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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1441 IGR1442 IGR1443 IGR1444 IGR1438 IGR1429 IGR1431 IGR1437 IGR1440 IGR1433 IGR1435 IGR1432 IGR1436 IGR1428 IGR1430 IGR1439 IGR1434 rpL36, - HD1955 rpL30,rpmD, - HD1960 rpS16, - HD1949 rpL19, - HD1946 rpL18, - HD1962 rpS13, - HD1954 rpL17,rplQ, - HD1950 rpS11, - HD1953 rpL15, - HD1959 rps5,rpsE, - HD1961 rimM, - HD1948 rpS4, - HD1952 trmD, - HD1947 glyQ, - HD1943 rpoA, - HD1951 secY, - HD1957 HD1944 HD1945 rpL36, - HD1955 rpL30,rpmD, - HD1960 rpS16, - HD1949 rpL19, - HD1946 rpL18, - HD1962 rpS13, - HD1954 rpL17,rplQ, - HD1950 rpS11, - HD1953 rpL15, - HD1959 rps5,rpsE, - HD1961 rimM, - HD1948 rpS4, - HD1952 trmD, - HD1947 glyQ, - HD1943 rpoA, - HD1951 secY, - HD1957 HD1944 HD1945 rpL36, - HD1955 rpL19, - HD1946 rpL17,rplQ, - HD1950 rpS11, - HD1953 rpL15, - HD1959 rps5,rpsE, - HD1961 rimM, - HD1948 rpS4, - HD1952 trmD, - HD1947 glyQ, - HD1943 rpoA, - HD1951 secY, - HD1957 rpL30,rpmD, - HD1960 rpS16, - HD1949 rpL18, - HD1962 rpS13, - HD1954 HD1944 HD1945
* Calculated from Protein Sequence

Gene ID: HD1951

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rpoA  

Definition:
DNA-directed RNA polymerase alpha subunit

Gene Start:
1638131

Gene Stop:
1637142

Gene Length:
990

Molecular Weight*:
36404

pI*:
4.90

Net Charge*:
-13.94

EC:
2.7.7.6  

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

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Peck MC, Gaal T, Fisher RF, Gourse RL, Long SR.
The RNA polymerase alpha subunit from Sinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro.
J Bacteriol. 2002 Jul;184(14):3808-14.
PMID: 12081950

Olekhnovich IN, Kadner RJ.
Mutational scanning and affinity cleavage analysis of UhpA-binding sites in the Escherichia coli uhpT promoter.
J Bacteriol. 2002 May;184(10):2682-91.
PMID: 11976297

Bedwell D, Davis G, Gosink M, Post L, Nomura M,
Kestler H, Zengel JM, Lindahl L.
Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli.
Nucleic Acids Res. 13(11): 3891-3903.1985.
Medline: 85242076.

Lombardo,M.J., Bagga,D. and Miller,C.G.
Mutations in rpoA affect expression of anaerobically regulated
genes in Salmonella typhimurium
J. Bacteriol. 173 (23), 7511-7518 (1991)
Medline: 92041662



Comment:
For other "rpo" genes, see HD1172 (rpoE), HD1876 (rpoC), HD1877 (rpoB), HD1923 (rpoZ), HD0086 (rpoH), HD0691 (rpoD), HD0692 (rpoD).

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to from H. influenzae (), E. coli (133396, 42799), H. influenzae (1173145), Shewanella sp (7434688), Shewanella violacea (5913932), among others.

HD1951 is similar to DNA-directed RNA polymerase alpha subunit from C. pneumoniae (CPn0626), C. trachomatis (CT507), T. pallidum (TP0212), U. urealyticum (UU257), M. pneumoniae (MP0640), M. genitalium (MG177).

COGS Summary:  COGS Search
BeTs to 15 clades of COG0202
COG name: DNA-dependent RNA polymerase alpha subunit
Functional Class: K
The phylogenetic pattern of COG0202 is amtkYqvcebrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001700 (Bacterial RNA polymerase, alpha chain) with a combined E-value of 3e-90.
    IPB001700A    23-67
    IPB001700B    131-147
    IPB001700C    173-187
    IPB001700D    199-231
    IPB001700E    257-299


ProDom Summary:  Protein Domain Search
Residues 7-307 are 92% similar to a (RNA POLYMERASE ALPHA DNA-DIRECTED) protein domain (PD001179) which is seen in RPOA_PASMU.



Paralogs:  Local Blast Search

HD1951 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 17 to 233 (E-value = 1.3e-19) place HD1951 in the RNA_pol_L family which is described as RNA polymerase Rpb3/Rpb11 dimerisation domain (PF01193)
Residues 59 to 178 (E-value = 1.9e-55) place HD1951 in the RNA_pol_A_bac family which is described as RNA polymerase Rpb3/RpoA insert domain (PF01000)
Residues 242 to 309 (E-value = 7.6e-34) place HD1951 in the RNA_pol_A_CTD family which is described as Bacterial RNA polymerase, alpha chain C terminal domain (PF03118)

PDB Hit:
pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymeras... 410 1e-115
pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core... 199 4e-052
pdb|1COO| The Cooh-Terminal Domain Of Rna Polymerase Alpha S... 190 2e-049

Gene Protein Sequence:
MQGSVIEFLKPHLVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSS
MPGCAVAEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKNDVTL
TLNKSGIGPVLAADITHDGDVEIINPNHVICHLTDKDASINMRIYVQRGR
GYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDK
LIIDMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEIKEEKPEFD
PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIAED$

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAGGGTTCTGTGATAGAATTTTTAAAGCCGCACTTAGTGAATATTGA
GCAAATTAGTTCAACTCACGCAAAAGTGACCTTAGAGCCGTTAGAACGTG
GTTTTGGTCATACATTAGGTAACGCACTTCGTCGCATTTTACTTTCGTCT
ATGCCTGGCTGTGCAGTTGCAGAAGTTGAAATTGATGGTGTATTACATGA
ATACAGCAGCAAAGAAGGCGTACAAGAAGATATTCTTGAAGTATTGTTAA
ACCTTAAAGGTCTAGCGGTAAAAGTATCAGGTAAAAATGATGTTACTCTG
ACACTTAATAAGTCTGGAATTGGCCCTGTACTTGCAGCCGACATTACGCA
CGATGGTGATGTGGAAATTATAAATCCGAATCATGTTATTTGTCATTTGA
CAGATAAAGATGCATCAATCAATATGCGTATCTACGTTCAACGTGGTCGT
GGTTATGTACCAGCATCGGCTCGAGTACATTCACAGGATGAAGACCGTCC
AATTGGTCGCTTATTAGTTGATGCTCGTTTCAGTCCAGTAGATCGTATAG
CTTATAATGTAGAAGCTGCACGTGTTGAACAACGAACAGACTTAGATAAG
CTGATTATTGATATGGAAACAAATGGCACAATCGATCCAGAAGAAGCCAT
TCGTCGTGCTGCAACGATTTTAGCAGAACAATTAGATGCATTCGTTGATT
TACGTGATGTTCGTCAACCCGAAATCAAAGAAGAAAAACCGGAATTTGAT
CCAATTTTACTTCGCCCTGTAGATGATTTAGAGTTGACAGTTCGTTCTGC
TAACTGTTTGAAAGCAGAGACAATTCATTATATCGGTGATTTAGTACAAC
GTACTGAAGTTGAGTTATTAAAAACGCCTAATCTTGGTAAGAAATCACTT
ACTGAGATTAAGGATGTCCTTGCTTCGCGTGGTTTGTCACTGGGTATGCG
CCTTGAAAATTGGCCTCCAGCAAGTATTGCTGAAGATTAG


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