HHsearch alignment for GI: 254780306 and conserved domain: TIGR01057
>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739 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 archaea, which is more closely related to bacterial 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. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=91.38 E-value=0.75 Score=25.44 Aligned_cols=56 Identities=18% Similarity=0.434 Sum_probs=40.2
Q ss_pred EEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHH
Q ss_conf 999998748805885676326777632100101488645688211001101112346431017899874
Q gi|254780306|r 410 GHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIK 478 (837)
Q Consensus 410 ~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik 478 (837)
T Consensus 234 ~~~~A~~-----~~~K-~~-------~~e~a~~i~~~~~~~~~~~V~~v~~~~~~~~PP~pFdLGtLQ~ 289 (637)
T TIGR01057 234 GVFKAES-----EKEK-IW-------KEEEAKSILEEVKKSKSAKVEEVRVKRSILKPPPPFDLGTLQR 289 (637)
T ss_pred CEEEEEC-----CCCC-CC-------HHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCHHHH
T ss_conf 5587522-----5787-41-------2465556888616798842332455311168325987552589