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The map label for this gene is rpoD [H]

Identifier: 159901184

GI number: 159901184

Start: 5967897

End: 5969024

Strand: Reverse

Name: rpoD [H]

Synonym: Haur_4672

Alternate gene names: 159901184

Gene position: 5969024-5967897 (Counterclockwise)

Preceding gene: 159901188

Following gene: 159901183

Centisome position: 94.05

GC content: 52.75

Gene sequence:

>1128_bases
ATGGGGGCAGCCCGTCAGCATCGTTATCTAACGCACGACCAAGTGCTGCTCCACCTTCCTCCCTCCGACAAAAACACAGC
GCTGTTCGACGAATTGTGTGTCCGCTGCCAAGCAGAAGATATTCCAATTTTGGAAGAACCGCCAACCGCTGCAGTGCATC
TCCGTTCACGCGATGTCGATGATGACGATCTCGAACGGTCTCTGATTCGGGAAGGGGTAAGCCTCGATGATCCGGTGCGC
ATGTATTTGCGCGAAATTGGCCAAGTGCATCTCTTAACCGCCCACGAAGAAACCATGTTGGCCAAACAATTGGAACGCGG
CGAACGCGCAATGATTCGGCTCGCCCGCCACGAATATCTCCTCGAAGAAAAAGCCCGCCTGCAACAGCAAGTTCTCGAAA
GCGAAGCAGCCCGTCAACATCTCATCCAAGCCAATTTACGCCTCGTGGTGTCGATTGCAAAAAAATATGTTGGCCGCGGC
ATGTCGTTTTTAGATTTAATTCAAGAGGGCAATATTGGCCTGATGCGGGCAACCGAGAAGTTCGATTATCACAAGGGCTT
TAAGTTCTCAACCTATGCAACATGGTGGATTCGCCAAGCAATTACGCGCTCGATCTCTGATCATAGTCGCACTATTCGCC
TGCCAGTTCACGTGGGCGAGACGATCAATCGGGTCAAGCGCACGGCCCACAAGTTGCAACAAGCCTTAGAGCGTGAGCCA
AGTGCCGAGGAGATTGGCGAAGCCCTTGGGTTGCCCGCCGATAAAGTGCGGCGCGTGCTCGAAGTTGCCCGTCAGCCAGT
TTCGCTGGAAACGCCCGTTGGCAACGAAGGCGATAGTGTGTTAGGCGATTTTATCGAAGATGATCGCTCATCCGAGCCAC
TTGATCATGCGACCGAGCATTTATTGCGCGAACAACTTGATGAAGTGCTGTGCAAGCTCGATGAGCGTGAACGGCGGATT
ATTGAGCTACGCTATGGCTTGGTCGATGGCAAATATCGTACCCTTGAAGAAGTTGGCCGCGAATTTGGCATTACCCGCGA
GCGAATTCGCCAAATTGAGGCCAAAGTACTGCGAAAACTGCGCCACCCAGCGTTTGGTGGGCGCAAATTGCGAGCCTATC
TTGAATAA

Upstream 100 bases:

>100_bases
ATTGAATCGCAGATCTATCCGTGATATAGTGGTCTATCATTAGGCTTTTCTATAGCAGTAGAAAGTCGGTGCTTACTTGA
AAAACGTACTCGAAGTTCTG

Downstream 100 bases:

>100_bases
CTAAGTTGCAGATTGAACGGCAAAGCAACACACGCGTAGCGCGGACATAATGCCGTGATGCGCGTGTGTTAGTTTTTAAT
CAACACCACAATCGGAGGTT

Product: RpoD family RNA polymerase sigma factor

Products: NA

Alternate protein names: NA

Number of amino acids: Translated: 375; Mature: 374

Protein sequence:

>375_residues
MGAARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVDDDDLERSLIREGVSLDDPVR
MYLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYLLEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRG
MSFLDLIQEGNIGLMRATEKFDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREP
SAEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEHLLREQLDEVLCKLDERERRI
IELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKLRHPAFGGRKLRAYLE

Sequences:

>Translated_375_residues
MGAARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVDDDDLERSLIREGVSLDDPVR
MYLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYLLEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRG
MSFLDLIQEGNIGLMRATEKFDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREP
SAEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEHLLREQLDEVLCKLDERERRI
IELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKLRHPAFGGRKLRAYLE
>Mature_374_residues
GAARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVDDDDLERSLIREGVSLDDPVRM
YLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYLLEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRGM
SFLDLIQEGNIGLMRATEKFDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREPS
AEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEHLLREQLDEVLCKLDERERRII
ELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKLRHPAFGGRKLRAYLE

Specific function: Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This may be 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=239, Percent_Identity=56.4853556485356, Blast_Score=291, Evalue=5e-80,
Organism=Escherichia coli, GI1789098, Length=338, Percent_Identity=39.6449704142012, Blast_Score=237, Evalue=1e-63,
Organism=Escherichia coli, GI1789871, Length=242, Percent_Identity=29.3388429752066, Blast_Score=93, Evalue=4e-20,
Organism=Escherichia coli, GI1788231, Length=200, Percent_Identity=28.5, Blast_Score=70, Evalue=3e-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:   IPR007127
- InterPro:   IPR013325
- InterPro:   IPR013324
- InterPro:   IPR012760
- InterPro:   IPR011991 [H]

Pfam domain/function: PF03979 Sigma70_r1_1; PF00140 Sigma70_r1_2; PF04542 Sigma70_r2; PF04539 Sigma70_r3; PF04545 Sigma70_r4 [H]

EC number: NA

Molecular weight: Translated: 43296; Mature: 43165

Theoretical pI: Translated: 6.80; Mature: 6.80

Prosite motif: PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.8 %Cys     (Translated Protein)
1.6 %Met     (Translated Protein)
2.4 %Cys+Met (Translated Protein)
0.8 %Cys     (Mature Protein)
1.3 %Met     (Mature Protein)
2.1 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MGAARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVD
CCCCHHCCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC
DDDLERSLIREGVSLDDPVRMYLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYL
HHHHHHHHHHCCCCCCHHHHHHHHHCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHH
LEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATEK
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEHHHH
FDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREP
HHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCC
SAEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEH
CHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHH
LLREQLDEVLCKLDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKL
HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
RHPAFGGRKLRAYLE
HCCCCCCHHHHHHCC
>Mature Secondary Structure 
GAARQHRYLTHDQVLLHLPPSDKNTALFDELCVRCQAEDIPILEEPPTAAVHLRSRDVD
CCCHHCCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCC
DDDLERSLIREGVSLDDPVRMYLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYL
HHHHHHHHHHCCCCCCHHHHHHHHHCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHH
LEEKARLQQQVLESEAARQHLIQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATEK
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCEEEHHHH
FDYHKGFKFSTYATWWIRQAITRSISDHSRTIRLPVHVGETINRVKRTAHKLQQALEREP
HHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCC
SAEEIGEALGLPADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIEDDRSSEPLDHATEH
CHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHH
LLREQLDEVLCKLDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKL
HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
RHPAFGGRKLRAYLE
HCCCCCCHHHHHHCC

PDB accession: NA

Resolution: NA

Structure class: Unstructured

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: 1923759 [H]