HHsearch alignment for GI: 254780134 and conserved domain: cd00659
>cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.
Probab=95.19 E-value=0.037 Score=32.49 Aligned_cols=102 Identities=16% Similarity=0.230 Sum_probs=62.9
Q ss_pred HHHHHHHHCCCCCC-----------CCCCCCCCEE--EEECCCCC-CCCCHHHHHHCCH--HHHHHHHHHHC--CCCCCC
Q ss_conf 99898986188731-----------0025664014--43023321-1331024331121--68999996420--133221
Q gi|254780134|r 194 LAFEFLLYSGLRCS-----------DSCRAGVQHL--QNNIFSIK-TQKTGTIITVELP--DGFMKLLAMTP--IGKETF 255 (348)
Q Consensus 194 ~~~~l~~~TG~R~~-----------Ei~~L~~~di--d~~~i~~~-~~Kt~~~~~vpl~--~~l~~~l~~~~--~~~~~~ 255 (348)
T Consensus 45 ~~v~LlD~~~~RvGne~Ya~en~SyGltTLr~~Hv~~~~~~i~~~F~GK~gv~~~~~i~d~~~l~~~~~~~~~~~pg~~L 124 (218)
T cd00659 45 TAVYLIDKFALRVGNEKYERENDTVGLCTLRKEHVTLKPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFLDKLPGDDL 124 (218)
T ss_pred HHHHHHHHHCEECCCCCCCCCCCCEEEEEECHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHHHCCCCHHH
T ss_conf 99999998564168823331379762554013116576998999985688828999970659999999999736990664
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf 12224577587789999999999838899814026999999998
Q gi|254780134|r 256 FINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISAD 299 (348)
Q Consensus 256 ~~~~~g~~~~~~~~~~~~~~~~~~agi~~~~H~lRht~at~l~~ 299 (348)
T Consensus 125 F~y~~~~~v~s~~vN~yLk~~~---~-~~TaKdFRTw~at~~~~ 164 (218)
T cd00659 125 FQYLQVDRLNSSKLNAYLREFM---E-GLTAKVFRTYNASLTAL 164 (218)
T ss_pred EECCCCCCCCHHHHHHHHHHHC---C-CCCHHCEEEHHHHHHHH
T ss_conf 0346788669899999999975---9-99700233137899999