HHsearch alignment for GI: 254780634 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=1.6e-07 Score=70.88 Aligned_cols=108 Identities=19% Similarity=0.258 Sum_probs=85.0
Q ss_pred CCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEHHHHCCHHHHHHHHHHHHHCCCCCCEEEECCC--CCCCC---CC
Q ss_conf 11236666625860134688279999998616881005524989999999998750288608821554--34457---23
Q gi|254780634|r 224 SNLTAITNSSQILDFCAGGGGKTLALSMLLNNKGQIHAWDNNKSRMAPIVARIKRAGIHNVQLHSSWE--SLRNL---QE 298 (429)
Q Consensus 224 ~~~l~~~~g~~vLD~CAapGGKt~~la~~~~~~g~i~A~D~~~~Rl~~l~~~~~r~g~~~v~~~~~~~--~~~~~---~~ 298 (429)
T Consensus 287 ~~~l~Lqg~e~V~DayCG~GtftLpLA~qak---~v~G~E~v~e~v~~a~~NAe~Ng~~N~~F~~g~~E~~~p~~~~e~~ 363 (434)
T TIGR00479 287 LEALELQGEEKVVDAYCGVGTFTLPLAKQAK---SVVGVEVVPESVEDAKRNAELNGIANVEFLAGTLETVLPKQPWEGI 363 (434)
T ss_pred HHHHHCCCCCEEEEEECCCCCCHHHHHHCCC---EEEEEECCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf 9997159865578631575520044440121---8888714376789998888860353201333123211014422267
Q ss_pred CCCEEEECCCCCC-C-HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf 2467896275445-0-44444223667249678999999878999999996089838999775888
Q gi|254780634|r 299 HFTTVLVDAPCSG-T-GTWRRRPDIKWRLSQKNLIERTEEQKKILEESAQFVRPEGYLVYITCSIL 362 (429)
Q Consensus 299 ~fd~vl~DaPCSg-~-G~~rr~Pe~~w~~~~~~~~~~~~lQ~~iL~~a~~~lk~gG~lvYsTCS~~ 362 (429)
T Consensus 364 ~~D~~llDPPR~GCa~~~L---------------~~I~~------------~kP~-rivYVSCNP~ 401 (434)
T TIGR00479 364 SPDVVLLDPPRKGCAAEVL---------------RTIIK------------LKPK-RIVYVSCNPA 401 (434)
T ss_pred CCCEEEECCCCCCCHHHHH---------------HHHHH------------CCCE-EEEEEECCCH
T ss_conf 7898888888987458999---------------98862------------0770-5999844853