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The map label for this gene is rpoD

Identifier: 21244512

GI number: 21244512

Start: 4456172

End: 4458049

Strand: Reverse

Name: rpoD

Synonym: XAC3788

Alternate gene names: 21244512

Gene position: 4458049-4456172 (Counterclockwise)

Preceding gene: 21244513

Following gene: 21244511

Centisome position: 86.14

GC content: 61.18

Gene sequence:

>1878_bases
ATGGCCAACGAACGTCCTGCCCAGCAATCCGACATCAAGCTACTGATCAGCAAGGGCCTGGAACAGGGCTATCTGACCTA
CGCCGAAGTCAATGACCATCTGCCCGACGACCTCGTCGACCCGGAGCAGATCGAAGACATCATCAGCATGATCAACGGCA
TGGGCATCGATGTCCATGAAGTTGCACCCGATGCCGAAACCCTGTTGCTCAACGATGGCAACACCGGCAACCGCGAGGTT
GACGACACCGCAGCCGAAGAAGCTGCCGCCGCGCTGACCGCGCTCGACACCGAAGGTGGCCGCACCACCGACCCGGTGCG
CATGTACATGCGCGAAATGGGCACGGTCGAGCTGCTGACCCGCGAAGGCGAAATCGCCATCGCCAAGCGCATCGAAGAAG
GCCTGAGCCAGGTCCAGGCCGCGTTGGGCGTGTTCCCGCTCTCGACCGAAATGCTGCTGGCCGACTACGAAGCGCACAAG
GAGGGCAAGAAGCGTCTGGCCGAGATCGTGGTCGGCTTCAACGACCTGATCGAAGAGGCCGATGCGGCCGCTGCTGCGCT
CGCCGCGGCCGGTCCGGTCGCCGTGTCCGACGATGAAGCAGTCGACGAAGACGACGACGAAGACGGCGATGACGAGGCCG
CCGAAGAAGAGGCCGGCCCGACCGGTCCGGACCCGGTGGAAGTGGCCACGCGCATGGAGAACCTGGCTAACGAATACGCC
AAGTTCAAGAAGGTCTATGCCAAGAACGGCGCCGAGCACAAGCTGGTGGTCAAGGCGCGCGAAGACATGGCCGCCATCTT
CACCACGCTCAAGCTGCCGCTGCCGCTGACCGACGCGCTGGTCACCCAGCTGCGTGGCGTGGTCAATGGCATCAAGGACC
ACGAGCGCAAGGTGCTGCACCTGGCCACCACCGTGGCCCGCATGCCGCGCAAGGATTTCATCCGCTCCTGGGAAGGCAAC
CAGACCAACCTGGAATGGGTGGAGGACGCACTCAAGCGCAAGCAGAAGTGGTCCTCGGCGCTGCGCGACGTCAAGGATCA
GATCATCTCCGAGCAGCAGGGCTCGATCGAGATGGAAAAGGCCAATTACCTGACCCTGGGCGAGATCAAGGAAATCAGCC
GTGCGATGGCCTATGGCGAAGCCAAGGCGCGCAAGGCTAAGAAGGAAATGGTCGAAGCCAACCTGCGTCTGGTGATCTCC
ATCGCCAAGAAGTACACCAACCGCGGCCTGCAGTTCCTGGATCTGATCCAGGAAGGCAACATCGGCCTGATGAAGGCCGT
GGACAAGTTCGAATACCGTCGCGGTTACAAGTTCTCGACGTATGCCACGTGGTGGATCCGTCAGGCCATCACCCGTTCGA
TCGCCGATCAGGCGCGCACCATCCGTATCCCGGTGCACATGATCGAAACGATCAACAAGTTGAACCGCATTTCCCGCCAG
ATGCTCCAGCAGTTCGGTCGCGAGGCCACGCCGGAGGAACTGGCCAAGGAAATGGACATGCCCGAGGACAAGATCCGCAA
GGTGATGAAAATCGCCAAGGAGCCGATCTCGATGGAAACCCCGATCGGCGACGACGAGGATTCGCATCTGGGCGACTTCA
TCGAGGACACCAATGTGGAGTCCCCGATCGACAACACCACCAACATCAATCTCTCCGAGACGGTGCGTGACGTGTTGGCC
GGCCTCACCCCGCGCGAGGCGAAGGTACTGCGCATGCGCTTCGGTATCGACATGAACACCGATCACACGCTGGAAGAGGT
CGGTAAGCAGTTCGACGTCACCCGTGAGCGGATTCGTCAGATAGAGGCCAAGGCATTGCGCAAGCTGCGTCACCCGAGCC
GTTCGGAACAGCTGCGCTCGTTCCTGGATATCGACTGA

Upstream 100 bases:

>100_bases
CGTCCACCAGCGGTCCCGTCTTGAATCCGGCAGACCGGGCTTCACGCTGGTATAATGCTAGGTTCTCTTTCCAATCTCAA
AGCCGGTGGCGCGAGCACTC

Downstream 100 bases:

>100_bases
GTCCTCGGTCGCGACCGTGCAGTGATCACACAGCAGCCCCGCTCATGCGGGGCTGTTGCGTTATGGCTCAGGCAGTTGGC
TATGCTTGGTACCTGGGCTG

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70

Number of amino acids: Translated: 625; Mature: 624

Protein sequence:

>625_residues
MANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREV
DDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHK
EGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYA
KFKKVYAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGN
QTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS
IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ
MLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLA
GLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLDID

Sequences:

>Translated_625_residues
MANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREV
DDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHK
EGKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYA
KFKKVYAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGN
QTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS
IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ
MLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLA
GLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLDID
>Mature_624_residues
ANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLNDGNTGNREVD
DTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKE
GKKRLAEIVVGFNDLIEEADAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAK
FKKVYAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDFIRSWEGNQ
TNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISI
AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM
LQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSETVRDVLAG
LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLDID

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

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

Homologues:

Organism=Escherichia coli, GI1789448, Length=615, Percent_Identity=59.349593495935, Blast_Score=681, Evalue=0.0,
Organism=Escherichia coli, GI1789098, Length=233, Percent_Identity=40.7725321888412, Blast_Score=208, Evalue=1e-54,
Organism=Escherichia coli, GI1789871, Length=241, Percent_Identity=29.4605809128631, Blast_Score=100, Evalue=3e-22,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=27.2277227722772, Blast_Score=67, Evalue=5e-12,

Paralogues:

None

Copy number: 700 (log & stationary phase) [C]

Swissprot (AC and ID): RPOD_XANAC (Q8PG33)

Other databases:

- EMBL:   AE008923
- RefSeq:   NP_644094.1
- ProteinModelPortal:   Q8PG33
- SMR:   Q8PG33
- GeneID:   1157859
- GenomeReviews:   AE008923_GR
- KEGG:   xac:XAC3788
- NMPDR:   fig|190486.1.peg.3738
- HOGENOM:   HBG745096
- OMA:   HPSRSET
- ProtClustDB:   PRK05658
- BioCyc:   XAXO190486:XAC3788-MONOMER
- InterPro:   IPR014284
- InterPro:   IPR000943
- InterPro:   IPR009042
- InterPro:   IPR007627
- InterPro:   IPR007624
- InterPro:   IPR007630
- InterPro:   IPR007631
- InterPro:   IPR007127
- InterPro:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991
- Gene3D:   G3DSA:1.10.10.10
- PRINTS:   PR00046
- TIGRFAMs:   TIGR02393
- TIGRFAMs:   TIGR02937

Pfam domain/function: PF04546 Sigma70_ner; PF03979 Sigma70_r1_1; PF00140 Sigma70_r1_2; PF04542 Sigma70_r2; PF04539 Sigma70_r3; PF04545 Sigma70_r4; SSF88946 Sigma_r2; SSF88659 Sigma_r3_r4

EC number: NA

Molecular weight: Translated: 70085; Mature: 69954

Theoretical pI: Translated: 4.61; Mature: 4.61

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)
3.4 %Met     (Mature Protein)
3.4 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHE
CCCCCCCCHHHHHHHHHHCCHHCCEEEEHHCCCCCCCCCCHHHHHHHHHHHHCCCCCHHH
VAPDAETLLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLT
CCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCEEEE
REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEA
CCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
DAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYA
HHHHHHHHHCCCCEECCCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
KFKKVYAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLH
HHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
LATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEK
HHHHHHHCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECC
ANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
CCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ
CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEECHHHHHHHHHHHHHHHHH
MLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVE
HHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCC
SPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ
CCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
IEAKALRKLRHPSRSEQLRSFLDID
HHHHHHHHHHCCCHHHHHHHHHCCC
>Mature Secondary Structure 
ANERPAQQSDIKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHE
CCCCCCCHHHHHHHHHHCCHHCCEEEEHHCCCCCCCCCCHHHHHHHHHHHHCCCCCHHH
VAPDAETLLLNDGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLT
CCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCEEEE
REGEIAIAKRIEEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEA
CCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
DAAAAALAAAGPVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYA
HHHHHHHHHCCCCEECCCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
KFKKVYAKNGAEHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLH
HHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
LATTVARMPRKDFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEK
HHHHHHHCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECC
ANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
CCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ
CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEECHHHHHHHHHHHHHHHHH
MLQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVE
HHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCC
SPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ
CCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
IEAKALRKLRHPSRSEQLRSFLDID
HHHHHHHHHHCCCHHHHHHHHHCCC

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: 12024217