HHsearch alignment for GI: 254780313 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=91.30 E-value=0.35 Score=27.84 Aligned_cols=85 Identities=25% Similarity=0.324 Sum_probs=59.3
Q ss_pred HHHHHHHHCCCCCCCCEEEEEECCCCHHHHHHHHHHCCCCCCEEEEEECCCC-----------CCCCCCCEEEECCCCHH
Q ss_conf 9999986458313796788850455306899999706878832786411213-----------33469817830112207
Q gi|254780313|r 54 KLLQINEKHQILQSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILD-----------MEPILGVKFFKFDFLDL 122 (227)
Q Consensus 54 KL~eId~kf~l~k~g~~VlDLGaaPGgWsQva~~~~~~~~~~~~VigVDl~~-----------~~~i~gv~~~~gDi~~~ 122 (227)
T Consensus 281 ~l~~~a~~~l~Lqg~e~V~DayCG~GtftLpLA~qak------~v~G~E~v~e~v~~a~~NAe~Ng~~N~~F~~g~~E~~ 354 (434)
T TIGR00479 281 KLVDRALEALELQGEEKVVDAYCGVGTFTLPLAKQAK------SVVGVEVVPESVEDAKRNAELNGIANVEFLAGTLETV 354 (434)
T ss_pred HHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHCCC------EEEEEECCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 9999999997159865578631575520044440121------8888714376789998888860353201333123211
Q ss_pred HHHHHHHHHCCCCCCEEEECCCHHHCC
Q ss_conf 999999973138874897532021102
Q gi|254780313|r 123 DSWEFIRQAIGGNPDLVLSDMAYPTIG 149 (227)
Q Consensus 123 ~~~~~i~~~l~~~~DlVlSDmapn~SG 149 (227)
T Consensus 355 --~p~~~~-e~~~~D~~llD--PPR~G 376 (434)
T TIGR00479 355 --LPKQPW-EGISPDVVLLD--PPRKG 376 (434)
T ss_pred --CCCCCC-CCCCCCEEEEC--CCCCC
T ss_conf --014422-26778988888--88987