HHsearch alignment for GI: 254780814 and conserved domain: cd03481
>cd03481 TopoIIA_Trans_ScTopoIIA TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. 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. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to t
Probab=99.88 E-value=3.8e-22 Score=191.06 Aligned_cols=130 Identities=22% Similarity=0.287 Sum_probs=96.9
Q ss_pred CCEEEEEEEEEEEEEEEEEECCCCCCEEEEEECCCCCCCCCCEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHCC
Q ss_conf 52036420036999733453177541212222462166677210356888999999999862420001235761343057
Q gi|254780814|r 246 SPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREG 325 (803)
Q Consensus 246 ~~i~~~~~~~~~~veval~~~~~~~e~i~SfvN~I~T~~GGtHv~gf~~al~~~i~~y~~~~~~~Kk~k~~~~~~Direg 325 (803)
T Consensus 22 ~~~~~e~~~--~rWeV~v~~s~~~f~qv-SFVNgI~T~~GGtHVd~i~~~I~~~l~~~i~kk---~K~~~~ik~~~Ik~~ 95 (153)
T cd03481 22 PPVVYEPVN--DRWEVAVALSDGQFQQV-SFVNSIATTKGGTHVDYVADQIVKKLDEVVKKK---NKGGINVKPFQVKNH 95 (153)
T ss_pred CCEEEECCC--CCEEEEEEECCCCCEEE-EEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHH---CCCCCCCCHHHHHHH
T ss_conf 977980379--98899999879982798-886660069998666999999999999999985---678877799999844
Q ss_pred CEEEEEEECCCCCCCCCCHHHHCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2156665213763357210020261111032111026899998740035799987789998
Q gi|254780814|r 326 FTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDAS 386 (803)
Q Consensus 326 l~~visvki~nP~F~gQTK~kL~s~~v~~~v~~~v~~~l~~~l~~n~~~ak~i~~k~~~a~ 386 (803)
T Consensus 96 l~ifv~~~I~NP~FdSQTKe~Ltt~~~~FGsk~~ls~~fi~k~~k~-----~i~~~v~~~a 151 (153)
T cd03481 96 LWIFVNCLIENPSFDSQTKETLTTKPKSFGSKCELSEKFLKKAVKS-----GIVESVLSWA 151 (153)
T ss_pred CEEEEEEEECCCCCCCHHHHHHCCCHHHCCCCCCCCHHHHHHHHHC-----HHHHHHHHHH
T ss_conf 1799999826998662123242485565698766799999999834-----1999999886