HHsearch alignment for GI: 254780277 and conserved domain: TIGR03674
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=99.86 E-value=8.3e-20 Score=163.04 Aligned_cols=256 Identities=23% Similarity=0.289 Sum_probs=176.9
Q ss_pred CEEEEEECCHHHHHHHHCC-----CCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHH----
Q ss_conf 7289996626999887426-----7544689885500699999999999998485547987999972748871324----
Q gi|254780277|r 5 NHLFLVDGSSFIYRAFYAT-----PLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVIFDYPAVTFRNE---- 75 (976)
Q Consensus 5 ~~~~liDg~~~~~ra~~a~-----p~~~~~~~G~~t~ai~gf~~~l~~~i~~~~~~~~~~~~~v~fD~~~~tfR~~---- 75 (976)
T Consensus 21 Gk~vAIDas~~lyqfl~~ir~~~g~~l~-~~~G~~Tshl~g~f~R~~~Ll~~-g-----I~PIfVFDGkpp~~K~~t~~~ 93 (338)
T TIGR03674 21 GKVVAVDAFNALYQFLSSIRQPDGTPLM-DSRGRITSHLSGLFYRTINLLEN-G-----IKPVYVFDGKPPELKAETLEE 93 (338)
T ss_pred CCEEEEECHHHHHHHHHHHHCCCCCCCC-CCCCCEEHHHHHHHHHHHHHHHC-C-----CEEEEEECCCCCCCCHHHHHH
T ss_conf 9889997589999999997066898142-67897408999999999999977-9-----989999799985100188999
Q ss_pred -------CCHHHHCCCCCC-CHHH-----------HHHHHHHHHHHHHCCCCEEEECCEEHHHHHHHHHHHHHHCCCCEE
Q ss_conf -------086521667987-9758-----------864899999999709979956890166589999999984899499
Q gi|254780277|r 76 -------IYPDYKANRPKI-PEML-----------LPQLPLVRLATQAFGIPAIEIQGFEADDIIATYTYIAEKEGFAVT 136 (976)
Q Consensus 76 -------~~~~YKa~R~~~-p~~l-----------~~q~~~i~~~l~~~gi~~~~~~~~EADDviatla~~~~~~~~~v~ 136 (976)
T Consensus 94 R~~~r~~a~~~~~~~~~~g~~e~~~k~~~r~~~it~~~i~~~k~lL~~~Gi~~i~Ap~-EAeaqca~L~k~----g~vda 168 (338)
T TIGR03674 94 RREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQAAYMAKK----GDVDY 168 (338)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCEEECCH-HHHHHHHHHHHC----CCEEE
T ss_conf 9999999999999999778999999998774749899999999999976987685672-799999999974----97259
Q ss_pred EECCCCHHHEECCCCEEEEEC--------CCC-------CEECHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 986870121223797599966--------788-------35389999888489887877778751874358998776360
Q gi|254780277|r 137 IISTDKDLMQLVSPTTCLYDT--------VKE-------EKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGY 201 (976)
Q Consensus 137 i~s~DkD~~Qlv~~~v~~~~~--------~~~-------~~~~~~~v~~~~gv~p~~~~d~~al~GD~sDnipGv~GiG~ 201 (976)
T Consensus 169 v~SeD~D~l~fG~~~virnl~~~g~~k~~~~~~~~~~~~e~i~l~~~l~~l~lt~eqfidlcIL~G--cDY~~gI~GIG~ 246 (338)
T TIGR03674 169 VGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVG--TDYNEGVKGIGP 246 (338)
T ss_pred EECCCHHHHHCCCCEEEHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCCCCCCH
T ss_conf 961540033228765101112455513566454332457783099888773899999999999708--756789998568
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCHHHHHHHH-HHHH
Q ss_conf 249989841367899986454200112232200357899976554320356422476355212676768899865-3233
Q gi|254780277|r 202 KTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFL-KALE 280 (976)
Q Consensus 202 KtA~~ll~~~gsle~i~~~~d~i~~~k~~~~l~~~~e~a~ls~~L~tL~~Dvpl~~~~~~l~~~~~d~~~l~~~~-~~le 280 (976)
T Consensus 247 k~A~klIkk~~~ie~i~~~~~~~~~---------~~~~~---r~lF---~~p~v~-d~~~~~~~~pd~e~l~~fL~~e~~ 310 (338)
T TIGR03674 247 KTALKLIKEHGDLEKVLKARGEDIE---------NYDEI---REFF---LNPPVT-DDYELKWRKPDKEGIIEFLCDEHD 310 (338)
T ss_pred HHHHHHHHHHCCHHHHHHHCCCCCC---------CHHHH---HHHH---CCCCCC-CCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf 9999999985999999986568877---------89999---9984---899989-877776799998999999553559
Q ss_pred HH-----HHHHHHHH
Q ss_conf 68-----99987653
Q gi|254780277|r 281 FT-----KLINRVAT 290 (976)
Q Consensus 281 f~-----~ll~rL~~ 290 (976)
T Consensus 311 fse~RV~~~i~kl~k 325 (338)
T TIGR03674 311 FSEDRVERALERLEA 325 (338)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 799999999999997