>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

Probab=100.00 E-value=0 Score=580.55 Aligned_cols=240 Identities=50% Similarity=0.806 Sum_probs=233.6 Q ss_pred CEEEEEECCHHHHHHHHCCCCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHCCHHHHCCC Q ss_conf 72899966269998874267544689885500699999999999998485547987999972748871324086521667 Q gi|254780277|r 5 NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVIFDYPAVTFRNEIYPDYKANR 84 (976) Q Consensus 5 ~~~~liDg~~~~~ra~~a~p~~~~~~~G~~t~ai~gf~~~l~~~i~~~~~~~~~~~~~v~fD~~~~tfR~~~~~~YKa~R 84 (976) T Consensus 1 k~lllIDg~~l~~R~~~a~~~~~~~~~G~~t~ai~gf~~~l~~l~~~~~p----~~i~v~fD~~~~t~R~~l~p~YKanR 76 (240) T cd00008 1 KRLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKP----TYVAVVFDAGGKTFRHELYPEYKANR 76 (240) T ss_pred CEEEEECCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCC----CEEEEEECCCCCCCHHHHHHHHHHCC T ss_conf 95999926299999997187778899998712899999999999986599----88999972899862387728877378 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCEEEECCEEHHHHHHHHHHHHHHCCCCEEEECCCCHHHEECCCCEEEEECCCCCEEC Q ss_conf 98797588648999999997099799568901665899999999848994999868701212237975999667883538 Q gi|254780277|r 85 PKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKID 164 (976) Q Consensus 85 ~~~p~~l~~q~~~i~~~l~~~gi~~~~~~~~EADDviatla~~~~~~~~~v~i~s~DkD~~Qlv~~~v~~~~~~~~~~~~ 164 (976) T Consensus 77 ~~~p~~l~~q~~~~~~~l~~~gi~~~~~~~~EADD~ia~la~~~~~~~~~v~IvS~DkD~~QLv~~~v~~~~~~~~~~~~ 156 (240) T cd00008 77 KKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPMKKKLVT 156 (240) T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCC T ss_conf 99958999999999999997799789746843899999999999866970699628806888724330013555576578 Q ss_pred HHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 99998884898878777787518743589987763602499898413678999864542001122322003578999765 Q gi|254780277|r 165 IEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSR 244 (976) Q Consensus 165 ~~~v~~~~gv~p~~~~d~~al~GD~sDnipGv~GiG~KtA~~ll~~~gsle~i~~~~d~i~~~k~~~~l~~~~e~a~ls~ 244 (976) T Consensus 157 ~~~v~~~~gv~p~q~~d~~aL~GD~sDnIpGV~GiG~KtA~kLl~~~gsle~i~~~~~~~~~-k~~~~l~~~~~~a~ls~ 235 (240) T cd00008 157 EENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKG-KLREKLEEGKEMAFLSK 235 (240) T ss_pred HHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCH-HHHHHHHHCHHHHHHHH T ss_conf 89999960989999987699728764688999985789999999980999999982985278-99999996899999999 Q ss_pred HHHHC Q ss_conf 54320 Q gi|254780277|r 245 KLVML 249 (976) Q Consensus 245 ~L~tL 249 (976) T Consensus 236 ~L~tl 240 (240) T cd00008 236 RLATI 240 (240) T ss_pred HHHCC T ss_conf 85349

HHsearch alignment for GI: 254780277 and conserved domain: cd00008