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