Click here to switch to the map view.

The map label for this gene is rpoD [H]

Identifier: 110633818

GI number: 110633818

Start: 1564810

End: 1566816

Strand: Direct

Name: rpoD [H]

Synonym: Meso_1465

Alternate gene names: 110633818

Gene position: 1564810-1566816 (Clockwise)

Preceding gene: 110633817

Following gene: 110633819

Centisome position: 35.46

GC content: 61.53

Gene sequence:

>2007_bases
ATGGCGACAAAGGAAAAGGAAGAGGTCGAGATCGAACGCGACGGCACCGATGGGCCGCTGCTCGACCTTTCCGACGACGC
AGTCAAGAAAATGATCAAGCTCGCGAAGAAGCGCGGCTATGTGACCATGGACGAGCTGAATGCGGTGCTGCCTTCCGGTG
AGGTGAGTTCCGAGCAGATCGAGGACACGATGGCCATGCTTTCGGACATGGGCATCAATGTCGTCGAGGACGAGGAGGCG
GGCGAGGAAGCCGAGGCTGACAGCGCGCCCGAAGAGGAAAGCGGTGAGCTGGCCGAGACCGGCAGCGCCGTTGCCACCGT
TGCCAAGAAAGAGCCGACCGACCGCACCGACGACCCCGTGCGCATGTATCTGCGCGAGATGGGTTCGGTGGAGCTGCTGT
CGCGCGAAGGCGAAATCGCCATCGCCAAGCGCATCGAGGCCGGCCGCGAGACCATGATCGCCGGGCTTTGCGAAAGCCCG
CTGACGTTCCAGGCGCTCATCATCTGGCGCGAAGAGCTTAACGACGGAAAGATCCTGCTGCGCGAGATCATCGATCTTGA
GGCGACCTATGCCGGCCCCGAGGGCAAGCAGGCGCCGGTGATCGCGCGGCCGGAAGATGTCGCCAGGCCCGCGCCCGAAG
AGAAGCTGATGCGGCGGGCGCGCGATGACGACGACATTACCAATGTCGGCGGAGAGTCGCGGCCCGAGGAAGACGACGAG
GAGGAGGACGAGACGAACCTCTCCCTCGCTGCCATGGAGGCCGAGCTCAAGCCCGGCTTCATGACGACGCTCGACTTCAT
CGCCGACACTTATTCCAAGCTGCGCAAGCTGCAGGACCAGGAGGTGGAGAGCCGCCTGGGCGATTCCGACAAGCTTTCGG
CTGGTCAGGAGCGCCGGTCCAAAGAGCTGAAGGACGAGCTCATCAAGGCGGTGAAGTCGCTCTCGCTCAACAACCAGCGC
ATCGAGACGCTGGTCGAGCAGCTTTACGATATCAATAAGCGCCTGGTGCAGAACGAGCTGAAGCTGTTCCGGCTTGCCGA
GAGTTATGGCGTGAGGCGCGAGGATTTCCTCAAGGCCTATCAGGGTTCCGAGCTTGACCCGAACTGGGGTTCCACGGTGG
CCGTCCTGCCGCAGCCCGGTTGGAGGGACTTCGTCAAGCACGAAGCCGACACGATCGAGGCCCTTCGCTCCGAGATCCAG
AATCTTGCGCAGGAAACCGGTATTTCGATTGGCGAGTTCCGCCGCATCGTCAATCAGGTTCAAAAGGGCGAGCGCGAGGC
GGCTATCGCCAAGAAGGAGATGGTGGAGGCCAATCTGCGCCTGGTCATCTCCATCGCCAAAAAATACACCAACCGTGGCC
TGCAGTTCCTTGACCTGATCCAGGAAGGCAATATCGGCCTCATGAAGGCCGTGGACAAGTTCGAGTATCGCCGCGGCTAT
AAGTTCTCGACCTATGCCACCTGGTGGATCAGGCAGGCGATCACCCGTTCGATCGCCGATCAGGCGCGGACGATCCGCAT
CCCTGTGCATATGATCGAGACGATCAACAAGATCGTGCGCACCTCGCGCCAGATGCTGCATGAGATCGGCCGGGAGCCGA
CGCCGGAAGAACTCGCCGAAAAGCTCGCAATGCCGCTTGAGAAGGTGCGCAAGGTTCTCAAGATCGCCAAGGAGCCGATC
AGCCTCGAAACGCCTGTGGGCGATGAGGAGGATTCGCATCTCGGCGATTTCATCGAAGACAAGAGTGCGATCCTGCCGAT
CGACGCGGCAATCCAGGCGAACCTTCGCGAGACGACGACGCGCGTTCTTGCTTCGCTCACTCCGCGCGAGGAACGCGTGC
TCCGCATGCGCTTCGGCATCGGAATGAACACCGATCACACGCTTGAGGAGGTGGGCCAGCAATTCTCGGTCACACGCGAG
CGCATTCGCCAGATCGAGGCGAAGGCGCTGCGCAAGCTCAAGCATCCGAGCCGCAGTCGCAAGCTGCGCAGCTTCCTGGA
CAGCTGA

Upstream 100 bases:

>100_bases
ACACTGGGCGCATAGAGCCTGACGGCGCGCATCCCGGCGATGAGTCGAGCTGTGGGTAGTGGCTGAGCCCGCTGCAAAGG
GCGGTTGGAGAAGGCAGAGC

Downstream 100 bases:

>100_bases
GGAAGCGTCTCTACTTCTCCTAAAAGCCGGGCCTTGGCCCGGCTTTTTTTGTGCCCGGCAGCCTCATCCAGCTTTGGTAG
GAATGCTTCCCAAAGCGGAT

Product: RNA polymerase sigma factor RpoD

Products: NA

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

Number of amino acids: Translated: 668; Mature: 667

Protein sequence:

>668_residues
MATKEKEEVEIERDGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQIEDTMAMLSDMGINVVEDEEA
GEEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESP
LTFQALIIWREELNDGKILLREIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNVGGESRPEEDDE
EEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDSDKLSAGQERRSKELKDELIKAVKSLSLNNQR
IETLVEQLYDINKRLVQNELKLFRLAESYGVRREDFLKAYQGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQ
NLAQETGISIGEFRRIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY
KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPI
SLETPVGDEEDSHLGDFIEDKSAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE
RIRQIEAKALRKLKHPSRSRKLRSFLDS

Sequences:

>Translated_668_residues
MATKEKEEVEIERDGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQIEDTMAMLSDMGINVVEDEEA
GEEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESP
LTFQALIIWREELNDGKILLREIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNVGGESRPEEDDE
EEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDSDKLSAGQERRSKELKDELIKAVKSLSLNNQR
IETLVEQLYDINKRLVQNELKLFRLAESYGVRREDFLKAYQGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQ
NLAQETGISIGEFRRIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY
KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPI
SLETPVGDEEDSHLGDFIEDKSAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE
RIRQIEAKALRKLKHPSRSRKLRSFLDS
>Mature_667_residues
ATKEKEEVEIERDGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQIEDTMAMLSDMGINVVEDEEAG
EEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPL
TFQALIIWREELNDGKILLREIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNVGGESRPEEDDEE
EDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDSDKLSAGQERRSKELKDELIKAVKSLSLNNQRI
ETLVEQLYDINKRLVQNELKLFRLAESYGVRREDFLKAYQGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQN
LAQETGISIGEFRRIVNQVQKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS
LETPVGDEEDSHLGDFIEDKSAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER
IRQIEAKALRKLKHPSRSRKLRSFLDS

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=396, Percent_Identity=58.3333333333333, Blast_Score=442, Evalue=1e-125,
Organism=Escherichia coli, GI1789098, Length=225, Percent_Identity=42.6666666666667, Blast_Score=213, Evalue=4e-56,
Organism=Escherichia coli, GI1789871, Length=248, Percent_Identity=27.4193548387097, Blast_Score=82, Evalue=1e-16,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=27.7227722772277, Blast_Score=70, Evalue=5e-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:   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: 75533; Mature: 75401

Theoretical pI: Translated: 4.66; Mature: 4.66

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.1 %Cys     (Translated Protein)
2.8 %Met     (Translated Protein)
3.0 %Cys+Met (Translated Protein)
0.1 %Cys     (Mature Protein)
2.7 %Met     (Mature Protein)
2.8 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MATKEKEEVEIERDGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQI
CCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEHHHHHHHCCCCCCCHHHH
EDTMAMLSDMGINVVEDEEAGEEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDPV
HHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCCCCCCHHH
RMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNDGKILL
HHHHHHCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHH
REIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNVGGESRPEEDDE
HHHHHHHHHCCCCCCCCCCEEECCHHHCCCCCHHHHHHHCCCCCHHHCCCCCCCCCCCCC
EEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDSDKLSAGQERRS
CHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
KELKDELIKAVKSLSLNNQRIETLVEQLYDINKRLVQNELKLFRLAESYGVRREDFLKAY
HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
QGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQNLAQETGISIGEFRRIVNQV
CCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
QKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY
HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHCCC
KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAE
CCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
KLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKSAILPIDAAIQANLRETTT
HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCEECCHHHHHHHHHHHHH
RVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSR
HHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
KLRSFLDS
HHHHHHCC
>Mature Secondary Structure 
ATKEKEEVEIERDGTDGPLLDLSDDAVKKMIKLAKKRGYVTMDELNAVLPSGEVSSEQI
CCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCEEHHHHHHHCCCCCCCHHHH
EDTMAMLSDMGINVVEDEEAGEEAEADSAPEEESGELAETGSAVATVAKKEPTDRTDDPV
HHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCCCCCCHHH
RMYLREMGSVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELNDGKILL
HHHHHHCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHH
REIIDLEATYAGPEGKQAPVIARPEDVARPAPEEKLMRRARDDDDITNVGGESRPEEDDE
HHHHHHHHHCCCCCCCCCCEEECCHHHCCCCCHHHHHHHCCCCCHHHCCCCCCCCCCCCC
EEDETNLSLAAMEAELKPGFMTTLDFIADTYSKLRKLQDQEVESRLGDSDKLSAGQERRS
CHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
KELKDELIKAVKSLSLNNQRIETLVEQLYDINKRLVQNELKLFRLAESYGVRREDFLKAY
HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
QGSELDPNWGSTVAVLPQPGWRDFVKHEADTIEALRSEIQNLAQETGISIGEFRRIVNQV
CCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
QKGEREAAIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY
HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHCCC
KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAE
CCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
KLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKSAILPIDAAIQANLRETTT
HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCEECCHHHHHHHHHHHHH
RVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSR
HHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
KLRSFLDS
HHHHHHCC

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]