>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. 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, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic 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. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal

Probab=100.00 E-value=0 Score=362.64 Aligned_cols=181 Identities=31% Similarity=0.390 Sum_probs=146.0 Q ss_pred EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC---EEEEECCCHHHHHHH----- Q ss_conf 998427877752225599999870108----23311520289999987552110123---078851567998520----- Q gi|254781076|r 27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA---IISISSASHQYIDKH----- 94 (209) Q Consensus 27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~---~~~i~~~~~~eID~~----- 94 (209) T Consensus 1 IGvDEaGRGplaGPvV~aav~~~~~~~~~l~~~gv~DSKkLs~kkRe~l~~~I~~~~~~~~~~i~~~~~~eId~~~l~~~ 80 (216) T cd07181 1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART 80 (216) T ss_pred CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHCCCCHHCCCCHHHHHHHHHHHHHHCCCEEEEEEEECHHHHHHHHHHHH T ss_conf 99778786662164057999970222303431487120119999999999999852735078999946999889898864 Q ss_pred --CHHHHHHHHHHH---HCCCCCCCCCCCCCCCCCCCC---------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf --479998865432---100257532110126532246---------621226871147865200236666547758999 Q gi|254781076|r 95 --NIHKATLDAIYH---AVENLQVIPRSALIDGRSIPE---------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRL 160 (209) Q Consensus 95 --ni~~A~~~a~~~---ai~~l~~~~~~ilIDg~~~~~---------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~ 160 (209) T Consensus 81 ~~~ln~l~~~~~~~~i~~~~~~~~~~~~i~iD~~g~~~~~~~~l~~~~~~~~~~~~~KgD~~~~~IaAASIlAKV~RD~~ 160 (216) T cd07181 81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA 160 (216) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCHH T ss_conf 75599999999999999999659998779981899867887653103899654772126545520237888999974599 Q ss_pred HHHHHHHCCCCCCCCC--CCCCC-HHHHHHHHH-----CCCCCCCCCCHHHHHHH Q ss_conf 9999887779881028--99999-899999998-----28583010784888640 Q gi|254781076|r 161 MRIAHKKYPDYGFDSH--VGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL 207 (209) Q Consensus 161 m~~l~~~~p~Ygf~~n--kGYgT-~~H~~ai~~-----~G~~~~HR~Sf~~vk~l 207 (209) T Consensus 161 m~~l~~~~~~~~~~~~~GsGYPsdp~t~~~L~~~~~~~~g~~~~hR~Sw~~v~~l 215 (216) T cd07181 161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFGFPSLVRFSWSTAKKL 215 (216) T ss_pred HHHHHHHCCCCCCCCCCCEECCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH T ss_conf 9987645645544688785789838899999955556689996640782999985

HHsearch alignment for GI: 254781076 and conserved domain: cd07181