HHsearch alignment for GI: 254780222 and conserved domain: cd03366

>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleava
Probab=100.00  E-value=0  Score=386.37  Aligned_cols=114  Identities=60%  Similarity=0.918  Sum_probs=112.8

Q ss_pred             EEEEEECCCCCCCCHHHCCCCCCEEEEEECCEECCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             37997327676421001011222012211231314454108776322889999988256654333334655251899977
Q gi|254780222|r  464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQYREEDLRYEKVIIMTD  543 (686)
Q Consensus       464 ~eL~lvEGDSA~gsAk~grdr~~qgi~PLRGKiLNv~~as~~ki~~N~Ei~~l~~~lGl~~g~~~~~~~LRYgkIiImTD  543 (686)
T Consensus         1 seL~l~EGDSA~g~a~~~Rd~~~qgv~PLrGK~lNv~~~~~~ki~~N~Ei~~l~~~lGl~~~~~~d~~~LRYgkIiImtD   80 (114)
T cd03366           1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD   80 (114)
T ss_pred             CEEEEECCCCCHHHHHCCCCCCCEEEEECCCCCHHHHHCCHHHHHCCHHHHHHHHHHCCCCCCCCCHHHCCCCEEEEEEC
T ss_conf             92899727674055652178786899870785000642878788629679999999687878645400078786999968


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
Q ss_conf             9877146889999999987088863393899309
Q gi|254780222|r  544 ADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISP  577 (686)
Q Consensus       544 aD~DGsHI~~Lll~ff~~~~p~Li~~g~v~~~~t  577 (686)
T Consensus        81 aD~DG~HI~~Lli~ff~~~~p~Li~~G~vyia~P  114 (114)
T cd03366          81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP  114 (114)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             9988068999999999998499998694788369