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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1415 IGR1418 IGR1412 IGR1411 IGR1413 IGR1409 IGR1417 IGR1414 IGR1410 IGR1416 IGR1419 HD1930 HD1926 HD1927 HD1920 proS, - HD1919 acpP, - HD1931 rpoZ, - HD1923 dod, - HD1929 menB, - HD1925 spoT, - HD1924 recG, - HD1921 HD1930 HD1926 HD1927 HD1920 proS, - HD1919 acpP, - HD1931 rpoZ, - HD1923 dod, - HD1929 menB, - HD1925 spoT, - HD1924 recG, - HD1921 Type: tandem, Name:  - 19 HD1930 HD1927 HD1920 proS, - HD1919 HD1926 acpP, - HD1931 rpoZ, - HD1923 dod, - HD1929 menB, - HD1925 spoT, - HD1924 recG, - HD1921
* Calculated from Protein Sequence

Gene ID: HD1923

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rpoZ  

Definition:
DNA-directed RNA polymerase, omega chain

Gene Start:
1617753

Gene Stop:
1618058

Gene Length:
306

Molecular Weight*:
11401

pI*:
4.50

Net Charge*:
-5.76

EC:
2.7.7.6  

Functional Class:
Transcription; RNA synthesis, modification, and DNA transcription  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Kojima I, Kasuga K, Kobayashi M, Fukasawa A, Mizuno S, Arisawa A, Akagawa H.
The rpoZ Gene, Encoding the RNA Polymerase Omega Subunit, Is Required for Antibiotic Production and Morphological Differentiation in Streptomyces kasugaensis.
J Bacteriol. 2002 Dec 1;184(23):6417-6423.
PMID: 12426327

Kormanec J, Novakova R, Homerova D, Rezuchova B.
Streptomyces aureofaciens sporulation-specific sigma factor sigma(rpoZ) directs expression of a gene encoding protein similar to hydrolases involved in degradation of the lignin-related biphenyl compounds.
Res Microbiol. 2001 Dec;152(10):883-8.
PMID: 11766963

Novakova R, Sevcikova B, Kormanec J.
A method for the identification of promoters recognized by RNA polymerase containing a particular sigma factor: cloning of a developmentally regulated promoter and corresponding gene directed by the Streptomyces aureofaciens sigma factor RpoZ.
Gene. 1998 Feb 16;208(1):43-50.
PMID: 9479043

Gentry,D.R. and Burgess,R.R.
The cloning and sequence of the gene encoding the omega subunit of
Escherichia coli RNA polymerase
Gene 48 (1), 33-40 (1986)
Medline: 87163514


Comment:
For other "rpo" genes, see HD1172 (rpoE), HD1876 (rpoC), HD1877 (rpoB), HD0086 (rpoH), HD1951 (rpoA), HD0691 (rpoD), HD0692 (rpoD).

Blast Summary:  PSI-Blast Search
Three significant hits using gapped BLAST to DNA-directed RNA polymerase omega chain from H. influenzae (1173169), E. coli (133464), and Neisseria meningitidis (7226913). One weakly significant hit to RNA-dependent nucleotide polymerase omega subunit homolog RnpO from Bradyrhizobium japonicu (6136305).

No similarities to C. trachomatis, C. pneumoniae, U. urealyticum, T. pallidum, M. genitalium, or M. pneumoniae.

COGS Summary:  COGS Search
BeTs to 4 clades of COG1758
COG name: RNA polymerase-associated protein RpoZ, omega subunit
Functional Class: K
The phylogenetic pattern of COG1758 is -----qv-ebrh--------x
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB003716 (RNA polymerase omega subunit) with a combined E-value of 3e-44.
    IPB003716A    1-31
    IPB003716B    37-60
    IPB003716C    68-88


ProDom Summary:  Protein Domain Search
Residues 1-64 are 89% similar to a (POLYMERASE RNA OMEGA CHAIN) protein domain (PD027461) which is seen in RPOZ_PASMU.



Paralogs:  Local Blast Search

HD1923 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 12 to 65 (E-value = 3.1e-19) place HD1923 in the RNA_pol_Rpb6 family which is described as RNA polymerase Rpb6 (PF01192)

PDB Hit:
No significant hits to the NCBI PDB database.

Gene Protein Sequence:
MARVTVQEAADKIGNRFDLILTAARRARQLQLHVREPLVPEENDKPTVIA
LREIEKGLINGSIMDQLENSDAVRQEVAEQEAISFLTDIQTNAYFYSFND
G$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCTCGTGTAACCGTCCAAGAAGCTGCCGATAAAATCGGTAACCGTTT
CGACCTAATTTTAACAGCCGCACGCCGTGCAAGACAATTACAACTTCACG
TTCGTGAGCCGCTTGTCCCTGAAGAAAATGATAAACCTACCGTGATCGCC
TTACGCGAAATTGAAAAAGGCTTGATTAACGGGTCAATTATGGATCAATT
AGAAAATAGCGATGCAGTCCGCCAAGAGGTGGCTGAACAAGAAGCGATTT
CTTTCTTAACCGATATTCAAACCAACGCTTATTTTTATTCATTTAATGAT
GGATAA


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