HHsearch alignment for GI: 254780814 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=391.90 Aligned_cols=114 Identities=79% Similarity=1.209 Sum_probs=112.0
Q ss_pred EEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCHHHCCHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf 17999825575432233465443023300562033443058766323667888876257877533212356737389985
Q gi|254780814|r 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMT 504 (803)
Q Consensus 425 ~eL~ivEGDSAggsak~gRdr~~qai~PLrGKilNv~~a~~~~i~~n~Ei~~l~~~lG~~~g~~~~~~~~lrY~kiiimt 504 (803)
T Consensus 1 seL~l~EGDSA~g~a~~~Rd~~~qgv~PLrGK~lNv~~~~~~ki~~N~Ei~~l~~~lGl~~~~~-~d~~~LRYgkIiImt 79 (114)
T cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGED-FDLEKLRYHKIIIMT 79 (114)
T ss_pred CEEEEECCCCCHHHHHCCCCCCCEEEEECCCCCHHHHHCCHHHHHCCHHHHHHHHHHCCCCCCC-CCHHHCCCCEEEEEE
T ss_conf 9289972767405565217878689987078500064287878862967999999968787864-540007878699996
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCEEEEECC
Q ss_conf 08888532899999999963077874895999438
Q gi|254780814|r 505 DADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKP 539 (803)
Q Consensus 505 DaD~DG~HI~~Llltff~~~~~~li~~g~~yia~p 539 (803)
T Consensus 80 DaD~DG~HI~~Lli~ff~~~~p~Li~~G~vyia~P 114 (114)
T cd03366 80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114 (114)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf 89988068999999999998499998694788369