HHsearch alignment for GI: 254780398 and conserved domain: COG0030
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis].
Probab=100.00 E-value=0 Score=548.63 Aligned_cols=254 Identities=42% Similarity=0.676 Sum_probs=235.8
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf 89843365841123989999999971989998799975898823467750235259984255430368878753220012
Q gi|254780398|r 18 KIIPKKYMGQNFLLDLNILKKIAESSGSLDGITVIEIGAGPGNLTQMLLTLGARKVIVIEKDQQFFPILKDISSQHPNRL 97 (284)
Q Consensus 18 ~~~p~k~lGQnFL~d~~i~~~iv~~~~~~~~~~VlEIGpG~G~LT~~Ll~~~~~~v~aiEiD~~~~~~l~~~~~~~~~~~ 97 (284)
T Consensus 1 ~~k~~K~~GQnFL~d~~v~~kIv~~a~~~~~d~VlEIGpG~GaLT~~Ll~~~-~~v~aiEiD~~l~~~L~~~~~~~-~n~ 78 (259)
T COG0030 1 MFRPNKRLGQNFLIDKNVIDKIVEAANISPGDNVLEIGPGLGALTEPLLERA-ARVTAIEIDRRLAEVLKERFAPY-DNL 78 (259)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHC-CEEEEEEECHHHHHHHHHHHCCC-CCE
T ss_conf 9988877664541478799999985578999869997898778899999606-95799996889999999750656-655
Q ss_pred CCCHHHHCCCCHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCCCHHHHEEEHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 20000000143155213322201120232246788999998520100000011020334478875301231233234543
Q gi|254780398|r 98 EIIQDDALKVDFEKFFNISSPIRIIANLPYNIGTRLLFNWISADTWPPFWESLTLLFQKEVGERITAQKNSPHYGRLSVL 177 (284)
Q Consensus 98 ~ii~~Dal~~d~~~~~~~~~~~~vvgNLPYnIss~Il~~ll~~~~~~~~~~~~vlmvQkEvA~Rl~a~pg~k~Yg~LSv~ 177 (284)
T Consensus 79 ~vi~~DaLk~d~~~l~---~~~~vVaNlPY~Isspii~kll~~~~~---~~~~v~M~QkEvaeRl~A~pgsk~Yg~LsV~ 152 (259)
T COG0030 79 TVINGDALKFDFPSLA---QPYKVVANLPYNISSPILFKLLEEKFI---IQDMVLMVQKEVAERLVAKPGSKDYGRLSVL 152 (259)
T ss_pred EEEECCHHCCCCHHHC---CCCEEEECCCCCCCHHHHHHHHHCCCC---CCEEEEEEHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf 9994724247513515---788899808976567999999846676---5428998299999997178898652066554
Q ss_pred HCCCCCEEEECCCCCCEECCCCCCCEEEEEECCCCC-CC-CCCHHHHHHHHHHHHCCCCHHHHHHHHHCCC-HHHHHHCC
Q ss_conf 201332012000110000105787578873012588-55-3476789999999972731389998763181-78999787
Q gi|254780398|r 178 TGWRTKATMMFDISPHVFFPSPKVTSTVIHFIPHLN-PI-PCCLESLKKITQEAFGKRRKTLRQSLKRLGG-ENLLHQAG 254 (284)
Q Consensus 178 ~q~~~~v~~~~~V~~~~F~P~PkVdS~vi~l~pk~~-~~-~~~~~~~~~~~~~~F~~RRK~l~~~L~~~~~-~~~l~~~~ 254 (284)
T Consensus 153 ~q~~~~v~~~~~Vpp~~F~P~PkVdSavv~L~~~~~~~~~~~d~~~~~~~~~~~F~~RRKtl~n~l~~~~~~~~~l~~~~ 232 (259)
T COG0030 153 VQYYADVEIVFDVPPSAFYPPPKVDSAVVRLVPKKEKPSPVKDEEKFFKFVKAAFSQRRKTLRNNLKNLFGLEEVLEAAG 232 (259)
T ss_pred HEEEEEEEEEEEECHHHCCCCCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 01058889998877565899997527999999678887764479999999999986006889998775411999998669
Q ss_pred CCCCCCHHCCCHHHHHHHHHHHHHC
Q ss_conf 7746571208999999999998636
Q gi|254780398|r 255 IETNLRAENLSIEDFCRITNILTDN 279 (284)
Q Consensus 255 i~~~~R~e~Ls~~~~~~L~~~l~~~ 279 (284)
T Consensus 233 i~~~~R~e~ls~~~f~~L~~~l~~~ 257 (259)
T COG0030 233 IDPNARAENLSPEDFLKLANALKGF 257 (259)
T ss_pred CCCCCCHHHCCHHHHHHHHHHHHHH
T ss_conf 9811395659999999999987640