HHsearch alignment for GI: 254780353 and conserved domain: TIGR01062
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742 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 A (parC) 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, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=97.70 E-value=0.0022 Score=44.95 Aligned_cols=189 Identities=8% Similarity=0.058 Sum_probs=130.8
Q ss_pred CCCCCCCCCEEEE---EECCCCCE-EEEECCCEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEE
Q ss_conf 2345555540121---11147817-8980688278755112121234444222235767653078999857998599997
Q gi|254780353|r 543 LHFKEGDSLKIAL---HAHTTDRI-LLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVS 618 (753)
Q Consensus 543 ~~~KegD~l~~~~---~~~t~d~L-LffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~T 618 (753)
T Consensus 484 ~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~D~~~---------l~YK~GD~~~~~~~~~~~~~v~~i~ 554 (747)
T TIGR01062 484 SSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDIDLST---------LKYKAGDSEKAIIEGKSNQKVVFID 554 (747)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCCCCCC---------CCCCCCCCEEEEEEECCCCEEEEEE
T ss_conf 5135678888887665303678817998277735504665667143---------5413686123345512775179997
Q ss_pred CCCCEEEEEHHHHHCCCCCCE-EEEE--ECCC-CCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCHHHCCEEEECC
Q ss_conf 489789963887402333562-7885--3689-80568896189-80999956993899557877833612141334218
Q gi|254780353|r 619 SKGNAFIVEESEIIANTRKGK-TFLK--VSSE-EKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYK 693 (753)
Q Consensus 619 k~G~ikr~~l~~~~~~~k~Gk-~~ik--Lk~~-D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lk 693 (753)
T Consensus 555 S~GR~y~l~~~~l~~a~g~G~Pl~~KL~l~~Gn~~i~~~l~~~~~Q~LL~AS~~G~GF~~~~~~liA~~k-~GK~l~~lP 633 (747)
T TIGR01062 555 STGRSYALDPLNLPSARGQGEPLTGKLLLPIGNATIENILMESENQKLLLASDAGYGFLVKFNDLIARNK-AGKALINLP 633 (747)
T ss_pred CCCCEEEECCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCEEEECHHHHHHCH-HCHHHCCCC
T ss_conf 2885266311204345677872268873268862310777635885321000168624740043333110-040200178
Q ss_pred CCCEEEEEEEECCCCC-EEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCC
Q ss_conf 7875689997338883-6999417756645114322544413666027552
Q gi|254780353|r 694 DGGISDVICFKICEGL-TWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKG 743 (753)
Q Consensus 694 d~~~~~~~~~~~~e~~-~il~~t~~g~~k~~~~~~~~~~~RggkG~~~~k~ 743 (753)
T Consensus 634 E~~~~-~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~K-G~G~~~~~~ 682 (747)
T TIGR01062 634 ENASV-LAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELSK-GKGNKLIRI 682 (747)
T ss_pred CCCEE-ECCEEECCCCCEEEEECCCCEEEEECHHHCCCCCC-CCCCEEEEE
T ss_conf 88611-04434237610244411367068742111776347-873057750