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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR625 IGR619 IGR620 IGR622 IGR623 IGR624 IGR621 HD0868 HD0876 fba, - HD0864 pheA, - HD0873 pgk, - HD0865 HD0866 ndh, - HD0874 parE, - HD0870 HD0869 HD0872 HD0868 HD0876 fba, - HD0864 pheA, - HD0873 pgk, - HD0865 HD0866 ndh, - HD0874 parE, - HD0870 HD0869 HD0872 HD0868 fba, - HD0864 pheA, - HD0873 pgk, - HD0865 HD0866 ndh, - HD0874 parE, - HD0870 sprT, - HD0875 HD0876 sprT, - HD0875 HD0869 HD0872
* Calculated from Protein Sequence

Gene ID: HD0870

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
parE  

Definition:
DNA topoisomerase IV subunit B (gyrase B)

Gene Start:
696247

Gene Stop:
694331

Gene Length:
1917

Molecular Weight*:
70712

pI*:
6.40

Net Charge*:
-5.94

EC:
5.99.1.-  

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

Pathway: pathway table

Secondary Evidence:
Springer,A.L. and Schmid,M.B.
Molecular characterization of the Salmonella typhimurium parE gene.
Nucleic Acids Res. 21(8): 1805-1809.
Medline: 93261812.

Peng,H. and Marians,K.J. 1993. Escherichia coli topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions. J. Biol. Chem. 268(32): 24481-24490. Medline: 94043292.

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

Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to topoisomerase IV subunit B proteins from H. influenzae (1172018), E. coli (464346), S. typhimurium (400731), among others.

HD0870 is similar to DNA topoisomerase subunit B (gyrase B) proteins form U. urealyticum (UU081 & UU466), T. pallidum (TP1006), C. trachomatis (CT190 & CT661), C. pneumoniae (CPn0275 & CPn0715), M. pneumoniae (MP0151 & MP0032), and M. genitalium (MG003 & MG203). It is also similar to a NIFS-related protein from C. trachomatis (CT721).

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 1e-118.
    IPB001241A    11-32
    IPB001241B    106-124
    IPB001241C    163-175
    IPB001241D    267-280
    IPB001241E    312-338
    IPB001241F    414-462
    IPB001241G    481-507
    IPB001241H    563-586


ProDom Summary:  Protein Domain Search
Residues 360-471 are 75% similar to a (TOPOISOMERASE ATP-BINDING DNA SUBUNIT GYRASE DNA-BINDING) protein domain (PD000714) which is seen in PARE_SALTY.

Residues 131-205 are 68% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA GYRASE IV COMPLETE) protein domain (PD242130) which is seen in Q9CNQ7_PASMU.

Residues 478-545 are 80% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA GYRASE PROTEOME IV) protein domain (PD000616) which is seen in Q9KPD9_VIBCH.

Residues 36-125 are 85% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING GYRASE) protein domain (PD404171) which is seen in PARE_HAEIN.

Residues 552-628 are 74% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA) protein domain (PD149633) which is seen in PARE_HAEIN.

Residues 474-578 are 36% similar to a (TOPOISOMERASE II DNA-BINDING ATP-BINDING NUCLEAR ISOZYME) protein domain (PD335861) which is seen in TP2A_MOUSE.

Residues 360-414 are 52% similar to a (PROTEOME COMPLETE PARE) protein domain (PD382895) which is seen in Q9CNQ7_PASMU.

Residues 238-359 are 71% similar to a (TOPOISOMERASE SUBUNIT ATP-BINDING DNA GYRASE PROTEOME IV) protein domain (PD001260) which is seen in Q9KPD9_VIBCH.

Residues 36-223 are 53% similar to a (TOPOISOMERASE ATP-BINDING DNA SUBUNIT GYRASE II) protein domain (PD000740) which is seen in Q9F7P0_BBBBB.



Paralogs:  Local Blast Search


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


Pfam Summary:  Pfam Search
Residues 28 to 173 (E-value = 1.4e-24) place HD0870 in the HATPase_c family which is described as Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (PF02518)
Residues 219 to 387 (E-value = 2.9e-54) place HD0870 in the DNA_gyraseB family which is described as DNA gyrase B (PF00204)
Residues 553 to 628 (E-value = 7.3e-28) place HD0870 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... 210 3e-055
pdb|1AJ6| Novobiocin-Resistant Mutant (R136h) Of The N-Termi... 164 4e-041
pdb|1BJT| Topoisomerase Ii Residues 409 - 1201 >gi|1633273|p... 81 4e-016

Gene Protein Sequence:
MSDKRYGADQITVLKDLEPVQLRPGMYTDTSRPNHLAQEVIDNSVDEALS
GFATQIDVILHSDNSLEVIDNGRGMPVDIHSTEQISGVELILTKLHAGGK
FSNKNYTFSGGLHGVGISVVNALSEQVKIKIKRDGNIYQIAFANGAKTEE
LHVVGSCAKKQTGTSVHFYPNPKYFDSPRFSVSRLRHLLRAKAVLCPKLT
INFTDHINHNQESWYYEDGLADYLSEALAETESLPNPPFIGNVTSETEAV
SWALTWLPEGGELLAESYVNLIPTAQGGTHVNGLRNGLLKAIVEFCEIHN
LLLKGIKLTADDVWNRCAYVLSLKMQEPQFAGQTKERLSSRQASSYVDNT
LKNAFSLWLNQNVQVGKSIAEMAIASAQSRLRAAKKVVRKKLVSGPALPG
KLADCTAQDLTRTELFLVEGDSAGGSAKQARDKEYQAILPLRGKILNTWE
VSSDQVLASQEVHDIAVAMGIDPDNDRLDELRYGKICILADADSDGLHIA
TLLCALFLRHFPNLVRQGHVYVAMPPLYRIDIGKDEVHYALDEVEKEAIL
ARLAHKKAKPNVQRFKGLGEMNPSQLRETTMDPSTRRLVQLVLDDSEEDQ
QDDALNTFAIMDMLLAKKRSEDRKQWLQKRGNEAALSV$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCTGATAAACGCTACGGAGCTGATCAAATTACTGTTCTAAAGGATTT
GGAACCAGTGCAACTTCGTCCTGGTATGTACACTGATACAAGCCGTCCAA
ATCACTTAGCTCAAGAAGTGATTGATAACAGTGTTGATGAAGCATTATCA
GGCTTTGCTACTCAAATTGATGTTATTCTACATTCAGACAACTCATTGGA
AGTGATTGATAATGGTAGAGGAATGCCAGTTGATATACATTCAACTGAAC
AAATCTCAGGCGTCGAATTAATTCTAACTAAATTGCACGCAGGCGGTAAG
TTTTCCAATAAAAATTATACTTTCTCAGGTGGCTTACACGGCGTAGGGAT
TTCCGTTGTCAATGCATTATCTGAACAAGTAAAAATTAAAATTAAACGTG
ATGGTAATATTTATCAAATTGCTTTTGCTAACGGTGCCAAAACGGAAGAA
TTACACGTAGTAGGAAGTTGTGCCAAAAAACAGACTGGCACTAGTGTTCA
TTTTTATCCTAATCCCAAATATTTTGACAGTCCGCGTTTTTCAGTGAGTC
GTTTACGCCATTTACTACGTGCCAAAGCGGTACTTTGTCCCAAATTAACG
ATTAATTTTACTGACCATATTAATCACAACCAAGAAAGCTGGTATTACGA
AGATGGTTTAGCCGATTATCTATCAGAAGCACTGGCAGAAACAGAATCTT
TACCTAACCCGCCTTTTATTGGCAACGTAACCAGTGAAACAGAAGCAGTG
AGTTGGGCATTAACATGGCTACCAGAAGGGGGCGAATTATTGGCAGAAAG
CTATGTCAATTTAATTCCGACAGCACAAGGCGGCACCCACGTTAATGGCT
TACGCAATGGCTTGTTAAAAGCCATAGTTGAATTTTGTGAAATACATAAT
TTGTTACTCAAAGGCATTAAATTAACGGCCGATGATGTGTGGAATCGTTG
CGCTTACGTACTTTCACTAAAAATGCAAGAACCCCAATTTGCTGGTCAAA
CAAAAGAACGGTTGTCTTCTCGCCAAGCTTCCAGTTATGTGGATAACACC
TTGAAAAATGCGTTTAGCTTATGGCTCAACCAAAATGTACAAGTAGGCAA
ATCTATCGCTGAAATGGCCATTGCCTCAGCACAAAGTCGCTTACGAGCAG
CCAAAAAAGTGGTACGTAAAAAATTAGTGAGTGGTCCTGCTTTGCCGGGT
AAATTGGCTGATTGTACTGCACAAGATTTAACACGTACCGAATTATTTTT
AGTCGAAGGTGATTCTGCGGGCGGTTCTGCTAAACAAGCACGCGATAAAG
AATATCAAGCGATTTTGCCATTACGTGGTAAAATTTTAAACACTTGGGAA
GTTTCTTCCGATCAAGTCCTAGCATCGCAAGAAGTGCATGATATTGCCGT
GGCAATGGGAATTGATCCAGATAATGATAGACTAGATGAATTACGTTACG
GCAAAATCTGTATTCTCGCCGATGCTGACTCAGATGGTTTACATATTGCA
ACCTTACTTTGTGCGCTATTTTTACGTCATTTCCCCAACTTAGTCCGGCA
AGGACACGTTTATGTGGCAATGCCCCCCTTATATCGCATTGATATCGGCA
AAGATGAAGTGCATTATGCTTTAGATGAAGTGGAAAAAGAGGCTATTTTA
GCACGTCTTGCTCACAAAAAAGCCAAACCAAATGTACAACGTTTTAAAGG
CTTAGGTGAAATGAATCCAAGCCAATTACGTGAAACCACTATGGATCCTA
GTACACGTCGCTTGGTGCAACTCGTGCTAGATGACAGTGAAGAGGATCAA
CAAGATGATGCTCTTAATACTTTCGCTATTATGGATATGTTATTAGCCAA
AAAACGCTCCGAAGATCGGAAACAATGGTTACAAAAACGCGGTAATGAAG
CCGCATTAAGTGTATAA


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