HHsearch alignment for GI: 254781149 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 ( from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes ( 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=96.39  E-value=0.014  Score=38.20  Aligned_cols=88  Identities=17%  Similarity=0.193  Sum_probs=63.4

Q ss_conf             777765-530168368870687414889999999996302-2323-641167534899999999630223234785---5
Q Consensus       131 ~LD~~~-gG~~~g~LiviaaRP~mGKTa~alnia~~~a~~-g~~V-l~fSlEMs~~ql~~R~ls~~t~~~~s~I~~---~  204 (266)
T Consensus        87 s~Qk~WAKRv~~~~SFai~APTGVGKttFG~~mslflA~kKGkR~y~ilPT~lLv~Qv~~kl~~~~~---k~g~~~~~l~  163 (1843)
T ss_conf             5679999996417964898058876779999999998654298789994707889999999875200---2575000022

Q ss_pred             HCCCCCCCHHHHHHHHH
Q ss_conf             50178899899999999
Q gi|254781149|r  205 NLIRGEINQEQYRISQG  221 (266)
Q Consensus       205 ~l~~g~l~~~e~~~i~~  221 (266)
T Consensus       164 ~~yhS~L~~~~kke~~E  180 (1843)
T TIGR01054       164 GAYHSKLSTKEKKEVKE  180 (1843)
T ss_pred             EEEECCCCHHHHHHHHH
T ss_conf             21011265456788999