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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR1523 IGR1521 IGR1524 IGR1519 IGR1520 IGR1522 rplL, - NG1852 rplK, - NG1855 rplJ, - NG1853 nusG, - NG1856 rplA, - NG1854 rpoC, - NG1850 rpoB, - NG1851 rplL, - NG1852 rplK, - NG1855 rplJ, - NG1853 nusG, - NG1856 rplA, - NG1854 rpoC, - NG1850 rpoB, - NG1851 rplL, - NG1852 rplK, - NG1855 rplJ, - NG1853 nusG, - NG1856 rplA, - NG1854 rpoC, - NG1850 rpoB, - NG1851
* Calculated from Protein Sequence

Gene ID: NG1851

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
rpoB  

Definition:
DNA-directed RNA polymerase, beta subunit

Gene Start:
1823626

Gene Stop:
1819451

Gene Length:
4176

Molecular Weight*:
155753

pI*:
5.30

Net Charge*:
-28.90

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:
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

BORODIN,A.M., DANILKOVICH,A.V., ALLIKMETS,R.L., ROSTAPSHOV,V.M.,
CHERNOV,I.P., AZHIKINA,T.L., MONASTYRSKAYA,S. and SVERDLOV,D.
Nucleotide sequence of the rpoB gene coding for the beta-subunit of RNA polymerase in Pseudomonas putida
Dokl. Biochem. 302, 1261-1265 (1988)

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



Comment:
Oklahoma ID: NGO.1851c

For other 'rpo' genes, see NG0999 (rpoD), NG1309 (rpoZ), NG1818 (rpoA), NG1850 (rpoC), NG0288 (rpoH).

Blast Summary:  PSI-Blast Search
Residues 1-1392 are 99% similar to DNA-directed RNA polymerase, beta chain from Neisseria meningitidis group B strain MD58 (11261160|).

Numerous hits in gapped BLAST to DNA-directed RNA polymerase sequences,e.g.residues 1-1390 are 64% similar to DNA-directed RNA polymerase beta chain from Escherichia coli (gb|AAB18647.1|). Residues 1-1390 are 64% similar to DNA-directed RNA polymerase beta chain from Pseudomonas aeruginosa strain PAO1 (11348463|). Residues 12-1166 are 45% similar to DNA-directed RNA polymerase beta chain from Chlamydia trachomatis serotype D, strain UW3/Cx (gb|AAC67908.1|).Residues 20-963 are 45% similar and residues 839-1389 are 38% similar to DNA-directed RNA polymerase, beta subunit from syphilis spirochete Treponema pallidum (gb|AAC65229.1|).

COGS Summary:  COGS Search
BeTs to 17 clades of COG0085
COG name: DNA-dependent RNA polymerase beta subunit (split gene in Mjan, Mthe, Aful)
Functional Class:  K
The phylogenetic pattern of COG0085 is AMTkYqvcebrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001572 (RNA polymerases beta subunit) with a combined E-value of 3.4e-230.
    IPB001572A    470-486
    IPB001572B    531-570
    IPB001572C    575-599
    IPB001572D    689-718
    IPB001572E    824-841
    IPB001572F    892-916
    IPB001572G    1104-1146
    IPB001572H    1281-1334


ProDom Summary:  Protein Domain Search
Residues 971-998 are identical to a (DNA-DIRECTED RNA POLYMERASE BETA) protein domain (PD036301) which is seen in RPOB_NEIME.

Residues 686-759 are 93% similar to a (POLYMERASE RNA DNA-DIRECTED BETA) protein domain (PD001760) which is seen in RPOB_NEIME.

Residues 211-278 are 51% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD152123) which is seen in RPOB_BUCAP.

Residues 1080-1169 are 65% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION TRANSFERASE) protein domain (PD000636) which is seen in O86094_LEGPN.

Residues 930-1073 are 25% similar to a (DNA-DIRECTED RNA POLYMERASE BETA SUBUNIT TRANSCRIPTION) protein domain (PD105072) which is seen in O25806_HELPY.

Residues 1172-1240 are 92% similar to a (RNA POLYMERASE SUBUNIT BETA DNA-DIRECTED TRANSCRIPTION) protein domain (PD007542) which is seen in RPOB_NEIME.

Residues 999-1079 are 97% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD013464) which is seen in RPOB_NEIME.

Residues 210-283 are 63% similar to a (DNA-DIRECTED RNA POLYMERASE BETA) protein domain (PD123255) which is seen in RPOB_NEIME.

Residues 1250-1389 are 99% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION TRANSFERASE) protein domain (PD000748) which is seen in RPOB_NEIME.

Residues 210-388 are 23% similar to a (DNA-DIRECTED RNA POLYMERASE BETA SUBUNIT TRANSCRIPTION) protein domain (PD123257) which is seen in O25806_HELPY.

Residues 285-382 are 86% similar to a (RNA POLYMERASE DNA-DIRECTED BETA TRANSCRIPTION SUBUNIT) protein domain (PD008608) which is seen in RPOB_NEIME.

Residues 769-820 are identical to a (POLYMERASE RNA DNA-DIRECTED BETA) protein domain (PD186074) which is seen in RPOB_NEIME.

Residues 619-682 are 98% similar to a (POLYMERASE RNA DNA-DIRECTED BETA) protein domain (PD186098) which is seen in RPOB_NEIME.

Residues 387-618 are identical to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION TRANSFERASE) protein domain (PD001006) which is seen in RPOB_NEIME.

Residues 21-209 are 98% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION TRANSFERASE) protein domain (PD001037) which is seen in RPOB_NEIME.

Residues 777-914 are 26% similar to a (PROTEIN ORF PUTATIVE KINASE) protein domain (PD000146) which is seen in RPOB_PLAFA.

Residues 821-929 are 98% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION TRANSFERASE) protein domain (PD001712) which is seen in RPOB_NEIME.



Paralogs:  Local Blast Search


NG1851 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 27 to 536 (E-value = 3.6e-26) place NG1851 in the RNA_pol_Rpb2_1 family which is described as RNA polymerase beta subunit (PF04563)
Residues 537 to 609 (E-value = 4.2e-46) place NG1851 in the RNA_pol_Rpb2_3 family which is described as RNA polymerase Rpb2, domain 3 (PF04565)
Residues 742 to 1314 (E-value = 7.4e-169) place NG1851 in the RNA_pol_Rpb2_6 family which is described as RNA polymerase Rpb2, domain 6 (PF00562)
Residues 1316 to 1392 (E-value = 1.5e-49) place NG1851 in the RNA_pol_Rpb2_7 family which is described as RNA polymerase Rpb2, domain 7 (PF04560)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
225  
364
transmembrane  
446  
462
transmembrane  
682  
698
non-globular  
727  
777
coil-coil  
1049  
1076

PDB Hit:
pdb|1IW7|1IW7-C CRYSTAL STRUCTURE OF THE RNA POLYMERASE 586.0 0e+00
pdb|1I6V|1I6V-C THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN578.0 0e+00
pdb|1L9U|1L9U-C THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4578.0 0e+00
pdb|1HQM|1HQM-C CRYS

Gene Protein Sequence:
MNYSFTEKKRIRKSFAKRENVLEVPFLLATQIDSYAKFLQLENAFDKRTD
DGLQAAFNSIFPIVSHNGYARLEFVYYTLGEPLFDIPECQLRGITYAAPL
RARIRLVILDKEASKPTVKEVRENEVYMGEIPLMTPSGSFVINGTERVIV
SQLHRSPGVFFEHDKGKTHSSGKLLFSARIIPYRGSWLDFEFDPKDLLYF
RIDRRRKMPVTILLKALGYNNEQILDIFYDKETFYLSSNGVQTDLVAGRL
KGETAKVDILDKEGNVLVAKGKRITAKNIRDITNAGLTRLDVEQESLLGK
ALAADLIDSETGEVLASANDEITEELLAKFDINGVKEITTLYINELDQGA
YISNTLRTDETAGRQAARVAIYRMMRPGEPPTEEAVEQLFNRLFFSEDSY
DLSRVGRMKFNTRTYEQKLSEAQQNSWYGRLLNETFAGAADKGGYVLSVE
DIVASIATLVELRNGHGEVDDIDHLGNRRVRSVGELTENQFRSGLARVER
AVKERLNQAESENLMPHDLINAKPVSAAIKEFFGSSQLSQFMDQTNPLSE
VTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIN
SLSVYARTNDYGFLETPYRRVIDGKVTEEIDYLSAIEEGRYVIAQANADL
DSDGNLIGDLVTCREKGETIMATPDRVQYMDVATGQVVSVAASLIPFLEH
DDANRALMGANMQRQAVPCLRPEKPMVGTGIERSVAVDSATAIVARRGGV
VEYVDANRVVIRVHDDEATAGEVGVDIYNLVKFTRSNQSTNINQRPAVKA
GDVLQRGDLVADGASTDLGELALGQNMTIAFMPWNGYNYEDSILISEKVA
ADDRYTSIHIEELNVVARDTKLGAEDITRDIPNLSERMQNRLDESGIVYI
GAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRMPTG
MSGTVIDVQVFTREGIQRDKRAQSIIDSELKRYRLDLNDQLRIFDNDAFD
RIERMIVGQKANGGPMKLTKGSEITTEYLAGLPSRHDWFDIRLTDEDLAK
QLELIKLSLQQKREEADELYEIKKKKLTQGDELQPGVQKMVKVFIAIKRR
LQAGDKMAGRHGNKGVVSRILPVEDMPYMADGRPVDIVLNPLGVPSRMNI
GQILEVHLGWAAKGIGERIDRMLKERRKAGELREFLNKLYNGSGKKEDLD
SLTDEEIIELASNLRKGASFASPVFDGAKESEIREMLNLAYPSEDPEVEK
LGFNDSKTQITLYDGRSGEAFDRKVTVGVMHYLKLHHLVDEKMHARSTGP
YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG
RTKMYENIVKGEHKIDAGMPESFNVLVKEIRSLGLDIDLERY

Gene Nucleotide Sequence:  Sequence Viewer
ATGAACTATTCGTTTACCGAGAAAAAACGTATCCGTAAGAGTTTTGCAAA
GCGGGAAAATGTTTTGGAAGTTCCTTTTCTACTGGCAACCCAAATTGATT
CTTATGCGAAATTTTTGCAGCTGGAAAATGCTTTTGACAAACGTACCGAT
GACGGTCTGCAAGCGGCATTTAATTCTATTTTCCCGATTGTGAGCCACAA
CGGTTATGCTCGTCTGGAGTTTGTATATTACACGCTGGGCGAGCCTTTGT
TCGATATCCCTGAATGTCAATTGCGCGGAATCACTTATGCTGCCCCTCTG
CGCGCGCGTATCCGTTTGGTGATTTTGGATAAGGAAGCGTCTAAACCGAC
GGTAAAAGAAGTTCGTGAAAACGAAGTGTATATGGGCGAAATTCCGTTGA
TGACCCCGAGCGGTTCTTTTGTGATTAACGGCACAGAGCGTGTGATTGTT
TCCCAGTTGCACCGTTCGCCCGGTGTGTTCTTCGAGCATGACAAAGGTAA
GACACACTCTTCCGGCAAATTGTTATTCTCCGCCCGCATCATTCCCTACC
GTGGTTCATGGTTGGATTTTGAATTTGATCCGAAAGATTTGCTGTATTTC
CGTATCGACCGCCGCCGTAAAATGCCGGTAACGATTTTGTTGAAGGCTTT
GGGCTACAACAATGAGCAAATCTTGGATATTTTCTACGACAAAGAAACGT
TTTATTTGTCTTCAAACGGTGTTCAAACCGATTTGGTCGCAGGCCGTCTG
AAAGGCGAAACTGCCAAGGTCGATATCTTGGATAAAGAAGGCAATGTATT
GGTTGCCAAAGGTAAGCGCATTACTGCGAAAAATATCCGTGATATTACCA
ATGCAGGCCTGACCCGTTTGGATGTAGAACAGGAAAGCCTGCTGGGCAAA
GCATTGGCTGCCGATTTGATTGATTCGGAAACCGGCGAGGTATTGGCTTC
TGCCAATGATGAAATTACAGAAGAGTTGTTGGCCAAATTTGATATTAACG
GCGTAAAAGAAATTACGACCCTTTACATCAATGAGTTGGATCAGGGTGCT
TATATTTCCAATACCTTGCGCACGGATGAGACTGCCGGCCGGCAGGCGGC
GCGTGTTGCGATTTACCGTATGATGCGTCCGGGCGAACCGCCCACCGAAG
AGGCGGTCGAGCAATTGTTTAACCGCTTGTTCTTCAGTGAAGACAGCTAC
GATTTGTCCCGCGTAGGCCGTATGAAATTTAATACGCGCACATACGAACA
AAAACTGTCCGAAGCCCAACAAAACTCTTGGTACGGCCGCCTGTTGAACG
AGACGTTTGCCGGTGCTGCCGACAAAGGCGGTTATGTCCTGAGCGTCGAA
GATATTGTCGCCTCGATTGCGACTTTGGTCGAGTTGCGTAACGGCCATGG
CGAAGTGGACGATATCGATCACTTGGGCAACCGTCGAGTACGGTCGGTAG
GCGAGCTGACTGAAAACCAATTCCGCAGCGGTTTGGCTCGTGTGGAACGT
GCCGTAAAAGAACGTTTGAATCAGGCGGAATCAGAAAACTTGATGCCGCA
CGACTTGATTAATGCGAAACCCGTTTCTGCCGCCATCAAAGAATTCTTCG
GCTCCAGCCAATTGAGTCAGTTTATGGATCAGACCAATCCCTTGTCTGAA
GTAACCCATAAACGCCGTGTATCTGCATTGGGTCCGGGCGGTTTGACCCG
CGAACGTGCCGGCTTCGAAGTGCGGGACGTGCATCCGACCCACTATGGAC
GTGTATGTCCTATTGAAACGCCTGAAGGTCCGAACATCGGTTTGATCAAC
TCATTGTCTGTTTACGCGCGCACCAATGATTACGGTTTCTTGGAAACGCC
TTACCGCCGCGTTATTGACGGCAAAGTAACCGAGGAAATTGATTACTTGT
CTGCCATCGAAGAAGGCCGCTATGTGATTGCACAGGCGAATGCCGATTTG
GATTCAGACGGCAATCTGATTGGCGATTTGGTTACCTGTCGTGAAAAAGG
CGAAACCATTATGGCAACGCCCGACCGCGTCCAATATATGGACGTGGCAA
CCGGTCAGGTGGTATCCGTTGCGGCATCCCTGATTCCGTTCTTGGAACAC
GATGACGCGAACCGCGCATTGATGGGTGCCAACATGCAACGTCAGGCAGT
GCCTTGTCTGCGTCCTGAAAAACCGATGGTCGGTACCGGTATCGAGCGTT
CCGTTGCCGTTGACTCTGCTACTGCAATCGTTGCCCGCCGAGGCGGCGTG
GTCGAGTATGTCGATGCCAACCGCGTTGTGATCCGTGTCCATGACGACGA
AGCGACTGCCGGTGAAGTGGGTGTCGATATTTACAATTTGGTTAAATTCA
CCCGTTCCAATCAATCTACCAACATCAACCAACGTCCGGCTGTCAAAGCA
GGCGATGTTTTGCAACGCGGCGATTTGGTGGCCGACGGCGCGTCCACCGA
TTTGGGCGAATTGGCTTTGGGTCAAAATATGACCATCGCCTTCATGCCGT
GGAACGGTTACAACTACGAAGACTCGATTCTGATTTCCGAAAAAGTGGCT
GCGGACGACCGCTATACTTCGATTCACATTGAGGAATTGAATGTCGTTGC
CCGCGATACCAAGCTGGGTGCGGAAGACATTACCCGCGATATTCCGAACT
TGTCCGAGCGTATGCAAAACCGTTTGGACGAATCCGGTATCGTTTACATC
GGTGCGGAAGTAGAAGCCGGCGATGTGTTGGTAGGCAAGGTAACGCCTAA
AGGCGAAACCCAGCTGACGCCGGAAGAAAAACTGCTGCGCGCCATCTTCG
GCGAAAAAGCGTCTGACGTAAAAGATACTTCATTGCGTATGCCTACCGGT
ATGAGCGGTACGGTTATCGACGTTCAAGTCTTTACCCGCGAAGGCATCCA
ACGCGACAAACGCGCCCAATCCATTATCGATTCCGAGTTGAAACGCTACC
GTTTGGATTTGAACGACCAATTGCGTATTTTCGACAACGACGCATTCGAC
CGTATCGAGCGTATGATTGTCGGTCAGAAAGCCAACGGCGGCCCGATGAA
GCTGACCAAAGGCAGCGAAATCACGACCGAATATCTGGCGGGTCTGCCGA
GCAGGCACGATTGGTTCGATATCCGTTTGACCGATGAAGATTTGGCCAAG
CAGTTGGAACTGATTAAATTGAGCCTGCAACAAAAACGCGAAGAAGCGGA
TGAGTTGTATGAGATCAAGAAGAAAAAACTGACCCAAGGCGACGAGCTGC
AACCCGGCGTACAAAAAATGGTGAAAGTCTTTATCGCCATCAAACGCCGT
CTGCAAGCCGGTGACAAAATGGCGGGCCGCCACGGTAATAAAGGTGTGGT
ATCTCGCATTCTGCCTGTGGAAGACATGCCGTACATGGCGGACGGCCGTC
CTGTGGACATCGTACTGAACCCGTTGGGCGTACCTTCCCGTATGAACATC
GGTCAGATTTTGGAAGTTCACTTGGGTTGGGCGGCAAAAGGTATCGGCGA
GCGCATCGACCGTATGCTGAAAGAGCGACGCAAAGCCGGCGAGCTGCGCG
AGTTCTTGAACAAACTCTACAACGGCAGCGGTAAGAAAGAAGATTTGGAC
AGCCTGACTGATGAAGAAATCATCGAATTGGCTTCCAATCTGCGTAAAGG
TGCATCTTTCGCCTCTCCTGTATTCGACGGTGCGAAAGAGTCTGAAATCC
GCGAAATGTTGAACTTGGCTTACCCAAGCGAAGATCCTGAGGTTGAGAAA
CTGGGCTTCAACGACAGTAAAACTCAAATCACGCTGTATGACGGCCGTTC
AGGCGAAGCATTTGACCGCAAGGTTACAGTCGGTGTGATGCACTATCTGA
AACTGCACCACTTGGTTGACGAAAAAATGCACGCGCGTTCTACCGGCCCG
TACAGTCTGGTTACTCAACAACCTCTGGGCGGTAAAGCTCAGTTTGGCGG
CCAACGTTTCGGTGAGATGGAGGTTTGGGCATTGGAAGCATACGGCGCGG
CATACACGCTGCAAGAGATGCTGACTGTGAAGTCTGACGACGTGAACGGC
CGTACCAAAATGTACGAAAACATCGTCAAAGGCGAACACAAAATCGATGC
CGGTATGCCCGAGTCCTTCAACGTATTGGTCAAAGAGATTCGCTCACTGG
GTTTGGATATCGATTTGGAACGCTAC


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