HHsearch alignment for GI: 254781215 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=97.57  E-value=0.0015  Score=41.08  Aligned_cols=145  Identities=19%  Similarity=0.190  Sum_probs=84.7

Q ss_pred             HHHHHHHHHH---HHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             6665288667---7642145577756555784589999999999987405655542101246502576597899999999
Q gi|254781215|r   23 EIKLSFSNFV---LHFFPWGEKGTPLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVL   99 (511)
Q Consensus        23 ~~~~~~~~~~---~~~~~w~~~~~~~~~~~~P~~WQ~e~l~~i~~~~~~~~~~~~~~~~r~aV~sgrG~GKS~l~a~l~l   99 (511)
T Consensus        68 ~~~k~f~~FF~~~~G~~pws~----------Qk~WAKRv~~~------------~----SFai~APTGVGKttFG~~msl  121 (1843)
T TIGR01054        68 EELKEFEEFFKKAVGSEPWSI----------QKSWAKRVLKG------------D----SFAIVAPTGVGKTTFGLVMSL  121 (1843)
T ss_pred             HHHHHHHHHHHHHHCCCCHHH----------HHHHHHHHHCC------------C----CEEEECCCCCCHHHHHHHHHH
T ss_conf             999999999999718884356----------79999996417------------9----648980588767799999999


Q ss_pred             HHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCHHCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             999808996699980858999999999999999855000134443--222222333444321112357861698530357
Q gi|254781215|r  100 WLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQ--SLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYS  177 (511)
Q Consensus       100 w~l~~~p~~kv~vtApt~~Q~~~ilw~Ei~k~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s  177 (511)
T Consensus       122 flA~k-KGkR~y~ilPT~lLv~Qv~-~kl~~~~~----k~g~~~~~l~~~yhS~L~~~~kke~~Eri~~GDfdi-litT~  194 (1843)
T TIGR01054       122 FLAKK-KGKRSYIILPTTLLVKQVA-EKLSSLAE----KEGVGIVRLLGAYHSKLSTKEKKEVKERIENGDFDI-LITTS  194 (1843)
T ss_pred             HHHHH-CCCEEEEEECHHHHHHHHH-HHHHHHCC----CCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCEEE-EHHHH
T ss_conf             98654-2987899947078899999-99875200----257500002221011265456788999873189178-61224


Q ss_pred             CCCCCHHHHCC-CCCCEEEEECCH
Q ss_conf             55610021202-676149997111
Q gi|254781215|r  178 EERPDTFVGHH-NTYGMAIINDEA  200 (511)
Q Consensus       178 ~~~~ea~~G~h-~~~~~lvI~DEA  200 (511)
T Consensus       195 ~FL~K~~~~L~~~y~F~liFVDDV  218 (1843)
T TIGR01054       195 MFLSKNFDKLKNQYKFDLIFVDDV  218 (1843)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEECH
T ss_conf             688876651789851448997153