HHsearch alignment for GI: 254781076 and conserved domain: cd07180
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears tha
Probab=100.00 E-value=0 Score=376.72 Aligned_cols=177 Identities=36% Similarity=0.585 Sum_probs=154.4
Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHH----HCHH
Q ss_conf 998427877752225599999870108----23311520289999987552110123-07885156799852----0479
Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDK----HNIH 97 (209)
Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~----~ni~ 97 (209)
T Consensus 1 ~GvDEaGRG~laGPvvvaav~~~~~~~~~l~~~gv~DSKkLs~kkR~~l~~~I~~~~~~~~i~~~s~~eID~~~~~~nln 80 (204)
T cd07180 1 CGIDEAGRGPVIGPMVVAGVAIDEESLKKLKSLGVKDSKKLTPKKREELYNEILKVADDVVIVIVSPEEIDERREAHNLN 80 (204)
T ss_pred CCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf 99987787662101168999984553335553677535008899999999999973537899997799997885899999
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCC---------C--CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99886543210025753211012653224---------6--621226871147865200236666547758999999988
Q gi|254781076|r 98 KATLDAIYHAVENLQVIPRSALIDGRSIP---------E--DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHK 166 (209)
Q Consensus 98 ~A~~~a~~~ai~~l~~~~~~ilIDg~~~~---------~--~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~ 166 (209)
T Consensus 81 ~~~~~a~~~~i~~l~~~~~~i~iD~~~~~~~~~~~~~~~~~~~~~~v~~~~KgD~k~~~IAAASIiAKv~RD~~M~~l~~ 160 (204)
T cd07180 81 ELEAEAFAELINRLSDKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAKYPVVSAASIIAKVERDREIEELKE 160 (204)
T ss_pred HHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999955778999998167876134433033235888726873375222177899999999999999999998
Q ss_pred HCCCCCCCCCCCCCC-HHHHHH----HHHCC-CCCCCCCCHHHHHHH
Q ss_conf 777988102899999-899999----99828-583010784888640
Q gi|254781076|r 167 KYPDYGFDSHVGYPT-AKHQQV----IKEKG-PSCIHRLTFRPLRNL 207 (209)
Q Consensus 167 ~~p~Ygf~~nkGYgT-~~H~~a----i~~~G-~~~~HR~Sf~~vk~l 207 (209)
T Consensus 161 ~yp~yG----~GYpsd~~t~~~l~~~i~~~g~~~~~hR~S~~~vk~~ 203 (204)
T cd07180 161 EYGDFG----SGYPSDPRTIKFLRNYYREHGELPPIVRKSWKTVKRL 203 (204)
T ss_pred HCCCCC----CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf 769989----8799977899999999873289996631881758975