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The map label for this gene is rpoD [H]

Identifier: 126208939

GI number: 126208939

Start: 1688201

End: 1690060

Strand: Direct

Name: rpoD [H]

Synonym: APL_1475

Alternate gene names: 126208939

Gene position: 1688201-1690060 (Clockwise)

Preceding gene: 126208938

Following gene: 126208946

Centisome position: 74.22

GC content: 43.6

Gene sequence:

>1860_bases
ATGGAACAACAATTAGAACAGCAATCTCAATTAGAACTTCTGATTGCCCAAGGGCGTGAACAAGGTTATTTAACCATTTC
GGAAGTGCACGACCACTTACCGGAAGAGTTGGTTGATGCGGAGCAGATCGAAGATATTATTCAAATGATCAACGATATGG
GGATTAAAGTTTTAGAAACCGCCCCGGATACCGACGAGTTAATGCTCGCGGAAAATATCGCTGATGAAGATGTCGTGGAA
GAAGCGACTAAAGTGCTTTCGACGGTAGAATCTGAATTAGGTAGAACGACCGATCCGGTACGTATGTATATGCGTGAAAT
GGGTACGGTGGAATTGCTTACCCGTGAAGGCGAAATTGATATTGCGAAACGTATTGAAGAAGGTATCAATGAAGTGCAAT
GTGCGGTTGCAGAATATCCGGAAGCCTTAACCGAATTAATCGGTTTCTATGCGCAAGTTGAAGAAGGTACGATGCGTTTA
TCGGATCTTGTTACCGCTTTCGTTGATCCGAATATCCAAGCGGACGAAGCGTTGGAAGATTTAGACGTAGATCTTGATGA
CGAAGAAGAAGCGGAAGATGTTGCGGATGTAGATGACGAGAGCGAAGAGGAAGAAAGCGACGGCAGTACGGATACCGGTG
ATGACAATTCAATCGATCCTGAACTTGCTCGCGAAAAATTCTATGCGTTACGCGAGCAACACGAAAAAGCCTTACAAGCG
ATTCAAAAACATGGTCGTAGCCATAAAAAATCAAGAGAGCAGATCCAAGCGCTTTCGGATATTTTCCGTGAGTTCCGTTT
AGTACCGAAACAATTTGATTTACTTGTCGAATCGATGCAAAAAATGATGAAACAAGTACGTTCGGAAGAGCGCCAAATTC
AACGTTATGCGGTTGAATATGCACAAATGAAAAAGGCTGACTTCTTAAAATTGTTCCAAGGTAACGAAACGTCGGAAGAA
TGGATTGAAAAAGCAATTAATGCGAAAAAAGGCGCCGCGCCTAAATTGGCGAACTATATCGACCAAATTCGCGTAAATAT
CGATAATTTACAACGTATGGAGCAAACGACCGGTCTGACTATCGCACAAATTCGTGAAATCGGCGGGCGTATCGCAAACG
GTGAATTAAAAGCTCGCCGTGCGAAAAAAGAGATGGTGGAAGCGAACTTACGTTTAGTAATCTCGATTGCGAAAAAATAT
ACCAACCGCGGTTTACAATTCCTAGATTTAATTCAGGAAGGTAACATCGGTTTGATGAAAGCGGTCGATAAATTCGAATA
TCGTCGCGGTTATAAGTTCTCTACTTATGCGACTTGGTGGATTCGTCAGGCGATTACCCGTTCAATCGCCGACCAAGCAC
GTACCATCCGTATTCCGGTACATATGATCGAAACCATCAATAAACTGAACCGTATTTCTCGTCAATGTTTACAAGAAATG
GGACGTGAAGCGACGCCGGAAGAGTTAGCGGAACGTATGGGAATGCCGGAAGATAAGATTCGTAAAGTATTGAAGATTGC
CAAAGAGCCGATTTCAATGGAAACGCCGATTGGCGATGACGACGATTCGCATTTAGGTGATTTCATTCAAGACGAAAGCC
TTGAATTACCGTTAGATTCGGCAACTGCGGAAAGTTTACGTTTAGCAACGAATGAAGTATTGGAAGGCTTAACGCCGCGT
GAAGCAAAAGTATTGCGTATGCGTTTCGGTATTGATATGAACACAGACCACACGCTTGAGGAAGTCGGTAAGCAGTTTGA
CGTAACGCGTGAACGTATTCGTCAGATTGAAGCGAAAGCGTTACGCAAACTTCGTCACCCAAGCCGTTCGGAAACTTTAC
GTAGTTTCTTAGACGACTAG

Upstream 100 bases:

>100_bases
GCGGTCATTTTTGAGAAATTTTTTGCAAAACTATCAAGAAAATTTTAATTAATGGTATAATCCAATACTATTTTTGCGCG
CACACAAAACGGATACAATT

Downstream 100 bases:

>100_bases
AATAGAGAAATAAAAATGCCCAGGCGAGTTAAACTTGGGCATTTTTATTTCTATGACAAGCGGTCGAATTTGCAAAAAAA
TTAACAAATTTAACCGCTTG

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70 [H]

Number of amino acids: Translated: 619; Mature: 619

Protein sequence:

>619_residues
MEQQLEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIADEDVVE
EATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRL
SDLVTAFVDPNIQADEALEDLDVDLDDEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQA
IQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEE
WIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKY
TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM
GREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPR
EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDD

Sequences:

>Translated_619_residues
MEQQLEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIADEDVVE
EATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRL
SDLVTAFVDPNIQADEALEDLDVDLDDEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQA
IQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEE
WIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKY
TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM
GREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPR
EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDD
>Mature_619_residues
MEQQLEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIADEDVVE
EATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRL
SDLVTAFVDPNIQADEALEDLDVDLDDEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQA
IQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKADFLKLFQGNETSEE
WIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKY
TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM
GREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRLATNEVLEGLTPR
EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLDD

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=619, Percent_Identity=71.40549273021, Blast_Score=843, Evalue=0.0,
Organism=Escherichia coli, GI1789098, Length=244, Percent_Identity=40.9836065573771, Blast_Score=204, Evalue=2e-53,
Organism=Escherichia coli, GI1789871, Length=242, Percent_Identity=28.5123966942149, Blast_Score=92, Evalue=1e-19,
Organism=Escherichia coli, GI1788231, Length=221, Percent_Identity=28.9592760180996, Blast_Score=72, Evalue=1e-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: 70965; Mature: 70965

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:

0.3 %Cys     (Translated Protein)
3.6 %Met     (Translated Protein)
3.9 %Cys+Met (Translated Protein)
0.3 %Cys     (Mature Protein)
3.6 %Met     (Mature Protein)
3.9 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MEQQLEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLET
CCHHHHHHHHHHHHHHCCCCCCCEEHHHHHHHCCHHHHCHHHHHHHHHHHHHCCCEEEEC
APDTDELMLAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEID
CCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCHH
IAKRIEEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALED
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
LDVDLDDEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQA
CCCCCCCCHHHHHHHCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
IQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEY
HHHHCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
AQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLT
HHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHCCH
IAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK
HHHHHHHCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHH
AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM
HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHH
GREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDS
CCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCH
ATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA
HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
LRKLRHPSRSETLRSFLDD
HHHHHCCCHHHHHHHHHCC
>Mature Secondary Structure
MEQQLEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLET
CCHHHHHHHHHHHHHHCCCCCCCEEHHHHHHHCCHHHHCHHHHHHHHHHHHHCCCEEEEC
APDTDELMLAENIADEDVVEEATKVLSTVESELGRTTDPVRMYMREMGTVELLTREGEID
CCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHCCCCHH
IAKRIEEGINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALED
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
LDVDLDDEEEAEDVADVDDESEEEESDGSTDTGDDNSIDPELAREKFYALREQHEKALQA
CCCCCCCCHHHHHHHCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
IQKHGRSHKKSREQIQALSDIFREFRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEY
HHHHCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
AQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLT
HHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHCCH
IAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK
HHHHHHHCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHH
AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM
HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHH
GREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDS
CCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCH
ATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA
HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
LRKLRHPSRSETLRSFLDD
HHHHHCCCHHHHHHHHHCC

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]