HHsearch alignment for GI: 254780306 and conserved domain: TIGR01051

>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=95.77  E-value=0.0072  Score=40.58  Aligned_cols=103  Identities=18%  Similarity=0.215  Sum_probs=57.5

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHEECCCEEEEEEEECC---CEEEEEEEEEEEECCCHHHHHCCCCCCCC------------
Q ss_conf             99999999999999-852221100100136774079---63999998748805885676326777632------------
Q gi|254780306|r  373 QFQLYNLIWKRSVA-SQMASAKFERTTVNIIATYND---QIGHLRTTGSLLCFDGFLKVWENQYDQEK------------  436 (837)
Q Consensus       373 e~klY~LI~~R~la-sqm~~a~~~~~~v~i~~~~~~---~~~~F~asg~~i~~~G~~~vy~~~~~~~~------------  436 (837)
T Consensus       188 QSVAlRLi~~RErEi~~Fvp~~YW~~~~~~~~~~~~~~~~~~~f~A~--l~~~~g~kl~~~~~~D~~~g~l~~G~~v~~L  265 (688)
T TIGR01051       188 QSVALRLIVDREREIKRFVPEEYWTVDAKLEAKNNQKVACKETFEAL--LTEVNGKKLKAGSDFDPLTGELRPGKEVVVL  265 (688)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCHHHHCCCCE--EEEECCCCCCCCCCCCCCCCCCCCCCEEEEE
T ss_conf             65567677754789861688611798999645666311111046321--2412470113212478010126899716881


Q ss_pred             CCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHH
Q ss_conf             10010148864568821100110111234643101789987
Q gi|254780306|r  437 NSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLI  477 (837)
Q Consensus       437 ~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLi  477 (837)
T Consensus       266 ~E~~A~~~~~~L~~~~~~V~~~e~K~~~~~P~~PF~TSTLQ  306 (688)
T TIGR01051       266 NEAEATALKEQLKGEEYVVEEIEKKPKKSRPPPPFTTSTLQ  306 (688)
T ss_pred             CHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCHHH
T ss_conf             86999999985078647998863043301763483354189