HHsearch alignment of GI: 254780995 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=98.25  E-value=2.6e-06  Score=53.59  Aligned_cols=103  Identities=14%  Similarity=0.123  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCH---------HHHHCCCCCC---CHHHCCCCCCCCCCCCC--CC
Q ss_conf             9999999999851169988999614777688310027---------8763265541---00002576768710388--75
Q gi|254780995|r    5 QGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDD---------FWQKMDPDGL---LIRFPQEKESTCNVIKR--NK   70 (125)
Q Consensus         5 Q~~~L~~~i~~~~~~~~pvIi~GDFN~~~~~~~~~~~---------~~~~l~~~~~---~~~~~~~~~~~~~~~~~--~~   70 (125)
                      +...+............+.+..||+|...........         ..........   ...........+++...  ..
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (238)
T 1vyb_A          122 PRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTY  201 (238)
T ss_dssp             HHHHHHHHHHTTTTCCTTEEEEEECSSCSSGGGBTTCCCCCHHHHHHHHHHHHTTEEEHHHHHCTTCCCCSEEETTTTEE
T ss_pred             HHHHHHHHHHHHCCCHHHEEEHHHHCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             78887777655202401114074533566344314532211457899999987566665543114565444005889977


Q ss_pred             CCCCCCCCCCHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             5433355210121002573211543024741125867887564999996
Q gi|254780995|r   71 SSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIEYD  119 (125)
Q Consensus        71 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SDH~PV~~~l~  119 (125)
                      ..+||++++..+..       ++..+.+     ....+|||+||+++|+
T Consensus       202 ~rID~i~~s~~~~~-------~~~~~~v-----~~~~~SDH~pv~~~l~  238 (238)
T 1vyb_A          202 SKIDHIVGSKALLS-------KCKRTEI-----ITNYLSDHSAIKLELR  238 (238)
T ss_dssp             ECCEEEEEEGGGGG-------GEEEEEE-----ECCSSSSSCEEEEEEC
T ss_pred             CEEEEEEECHHHHH-------HCCEEEE-----CCCCCCCCCCEEEEEC
T ss_conf             61689998628973-------2618998-----9897998234899949