HHsearch alignment for GI: 254780701 and conserved domain: TIGR01058
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit; InterPro: IPR005740 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 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, 0005694 chromosome.
Probab=92.02 E-value=0.29 Score=29.78 Aligned_cols=95 Identities=26% Similarity=0.440 Sum_probs=66.3
Q ss_pred CCCCHHC-CCCHHHHHHHHHHHHHHHHHCC--CCCCEEEEEEEEECCCEEEEEEEECCCCCCHHHH--------HHHC--
Q ss_conf 6761010-4798999988777655688606--7988799999997698599999878997898785--------4422--
Q gi|254780701|r 355 DPSLSSV-WADEKGMRQVILNLLSNAVKFT--AIGGRVHVTVGWTSGRGQYISIKDNGPGIAEGEI--------PTVL-- 421 (495)
Q Consensus 355 ~~~~~~v-~~D~~~L~qvl~NLi~NAiK~T--~~gG~V~v~~~~~~~~~~~i~V~DtG~GI~~e~~--------~~iF-- 421 (495)
T Consensus 28 RPGM-YIGSTds~GLHHl~wEIvdNsvDEvl~g~a~~I~V~l~--~dn--si~V~D~GRG~P~~~h~~~~isT~e~vlT~ 102 (655)
T TIGR01058 28 RPGM-YIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLH--KDN--SISVQDDGRGIPTGIHKQGKISTVETVLTV 102 (655)
T ss_pred CCCC-EECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEE--CCC--EEEEEECCCCCCCCHHCCCCCCCCCEEEEE
T ss_conf 8984-12256878505567878844688898226974799982--787--078875785376012216898851004544
Q ss_pred ----CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEE
Q ss_conf ----65231577767899988805899999999619859
Q gi|254780701|r 422 ----TSFGQGSIAIKSAEQGVGLGLPIAQSIMANHGGQF 456 (495)
Q Consensus 422 ----~~F~r~~~~~~~~~~GtGLGLaIvk~lve~hgG~i 456 (495)
T Consensus 103 LHAGGKFd~~--~YKtaGGLHGVGaSVVNALS~wL~v~v 139 (655)
T TIGR01058 103 LHAGGKFDQG--GYKTAGGLHGVGASVVNALSSWLEVEV 139 (655)
T ss_pred EECCCCCCCC--CEEECCCCCCCHHHHHHHCCCCEEEEE
T ss_conf 3077303786--501057322303677640226338999