HHsearch alignment of GI: 254780797 and MMDB domain: 1vyb_A_

>1vyb_A (A:) ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens}
Probab=99.52  E-value=2.5e-12  Score=83.87  Aligned_cols=147  Identities=18%  Similarity=0.210  Sum_probs=88.2

Q ss_pred             CCCEEEEEEEEHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEEEECCCC
Q ss_conf             66548998873100767775566676666879999999999975189899997279988999872623221677403578
Q gi|254780797|r    3 LAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTD   82 (231)
Q Consensus         3 ~~~~lrv~twNi~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~DVi~LQEv~~~~~~~~~~~~~~~~~~~~~~~~~   82 (231)
                      -+.+|||+||||+.+              +...+...|++.|.+.+||||||||+..............+.+.+.. ...
T Consensus         4 ~~~~lrV~T~Nv~g~--------------~~~~~~~~i~~~i~~~~pDIi~lQE~~~~~~~~~~~~~~~~~~~~~~-~~~   68 (238)
T 1vyb_A            4 SNSHITILTLNINGL--------------NSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQA-NGK   68 (238)
T ss_dssp             CCCCEEEEEEECSCC--------------CSHHHHHHHHHHHHHHCCSEEEEECCCCCTTSGGGCCCTTCCEEEEE-CCS
T ss_pred             CCCCCEEEEEECCCC--------------CCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHCCCCCCCCC-CCC
T ss_conf             989869999993886--------------22454789999998769909999846136555403332144430000-002


Q ss_pred             CCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             76503568861464101000012214675655445750499999849978999997511688887543002545788754
Q gi|254780797|r   83 KHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNL  162 (231)
Q Consensus        83 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~g~~~~v~n~HL~s~~~~~~~~~~~~~~~~~~~~  162 (231)
                      ......+++++.+...........          .........+...+..+.++++|+.....                 
T Consensus        69 ~~~~g~~i~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------  121 (238)
T 1vyb_A           69 QKKAGVAILVSDKTDFKPTKIKRD----------KEGHYIMVKGSIQQEELTILNIYAPNTGA-----------------  121 (238)
T ss_dssp             SSSCCEEEEECTTCCCEEEEEEEC----------TTSSEEEEEEEETTEEEEEEEEECCSSSH-----------------
T ss_pred             CCCCCCEEEEECCCCCCCCCCCCC----------CCCCEEEEEEEECCCCEEEEEECCCCCCC-----------------
T ss_conf             232342269841443324564211----------14521356886236866887522010220-----------------


Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCC
Q ss_conf             89999999997404887899991368884
Q gi|254780797|r  163 QATWLKQWVDQKNNLNMPFIIAGDFNRKI  191 (231)
Q Consensus       163 q~~~l~~~i~~~~~~~~~vii~GDFN~~~  191 (231)
                      +................+.+..||+|...
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (238)
T 1vyb_A          122 PRFIKQVLSDLQRDLDSHTLIMGDFNTPL  150 (238)
T ss_dssp             HHHHHHHHHHTTTTCCTTEEEEEECSSCS
T ss_pred             HHHHHHHHHHHHCCCHHHEEEHHHHCCCC
T ss_conf             78887777655202401114074533566