HHsearch alignment of GI: 254780134 and MMDB domain: 2khq_A_

>2khq_A (A:) Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp}
Probab=99.57  E-value=2.4e-14  Score=111.35  Aligned_cols=103  Identities=15%  Similarity=0.149  Sum_probs=95.4

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHHH
Q ss_conf             87899999999835543569788999999999999995699958969999999887515--9978999999999999964
Q gi|254780134|r   69 TTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRK--HTPSSAIQFLTSMRVLFKW  146 (348)
Q Consensus        69 ~Tl~~l~~~y~~~~~~~~l~~~T~~~~~~~~~~~~~~~g~~~l~~it~~~i~~~~~~~~--~~~~t~n~~~~~l~~~~~~  146 (348)
                      .||+++++.|+.+....+++++|...|+..++++.+.+|+.++.+|++.+|++|++.+.  .++.|++..++.|+++|+|
T Consensus         2 it~~~~~~~~~~~~~~~~~s~~T~~~y~~~~~~~~~~~~~~~i~~i~~~~i~~~~~~l~~~~s~~t~~~~~~~l~~~f~~   81 (110)
T 2khq_A            2 ITFADYFYQWYEVNKLPHVSESTKRHYESAYKHIKDHFRHKLLKDIKRTEYQKFLNEYGLTHSYETIRKLNSYIRNAFDD   81 (110)
T ss_dssp             CBHHHHHHHHHHHHTGGGSCHHHHHHHHHHHHHHHHHCSSCBGGGCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             EEHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHCCCHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             83899999999986427789999999999886017773810685436999999999863015889999999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             4552001056651034643244442
Q gi|254780134|r  147 AVRQEYVAINPCLSVERPKRKTEGI  171 (348)
Q Consensus       147 a~~~~~i~~NP~~~v~~~~~~~~~~  171 (348)
                      |++.|+++.||+.+++.++.+.+..
T Consensus        82 a~~~~~i~~nP~~~i~~~~~~~~~~  106 (110)
T 2khq_A           82 AIHEGYVIKNPTYKAELHASVLEHH  106 (110)
T ss_dssp             HHHTTCCCCCGGGGCCCCCGGGCCC
T ss_pred             HHHCCCCCCCCCCCCEECCCHHHHC
T ss_conf             9988791019877787464311211