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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1197 IGR1199 IGR1204 IGR1201 IGR1202 IGR1203 IGR1200 IGR1198 IGR1196 HD1645 HD1640 HD1650 glpR, - HD1648 ubiA, - HD1647 purB, - HD1649 gyrB, - HD1643 HD1644 HD1642 purR,rbsR, - HD1641 uhpT, - HD1639 HD1645 HD1640 HD1650 glpR, - HD1648 ubiA, - HD1647 purB, - HD1649 gyrB, - HD1643 HD1644 HD1642 purR,rbsR, - HD1641 uhpT, - HD1639 HD1645 HD1640 HD1650 glpR, - HD1648 ubiA, - HD1647 purB, - HD1649 gyrB, - HD1643 HD1642 purR,rbsR, - HD1641 uhpT, - HD1639 HD1646 HD1644 HD1646
* Calculated from Protein Sequence

Gene ID: HD1643

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
gyrB  

Definition:
DNA gyrase subunit B (type II topoisomerase)

Gene Start:
1365150

Gene Stop:
1362718

Gene Length:
2433

Molecular Weight*:
90071

pI*:
5.30

Net Charge*:
-18.18

EC:
5.99.1.3  

Functional Class:
Replication; DNA replication, restriction, modification, recombination, and repair  

Pathway: pathway table

Secondary Evidence:
Yamagishi,J., Yoshida,H., Yamayoshi,M. and Nakamura,S.
Nalidixic acid-resistant mutations of the gyrB gene of Escherichia
coli
Mol. Gen. Genet. 204 (3), 367-373 (1986)
Medline: 87014111

Adachi,T., Mizuuchi,M., Robinson,E.A., Appella,E., O'Dea,M.H.,
Gellert,M. and Mizuuchi,K.
DNA sequence of the E. coli gyrB gene: application of a new
sequencing strategy
Nucleic Acids Res. 15 (2), 771-784 (1987)
Medline: 87146392

Funatsuki,K., Tanaka,R., Inagaki,S., Konno,H., Katoh,K. and
Nakamura,H.
acrB mutation located at carboxyl-terminal region of gyrase B
subunit reduces DNA binding of DNA gyrase
J. Biol. Chem. 272 (20), 13302-13308 (1997)
Medline: 97294746

Adachi,T., Mizuuchi,K., Menzel,R. and Gellert,M.
DNA sequence and transcription of the region upstream of the E.
coli gyrB gene
Nucleic Acids Res. 12 (16), 6389-6395 (1984)
Medline: 84297235




Comment:
From Genbank:[gi:1170145]
DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.

For other "gyr" genes, see HD1587 (gyrA), HD1748 (gyrA), HD0870 (gyrB). For other topoisomerases, see HD0413 (I), HD0954 (I), HD1276 (III), HD1385 (I), HD1643(II)

Blast Summary:  PSI-Blast Search
Matches in gapped BLAST to DNA gyrase subunit B. Residues 1-810 are 71% similar to this enzyme from Haemophilus influenzae Rd (1170145|) and residues 7-810 are 70% similar to this enzyme from E.coli (121888|).

HD1643 is similar to DNA gyrase subunit B proteins from C. trachomatis (CT190 & CT661), C. pneumoniae (CPn0275 & CPn0715), T. pallidum (TP1006), M. pneumoniae (MP0151), U. urealyticum (UU081), and M. genitalium (MG003). It is also similar to topoisomerase IV subunit B proteins from U. urealyticum (UU466), M. genitalium (MG203), and M. pneumoniae (MP0032).

COGS Summary:  COGS Search
BeTs to 14 clades of COG0187
COG name: DNA gyrase (topoisomerase II) B subunit
Functional Class: L
The phylogenetic pattern of COG0187 is a---yqvCEBrHujGPOlINX
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
***** IPB001241 (DNA topoisomerase II family) with a combined E-value of 2.3e-149.
    IPB001241A    15-36
    IPB001241B    114-132
    IPB001241C    169-181
    IPB001241D    273-286
    IPB001241E    321-347
    IPB001241F    426-474
    IPB001241G    495-521
    IPB001241H    744-767


ProDom Summary:  Protein Domain Search
Residues 368-482 are 66% similar to a (TOPOISOMERASE ATP-BINDING DNA SUBUNIT GYRASE DNA-BINDING) protein domain (PD000714) which is seen in GYRB_BUCAI.

Residues 139-210 are 51% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA GYRASE IV COMPLETE) protein domain (PD242130) which is seen in Q9PHD9_XYLFA.

Residues 484-556 are 89% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA GYRASE PROTEOME IV) protein domain (PD000616) which is seen in Q9CKX5_PASMU.

Residues 185-236 are 51% similar to a (GYRASE DNA ATP-BINDING TOPOISOMERASE) protein domain (PD412132) which is seen in Q59957_STRPN.

Residues 561-732 are 50% similar to a (GYRASE SUBUNIT DNA ISOMERASE) protein domain (PD013226) which is seen in Q9CKX5_PASMU.

Residues 40-137 are 59% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING GYRASE) protein domain (PD404171) which is seen in GYRB_HALSQ.

Residues 735-800 are 80% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA) protein domain (PD149633) which is seen in GYRB_ECOLI.

Residues 488-550 are 42% similar to a (TOPOISOMERASE II DNA-BINDING ATP-BINDING NUCLEAR ISOZYME) protein domain (PD335861) which is seen in TP2B_CHICK.

Residues 371-422 are 57% similar to a (GYRASE DNA ISOMERASE ATP-BINDING) protein domain (PD336367) which is seen in Q9CKX5_PASMU.

Residues 588-741 are 26% similar to a (GYRASE B ATP-BINDING SUBUNIT) protein domain (PD358158) which is seen in GYRB_BUCAI.

Residues 246-368 are 76% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA) protein domain (PD001260) which is seen in GYRB_ECOLI.

Residues 588-719 are 31% similar to a (COMPLETE ORF MITOCHONDRION PROTEOME) protein domain (PD000146) which is seen in GYRB_BUCAP.

Residues 40-220 are 77% similar to a (TOPOISOMERASE ATP-BINDING DNA SUBUNIT GYRASE II) protein domain (PD000740) which is seen in GYRB_HAEIN.



Paralogs:  Local Blast Search


HD1643 is paralogously related to HD0870 (1e-106).


Pfam Summary:  Pfam Search
Residues 36 to 179 (E-value = 2e-33) place HD1643 in the HATPase_c family which is described as Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (PF02518)
Residues 226 to 398 (E-value = 5.2e-85) place HD1643 in the DNA_gyraseB family which is described as DNA gyrase B (PF00204)
Residues 425 to 537 (E-value = 4e-07) place HD1643 in the Toprim family which is described as Toprim domain (PF01751)
Residues 734 to 800 (E-value = 8.4e-48) place HD1643 in the DNA_gyraseB_C family which is described as DNA gyrase B subunit, carboxyl terminus (PF00986)

PDB Hit:
pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Provid... 583 2e-167
pdb|1AJ6| Novobiocin-Resistant Mutant (R136h) Of The N-Termi... 349 9e-097
pdb|1BJT| Topoisomerase Ii Residues 409 - 1201 >gi|1633273|p... 65 4e-011

Gene Protein Sequence:
MSEQNQTNSYDSSSIKVLRGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVD
NAIDEALAGHCQDIIVTIHSDNSISVQDDGRGIPVGIHPEEGVSAAEVIM
TVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSSKLQLTIRREGHVHEQFY
SLGEPDAPLTIIGNTDKTGTSVRFWPSLAIFKNKTEFEYKILSKRLRELS
FLNSGVSIKLIDEREGKEEHFKYEGGIKAYVEYLNEGKTHIHNTPFYLAT
EKDGIGVEVSLQWNDSYNENVYCFTNNIPQRDGGTHLAGFRGALTRALKN
YMDNSGVVKKVDANIDASGDDAREGLVAVISVKVPDPKFSSQTKDKLVSS
EVRGAVESSMNEALAEYLAENPDDAKNIVTKIIDAARAREAARKAREMTR
RKGALDLGGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKNQAI
LPLKGKILNVEKARFDKMLSSQEVATLITALGAGIGRDDYNIEKLRYHKI
IIMTDADVDGAHIRTLLLTFFYRQMPELIENGYVYIAQPPLYKVKKGKQE
RYIQDNDEMLQYEIDIALEGAGLYVSEGAPALSGLALEKLISQYNGVQKL
FERLVRRYPMTILNELIYSTALSVELAKQQLKITAWTEQLVNTLNTKEVN
GSSYQVSVYFNSERQIYEPQIVVTTHGMDTTYRIDFNFITSNEYGLIVKL
GEQLNDLLADSAYVVRGERRQAVSTFAEALDWLVKESRKGLTIQRYKGLG
EMNPEQLWETTMDPVARKMLQVNISDAIAADKLFSTLMGDEVEPRRDFIE
SNALYANLDI$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCTGAACAAAATCAAACAAATAGTTATGATTCTTCGAGTATTAAAGT
CTTACGGGGCTTAGATGCGGTGCGTAAACGTCCGGGAATGTATATCGGCG
ATACTGATGATGGCACGGGGTTACATCATATGGTGTTTGAAGTGGTGGAT
AATGCCATTGATGAAGCATTAGCAGGCCATTGTCAAGATATTATTGTTAC
CATTCATTCAGATAATTCTATTTCTGTACAAGATGATGGACGTGGTATCC
CAGTTGGTATTCATCCTGAAGAAGGCGTTTCTGCGGCAGAAGTAATTATG
ACCGTCTTACACGCAGGCGGTAAATTTGATGATAATTCATATAAAGTCTC
CGGTGGTTTACACGGCGTGGGGGTTTCGGTTGTTAATGCGCTGTCATCAA
AATTACAATTAACAATTCGCCGAGAAGGGCATGTACACGAACAATTTTAT
AGTTTAGGCGAGCCTGATGCGCCTTTAACAATTATTGGTAATACAGATAA
AACAGGCACCAGTGTACGCTTTTGGCCTAGTTTAGCGATTTTTAAAAATA
AAACTGAATTTGAATATAAAATTTTATCTAAAAGACTGCGTGAGTTATCA
TTTTTAAACTCAGGTGTTTCGATAAAATTAATTGATGAACGCGAAGGTAA
AGAAGAGCACTTTAAATATGAAGGTGGTATTAAAGCCTATGTTGAATATT
TAAATGAAGGCAAAACGCATATTCATAACACTCCTTTTTACCTTGCTACA
GAGAAAGACGGCATCGGTGTAGAAGTTTCATTACAATGGAATGATAGCTA
TAACGAAAATGTTTATTGCTTCACGAATAATATTCCACAACGTGATGGTG
GTACCCATTTAGCGGGTTTTCGTGGTGCTTTAACACGCGCTTTAAAAAAT
TATATGGATAATAGTGGTGTCGTTAAAAAGGTAGACGCTAATATTGATGC
TTCAGGTGATGATGCGCGTGAAGGGCTTGTTGCGGTGATTTCCGTTAAAG
TACCCGATCCAAAGTTTTCTTCACAAACAAAGGATAAGCTTGTTTCATCT
GAAGTGAGAGGGGCGGTTGAAAGCTCAATGAATGAAGCATTAGCAGAATA
TTTAGCTGAAAACCCAGATGATGCAAAAAATATTGTCACAAAAATTATTG
ATGCTGCTCGTGCAAGAGAAGCCGCGCGTAAAGCACGTGAGATGACACGT
CGTAAAGGAGCACTAGATTTAGGTGGTTTGCCGGGGAAATTAGCGGATTG
TCAGGAAAAAGATCCAGCCTTGTCTGAATTATATTTAGTGGAGGGAGATT
CTGCGGGGGGATCCGCTAAACAAGGTCGTGATCGTAAAAATCAAGCGATT
TTACCCTTGAAAGGTAAGATTCTAAATGTAGAAAAAGCACGTTTCGATAA
AATGCTTTCATCGCAAGAAGTGGCAACTTTAATTACTGCGTTAGGTGCAG
GAATTGGGCGAGATGATTACAATATTGAAAAGTTACGTTATCACAAAATT
ATTATTATGACCGATGCGGATGTTGACGGTGCGCATATTCGTACGTTACT
GCTGACGTTCTTCTATCGTCAAATGCCGGAATTGATAGAAAACGGTTATG
TTTACATTGCTCAACCGCCTTTGTATAAAGTGAAAAAAGGTAAGCAAGAG
CGTTATATCCAAGATAATGATGAAATGTTGCAGTATGAAATTGATATTGC
GCTAGAAGGAGCCGGATTATATGTTAGTGAAGGCGCTCCAGCATTAAGCG
GTTTAGCTTTAGAAAAGCTAATCAGTCAATATAATGGCGTGCAGAAATTA
TTTGAACGTTTAGTTCGTCGTTATCCAATGACGATATTAAATGAATTGAT
TTACAGCACAGCCCTCTCAGTTGAATTAGCCAAACAACAGCTAAAAATAA
CCGCTTGGACGGAACAATTAGTCAACACACTTAATACAAAAGAAGTGAAT
GGCAGTAGCTATCAAGTCAGTGTTTATTTTAATAGTGAACGGCAAATATA
CGAGCCACAAATTGTGGTAACAACACATGGTATGGATACGACTTATCGTA
TTGATTTTAATTTTATCACCAGCAATGAGTATGGTCTTATTGTGAAATTA
GGTGAGCAATTAAATGATTTATTAGCTGATTCAGCTTATGTTGTGCGAGG
TGAGCGTCGTCAAGCGGTATCAACTTTTGCAGAAGCATTAGATTGGTTAG
TGAAAGAATCTCGGAAAGGTTTAACCATTCAACGTTATAAAGGATTAGGT
GAAATGAATCCAGAACAGTTATGGGAAACAACTATGGATCCCGTTGCCCG
TAAAATGTTGCAAGTAAATATTAGTGATGCGATTGCAGCGGATAAATTGT
TTAGTACGCTAATGGGCGATGAAGTTGAACCACGCCGTGATTTCATTGAA
AGCAATGCATTATATGCTAATTTAGATATTTAG


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