HHsearch alignment for GI: 254780872 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=99.01  E-value=6.6e-09  Score=75.88  Aligned_cols=116  Identities=19%  Similarity=0.414  Sum_probs=93.9

Q ss_pred             HHHCHHHHHHHHHHHHHHCCCCCCCCCCHHHCCEEEECCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHCCCC-CC
Q ss_conf             75175659999999886518764445880016288856985699999973198169952135677888865310112-11
Q gi|254780872|r   37 HQINPVRIKYIQDKIMQHFQCKSDDTHPFKGLRILDLGCGGGLLSEPMAQMGATVTGIDPSTKNIAIAKNHANMKNI-NI  115 (254)
Q Consensus        37 h~~N~~R~~~I~~~i~~~~~~~~~~~~~l~g~~VLDiGCG~G~~s~~la~~g~~V~giD~S~~~i~~Ak~~a~~~~~-~i  115 (254)
T Consensus       272 ~QVN~~~~~~l~~~a~~~l~Lqg~-------e~V~DayCG~GtftLpLA~qak~v~G~E~v~e~v~~a~~NAe~Ng~~N~  344 (434)
T TIGR00479       272 FQVNSEQTEKLVDRALEALELQGE-------EKVVDAYCGVGTFTLPLAKQAKSVVGVEVVPESVEDAKRNAELNGIANV  344 (434)
T ss_pred             EECCHHHHHHHHHHHHHHHHCCCC-------CEEEEEECCCCCCHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCCCCH
T ss_conf             201876779999999999715986-------5578631575520044440121888871437678999888886035320


Q ss_pred             CCCCCCCCC-CCC---CCCCHHHHEECCCHHCCCCH------HHHHHHHHHHCCCCCEEEEEC
Q ss_conf             112210012-321---11530130012431026888------899888875213332157743
Q gi|254780872|r  116 DYRVSCAEE-IAE---TDEKFDIILNMEVIEHVDNI------PYFIKTCCSLLLSNGLMFIST  168 (254)
Q Consensus       116 ~~~~~~~~~-l~~---~~~~FD~V~~~~vleHv~d~------~~~l~~~~~~LkpgG~liist  168 (254)
T Consensus       345 ~F~~g~~E~~~p~~~~e~~~~D~~ll--------DPPR~GCa~~~L~~I~~-~kP~rivYVSC  398 (434)
T TIGR00479       345 EFLAGTLETVLPKQPWEGISPDVVLL--------DPPRKGCAAEVLRTIIK-LKPKRIVYVSC  398 (434)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCEEEE--------CCCCCCCHHHHHHHHHH-CCCEEEEEEEC
T ss_conf             13331232110144222677898888--------88898745899998862-07705999844