HHsearch alignment for GI: 254780303 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=91.63 E-value=0.29 Score=28.54 Aligned_cols=44 Identities=30% Similarity=0.434 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 889999999999986--------58968999999999749999999970999
Q gi|254780303|r 12 SLTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 12 ~ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
T Consensus 4 g~~p~q~~d~~~L~GD~sDnipGV~GIG~ktA~~ll~~~~~l~~i~~~~~~~ 55 (75)
T cd00080 4 GLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9799999999999196545887758637999999999909999999838777