HHsearch alignment for GI: 254780875 and conserved domain: TIGR00479

>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA; InterPro: IPR001566 This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from Escherichia coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA .; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing.
Probab=99.10  E-value=3.2e-10  Score=87.72  Aligned_cols=169  Identities=23%  Similarity=0.303  Sum_probs=124.3

Q ss_pred             HCCCCHHHHCCC-----------EE-EEEEEEEEECCCCCHH--HHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             749837685363-----------14-4237677504620512--235655531012332110124686056642142112
Q gi|254780875|r   46 LKHESIHRILGW-----------RD-FYNVRLTLSSDTFEPR--PETELLVDSALAFSLPRIEKRDVVRILDLGTGTGAV  111 (264)
Q Consensus        46 ~~g~Pl~YIlg~-----------~~-F~~~~f~v~~~vLIPR--peTE~lv~~~l~~~~~~~~~~~~~~vLDlG~GsG~i  111 (264)
T Consensus       233 inp~ktnvIFG~~t~~i~G~~~~y~~~~d~~f~lsaR~F~QVN~~~~~~l~~~a~~~l----~Lqg~e~V~DayCG~Gtf  308 (434)
T TIGR00479       233 INPEKTNVIFGEETEVIAGEEPIYELSGDVKFELSARDFFQVNSEQTEKLVDRALEAL----ELQGEEKVVDAYCGVGTF  308 (434)
T ss_pred             CCCCCCCEECCCCEEEEECCEEHHHHHCCEEEEECCCCCEECCHHHHHHHHHHHHHHH----HCCCCCEEEEEECCCCCC
T ss_conf             3789874220771168877700322128846875576502018767799999999997----159865578631575520


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCC------CHHHHHHHCCHHHHHHCCCCCCC
Q ss_conf             331222233321001333222002444201100012222222222222221------00233320113332100122111
Q gi|254780875|r  112 CLALLKESPFFKGVGVDISCKALEIAKSNAVTNGVSERFDTLQSDWFSSVE------GLFDVIVSNPPYIESVIVDCLGL  185 (264)
Q Consensus       112 ~i~la~~~~~~~v~~~Dis~~al~~A~~N~~~~~~~~~i~~~~~d~~~~~~------~~fD~IvsNPPYI~~~~~~~l~~  185 (264)
T Consensus       309 tLpLA~qak--~v~G~E~v~e~v~~a~~NAe~Ng~~N-~~F~~g~~E~~~p~~~~e~~~~D~~llDPP------------  373 (434)
T TIGR00479       309 TLPLAKQAK--SVVGVEVVPESVEDAKRNAELNGIAN-VEFLAGTLETVLPKQPWEGISPDVVLLDPP------------  373 (434)
T ss_pred             HHHHHHCCC--EEEEEECCHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCCCCCCCCCEEEECCC------------
T ss_conf             044440121--88887143767899988888603532-013331232110144222677898888888------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf             11235754332101123210256899999853788789998176679999999997898058998
Q gi|254780875|r  186 EVRDFDPRISLDGGIDGLSHYRTIADGVSRHLNKDGLCSVEIGYNQKVDVVRIFESRKLFLVNAF  250 (264)
Q Consensus       186 ~v~~~EP~~AL~gg~dGl~~~~~ii~~~~~~L~~~G~l~lEig~~q~~~v~~ll~~~gf~~v~~~  250 (264)
T Consensus       374 --------R~------GCa--~~~L~~I~-~~kP~rivYVSCNP~TLARDl~~L~~~GfY~i~~~  421 (434)
T TIGR00479       374 --------RK------GCA--AEVLRTII-KLKPKRIVYVSCNPATLARDLEVLCKEGFYKIEKV  421 (434)
T ss_pred             --------CC------CCH--HHHHHHHH-HCCCEEEEEEECCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             --------98------745--89999886-20770599984485347999999973796267888