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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1380 IGR1376 IGR1378 IGR1381 IGR1377 IGR1379 IGR1375.1 rpL7/L12,rplL, - HD1879 rpL11, - HD1884 rpL10,rplJ, - HD1881 nusG, - HD1885 rpL1, - HD1882 rpoC, - HD1876 rpoB, - HD1877 HD1878 rpL7/L12,rplL, - HD1879 rpL11, - HD1884 rpL10,rplJ, - HD1881 nusG, - HD1885 rpL1, - HD1882 rpoC, - HD1876 rpoB, - HD1877 HD1878 rpL10,rplJ, - HD1881 nusG, - HD1885 rpL1, - HD1882 rpoC, - HD1876 rpoB, - HD1877 rpL7/L12,rplL, - HD1879 rpL11, - HD1884 HD1878
* Calculated from Protein Sequence

Gene ID: HD1877

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rpoB  

Definition:
DNA-directed RNA polymerase beta chain (transcriptase beta chain)

Gene Start:
1580506

Gene Stop:
1576478

Gene Length:
4029

Molecular Weight*:
149857

pI*:
5.10

Net Charge*:
-37.62

EC:
2.7.7.6  

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

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Morse R, O'Hanlon K, Collins MD.
The spectrum of spontaneous rifampin resistance mutations in the rpoB gene of Bacillus subtilis 168 spores differs from that of vegetative cells and resembles that of Mycobacterium tuberculosis.
J Bacteriol. 2002 Sep;184(17):4936-40.
PMID: 12204372

Ko KS, Lee HK, Park MY, Lee KH, Yun YJ, Woo SY, Miyamoto H, Kook YH.
Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species.
J Clin Microbiol. 2002 Jul;40(7):2653-8.
PMID: 12089300

Aboshkiwa M, Rowland G, Coleman G.
Nucleotide sequence of the Staphylococcus aureus RNA polymerase rpoB gene and comparison of its predicted amino acid sequence with those of other bacteria.
Biochim Biophys Acta 1262(1):73-8.1995
Medline: 7772603.

Comment:
For other "rpo" genes, see HD1172 (rpoE), HD1876 (rpoC), HD0086(rpoH), HD1923 (rpoZ), HD1951 (rpoA), HD0691 (rpoD), HD0692 (rpoD).

Blast Summary:  PSI-Blast Search
Numerous stongly significant hits using gapped BLAST to DNA-dependent RNA polymerase beta subunit from H. influenzae (1173148), E. coli (2507343), Salmonella typhimurium (6960339), among others.

HD1877 is similar to DNA-dependent RNA polymerase beta subunit from C. trachomatis (CT315), C. pneumonia (CPn0081), T. pallidum (TP0241), M. genitalium (MG341), M. pneumoniae (MP0326), U. urealyticum (UU187).


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 1.3e-225.
    IPB001572A    443-459
    IPB001572B    504-543
    IPB001572C    548-572
    IPB001572D    663-692
    IPB001572E    798-815
    IPB001572F    866-890
    IPB001572G    1064-1106
    IPB001572H    1231-1284


ProDom Summary:  Protein Domain Search
Residues 600-793 are 87% similar to a (POLYMERASE RNA BETA DNA-DIRECTED) protein domain (PD001760) which is seen in Q9CK91_PASMU.

Residues 224-291 are 83% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD152123) which is seen in Q9CK91_PASMU.

Residues 1070-1120 are 98% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSFERASE TRANSCRIPTION) protein domain (PD000636) which is seen in RPOB_HAEIN.

Residues 888-935 are 70% similar to a (POLYMERASE RNA BETA DNA-DIRECTED) protein domain (PD105072) which is seen in Q9KJM5_BARQU.

Residues 380-591 are 84% similar to a (POLYMERASE RNA DNA-DIRECTED BETA) protein domain (PD011517) which is seen in RPOB_HAEIN.

Residues 1121-1182 are 53% similar to a (BETA POLYMERASE RNA CHAIN) protein domain (PD412613) which is seen in RPOB_BUCAI.

Residues 1121-1182 are 88% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD007542) which is seen in Q9CK91_PASMU.

Residues 954-1069 are 69% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD013464) which is seen in RPOB_HAEIN.

Residues 904-948 are 73% similar to a (BETA POLYMERASE RNA CHAIN) protein domain (PD174240) which is seen in RPOB_COXBU.

Residues 1183-1340 are 93% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSFERASE BETA) protein domain (PD000748) which is seen in Q9CK91_PASMU.

Residues 292-379 are 84% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD123257) which is seen in Q9CK91_PASMU.

Residues 202-295 are 55% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD328160) which is seen in RPOB_PSEPU.

Residues 390-507 are 30% similar to a (POLYMERASE RNA DNA-DIRECTED TRANSCRIPTION) protein domain (PD407541) which is seen in RPOB_TOBAC.

Residues 511-595 are 43% similar to a (RNA POLYMERASE DNA-DIRECTED TRANSCRIPTION) protein domain (PD008835) which is seen in O28393_ARCFU.

Residues 167-221 are 98% similar to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD383640) which is seen in RPOB_HAEIN.

Residues 168-200 are identical to a (RNA POLYMERASE BETA DNA-DIRECTED) protein domain (PD415995) which is seen in Q9CK91_PASMU.

Residues 794-953 are 98% similar to a (POLYMERASE RNA DNA-DIRECTED BETA TRANSFERASE) protein domain (PD001712) which is seen in RPOB_HAEIN.

Residues 11-231 are 78% similar to a (POLYMERASE RNA DNA-DIRECTED BETA TRANSFERASE) protein domain (PD001037) which is seen in Q9KW14_SHEVI.



Paralogs:  Local Blast Search

HD1877 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 27 to 509 (E-value = 1.9e-33) place HD1877 in the RNA_pol_Rpb2_1 family which is described as RNA polymerase beta subunit (PF04563)
Residues 151 to 454 (E-value = 2.3e-08) place HD1877 in the RNA_pol_Rpb2_2 family which is described as RNA polymerase Rpb2, domain 2 (PF04561)
Residues 510 to 582 (E-value = 5.3e-45) place HD1877 in the RNA_pol_Rpb2_3 family which is described as RNA polymerase Rpb2, domain 3 (PF04565)
Residues 716 to 1264 (E-value = 1e-178) place HD1877 in the RNA_pol_Rpb2_6 family which is described as RNA polymerase Rpb2, domain 6 (PF00562)
Residues 1266 to 1342 (E-value = 1.8e-50) place HD1877 in the RNA_pol_Rpb2_7 family which is described as RNA polymerase Rpb2, domain 7 (PF04560)

PDB Hit:
pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core... 566 8e-162

Gene Protein Sequence:
MAYSYSEKKRIRKSFGKRPQVLNVPYLLTIQLDSYEKFIHRDLDGQQGLE
AAFRSVFPIVSNNGSTELQYVSYELGEPVFDVRECQIRGTTYAAPLRVKL
RLVAFDREAAAGTVKDIKEQNVYMGEIPLMTDNGTFVINGTERVIVSQLH
RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDR
RRKLPATIILRALGYTTEEILTMFFEKVLFEIQDNKLLMILVPERLRGET
AAFDIEANGKIYVERGRRITARHIRTLEKDGITQIEVPVEYIVGKVAAKD
YVDLSTGELVCPANTEISMDMLAKLSQAGYKELEVLFTNDLDHGPYISET
LRVDSTYDRLSALVEIYRMMRPGEPPTKEAAEALFDNMFFSADRYDLSAV
GRMKFNRSLNIPEGVGTGILTNDDITGVMKKLIEIRNGRGEVDDIDHLGN
RRIRSVGEMAENQFRIGLVRVERAVRERLSLGDLDGITPQDLINAKPISA
AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDV
HPTHYGRLCPIETPEGPNIGLINSLSVYARTNNYGFLETPFHKVVNGQVT
EEIEYLSAIEEGNYVVAQANSNLDEHFRFTDTYVTCRGEHGESGLYKPED
IHYMDISTQQVVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPL
VGTGMEKPIALDSGVAIVAKRGGIIQRVDASRIVVKVNEDETIPGEAGID
IYNLIKYTRSNQNTCINQIPCVNLGEPVARGEILADGPSTDLGELALGQN
IRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGAEE
ITADIPNVGESALSKLDESGIVYVGAEVKGGDILVGKVTPKGETQLTPEE
KLLRAIFGEKASDVKDSSLRVPNGTSGTVIDVQVFTRDSVEKDKRALEIE
EMQLREAKKDLTEELEILEAGLFTRVRNLLIESGVSEVNLNNVAREKWLE
QTLDDEAKQNQLEQLAEQHEELCKEFERKLEIKRNKIIQGDDLAPGVLKV
VKVYLAVRRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGEPVEIVLN
PLGVPSRMNIGQILETHLGLAARGIGDQINAMIKQQQEVTKLREYIQKAY
DLGHGSQVVDLSTFTDEEVMRLAQNLRKGLPLATPVFDGAHEAEIKGLLE
LGGLPTSGQITLFDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGS
YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG
RTKMYKNIVDGTHQMEPGMPESFNVLLKEIRALGIDMELDED$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCATACTCATATTCCGAGAAAAAGCGTATTCGTAAGAGCTTTGGTAA
ACGTCCACAAGTTCTTAATGTACCTTACCTATTAACAATTCAGCTTGATT
CTTATGAAAAATTTATTCATAGAGATTTAGATGGACAACAAGGTTTAGAA
GCGGCATTCCGTTCAGTGTTTCCAATCGTTAGTAATAATGGTTCTACTGA
ATTGCAATACGTTTCTTATGAATTAGGTGAACCTGTATTTGATGTGCGTG
AATGTCAAATTCGTGGTACCACTTATGCTGCCCCATTACGCGTAAAACTT
CGTTTAGTTGCGTTCGATCGTGAAGCTGCTGCTGGCACGGTGAAGGATAT
TAAAGAACAAAATGTGTATATGGGCGAAATTCCATTAATGACAGATAATG
GTACTTTTGTAATTAATGGTACAGAGCGTGTAATCGTTTCACAATTACAT
CGTAGTCCTGGCGTTTTCTTTGATTCAGATAAAGGTAAAACGCATTCTTC
AGGTAAAGTGTTGTATAACGCACGTATTATCCCTTATCGTGGTTCATGGT
TAGACTTTGAGTTTGATCCAAAAGATAACCTTTATGCGCGTATTGATCGC
CGTCGTAAATTACCTGCTACCATCATTTTACGTGCATTAGGCTATACCAC
AGAAGAAATCTTAACGATGTTCTTCGAGAAAGTATTGTTTGAAATTCAAG
ATAATAAATTATTAATGATATTGGTGCCGGAACGCTTACGTGGTGAGACT
GCGGCATTTGATATTGAAGCTAATGGTAAAATTTATGTAGAACGTGGTCG
CCGTATTACGGCTCGCCATATTCGTACATTAGAAAAAGATGGTATTACTC
AAATTGAGGTGCCGGTAGAGTATATTGTGGGTAAAGTTGCTGCGAAAGAT
TATGTTGATCTTTCAACAGGCGAATTAGTGTGCCCAGCTAATACGGAAAT
CTCTATGGATATGCTAGCGAAGTTATCGCAAGCGGGCTATAAAGAGCTTG
AAGTATTATTTACTAATGATTTAGATCACGGTCCTTATATTTCAGAAACG
TTACGTGTTGACTCAACTTATGATCGTTTAAGCGCATTAGTTGAAATTTA
TCGAATGATGCGTCCGGGAGAGCCACCAACAAAAGAAGCGGCAGAAGCAT
TATTTGATAATATGTTCTTCTCTGCGGATCGTTACGATTTATCAGCAGTG
GGTCGAATGAAATTTAATCGTTCATTAAATATTCCAGAAGGTGTAGGAAC
GGGTATTTTAACGAATGATGACATCACCGGTGTGATGAAAAAATTAATTG
AAATCCGTAATGGTCGTGGTGAAGTAGATGATATTGACCACTTAGGTAAT
CGTCGTATTCGTTCAGTAGGGGAAATGGCAGAAAATCAATTCCGCATTGG
TTTAGTACGTGTTGAACGTGCCGTACGTGAACGTTTATCCTTAGGTGATT
TAGATGGAATTACCCCGCAAGATTTAATTAATGCGAAACCTATTTCAGCG
GCAGTTAAAGAATTTTTTGGTTCTTCACAACTTTCGCAATTTATGGATCA
AAACAATCCGCTTTCAGAGGTTACACATAAACGTCGTATTTCAGCATTAG
GTCCTGGTGGTTTAACACGTGAGCGTGCAGGCTTTGAGGTGCGAGATGTA
CACCCAACGCACTATGGTCGCTTATGTCCGATTGAAACGCCAGAGGGGCC
AAACATTGGTTTGATTAACTCACTTTCTGTATATGCACGTACCAATAACT
ATGGTTTCTTAGAAACGCCATTCCATAAAGTAGTGAATGGGCAAGTTACA
GAAGAGATTGAATATTTATCAGCGATTGAAGAAGGTAATTATGTTGTTGC
TCAGGCTAACTCAAACTTAGATGAGCACTTCCGTTTTACAGATACGTATG
TCACTTGTCGTGGTGAACACGGTGAATCAGGCTTATATAAACCTGAAGAT
ATTCACTATATGGATATTTCAACACAACAAGTGGTTTCTGTCGCTGCAGC
ATTAATTCCATTCTTAGAACACGATGATGCAAACCGTGCCTTAATGGGCG
CGAACATGCAACGTCAAGCAGTTCCAACATTACGTGCAGATAAACCGCTT
GTTGGTACGGGTATGGAAAAACCGATTGCGCTTGACTCTGGTGTGGCAAT
TGTTGCCAAACGTGGTGGTATTATACAGCGTGTTGATGCATCGCGTATTG
TGGTTAAGGTGAATGAAGATGAAACTATTCCGGGCGAAGCGGGCATTGAT
ATCTATAACTTAATTAAATATACCCGTTCAAACCAAAATACGTGTATCAA
TCAAATTCCTTGTGTGAATTTAGGCGAACCAGTGGCGCGTGGTGAGATCT
TGGCAGATGGTCCTTCAACCGATTTAGGTGAGTTAGCATTAGGTCAAAAT
ATCCGCGTGGCATTTATGCCTTGGAATGGCTATAACTTTGAAGACTCAAT
GTTAGTGTCTGAACGCGTGGTGCAAGAAGATCGCTTTACCACAATTCATA
TTCAAGAATTATCTTGTGTAGCACGTGATACTAAATTAGGTGCAGAAGAA
ATTACGGCAGATATTCCGAATGTGGGTGAATCAGCATTAAGTAAACTAGA
TGAATCTGGTATTGTTTATGTTGGTGCAGAGGTTAAAGGTGGTGATATCT
TAGTCGGTAAAGTAACGCCAAAAGGTGAAACCCAATTAACACCAGAAGAA
AAATTATTACGTGCAATTTTTGGTGAAAAAGCATCGGATGTAAAGGATTC
TTCGTTACGTGTACCAAATGGTACTTCAGGTACGGTAATTGACGTACAAG
TATTTACGCGTGATAGCGTTGAGAAAGATAAACGCGCTTTAGAAATCGAA
GAAATGCAACTTCGTGAAGCGAAAAAAGATTTAACTGAAGAGTTAGAGAT
TTTAGAAGCGGGTTTATTTACTCGTGTACGTAACTTGTTAATTGAAAGTG
GTGTATCTGAAGTTAACTTAAATAATGTAGCACGTGAGAAATGGCTAGAA
CAGACATTAGATGACGAAGCAAAACAAAATCAGTTAGAACAACTTGCAGA
ACAGCACGAAGAATTATGCAAAGAGTTTGAGCGTAAACTTGAAATCAAAC
GCAATAAGATCATTCAAGGTGATGATTTAGCCCCGGGCGTGTTAAAGGTT
GTTAAAGTTTATTTAGCGGTTCGTCGTCAAATTCAACCGGGCGATAAAAT
GGCCGGTCGCCATGGTAATAAGGGTGTTATCTCAAAAATCAACCCTGTTG
AAGATATGCCATACGATGAAAATGGTGAGCCAGTTGAGATTGTGTTAAAT
CCATTAGGTGTACCGTCGCGTATGAACATTGGTCAGATTTTAGAAACTCA
TTTAGGCTTAGCGGCCAGAGGGATTGGCGATCAGATCAATGCTATGATTA
AACAACAGCAAGAAGTAACTAAATTACGCGAATATATCCAAAAAGCGTAT
GACTTAGGTCATGGTTCACAAGTTGTTGATTTAAGTACCTTTACGGATGA
AGAGGTCATGCGTTTAGCGCAAAATTTACGTAAAGGATTACCGCTTGCTA
CACCAGTATTTGATGGTGCGCATGAAGCGGAAATTAAAGGCTTATTAGAA
TTAGGTGGTTTACCGACTTCAGGCCAAATTACCTTATTTGATGGTCGTAC
GGGAGAGAAATTTGAGCGTCCTGTAACAGTTGGTTACATGTATATGCTCA
AATTGAACCACTTAGTTGATGACAAAATGCATGCTCGTTCAACCGGTTCT
TATAGTCTTGTTACCCAACAACCGCTTGGTGGTAAAGCACAATTCGGTGG
TCAGCGTTTTGGTGAGATGGAGGTTTGGGCATTAGAAGCATATGGTGCAG
CTTATACCTTACAAGAAATGCTAACGGTTAAATCGGATGACGTGAATGGC
CGTACTAAGATGTATAAAAACATTGTAGACGGTACACATCAAATGGAACC
GGGTATGCCAGAATCATTCAACGTATTGTTGAAAGAGATTCGCGCATTGG
GTATTGATATGGAGTTAGACGAAGATTAA


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