HHsearch alignment for GI: 254780624 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=98.49  E-value=9e-08  Score=70.26  Aligned_cols=104  Identities=22%  Similarity=0.310  Sum_probs=82.5

Q ss_pred             HHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCC---
Q ss_conf             99998520644679977986023355777776641388632787213322221111000001122222222222333---
Q gi|254780624|r   57 KEAMVTNLNPRKSKDYRVLDVAGGTGDVAFRIAEASDNRSQIVVADINNEMLSVGRDRAFKENLQDCITFIEANAET---  133 (265)
Q Consensus        57 r~~~i~~l~~~~~~~~~iLDiGcGTG~~~~~l~~~~~~~~~v~giD~s~~Ml~~a~~r~~~~~~~~~i~~~~~da~~---  133 (265)
T Consensus       283 ~~~a~~~l~Lqg~e--~V~DayCG~GtftLpLA~qak---~v~G~E~v~e~v~~a~~NAe~Ng~-~N~~F~~g~~E~~~p  356 (434)
T TIGR00479       283 VDRALEALELQGEE--KVVDAYCGVGTFTLPLAKQAK---SVVGVEVVPESVEDAKRNAELNGI-ANVEFLAGTLETVLP  356 (434)
T ss_pred             HHHHHHHHHCCCCC--EEEEEECCCCCCHHHHHHCCC---EEEEEECCHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHCC
T ss_conf             99999997159865--578631575520044440121---888871437678999888886035-320133312321101


Q ss_pred             -CCCCCCCCCCCEEEEEECCCHHHH------HHHCCCCHHCCCCCEEEE
Q ss_conf             -457554467403664201321344------320121000485211776
Q gi|254780624|r  134 -LPFEANSFDACTLAFGIRNMPHIT------LVLQEIYRILKCGGRLLV  175 (265)
Q Consensus       134 -lp~~d~sfD~V~~sf~l~~~~d~~------~~l~e~~RvLKpGG~~~i  175 (265)
T Consensus       357 ~~~~e~~~~D~~ll--------DPPR~GCa~~~L~~I~~-~kP~rivYV  396 (434)
T TIGR00479       357 KQPWEGISPDVVLL--------DPPRKGCAAEVLRTIIK-LKPKRIVYV  396 (434)
T ss_pred             CCCCCCCCCCEEEE--------CCCCCCCHHHHHHHHHH-CCCEEEEEE
T ss_conf             44222677898888--------88898745899998862-077059998