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