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