HHsearch alignment for GI: 255764515 and conserved domain: TIGR01054
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 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. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . 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=99.34 E-value=2.7e-10 Score=80.60 Aligned_cols=123 Identities=19% Similarity=0.207 Sum_probs=92.9
Q ss_pred HHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCCEE----EEEEC
Q ss_conf 99999999967980999588998689999999999975999499991604656999999998558888159----99858
Q gi|255764515|r 7 QTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNI----SVITG 82 (458)
Q Consensus 7 Q~~~v~~~~~~~~~ll~~~~G~GKT~~al~~~~~l~~~~~~~~LIv~P~~l~~~~W~~Ei~kf~~~~~~~~----~~~~g 82 (458)
T Consensus 89 Qk~WAKRv~~~~SFai~APTGVGKttFG~~mslflA~kKGkR~y~ilPT~lLv~Qv~~kl~~~~~k~g~~~~~l~~~yhS 168 (1843)
T TIGR01054 89 QKSWAKRVLKGDSFAIVAPTGVGKTTFGLVMSLFLAKKKGKRSYIILPTTLLVKQVAEKLSSLAEKEGVGIVRLLGAYHS 168 (1843)
T ss_pred HHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEC
T ss_conf 79999996417964898058876779999999998654298789994707889999999875200257500002221011
Q ss_pred --CHHHH----HHHHCCCCCEEEECCCCHHHHHHHCCCCCCCCEEECCCCCCC
Q ss_conf --97898----887307798699806420233442000113220440453100
Q gi|255764515|r 83 --TVKQR----TKVLKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKL 129 (458)
Q Consensus 83 --~~~~r----~~~~~~~~~i~i~s~e~~~~~~~~~~~~~~~~~iIiDEaH~l 129 (458)
T Consensus 169 ~L~~~~kke~~Eri~~GDfdilitT~~FL~K~~~~L~~~y~F~liFVDDVDa~ 221 (1843)
T TIGR01054 169 KLSTKEKKEVKERIENGDFDILITTSMFLSKNFDKLKNQYKFDLIFVDDVDAL 221 (1843)
T ss_pred CCCHHHHHHHHHHHHCCCEEEEHHHHHHHHHHHHHCCCCCEEEEEEEECHHHH
T ss_conf 26545678899987318917861224688876651789851448997153676