HHsearch alignment for GI: 254780229 and conserved domain: cd00221

>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=98.46  E-value=1.2e-06  Score=84.26  Aligned_cols=82  Identities=30%  Similarity=0.525  Sum_probs=72.6

Q ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCCCCCEECCEEEECCCCCCCEEEEEECCCHHHCCCC-------------------C
Q ss_conf             689989999999999789989706575771012573368988831799974580236832-------------------4
Q gi|254780229|r 1660 KQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIECDGAMYNSAK-------------------S 1720 (1775)
Q Consensus      1660 ~~ds~fe~~v~~~L~~~G~~v~~qvg~~~~riDl~v~~p~~pg~~~l~iecDG~~yh~~~-------------------~ 1720 (1775)
T Consensus        15 sk~TkpE~~vrk~L~~~G~Ryr~~~k~lpG~PDiv~~------~~k~aIFvdGCFWHgh~~~~~~~pk~n~~fW~~Ki~~   88 (115)
T cd00221          15 SKDTKPERAVRSALWELGYRFRKQDKDLPGKPDIVVP------GYRLAIFVDGCFWHGHPCHKRKPPPKNTEFWLEKIER   88 (115)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCCCCCCCCCEEEC------CCCEEEEECCEEECCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             7998699999999998899899668877999999735------7628999324043388875788898538999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEECHHH
Q ss_conf             867774448999956990999322164
Q gi|254780229|r 1721 ARDRDRLRQEVLERMGWRIRRIWSVDW 1747 (1775)
Q Consensus      1721 ardrD~~Rq~vLe~~GW~~~Riws~dw 1747 (1775)
T Consensus        89 N~~RD~~~~~~L~~~GW~v~~vWEcel  115 (115)
T cd00221          89 NVERDRRVQAALERLGWRVLRVWECEL  115 (115)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             999899999999988998999983059