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