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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR1516 IGR1519 IGR1515 IGR1517 IGR1518 NG1846 NG1847 NG1849 rpoC, - NG1850 rpoB, - NG1851 NG1846 NG1847 NG1849 rpoC, - NG1850 rpoB, - NG1851 NG1847 NG1849 rpoC, - NG1850 rpoB, - NG1851 NG1848 NG1848 NG1846
* Calculated from Protein Sequence

Gene ID: NG1850

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
rpoC  

Definition:
DNA-directed RNA polymerase,beta subunit

Gene Start:
1819295

Gene Stop:
1815123

Gene Length:
4173

Molecular Weight*:
153799

pI*:
7.20

Net Charge*:
2.79

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:
Monastyrskaya,G.S.,Guryev,S.O.,Kalinina,N.F.,Sorokin,A.V.,
Salomatina,I.S.,Shuvaeva,T.M.,Lipkin,V.M.,Sverdlov,E.D.and
Ovchinnikov,Y.A.
Primary structure of EcoRI-D fragment of rpoC gene and
corresponding fragment of beta-subunit of RNA polymerase from
E.coli
Bioorg. Khim. 8, 130-134 (1982)

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

Blattner,F.R., Burland,V., Plunkett,G. 3rd, Sofia,H.J. and
Daniels,D.L.
Analysis of the Escherichia coli genome. IV. DNA sequence of the
region from 89.2 to 92.8 minutes
Nucleic Acids Res. 21 (23), 5408-5417 (1993)
Medline: 94089392

Ovchinnikov,Y.A., Monastyrskaya,G.S., Gubanov,V.V., Guryev,S.O.,
Chertov,O.Y., Modyanov,N.N., Grinkevich,V.A., Makarova,I.A.,
Marchenko,T.V., Polovnikova,I.N., Lipkin,V.M. and Sverdlov,E.D.
The primary structure of Escherichia coli RNA polymerase.
Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit
Eur. J. Biochem. 116 (3), 621-629 (1981)
Medline: 81260785

Gurevich,A.I., Igoshin,A.V. and Kolosov,M.N.
Structure of a central part of E.coli operon rpoBC. Nucleotide
sequence of the gene for beta subunit of RNA polymerase
Bioorg. Khim. 6, 1580-1584 (1980)

Monastyrskaya,G.S., Guryev,S.O., Kalinina,N.F., Sorokin,A.V.,
Salomatina,I.S., Shuvaeva,T.M., Lipkin,V.M., Sverdlov,E.D. and
Ovchinnikov,Y.A.
Primary structure of EcoRI-D fragment of rpoC gene and
corresponding fragment of beta-subunit of RNA polymerase from
E.coli
Bioorg. Khim. 8, 130-134 (1982)

Ovchinnikov,Y.A., Monastyrskaya,G.S., Gubanov,V.V.,
Salomatina,I.S., Shuvaeva,T.M., Lipkin,V.M. and Sverdlov,E.D.
Primary structure of RNA polymerase from E.coli. Nucleotide
sequence of E.coli DNA fragment containing a part of the rpoC gene
and the corresponding C-terminal amino acid sequence of
beta'-subunit
Bioorg. Khim. 7, 1107-1112 (1981)





Comment:
Oklahoma ID: NGO.1850c

For other 'rpo' genes, see NG0999 (rpoD), NG1309 (rpoZ), NG1818 (rpoA), NG0288 (rpoH), NG1851 (rpoB).

Blast Summary:  PSI-Blast Search
Residues 1-1391 are 99% similar to DNA-directed RNA polymerase, beta' chain from Neisseria meningitidis group B strain MD58 (gb|AAF40592.1|).


Numerous hits in gapped BLAST to DNA-dependent RNA polymerase sequences,e.g.residues 177-990 are 70% similar to RNA polymerase from Escherichia coli (gb|AAA24586.1|).Residues 18-1370 are 48% similar to DNA-directed RNA polymerase, beta' subunit from syphilis spirochete Treponema pallidum (gb|AAC65230.1|).Residues 5-1390 are 68% similar to DNA-directed RNA polymerase beta* chain from Pseudomonas aeruginosa strain PAO1 (gb|AAG07657.1|).Residues 19-1382 are 50% similar to DNA-directed RNA polymerase from Chlamydia trachomatis serotype D, strain UW3/Cx (7434734|).

COGS Summary:  COGS Search
BeTs to 17 clades of COG0086
COG name: DNA-dependent RNA polymerase beta' subunit (split gene in Mjan, Mthe, Aful, and Synechocystis)
Functional Class:  K
The phylogenetic pattern of COG0086 is AMTKYqVCebrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000722 (RNA polymerase, alpha subunit) with a combined E-value of 4.9e-99.
    IPB000722A    90-118
    IPB000722B    236-253
    IPB000722C    334-351
    IPB000722D    423-441
    IPB000722E    459-473
    IPB000722F    477-516
***** IPB000684 (Eukaryotic RNA polymerase II heptapeptide repeat) with a combined E-value of 4.4e-50.
    IPB000684A    89-135
    IPB000684B    334-388
    IPB000684C    434-481
    IPB000684E    768-819
    IPB000684F    894-933
    IPB000684K    1343-1377


ProDom Summary:  Protein Domain Search
Residues 1305-1365 are 86% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD000751) which is seen in RPOC_HAEIN.

Residues 1192-1300 are 56% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD003181) which is seen in RPOC_ECOLI.

Residues 1000-1186 are 50% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD005798) which is seen in RPOC_PSEPU.

Residues 807-911 are 57% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD002641) which is seen in RPOC_ECOLI.

Residues 470-550 are 65% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD001471) which is seen in RPOC_HAEIN.

Residues 328-411 are 85% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD000691) which is seen in RPOC_PSEPU.

Residues 22-241 are 73% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD002077) which is seen in RPOC_HAEIN.

Residues 417-469 are 98% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD000656) which is seen in RPOC_HAEIN.

Residues 594-736 are 58% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD000956) which is seen in RPOC_PSEPU.

Residues 912-999 are 48% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD001579) which is seen in RPOC_ECOLI.

Residues 738-805 are 92% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD001122) which is seen in RPOC_PSEPU.

Residues 259-327 are 71% similar to a (RNA POLYMERASE DNA-DIRECTED SUBUNIT) protein domain (PD186054) which is seen in RPOC_ECOLI.

Residues 297-388 are 40% similar to a (PROTEIN ORF PUTATIVE KINASE) protein domain (PD000146) which is seen in RPOC_PLAFA.



Paralogs:  Local Blast Search


NG1850 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 16 to 344 (E-value = 3.9e-146) place NG1850 in the RNA_pol_Rpb1_1 family which is described as RNA polymerase Rpb1, domain 1 (PF04997)
Residues 346 to 488 (E-value = 4.6e-83) place NG1850 in the RNA_pol_Rpb1_2 family which is described as RNA polymerase Rpb1, domain 2 (PF00623)
Residues 491 to 646 (E-value = 1.7e-51) place NG1850 in the RNA_pol_Rpb1_3 family which is described as RNA polymerase Rpb1, domain 3 (PF04983)
Residues 671 to 766 (E-value = 2.3e-36) place NG1850 in the RNA_pol_Rpb1_4 family which is described as RNA polymerase Rpb1, domain 4 (PF05000)
Residues 768 to 1325 (E-value = 7.1e-135) place NG1850 in the RNA_pol_Rpb1_5 family which is described as RNA polymerase Rpb1, domain 5 (PF04998)

Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
164  
213
non-globular  
242  
287

PDB Hit:
pdb|1HQM|1HQM-D CRYSTAL STRUCTURE OF THERMUS AQUATICUS CORE RNA 862.0 0.000000
pdb|1I6V|1I6V-D THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN860.0 0.000000
pdb|1IW7|1IW7-D CRYSTAL STRUCTURE OF THE RNA POLYMERASE HOLOENZYME685.0 0.000000
pdb|1L9U|1L9U

Gene Protein Sequence:
MNLLNLFNPLQTAGMEEEFDAIKIGIASPETIRSWSYGEVKKPETINYRT
FKPERDGLFCAKIFGPVKDYECLCGKYKRLKFKGVTCEKCGVEVTLSKVR
RERMGHIELAAPVAHIWFLKSLPSRLGMVLNMTLRDIERVLYFEAFVVTD
PGMTPLQRRQLLTEDDYYNKLDEYGDDFDAKMGAEGIRELLRTLDVAGEI
EILRQELESTGSDTKIKKIAKRLKVLEAFHRSGMKLEWMIMDVLPVLPPD
LRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELHAPDIIVRNEKRM
LQEAVDSLLDNGRRGKAMTGANKRPLKSLADMIKGKGGRFRQNLLGKRVD
YSGRSVITVGPYLRLHQCGLPKKMALELFKPFIFHKLEKQGLASTVKAAK
KLVEQEVPEVWDILEEVIREHPIMLNRAPTLHRLGIQAFEPILIEGKAIQ
LHPLVCAAFNADFDGDQMAVHVPLSLEAQMEARTLMLASNNVLSPANGEP
IIVPSQDIVLGLYYMTRDRINAKGEGSLFADVKEVHRAYHTKQVELGTKI
TVRLREWVKNEAGEFEPVVNRYETTVGRALLSEILPKGLPFEYVNKALKK
KEISKLINASFRLCGLRDTVIFADHLMYTGFGFAAKGGISIAVDDMEIPK
EKAALLAEANAEVKEIEDQYRQGLVTNGERYNKVVDIWGRAGDKIAKAMM
DNLSKQKVIDRDGNEVDQESFNSIYMMADSGARGSAAQIKQLSGMRGLMA
KPDGSIIETPITSNFREGLTVLQYFIATHGARKGLADTALKTANSGYLTR
RLVDVTQDLVVVEDDCGTSDGFVMKAVVQGGDVIEALRDRILGRVTASDV
VDPSSGETLVEAGTLLTEKLVDMIDQSGVDEVKVRTPITCKTRHGLCAHC
YGRDLARGKLVNAGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAAS
QVEAKSNGTARFSSQMRYVANNKGELVVIGRSCEVVIHDDIGRERERHKV
PYGAILLVQDGMAIKAGQTLATWDPHTRPMITEHAGMVKFENMEEGVTVA
KQTDDVTGLSTLVVIDGKRRSSSASKLLRPTVKLLDENGVEICIPGTSTP
VSMAFPVGAVITVREGQEIGKGDVLARIPQASSKTRDITGGLPRVAELFE
ARVPKDAGMLAEITGTVSFGKETKGKQRLIITDVDGVAYETLISKEKQIL
VHDGQVVNRGETIVDGAVDPHDILRLQGIEALARYIVQEVQEVYRLQGVK
ISDKHIEVIIRQMLRRVNIADAGETGFITGEQVERGDVMAANEKALEEGK
EPARYENILLGITKASLSTDSFISAASFQETTRVLTEAAIMGKQDELRGL
KENVIVGRLIPAGTGLTYHRSRHQQWQGVEQETAETQVTDE

Gene Nucleotide Sequence:  Sequence Viewer
ATGAATTTGTTGAACTTATTTAATCCGTTGCAAACCGCAGGTATGGAAGA
AGAGTTTGATGCCATCAAAATCGGTATTGCCTCTCCCGAAACCATCCGCT
CATGGTCTTATGGCGAAGTTAAAAAACCTGAAACCATCAACTACCGTACG
TTCAAACCCGAGCGCGACGGCTTGTTCTGCGCCAAAATCTTTGGCCCGGT
CAAAGACTACGAATGCTTGTGCGGAAAATACAAACGATTGAAATTTAAAG
GCGTAACCTGTGAAAAATGTGGCGTAGAAGTTACCCTGTCCAAAGTGCGC
CGCGAACGCATGGGCCATATCGAATTGGCTGCACCCGTTGCCCATATTTG
GTTCTTGAAATCCCTGCCTTCCCGCTTGGGTATGGTATTGAACATGACGT
TGCGTGATATCGAACGCGTATTGTACTTTGAAGCATTCGTGGTGACCGAT
CCCGGCATGACTCCGTTGCAACGTCGTCAATTGCTGACTGAAGACGATTA
CTACAACAAACTGGACGAATACGGCGACGACTTCGATGCCAAAATGGGTG
CGGAAGGTATCCGCGAATTGTTGCGAACCTTGGATGTAGCAGGCGAAATC
GAAATCCTGCGCCAAGAGCTTGAATCGACCGGTTCTGACACCAAAATCAA
AAAAATCGCTAAACGCTTGAAAGTATTGGAAGCCTTCCATCGTTCCGGTA
TGAAGCTGGAGTGGATGATTATGGATGTGCTGCCGGTATTGCCGCCTGAT
TTGCGTCCGTTGGTTCCGTTGGACGGCGGCCGTTTTGCCACTTCCGATTT
GAACGATTTGTACCGCCGCGTCATCAACCGCAACAACCGTCTGAAACGCC
TGCTGGAACTGCATGCGCCTGACATCATCGTCCGCAACGAAAAACGTATG
TTGCAAGAAGCGGTTGATTCGCTGTTGGATAACGGCCGTCGCGGTAAAGC
CATGACCGGAGCCAACAAACGTCCGCTGAAATCGTTGGCAGATATGATTA
AAGGTAAAGGCGGCCGCTTCCGTCAAAACCTGTTGGGCAAACGTGTGGAC
TACTCCGGCCGTTCCGTGATTACCGTAGGCCCATACCTGCGTCTGCACCA
ATGCGGTTTGCCGAAAAAAATGGCGTTGGAACTGTTCAAACCATTTATTT
TCCACAAATTGGAAAAACAAGGTTTGGCGTCTACCGTTAAAGCTGCGAAA
AAATTGGTAGAACAAGAAGTACCTGAAGTATGGGATATCTTGGAAGAAGT
CATCCGCGAACATCCGATTATGTTGAACCGTGCGCCGACCCTGCACCGTT
TGGGTATTCAAGCGTTCGAGCCTATTCTGATCGAAGGTAAAGCGATTCAG
TTGCACCCATTGGTGTGTGCCGCATTTAATGCCGACTTTGACGGTGACCA
AATGGCAGTACACGTTCCATTGAGCTTGGAAGCGCAAATGGAAGCACGCA
CGCTGATGCTGGCTTCAAACAACGTATTGTCTCCTGCCAACGGCGAACCG
ATTATCGTACCTTCCCAAGACATCGTATTGGGTCTGTACTACATGACCCG
CGACCGTATCAATGCCAAAGGCGAGGGCAGCCTGTTTGCCGATGTGAAAG
AAGTGCATCGTGCATACCATACCAAACAGGTCGAGCTGGGTACAAAAATC
ACCGTACGTCTGCGCGAATGGGTGAAAAACGAAGCAGGTGAGTTTGAGCC
TGTCGTTAACCGTTACGAAACAACCGTCGGCCGTGCATTGTTGAGCGAAA
TCCTGCCGAAAGGCCTGCCGTTTGAATATGTCAACAAAGCGTTGAAGAAA
AAAGAAATTTCCAAGCTGATTAACGCATCGTTCCGCCTGTGCGGCTTGCG
CGATACGGTTATCTTCGCCGACCACCTGATGTACACCGGTTTCGGATTTG
CGGCAAAAGGCGGTATTTCCATTGCCGTTGACGATATGGAAATTCCAAAA
GAAAAAGCGGCCTTGCTGGCTGAAGCCAATGCCGAAGTTAAAGAAATCGA
AGACCAATACCGTCAAGGTTTGGTTACCAACGGCGAACGCTACAACAAAG
TGGTCGATATTTGGGGTCGTGCCGGCGATAAGATTGCTAAAGCGATGATG
GACAACCTGTCCAAACAAAAAGTTATCGACCGTGACGGCAACGAAGTCGA
TCAAGAGTCATTCAACTCCATTTATATGATGGCGGACTCCGGTGCCCGTG
GTTCTGCGGCTCAGATTAAACAGTTGTCCGGTATGCGCGGTTTGATGGCG
AAACCTGACGGATCGATTATTGAAACGCCGATTACCTCAAACTTCCGCGA
AGGTCTGACCGTATTGCAATACTTTATTGCGACCCACGGTGCGCGTAAGG
GTTTGGCGGATACCGCGTTGAAAACCGCGAACTCCGGTTACCTGACCCGT
CGTCTGGTGGATGTAACTCAAGACTTGGTCGTTGTTGAAGACGATTGCGG
TACTTCAGACGGCTTTGTCATGAAGGCAGTGGTACAAGGCGGTGATGTGA
TTGAAGCATTGCGCGATCGTATTTTGGGTCGTGTTACCGCGTCTGACGTT
GTCGATCCGTCAAGCGGCGAGACTTTGGTTGAAGCCGGTACGTTGTTGAC
TGAAAAACTGGTGGATATGATTGACCAATCCGGTGTCGATGAAGTCAAAG
TCCGTACTCCGATTACTTGTAAAACCCGCCACGGTCTGTGCGCGCACTGT
TACGGCCGCGACTTGGCGCGCGGCAAACTGGTCAATGCCGGCGAGGCAGT
CGGCGTGATTGCGGCTCAGTCTATTGGTGAACCGGGTACCCAGTTGACCA
TGCGTACGTTCCACATCGGTGGTGCGGCATCCCGTGCGGCAGCAGCCAGC
CAAGTCGAAGCCAAATCCAACGGTACGGCACGTTTCAGCAGCCAAATGCG
TTATGTTGCCAACAACAAAGGCGAGTTGGTTGTCATCGGCCGTTCTTGCG
AAGTCGTGATTCACGATGACATCGGCCGTGAACGCGAACGCCACAAAGTA
CCTTACGGTGCCATCCTGCTGGTACAAGACGGTATGGCCATTAAAGCCGG
TCAAACCTTGGCAACTTGGGATCCGCATACCCGTCCGATGATTACCGAAC
ATGCAGGTATGGTGAAATTCGAGAACATGGAAGAGGGCGTTACCGTTGCA
AAACAAACCGATGATGTAACCGGTTTGTCCACTTTGGTAGTGATTGACGG
TAAACGCCGTTCCTCTAGTGCTTCCAAACTGCTGCGTCCGACTGTGAAAC
TCTTGGACGAAAACGGCGTGGAAATCTGTATTCCCGGTACGTCCACTCCG
GTTTCGATGGCATTCCCCGTTGGTGCGGTGATTACCGTACGCGAAGGTCA
GGAAATCGGTAAAGGCGACGTATTGGCGCGTATTCCGCAAGCCTCTTCCA
AAACCCGCGACATTACCGGCGGTCTGCCGCGCGTTGCCGAGCTGTTTGAA
GCACGCGTGCCGAAAGATGCCGGTATGCTGGCGGAAATTACCGGTACCGT
TTCCTTCGGTAAGGAGACCAAAGGCAAACAACGTCTGATTATCACTGACG
TGGACGGTGTAGCATACGAGACTTTGATTTCCAAAGAGAAACAAATTCTG
GTACATGACGGTCAAGTGGTAAACCGAGGCGAAACCATTGTGGACGGCGC
GGTCGATCCGCACGATATTCTGCGTCTGCAAGGTATCGAAGCACTGGCAC
GCTACATTGTCCAAGAGGTGCAAGAGGTTTACCGCCTGCAAGGTGTGAAG
ATTTCCGATAAACACATCGAAGTCATCATCCGTCAAATGTTGCGCCGTGT
GAACATTGCGGATGCCGGCGAAACCGGGTTTATTACCGGAGAGCAGGTCG
AACGCGGCGATGTGATGGCGGCCAATGAAAAAGCTTTGGAAGAAGGCAAA
GAGCCGGCACGTTACGAAAACATATTGCTGGGTATTACCAAAGCCTCCCT
GTCCACCGACAGCTTCATTTCTGCCGCATCGTTCCAAGAAACCACCCGTG
TGTTGACCGAAGCTGCCATCATGGGCAAACAAGACGAACTGCGCGGTCTG
AAAGAGAATGTCATCGTCGGTCGCCTGATTCCTGCCGGTACCGGTTTGAC
TTATCACCGCAGCCGTCATCAGCAATGGCAAGGGGTAGAGCAGGAGACTG
CTGAAACCCAAGTAACGGATGAA


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