HHsearch alignment for GI: 254780553 and conserved domain: cd00080

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=90.25  E-value=0.33  Score=28.72  Aligned_cols=42  Identities=21%  Similarity=0.368  Sum_probs=28.2

Q ss_pred             EEEECHHHHHHHHHHHH--------HHHCCCHHHHHHHCCCC-HHHHHHHHH
Q ss_conf             99706779999999850--------10005101124431578-999999985
Q gi|254780553|r   61 FGFLSDLDRQWFMLLQS--------VQGVGARVAMGVLSRIT-ATELVESII  103 (207)
Q Consensus        61 yGF~~~~Er~~F~~Li~--------V~GIGpK~AL~iLs~l~-~~~l~~aI~  103 (207)
T Consensus         3 ~g~-~p~q~~d~~~L~GD~sDnipGV~GIG~ktA~~ll~~~~~l~~i~~~~~   53 (75)
T cd00080           3 LGL-TPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLD   53 (75)
T ss_pred             CCC-CHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             897-999999999991965458877586379999999999099999998387