HHsearch alignment for GI: 254780545 and conserved domain: COG0542

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones].
Probab=99.24  E-value=6e-10  Score=90.96  Aligned_cols=126  Identities=29%  Similarity=0.457  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCEEECCCCCHHHHHHHHHHHCCCC---CCEECCCHHHHHHH
Q ss_conf             8898528899999999987433567664201233----3110037874258889999742469---97020585788644
Q gi|254780545|r  148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIP----HGVLLVGPPGTGKTLLARAVAGEAN---VPFFTISGSDFVEL  220 (647)
Q Consensus       148 ~dv~g~~~~k~~~~~~v~~l~~~~~~~~~g~~~p----~g~ll~GppGtGKTlla~a~a~e~~---~~f~~~~~s~~~~~  220 (647)
T Consensus       491 ~rViGQd~AV~~v~~aIr-------raRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~Ek  563 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIR-------RARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEK  563 (786)
T ss_pred             CCEECHHHHHHHHHHHHH-------HHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEEECHHHHHHH
T ss_conf             650173999999999999-------9856999999873578866788656999999999996599744455456877778


Q ss_pred             ------------HHHCCHHHHHHHHHHHHHHCCHHEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC-C-CCC--
Q ss_conf             ------------420332459999999987378012063235641445578988626889889989985303-2-357--
Q gi|254780545|r  221 ------------FVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDG-F-ESS--  284 (647)
Q Consensus       221 ------------~~g~g~~~vr~lf~~a~~~~p~iifiDeida~~~~r~~~~~~~~~e~~~~ln~ll~~mdg-~-~~~--  284 (647)
T Consensus       564 HsVSrLIGaPPGYVGyeeG--G~LTEaVRr~PySViLlDEIEK-----------AH---pdV~nilLQVlDdGrLTD~~G  627 (786)
T COG0542         564 HSVSRLIGAPPGYVGYEEG--GQLTEAVRRKPYSVILLDEIEK-----------AH---PDVFNLLLQVLDDGRLTDGQG  627 (786)
T ss_pred             HHHHHHHCCCCCCCEECCC--CCHHHHHHCCCCEEEEECHHHH-----------CC---HHHHHHHHHHHCCCCEECCCC
T ss_conf             7799872799987200655--4003766069986888412644-----------08---899999999846780554899


Q ss_pred             -----CCEEEEEECCCC
Q ss_conf             -----782999962981
Q gi|254780545|r  285 -----EGVILIAATNRP  296 (647)
Q Consensus       285 -----~~v~vi~aTn~~  296 (647)
T Consensus       628 r~VdFrNtiIImTSN~G  644 (786)
T COG0542         628 RTVDFRNTIIIMTSNAG  644 (786)
T ss_pred             CEEECCEEEEEEECCCC
T ss_conf             88843002899845026