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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR1485 IGR1486 IGR1493.1 IGR1494 IGR1496 IGR1491 IGR1492 IGR1489 IGR1490 IGR1487 IGR1488 IGR1495 IGR1493 IGR1484 IF-1, - NG1821.1 minE, - NG1814 rl18, - NG1824.1 rpsM, - NG1821 rplQ, - NG1817 rpsK, - NG1820 rplO, - NG1823 rpsE, - NG1824 rpsD, - NG1819 minC, - NG1816 minD, - NG1815 oxyR, - NG1813 rpoA, - NG1818 secY, - NG1822 pIB, - NG1812 IF-1, - NG1821.1 minE, - NG1814 rl18, - NG1824.1 rpsM, - NG1821 rplQ, - NG1817 rpsK, - NG1820 rplO, - NG1823 rpsE, - NG1824 rpsD, - NG1819 minC, - NG1816 minD, - NG1815 oxyR, - NG1813 rpoA, - NG1818 secY, - NG1822 pIB, - NG1812 Type: tandem, Name:  - 84 IF-1, - NG1821.1 minE, - NG1814 rpsM, - NG1821 rplQ, - NG1817 rpsK, - NG1820 rplO, - NG1823 rpsE, - NG1824 rpsD, - NG1819 minC, - NG1816 minD, - NG1815 oxyR, - NG1813 rpoA, - NG1818 secY, - NG1822 rl18, - NG1824.1 pIB, - NG1812
* Calculated from Protein Sequence

Gene ID: NG1818

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
rpoA  

Definition:
DNA-directed RNA polymerase alpha chain (RpoA)

Gene Start:
1794548

Gene Stop:
1793565

Gene Length:
984

Molecular Weight*:
35988

pI*:
4.80

Net Charge*:
-13.38

EC:
2.7.7.6  

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

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism
RNA polymerase

Secondary Evidence:
Sarubbi,E., Rudd,K.E., Xiao,H., Ikehara,K., Kalman,M. and Cashel,M. Characterization of the spoT gene of Escherichia coli. J. Biol. Chem. 264 (25), 15074-15082 (1989) Medline: 89359321.
Engel,J.N., Pollack,J., Malik,F. and Ganem,D. Cloning and characterization of RNA polymerase core subunits of Chlamydia trachomatis by using the polymerase chain reaction J. Bacteriol. 172 (10), 5732-5741 (1990) Medline: 91008945.
Ovchinnikov,Yu.A., Monastyrskaya,G.S., Gubanov,V.V., Guryev,S.O., Salomatina,I.S., Shuvaeva,T.M., Lipkin,V.M. and Sverdlov,E.D. The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit Nucleic Acids Res. 10 (13), 4035-4044 (1982) Medline: 82274235.
Borodin,A.M., Danilkovich,A.V., Chernov,I.P., Azhikina,T.L. and Rostapshov,V.M. Genes coding for RNA polymerase in bacteria. III. The use of modified Sanger's method for sequencing the C-terminal region of rpoB gene, N-terminal region of rpoC gene and intercistron region of RNA polymerase in Pseudomonas putida Bioorg. Khim. 14 (9), 1179-1182 (1988) Medline: 89117617

Comment:
Oklahoma ID: NGO.1818c

For other 'rpo' genes, see NG0999 (rpoD), NG1309 (rpoZ), NG0288 (rpoH), NG1850 (rpoC), NG1851 (rpoB).

Blast Summary:  PSI-Blast Search
Matches in gapped BLAST to RpoA sequences. Residues 4-328 are 70% similar to RPOA_BORPE (585918).

Residues 1-328 are 98% similar to RPOA_NEIMA (12230592).

COGS Summary:  COGS Search
BeTs to 14 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 2

Blocks Summary:  Blocks Search
***** IPB001700 (Bacterial RNA polymerase, alpha chain) with a combined E-value of 1.1e-90.
    IPB001700A    23-67
    IPB001700B    130-146
    IPB001700C    172-186
    IPB001700D    198-230
    IPB001700E    256-298


ProDom Summary:  Protein Domain Search
Residues 15-306 are 70% similar to a (RNA POLYMERASE ALPHA SUBUNIT) protein domain (PD001179) which is seen in RPOA_BORPE.



Paralogs:  Local Blast Search


NG1818 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 19 to 232 (E-value = 7.3e-20) place NG1818 in the RNA_pol_L family which is described as RNA polymerase Rpb3/Rpb11 dimerisation domain (PF01193)
Residues 59 to 177 (E-value = 3.1e-56) place NG1818 in the RNA_pol_A_bac family which is described as RNA polymerase Rpb3/RpoA insert domain (PF01000)
Residues 241 to 308 (E-value = 7.5e-29) place NG1818 in the RNA_pol_A_CTD family which is described as Bacterial RNA polymerase, alpha chain C terminal domain (PF03118)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
280  
328

PDB Hit:
pdb|1BDF|1BDF-A STRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE 274.0 1e-74
pdb|1IW7|1IW7-A CRYSTAL STRUCTURE OF THE RNA POLYMERASE 213.0 4e-56
pdb|1L9U|1L9U-A THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4211.0 2e-55
pdb|1HQM|1HQM-A CRYS

Gene Protein Sequence:
MQNSTTEFLKPRQIDVNTFSATRAKVSMQPFERGFGHTLGNALRRILLSS
MNGFAPTEVAIAGVLHEYSTVGGVQEDVVDILLNIKGIVFKLHGRSQVQL
VLKKSGSGVVSAGDIELPHDVEILNPGHVICHLADNGQIEMEIKVEQGRG
YQSVSGRQVVRDENRQIGAIQLDASFSPISRVSFEVEPARVEQRTDLDKL
VLDIETDGSIDPEEAVRSAARILIDQMSIFADLQGTPVEEVEEKSPPIDP
VLLHPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLGRKSLN
EIKEVLASKGLTLGSKLEAWPPVGLEKP

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAGAATAGCACAACCGAATTTTTGAAACCTCGTCAAATTGATGTAAA
TACTTTTTCTGCAACTCGTGCAAAAGTATCTATGCAGCCATTTGAACGTG
GTTTCGGTCATACCTTAGGTAATGCTTTGCGCCGTATCTTACTGTCATCC
ATGAATGGTTTTGCTCCTACTGAAGTAGCTATTGCCGGTGTATTGCACGA
ATATTCTACTGTTGGTGGTGTTCAGGAAGATGTTGTTGACATTTTGCTGA
ATATTAAAGGTATTGTGTTTAAACTCCATGGTCGTAGCCAAGTTCAACTT
GTGTTGAAGAAATCAGGTTCAGGTGTCGTATCTGCCGGTGATATTGAGTT
GCCGCATGATGTAGAAATTCTGAATCCTGGTCATGTCATTTGTCATTTGG
CTGATAACGGTCAAATTGAAATGGAAATTAAAGTAGAGCAAGGTCGTGGT
TATCAATCTGTTTCAGGTCGTCAGGTAGTTCGTGATGAGAACCGTCAGAT
TGGTGCAATCCAGTTGGATGCGAGCTTTTCGCCCATCAGCCGTGTTAGCT
TTGAGGTTGAACCTGCACGTGTAGAGCAGCGGACGGATCTTGATAAGTTG
GTTTTGGATATCGAAACCGACGGTTCTATTGATCCTGAGGAAGCTGTACG
CAGTGCGGCACGTATTTTGATTGATCAGATGTCTATTTTTGCTGATTTGC
AGGGTACTCCTGTGGAGGAGGTTGAAGAAAAATCACCTCCTATCGACCCT
GTTCTTTTGCATCCGGTGGATGATCTGGAATTGACAGTACGTTCAGCTAA
TTGTTTGAAAGCTGAGGATATTTATTATATTGGCGATTTGATTCAACGCA
CTGAAACCGAGCTTCTTAAAACGCCGAATTTGGGACGTAAATCTTTGAAT
GAGATTAAGGAAGTATTGGCATCTAAAGGTTTGACACTGGGTTCTAAGTT
GGAAGCATGGCCACCTGTAGGCTTGGAAAAGCCT


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