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The map label for this gene is rpoD

Identifier: 39546362

GI number: 39546362

Start: 3376401

End: 3378248

Strand: Direct

Name: rpoD

Synonym: STM3211.S

Alternate gene names: 39546362

Gene position: 3376401-3378248 (Clockwise)

Preceding gene: 16766510

Following gene: 16766514

Centisome position: 69.51

GC content: 52.71

Gene sequence:

>1848_bases
ATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCTGAGGT
CAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAAATTGAAGATATCATCCAAATGATCAACGACATGGGTATTC
AGGTAATGGAAGAAGCGCCTGATGCCGATGATCTGCTGCTGGCTGAAAATACCACCAGCACCGATGAAGATGCGGAAGAA
GCTGCTGCACAAGTTCTGTCCAGTGTTGAGTCTGAAATCGGTCGTACGACTGACCCGGTACGCATGTATATGCGTGAAAT
GGGCACTGTTGAACTGTTGACCCGGGAAGGCGAAATCGACATCGCTAAACGTATCGAAGACGGGATCAACCAGGTTCAAT
GCTCCGTTGCCGAATACCCGGAAGCCATTACCTATCTGCTGGAACAGTACGATCGCGTTGAGGCTGAAGAGGCTCGTTTG
TCCGATCTTATCACCGGCTTTGTCGATCCGAACGCGGAAGAAGAGATGGCGCCGACCGCAACTCACGTCGGTTCTGAACT
CTCCCAGGAAGACCTGGATGATGACGAAGACGAAGATGAAGAAGACGGCGACGATGACGCCGCCGATGACGACAACAGCA
TTGACCCTGAACTGGCACGCGAAAAATTCGCTGAGCTGCGCGCGCAATACGTCGTTACGCGCGACACCATCAAAGCGAAA
GGCCGCAGCCATGCTGCCGCGCAGGAAGAGATTCTGAAGCTGTCTGAAGTGTTCAAACAGTTCCGTCTGGTACCGAAGCA
ATTCGACTATCTGGTCAACAGTATGCGCGTGATGATGGATCGCGTGCGTACCCAGGAACGTCTGATCATGAAGCTCTGCG
TCGAGCAGTGCAAAATGCCGAAGAAGAACTTTATCACGCTGTTTACCGGTAATGAAACCAGCGAAACCTGGTTCAATGCC
GCTATCGCGATGAACAAACCGTGGTCGGAAAAACTGCACGATGTCGCGGAAGAAGTGCAACGCTGCCTGCAAAAACTGCG
GCAGATTGAAGAAGAGACCGGTCTGACCATCGAACAGGTGAAAGACATCAACCGTCGCATGTCCATCGGGGAAGCGAAAG
CCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTGCGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGC
TTGCAATTCCTTGATCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTAGATAAGTTCGAATACCGTCGCGGCTA
CAAATTCTCCACCTATGCAACCTGGTGGATCCGTCAGGCGATCACCCGTTCTATCGCCGATCAGGCGCGCACCATCCGTA
TTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGCGAGCCA
ACGCCGGAAGAGCTGGCTGAACGGATGCTGATGCCGGAAGATAAAATTCGTAAGGTGCTAAAGATTGCCAAAGAGCCAAT
CTCCATGGAAACGCCGATCGGCGACGATGAAGATTCGCATCTGGGTGATTTCATCGAGGATACCACCCTCGAGCTGCCGC
TGGACTCTGCCACTACCGAGAGCCTGCGTGCCGCCACTCACGACGTTTTGGCTGGCCTGACCGCTCGTGAAGCGAAAGTG
CTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGATGTTACCCGCGA
ACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGTAAACTGCGCCACCCGAGCCGTTCTGAAGTGCTGCGCAGCTTCCTCG
ACGATTAA

Upstream 100 bases:

>100_bases
CAGTGAGAGGCAGCGGCCAAAATATAAGTATGCCCTCGCTTTAAATGTCGACAGCTATACCGTCGACACCAATCAAACGA
ATAAGTGTGGATACCGTCTT

Downstream 100 bases:

>100_bases
TTCGCCGCACACGTATAAACGCCGCCGCAAGGCGGCGTTTTTTTATCAGGCCATGCGCAAGCGCCCTATTTGGCCTGCAG
AATTTCTACACAGCGCGAGT

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-70

Number of amino acids: Translated: 615; Mature: 615

Protein sequence:

>615_residues
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEE
AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARL
SDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNA
AIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG
LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV
LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

Sequences:

>Translated_615_residues
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEE
AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARL
SDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNA
AIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG
LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV
LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD
>Mature_615_residues
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEE
AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARL
SDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNA
AIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG
LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV
LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

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=97.2357723577236, Blast_Score=1159, Evalue=0.0,
Organism=Escherichia coli, GI1789098, Length=280, Percent_Identity=40.3571428571429, Blast_Score=209, Evalue=4e-55,
Organism=Escherichia coli, GI1789871, Length=242, Percent_Identity=28.5123966942149, Blast_Score=89, Evalue=8e-19,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=28.7128712871287, Blast_Score=65, Evalue=1e-11,

Paralogues:

None

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

Swissprot (AC and ID): RPOD_SALTI (P0A2E4)

Other databases:

- EMBL:   AL627278
- EMBL:   AE014613
- ProteinModelPortal:   P0A2E4
- SMR:   P0A2E4
- PRIDE:   P0A2E4
- GenomeReviews:   AE014613_GR
- GenomeReviews:   AL513382_GR
- KEGG:   stt:t3131
- KEGG:   sty:STY3390
- HOGENOM:   HBG745096
- OMA:   HPSRSET
- ProtClustDB:   PRK05658
- BioCyc:   SENT209261:T3131-MONOMER
- BioCyc:   SENT220341:STY3390-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: 70532; Mature: 70532

Theoretical pI: Translated: 4.42; Mature: 4.42

Prosite motif: PS00715 SIGMA70_1; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.7 %Cys     (Translated Protein)
4.1 %Met     (Translated Protein)
4.7 %Cys+Met (Translated Protein)
0.7 %Cys     (Mature Protein)
4.1 %Met     (Mature Protein)
4.7 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
CCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHCCHHHHHHHHHHHHHCCHHHHHCCC
DADDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCHH
IAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTA
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHH
THVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP
CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
KKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQV
CCCEEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK
HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHH
FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHHCCCC
TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE
CHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCEECCCCCHHHH
SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL
HHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
RHPSRSEVLRSFLDD
CCCCHHHHHHHHHCC
>Mature Secondary Structure
MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAP
CCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHCCHHHHHHHHHHHHHCCHHHHHCCC
DADDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEID
CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCHH
IAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTA
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHH
THVGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAK
HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
GRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP
CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
KKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQV
CCCEEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK
HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHH
FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP
HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHHHHHHHCCCC
TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE
CHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCEECCCCCHHHH
SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL
HHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
RHPSRSEVLRSFLDD
CCCCHHHHHHHHHCC

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