HHsearch alignment for GI: 254780875 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=99.10 E-value=3.2e-10 Score=87.72 Aligned_cols=169 Identities=23% Similarity=0.303 Sum_probs=124.3
Q ss_pred HCCCCHHHHCCC-----------EE-EEEEEEEEECCCCCHH--HHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf 749837685363-----------14-4237677504620512--235655531012332110124686056642142112
Q gi|254780875|r 46 LKHESIHRILGW-----------RD-FYNVRLTLSSDTFEPR--PETELLVDSALAFSLPRIEKRDVVRILDLGTGTGAV 111 (264)
Q Consensus 46 ~~g~Pl~YIlg~-----------~~-F~~~~f~v~~~vLIPR--peTE~lv~~~l~~~~~~~~~~~~~~vLDlG~GsG~i 111 (264)
T Consensus 233 inp~ktnvIFG~~t~~i~G~~~~y~~~~d~~f~lsaR~F~QVN~~~~~~l~~~a~~~l----~Lqg~e~V~DayCG~Gtf 308 (434)
T TIGR00479 233 INPEKTNVIFGEETEVIAGEEPIYELSGDVKFELSARDFFQVNSEQTEKLVDRALEAL----ELQGEEKVVDAYCGVGTF 308 (434)
T ss_pred CCCCCCCEECCCCEEEEECCEEHHHHHCCEEEEECCCCCEECCHHHHHHHHHHHHHHH----HCCCCCEEEEEECCCCCC
T ss_conf 3789874220771168877700322128846875576502018767799999999997----159865578631575520
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCC------CHHHHHHHCCHHHHHHCCCCCCC
Q ss_conf 331222233321001333222002444201100012222222222222221------00233320113332100122111
Q gi|254780875|r 112 CLALLKESPFFKGVGVDISCKALEIAKSNAVTNGVSERFDTLQSDWFSSVE------GLFDVIVSNPPYIESVIVDCLGL 185 (264)
Q Consensus 112 ~i~la~~~~~~~v~~~Dis~~al~~A~~N~~~~~~~~~i~~~~~d~~~~~~------~~fD~IvsNPPYI~~~~~~~l~~ 185 (264)
T Consensus 309 tLpLA~qak--~v~G~E~v~e~v~~a~~NAe~Ng~~N-~~F~~g~~E~~~p~~~~e~~~~D~~llDPP------------ 373 (434)
T TIGR00479 309 TLPLAKQAK--SVVGVEVVPESVEDAKRNAELNGIAN-VEFLAGTLETVLPKQPWEGISPDVVLLDPP------------ 373 (434)
T ss_pred HHHHHHCCC--EEEEEECCHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCCCCCCCCCEEEECCC------------
T ss_conf 044440121--88887143767899988888603532-013331232110144222677898888888------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCCCEEEEE
Q ss_conf 11235754332101123210256899999853788789998176679999999997898058998
Q gi|254780875|r 186 EVRDFDPRISLDGGIDGLSHYRTIADGVSRHLNKDGLCSVEIGYNQKVDVVRIFESRKLFLVNAF 250 (264)
Q Consensus 186 ~v~~~EP~~AL~gg~dGl~~~~~ii~~~~~~L~~~G~l~lEig~~q~~~v~~ll~~~gf~~v~~~ 250 (264)
T Consensus 374 --------R~------GCa--~~~L~~I~-~~kP~rivYVSCNP~TLARDl~~L~~~GfY~i~~~ 421 (434)
T TIGR00479 374 --------RK------GCA--AEVLRTII-KLKPKRIVYVSCNPATLARDLEVLCKEGFYKIEKV 421 (434)
T ss_pred --------CC------CCH--HHHHHHHH-HCCCEEEEEEECCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf --------98------745--89999886-20770599984485347999999973796267888