGGCTCGGGCGCCGGTCCCGACGTGGTGGCCGAAGGCCTGGAAGACTCGGTGGTGCCGCTGTCGCCGT
TGGCCCTGTCTCCGGCCCGCGCCCTTCCCAAAGAGGCCGACGAGGCCGAAGAGGCCGTGACGCCCGGGCGCGATGACGAC
TCCGAAGATGAGGACGAGGGCGACGACGCCAAGCCCGCCGATGGGGCGGGCGACGAGGAGGCCGCGCCGAGCGGCGAGGA
CGAGGGCGACGGCAGCGAGAACAACGTGTCCCTCGCCGCCATGGAACAGGAGCTGATGCCCCGGGTTCTGGAAACCTTCG
AGCATATCGCCACCACCTATGGCAAGCTGAAGAAGGCCCAGGATCAGCGCATCGCCGCCTTGCAAAAGGGCGAGGAGCCG
GGCGCGGCGCTGGAGCGCAAATACGACAAGCTGAAGCTGGAGCTGGTCGGGCTGATGGAGGATGTCCATCTGAACAACGC
CCGCATCGAGCAGCTGGTCGAGCAGCTCAACGCGCTGAACAAGGGCCTGATCACCCAGGAAGGCAAGCTGCTGCGTCTGG
CCGAACGGGCCAAGATCCGCCGCGATGAATTCCTTGATCACTACTTCGGCCGCGAGATGGACCCGAGCTGGCGCGAGGAT
GTCGCCGCGCTGCCGGGCAAGGGCTGGCGCGATTTCACCACGCGCTTCGCCGATGAGATCAAGGATATCCGGGGCTCGAT
CGCCGAGATCGCCGAGCGCTCCTTGCTGCCCATCCCCGAGTTCCGCCGCATCGTGTCGACGGTGCAGAAGGGCGAGCGCG
AGGCCAGCCGGGCCAAGAAGGAGATGATCGAAGCCAACCTGCGCCTCGTCATCTCGATCGCCAAGAAATACACCAACCGC
GGTCTGCAGTTCCTCGACCTGATTCAGGAAGGCAACATCGGCCTGATGAAGGCGGTTGATAAGTTCGAATACCGCCGGGG
CTACAAGTTCTCGACCTATGCCACGTGGTGGATCAGACAGGCGATCACCCGCTCGATCGCCGATCAGGCCCGCACCATCC
GCATTCCGGTGCATATGATCGAGACGATCAACAAGCTGGTCCGCACCTCGCGCCAGATGCTCCACGAGATCGGCCGCGAG
CCGACCCCCGAGGAACTGGCCGAAAAGCTTCAGATGCCCTTGGAGAAAGTGCGCAAGGTTCTGAAGATCGCCAAGGAGCC
GATCAGCCTGGAAACGCCGATCGGCGACGAGGAAGACAGCCACCTGGGCGATTTCATCGAGGACAAGAACGCCGTTCAGC
CTTTGGACGCGGCGATCAACTCGAACCTGCGCGAAACCTGCACCCGGGTGCTGGCCAGCCTGACACCACGCGAGGAGCGC
GTGCTGCGCATGCGCTTTGGCATCGGCATGAACACCGACCACACCCTGGAAGAGGTGGGCCAGCAGTTCAGCGTGACCCG
CGAGCGTATCCGCCAGATCGAAGCCAAGGCCCTGCGCAAGCTCAAGCATCCCTCGCGCTCGCGCAAGCTGCGCTCTTTCC
TCGACAACTGA

Upstream 100 bases:

>100_bases
GACCCCCGGGCGCGATGGGACGAGGGCAGGCGGTCACGGATGATCCCAAGATTTCAAGGGGACACGGGGGGCCGGATATC
GGGCAAGGATGGAAAACCGT

Downstream 100 bases:

>100_bases
TCAACGATCGCTAAACTGCCGACAGCCGCCGCCCAAGCCCGCTTGGCGCGGCGCTCTGGTGGGCCTGTAGCTCAATGGTT
AGAGCCGGCGGCTCATAACC

Product: RNA polymerase sigma factor RpoD

Products: NA

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

Number of amino acids: Translated: 696; Mature: 695

Protein sequence:

>696_residues
MATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSSEQIEDTMAMLSDMGINVVED
EEEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICES
PLTIRALLQWHDALVDGRMLLRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDD
SEDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTYGKLKKAQDQRIAALQKGEEP
GAALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALNKGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWRED
VAALPGKGWRDFTTRFADEIKDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNR
GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGRE
PTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREER
VLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN

Sequences:

>Translated_696_residues
MATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSSEQIEDTMAMLSDMGINVVED
EEEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICES
PLTIRALLQWHDALVDGRMLLRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDD
SEDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTYGKLKKAQDQRIAALQKGEEP
GAALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALNKGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWRED
VAALPGKGWRDFTTRFADEIKDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNR
GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGRE
PTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREER
VLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN
>Mature_695_residues
ATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSSEQIEDTMAMLSDMGINVVEDE
EEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESP
LTIRALLQWHDALVDGRMLLRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDDS
EDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTYGKLKKAQDQRIAALQKGEEPG
AALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALNKGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWREDV
AALPGKGWRDFTTRFADEIKDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNRG
LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREP
TPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREERV
LRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN

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: Non_Essential [C]

Operon status: Not Known

Operon components: None

Similarity: Belongs to the sigma-70 factor family [H]

Homologues:

Organism=Escherichia coli, GI1789098, Length=233, Percent_Identity=42.0600858369099, Blast_Score=216, Evalue=4e-57,
Organism=Escherichia coli, GI1789448, Length=158, Percent_Identity=44.9367088607595, Blast_Score=121, Evalue=1e-28,
Organism=Escherichia coli, GI1789871, Length=242, Percent_Identity=28.5123966942149, Blast_Score=84, Evalue=3e-17,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=28.7128712871287, Blast_Score=72, Evalue=1e-13,

Paralogues:

None

Copy number: <10 (log phase) 250 (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: 77641; Mature: 77509

Theoretical pI: Translated: 4.55; Mature: 4.55

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2 ; PS00867 CPSASE_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.3 %Cys     (Translated Protein)
3.0 %Met     (Translated Protein)
3.3 %Cys+Met (Translated Protein)
0.3 %Cys     (Mature Protein)
2.9 %Met     (Mature Protein)
3.2 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSS
CCCCCCCHHHHHCCHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEHHHHCCCCCCCCCCH
EQIEDTMAMLSDMGINVVEDEEEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDP
HHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCHH
VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRALLQWHDALVDGRML
HHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
LRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDD
HHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCCCCCCCC
SEDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTY
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
GKLKKAQDQRIAALQKGEEPGAALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALN
HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
KGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWREDVAALPGKGWRDFTTRFADEI
CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHH
KDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNR
HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
CHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHH
ETINKLVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDS
HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
HLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
HHHHHHHCCCCCCHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHH
QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN
HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC
>Mature Secondary Structure 
ATKATNTAEAVNTQEEGGDSPLLDSMNAAVKKLVNRGKDRGYITYDELNNALPPDDVSS
CCCCCCHHHHHCCHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEHHHHCCCCCCCCCCH
EQIEDTMAMLSDMGINVVEDEEEGEASAAPPAEAGEEEPGREVAATGNVSEDDIGRTDDP
HHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCHH
VRMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLTIRALLQWHDALVDGRML
HHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
LRDIIDLDATYGSGAGPDVVAEGLEDSVVPLSPLALSPARALPKEADEAEEAVTPGRDDD
HHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCCCCCCCC
SEDEDEGDDAKPADGAGDEEAAPSGEDEGDGSENNVSLAAMEQELMPRVLETFEHIATTY
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
GKLKKAQDQRIAALQKGEEPGAALERKYDKLKLELVGLMEDVHLNNARIEQLVEQLNALN
HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
KGLITQEGKLLRLAERAKIRRDEFLDHYFGREMDPSWREDVAALPGKGWRDFTTRFADEI
CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHH
KDIRGSIAEIAERSLLPIPEFRRIVSTVQKGEREASRAKKEMIEANLRLVISIAKKYTNR
HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
CHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHH
ETINKLVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEEDS
HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH
HLGDFIEDKNAVQPLDAAINSNLRETCTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG
HHHHHHHCCCCCCHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHH
QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDN
HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC

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: 8491721; 11743193; 11743194 [H]