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The map label for this gene is rpoD

Identifier: 15889446

GI number: 15889446

Start: 2134533

End: 2136587

Strand: Reverse

Name: rpoD

Synonym: Atu2167

Alternate gene names: 15889446

Gene position: 2136587-2134533 (Counterclockwise)

Preceding gene: 15889447

Following gene: 159185083

Centisome position: 75.19

GC content: 59.76

Gene sequence:

>2055_bases
ATGGCAACCAAAGTCAAAGAAAACGAAGAAGCAGAAAACGAACGCGACGGTGCGACGGACGGTCCGCTTCTCGATCTTTC
GGATGACGCGGTCAAAAAGATGATCAAGGCCGCCAAGAAGCGCGGCTATGTGACGATGGACGAGCTGAATTCCGTCCTGC
CGTCCGAAGAGGTGACGTCCGAGCAGATCGAAGACACGATGGCGATGCTGTCCGATATGGGCATCAACGTTATCGAGGAC
GAGGATGCCGAGGAAGCCGCGCCTGCCGAAGACGACGGCGATTCCGACAATGAGGAGTCCGAAGGCGGCGAACTGGCGCC
GTCCGGCGGCACGGCGCTTGCGACCGCCAAGAAGAAAGAACCGACCGACCGCACCGATGATCCCGTGCGCATGTATCTGC
GCGAAATGGGTTCCGTCGAGCTTCTGTCGCGCGAAGGCGAAATCGCCATCGCCAAGCGCATCGAGGCCGGCCGCGAAACG
ATGATTTCGGGCCTGTGCGAAAGCCCGCTGACGTTCCAGGCGCTGATCATCTGGCGCGACGAACTGAACGAGGGCACGAC
GCTGCTGCGCGAGATCATCGATCTCGAAACGACCTATTCCGGTCCGGAAGCCAAGGCTGCACCGCAGTTCCAGAGCCCGG
AAAAGATCGAGGCTGACCGCAAGGCCGCCGAAGAAAAGGAAAAGACCCGCAGGCTGCGTGCGCCAACCGGCGACGAAGAC
GTGACTGACGTGGGTGGCGATGGCCTGCCTCCGGAAGAGGAAGAAGAGGACGACGACGAGTCCAATCTTTCGCTTGCCGC
GATGGAAGCCGAGCTGCGCCCGCAGGTCATGGAAACGCTCGACACCATTGCCGACACCTACAAGAAGCTGCGCAAGCTTC
AGGATCAGCAGGTCGAGGCCCGTCTCGCCTGCACCGGTACCCTGTCTTCCGGCCAGGAGCGTCGTTACAAGGAACTGAAG
GATCAGCTGATCACGGCCGTCAAGTCGCTGTCGCTGAACCAGAACCGCATCGACAGCCTCGTCGAGCAGCTCTACGACAT
TTCCAAGCGGCTGATGCAGAACGAAGGCCGGCTGCTGCGTCTTGCCGAATCCTATGGCGTCAAGCGCGACAGCTTCCTCG
AGCAGTATCACGGTGCGGAACTCGATCCGAACTGGATGAAGTCGATCACCAATCTGGCCGCGCGCGGCTGGAAGGAATTC
GCCCGCGAGGAAAGCAACACGATCCGGGAAATCCGTCAGGAAATCCAGAACCTCTCCACGGAAACCGGCATTTCCATTGC
CGAATTCCGCCGCATCGTTTCGATGGTGCAGAAGGGCGAACGTGAAGCGCGTATCGCCAAGAAGGAGATGGTCGAAGCGA
ACCTGCGTCTCGTGATCTCGATTGCGAAGAAATACACCAACCGCGGTCTGCAGTTCCTCGACCTCATTCAAGAAGGCAAT
ATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATATCGCCGTGGTTACAAGTTCTCGACCTATGCGACCTGGTGGATCAG
GCAGGCGATCACCCGCTCGATCGCCGACCAGGCCCGCACGATCCGTATTCCGGTTCACATGATCGAGACGATCAACAAGA
TCGTTCGCACCTCGCGCCAGATGCTTCACGAGATCGGCCGCGAGCCGACCCCGGAAGAACTGGCGGAAAAGCTGGCCATG
CCGCTTGAAAAGGTGCGCAAGGTTCTGAAGATCGCCAAGGAGCCGATCTCGCTCGAAACCCCTGTTGGTGACGAAGAGGA
TTCGCATCTCGGCGACTTCATCGAGGACAAGAACGCGCTGCTGCCGATCGACGCCGCCATTCAGGCGAACCTGCGTGAGA
CGACCACCCGGGTTCTCGCCTCGCTGACGCCGCGTGAGGAACGTGTTCTGCGCATGCGCTTCGGCATCGGCATGAATACC
GACCATACGCTGGAAGAAGTCGGCCAGCAGTTCTCGGTCACGCGCGAACGTATTCGCCAGATCGAGGCAAAGGCGTTGCG
CAAGCTGAAGCACCCGAGCCGCTCGAGAAAGCTGCGCAGCTTCCTCGACAGCTAA

Upstream 100 bases:

>100_bases
TAGGTGTCTGACAGTGATTCGCGGCAAACCGCTGGATGCTCAAGGGGCGGACGGCGATGCGGCGGAACAGGTGTTAGCGT
CAGGGAAAGCGACGAGATAG

Downstream 100 bases:

>100_bases
GTTTCCCGCTTCCTTCAAAATTGAACCCGGTCAGTGAGCGCTGGCCGGGTTTTTTGTTTCCCGCACTGGCGAACTCTGCG
ACAAGCCTTATGTGTGAAAA

Product: RNA polymerase sigma factor RpoD

Products: NA

Alternate protein names: Sigma-A; Major vegetative sigma factor

Number of amino acids: Translated: 684; Mature: 683

Protein sequence:

>684_residues
MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINVIED
EDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRET
MISGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRAPTGDED
VTDVGGDGLPPEEEEEDDDESNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELK
DQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEF
AREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAM
PLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT
DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS

Sequences:

>Translated_684_residues
MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINVIED
EDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRET
MISGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRAPTGDED
VTDVGGDGLPPEEEEEDDDESNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELK
DQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEF
AREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAM
PLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNT
DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS
>Mature_683_residues
ATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINVIEDE
DAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETM
ISGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRAPTGDEDV
TDVGGDGLPPEEEEEDDDESNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKD
QLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEFA
REESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI
GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMP
LEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTD
HTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS

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=654, Percent_Identity=47.7064220183486, Blast_Score=514, Evalue=1e-147,
Organism=Escherichia coli, GI1789098, Length=233, Percent_Identity=41.6309012875536, Blast_Score=213, Evalue=4e-56,
Organism=Escherichia coli, GI1789871, Length=241, Percent_Identity=27.3858921161826, Blast_Score=84, Evalue=3e-17,
Organism=Escherichia coli, GI1788231, Length=202, Percent_Identity=27.7227722772277, Blast_Score=69, Evalue=8e-13,

Paralogues:

None

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

Swissprot (AC and ID): RPOD_AGRT5 (P33452)

Other databases:

- EMBL:   X69388
- EMBL:   AE007869
- PIR:   A36913
- PIR:   AF2842
- PIR:   G97619
- RefSeq:   NP_355127.1
- ProteinModelPortal:   P33452
- SMR:   P33452
- STRING:   P33452
- GeneID:   1134205
- GenomeReviews:   AE007869_GR
- KEGG:   atu:Atu2167
- HOGENOM:   HBG745096
- OMA:   IWRDELN
- PhylomeDB:   P33452
- ProtClustDB:   PRK05658
- BioCyc:   ATUM176299-1:ATU2167-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: 77400; Mature: 77269

Theoretical pI: Translated: 4.69; Mature: 4.69

Prosite motif: PS00715 SIGMA70_1; PS00716 SIGMA70_2

Important sites: NA

Signals:

None

Transmembrane regions:

None

Cys/Met content:

0.3 %Cys     (Translated Protein)
3.1 %Met     (Translated Protein)
3.4 %Cys+Met (Translated Protein)
0.3 %Cys     (Mature Protein)
2.9 %Met     (Mature Protein)
3.2 %Cys+Met (Mature Protein)

Secondary structure:

>Translated Secondary Structure
MATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS
CCCCCCCCHHHHHHCCCCCCCCEECCCHHHHHHHHHHHHHCCCEEHHHHHHHCCCHHHHH
EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKE
HHHHHHHHHHHHCCCCEECCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCC
PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWRD
CCCCCCHHHHHHHHHHCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEHEEEHH
ELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRAPTGDED
HCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
VTDVGGDGLPPEEEEEDDDESNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQQVEA
CHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
RLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLR
HHHEECCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEE
LAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEFAREESNTIREIRQEIQNLST
EHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
ETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
HCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ
CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHH
MLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNAL
HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCE
LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ
ECCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
IEAKALRKLKHPSRSRKLRSFLDS
HHHHHHHHHHCCHHHHHHHHHHCC
>Mature Secondary Structure 
ATKVKENEEAENERDGATDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNSVLPSEEVTS
CCCCCCCHHHHHHCCCCCCCCEECCCHHHHHHHHHHHHHCCCEEHHHHHHHCCCHHHHH
EQIEDTMAMLSDMGINVIEDEDAEEAAPAEDDGDSDNEESEGGELAPSGGTALATAKKKE
HHHHHHHHHHHHCCCCEECCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCC
PTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMISGLCESPLTFQALIIWRD
CCCCCCHHHHHHHHHHCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEHEEEHH
ELNEGTTLLREIIDLETTYSGPEAKAAPQFQSPEKIEADRKAAEEKEKTRRLRAPTGDED
HCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
VTDVGGDGLPPEEEEEDDDESNLSLAAMEAELRPQVMETLDTIADTYKKLRKLQDQQVEA
CHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
RLACTGTLSSGQERRYKELKDQLITAVKSLSLNQNRIDSLVEQLYDISKRLMQNEGRLLR
HHHEECCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEE
LAESYGVKRDSFLEQYHGAELDPNWMKSITNLAARGWKEFAREESNTIREIRQEIQNLST
EHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
ETGISIAEFRRIVSMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN
HCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC
IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQ
CHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHHHHHHH
MLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNAL
HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCE
LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ
ECCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
IEAKALRKLKHPSRSRKLRSFLDS
HHHHHHHHHHCCHHHHHHHHHHCC

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: 8491721; 11743193; 11743194