HHsearch alignment for GI: 254780399 and conserved domain: TIGR01055

>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=98.27  E-value=5.3e-06  Score=62.77  Aligned_cols=160  Identities=23%  Similarity=0.355  Sum_probs=116.1

Q ss_pred             CCCHHHHHHHHHHHHHH---CC-CCEEEEEEECCCEEEEEEEECCCCCCHHHHH----------HHHCCCCCCCCHHHHH
Q ss_conf             26978999999987772---69-9679999980984399999888998898999----------8750246656312441
Q gi|254780399|r   20 IERPSIAIKELIENSLD---AE-SSRVETVIAGGGKSFFQITDNGFGMTSEEIP----------MAVQRHCTSKISDDFS   85 (594)
Q Consensus        20 i~~~~svVkELveNSlD---Ag-At~I~v~i~~~g~~~i~V~DnG~Gi~~~dl~----------~~~~rh~TSKi~~dl~   85 (594)
T Consensus        31 ~~~~~HL~~EV~DN~~DEA~AGfA~~i~v~lH~D--~Si~v~D~GRG~PvD~HP~~P~~sa~EvILt~LHaG~KFSN~~Y  108 (647)
T TIGR01055        31 TTRPNHLVQEVIDNSVDEALAGFASKIEVILHQD--QSIEVIDNGRGMPVDIHPKEPGVSAVEVILTKLHAGGKFSNKNY  108 (647)
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCC--CEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCC
T ss_conf             6530134555443335555406530788998289--61799888830344278888888623556430057852114440


Q ss_pred             HCCCCCCCHHHHHHHHHHE-EEEEEEECCCCCCCEEEEECCC-CCCC---CCCC-CCCCCCEEEEEHHHHHHHHHHHCCC
Q ss_conf             1214884048999876202-4899980489863015511010-0000---2110-1256757885210121125431034
Q gi|254780399|r   86 NIHTFGFRGEALPSIGAVS-HLTLMSRPPQNNTGAQIAISGE-KISS---VRPV-AMNPGTIVEVRDLFFTIPARLNFLK  159 (594)
Q Consensus        86 ~i~t~GFRGEAL~sIa~vs-~l~i~s~~~~~~~~~~~~~~~g-~~~~---~~~~-~~~~GT~V~V~~LF~N~PvRrkflk  159 (594)
T Consensus       109 ~~-sGGLHGVGISVVNALS~~~~i~V~~~G~--~Y~~af~~G~K~~dL~~~~~~GkR~~GT~v~F----~Pd~---~~F~  178 (647)
T TIGR01055       109 EF-SGGLHGVGISVVNALSKRVKIKVKRQGK--LYSIAFENGAKVTDLEVVGTCGKRLTGTSVHF----TPDP---EIFD  178 (647)
T ss_pred             CC-CCCEECCHHHHEEECCCEEEEEEEECCE--EEEHHHHCCCCHHHHHHHHCCCCCCCCCEEEE----CCCC---CHHC
T ss_conf             13-6860021432022013236789974670--43202215751102332112677655635773----1682---0103


Q ss_pred             C-HHHHHHHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             5-3689999999999987318997499998798
Q gi|254780399|r  160 S-EQVETNLITDVIRRMAIAYPKVSFTFSTIKS  191 (594)
Q Consensus       160 s-~~~e~~~I~~~v~~~aL~~P~V~f~l~~~~~  191 (594)
T Consensus       179 ~k~~F~~~~l~~~~raKA~L~~Gv~I~f~~~v~  211 (647)
T TIGR01055       179 SKLKFSVSRLYHILRAKAVLCRGVEIEFEDEVN  211 (647)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             122557899999986324202672078975106