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The map label for this gene is rpoD [H]

Identifier: 227080700

GI number: 227080700

Start: 507852

End: 509729

Strand: Reverse

Name: rpoD [H]

Synonym: VCM66_0475

Alternate gene names: 227080700

Gene position: 509729-507852 (Counterclockwise)

Preceding gene: 227080701

Following gene: 227080699

Centisome position: 17.62

GC content: 47.39

Gene sequence:

>1878_bases
ATGGATCAAAATCCGCAGTCACAGCTTAAACAACTTGTCCTTCGCGGCAAGGAACAGGGCTATCTGACCTACGCCGAAGT
AAATGACCACTTGCCTGCTGAAATCGTTGATTCAGAGCAGGTGGAAGATATTATTCAGATGATTAATGACATGGGCATTA
AGGTGGTGGAAACCGCACCTGATGCCGATGATCTTGCCCTCAGCGATGATACTACCATCACTGACGAAGATGCTGCTGAA
GCAGCCGCCGCGGCACTTTCTAGCGTAGAGAGTGAGATTGGCCGCACCACCGATCCAGTACGTATGTATATGCGTGAAAT
GGGTACGGTTGAGCTTTTGACACGTGAAGGTGAAATCGATATTGCCAAGCGCATTGAAGATGGTATTAACCAAGTTCAAA
GTGCGATTGCTGAGTATCCTGGAACCATCCCTTATATTCTTGAGCAGTTTGATCGTGTTCAGGCCGAAGAGCTACGTCTC
ACTGACCTGATTTCAGGTTTCGTTGACCCTAACGACATGGAAACCGAAGCGCCAACCGCGACTCACATCGGTTCTGAGCT
TTCTGAAGCGGATCTCGCGGATGAAGATGATGCTGTCGTCGAAGATGAAGACGAAGATGAAGACGAAGATGGCGACGGTG
AAAGCAGCGACAGCGAAGAAGAAGTCGGTATCGACCCTGAACTGGCTCGTGAGAAATTCAATGAACTGCGCGGTAAGTTC
CAAAACCTGCAATTAGCGGTTAATGAATTTGGTCGTGACAGTCATCAAGCTTCTGAAGCGTCAGACTTAGTGCTGGATAT
CTTCCGTGAATTCCGCCTAACACCAAAGCAATTCGACCACTTGGTTGAAACTCTGCGCACTTCAATGGATCGTGTTCGCA
CCCAAGAACGTTTGGTAATGAAAGCGGTAGTTGAAGTCGCGAAGATGCCGAAGAAATCGTTCATCGCCCTATTTACAGGC
AATGAATCGAATGAAGAGTGGCTGGATAAAGTCCTTGCTTCTGACAAGCCTTACGTAGCGAAAGTCCGTGAGCAAGAAGA
AGAGATCCGCCGTTCAATTCAGAAACTACAAATGATCGAGCAAGAGACATCACTGTCTGTTGAACGCATCAAAGACATCA
GCCGTCGTATGTCAATCGGTGAGGCGAAAGCTCGCCGTGCGAAGAAAGAGATGGTTGAAGCAAACTTACGTCTGGTAATT
TCGATTGCTAAGAAATACACCAACCGTGGTCTGCAATTCTTGGATCTGATCCAAGAAGGTAACATCGGTTTGATGAAAGC
CGTCGATAAGTTTGAATACCGTCGTGGTTATAAATTCTCAACTTATGCGACTTGGTGGATCCGTCAGGCAATCACTCGTT
CTATTGCTGACCAAGCACGTACGATTCGTATTCCAGTACACATGATCGAGACGATCAATAAACTGAATCGAATTTCGCGC
CAAATGCTGCAAGAGATGGGTCGTGAGCCACTGCCTGAAGAATTGGCAGAACGCATGCAAATGCCAGAAGACAAAATCCG
CAAAGTGCTGAAAATTGCCAAAGAACCCATCTCCATGGAAACACCGATTGGTGATGATGAAGATTCGCATCTGGGTGATT
TTATCGAGGATACCACCCTCGAGCTGCCACTGGATTCTGCGACCGCAACCAGCCTTAAAGCTGCCACTCGCGATGTATTA
GCAGGCCTAACACCTCGTGAAGCGAAAGTGCTACGTATGCGTTTCGGTATCGATATGAATACCGACCATACTCTGGAAGA
AGTGGGCAAGCAGTTTGATGTAACTCGTGAACGTATTCGTCAGATTGAAGCAAAAGCACTGCGTAAACTGCGTCATCCAA
GCCGCTCAGAAGTTCTGCGCAGCTTCTTGGATGAATAA

Upstream 100 bases:

>100_bases
AACTCTGTTGAGATAGTCAGCAAAGAATAAATTTGTTAGTATACGTGGTTTGCATTGCGCATACTTATTCCTTCACCAGA
TACGAAGTTGGATACCGTCT

Downstream 100 bases:

>100_bases
TTCAAGTTGGTTATGAACTGAAAAAGGTGAGCTGAGCTCACCTTTTCTTTTTTATACAAGCTAAGTGAATAAATTGTAAG
CACTATTGAACCCGCTTTGG

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70 [H]

Number of amino acids: Translated: 625; Mature: 625

Protein sequence:

>625_residues
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAE
AAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRL
TDLISGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTG
NESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVI
SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVL
AGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDE

Sequences:

>Translated_625_residues
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAE
AAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRL
TDLISGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTG
NESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVI
SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVL
AGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDE
>Mature_625_residues
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAE
AAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRL
TDLISGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTG
NESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVI
SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVL
AGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDE

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=625, Percent_Identity=76.48, Blast_Score=929, Evalue=0.0,
Organism=Escherichia coli, GI1789098, Length=239, Percent_Identity=42.2594142259414, Blast_Score=206, Evalue=4e-54,
Organism=Escherichia coli, GI1789871, Length=243, Percent_Identity=28.8065843621399, Blast_Score=91, Evalue=3e-19,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=27.2277227722772, Blast_Score=63, Evalue=7e-11,

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: 71167; Mature: 71167

Theoretical pI: Translated: 4.39; Mature: 4.39

Prosite motif: PS00715 SIGMA70_1 ; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.0 %Cys     (Translated Protein)
3.5 %Met     (Translated Protein)
3.5 %Cys+Met (Translated Protein)
0.0 %Cys     (Mature Protein)
3.5 %Met     (Mature Protein)
3.5 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAP
CCCCHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHCCHHHHHHHHHHHHHCCCEEEECCC
DADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHEECCCCCHH
IAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTA
HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCH
THIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVM
HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
KAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIE
HHHHHHHHCCCHHEEEEEECCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
QETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHH
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL
HHHHHHCCCCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCE
ELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR
ECCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
QIEAKALRKLRHPSRSEVLRSFLDE
HHHHHHHHHHCCCCHHHHHHHHHCC
>Mature Secondary Structure
MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAP
CCCCHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHCCHHHHHHHHHHHHHCCCEEEECCC
DADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHEECCCCCHH
IAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTA
HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCH
THIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKF
HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
QNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVM
HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
KAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIE
HHHHHHHHCCCHHEEEEEECCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
QETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR
CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHH
QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL
HHHHHHCCCCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCE
ELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR
ECCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
QIEAKALRKLRHPSRSEVLRSFLDE
HHHHHHHHHHCCCCHHHHHHHHHCC

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: 11677608; 12644504 [H]