HHsearch alignment for GI: 254780353 and conserved domain: TIGR01061
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741 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 positive 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=98.98 E-value=2.2e-08 Score=82.53 Aligned_cols=176 Identities=19% Similarity=0.299 Sum_probs=134.6
Q ss_pred CCC-CCCEEEEECCCEEECCCCCCC-----------CCCCCC-CCCCCCCEEEEEECCCC----CEEEEECCCEEEEEEH
Q ss_conf 456-670599871010202565544-----------553223-45555540121111478----1789806882787551
Q gi|254780353|r 515 IEK-EPITVVISNRGWIRSLKSHSV-----------DLSALH-FKEGDSLKIALHAHTTD----RILLLSTDGKAYTLPA 577 (753)
Q Consensus 515 I~~-E~v~V~LS~~GyIKr~k~~~~-----------~~~~~~-~KegD~l~~~~~~~t~d----~LLffTs~GkvY~l~a 577 (753)
T Consensus 539 ~~nttd~lL~~Ts~g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fdv~~~~L~l~sklg~vKriel 618 (745)
T TIGR01061 539 IANTTDKLLIFTSKGNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFDVDEAILVLASKLGMVKRIEL 618 (745)
T ss_pred HHHCCCEEEEEECCCCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHCCCEEEEEC
T ss_conf 52122537887616666421303145665668998720001102106848999861322574689899875587478760
Q ss_pred HHCCCCC---CCCCCCCCCCCCCCCCEEEEEEEECC--CCEEEEEECCCCEEEEEHHHHH--CCCCCCEEEEEECCCCCE
Q ss_conf 1212123---44442222357676530789998579--9859999748978996388740--233356278853689805
Q gi|254780353|r 578 GNLLSGR---GHGEAIQLLIDLNHNQDIVTAFVYDS--TCKLLVVSSKGNAFIVEESEII--ANTRKGKTFLKVSSEEKM 650 (753)
Q Consensus 578 ~~Ips~~---~kG~pI~~ll~l~~~EkIv~~~~~~~--~~~lll~Tk~G~ikr~~l~~~~--~~~k~Gk~~ikLk~~D~l 650 (753)
T Consensus 619 ~~l~~~~~y~sK~~---~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~GvK~mkLK~~D~v 695 (745)
T TIGR01061 619 TELDIKRNYRSKAI---LILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAAGVKGMKLKEDDEV 695 (745)
T ss_pred CCCCCCCCCHHHHH---HHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCCCEEEEECCCCCEE
T ss_conf 32477865101223---321117895438999841888441899973683577302033231446673113305767638
Q ss_pred EEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCHH-HCCEEE-ECC
Q ss_conf 68896189-80999956993899557877833612-141334-218
Q gi|254780353|r 651 KLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSRG-KGVRLQ-SYK 693 (753)
Q Consensus 651 i~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gRg-kGVk~i-~Lk 693 (753)
T Consensus 696 ~~~~i~~~~~~~vll~~~Gs~k~~~~~El~~~sRa~~~~~llRp~k 741 (745)
T TIGR01061 696 KSGLILEANESLVLLTQRGSVKRLSISELKVTSRAATGVKLLRPLK 741 (745)
T ss_pred EEEEEECCCCCEEEEEECCCEEEEEHHHHHHHHHHCCCCHHHCCCC
T ss_conf 9999982799558997368256510365555343116511110000