HHsearch alignment for GI: 254780405 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=99.62 E-value=4.5e-16 Score=116.20 Aligned_cols=123 Identities=25% Similarity=0.350 Sum_probs=104.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCCCC-CEEEECCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf 8867785899999998776333645589-678611001222100110168733011100012356676420013322100
Q gi|254780405|r 22 RSIRPSDSRTKKALFDILTHVYPVFLDS-TRMLNIFAGTGSVGFEALSRGCHYVLFVDNNSESIRLIRRNSELLGVEKNC 100 (189)
Q Consensus 22 ~~~RPt~~~vrealFniL~~~~~~~~~~-~~vlDlfaGsG~lgiEalSrGA~~v~~vE~~~~a~~~lk~N~~~~~~~~~~ 100 (189)
T Consensus 277 ~~~~~l~~~a~~~l----------~Lqg~e~V~DayCG~GtftL-pLA~qak~v~G~E~v~e~v~~a~~NAe~Ng~~-N~ 344 (434)
T TIGR00479 277 EQTEKLVDRALEAL----------ELQGEEKVVDAYCGVGTFTL-PLAKQAKSVVGVEVVPESVEDAKRNAELNGIA-NV 344 (434)
T ss_pred HHHHHHHHHHHHHH----------HCCCCCEEEEEECCCCCCHH-HHHHCCCEEEEEECCHHHHHHHHHHHHHCCCC-CH
T ss_conf 67799999999997----------15986557863157552004-44401218888714376789998888860353-20
Q ss_pred HHHHHHHHHHHHHCC--CCCCCCCCCCHHHHHCCHHHHHHHHHHCCCCCCCEEEEEECCCCC
Q ss_conf 223445665421003--444431015134310002888988874488889749999817788
Q gi|254780405|r 101 NIFFRDVLRLGKIGN--ISPFQLVYLDPPYGQGLAQQALAIIDKEGWLEPNALVIIEEYAGT 160 (189)
Q Consensus 101 ~ii~~D~~~~~~~~~--~~~fDiIf~DPPY~~~~~~~~l~~l~~~~~L~~~gliiiE~~~~~ 160 (189)
T Consensus 345 ~F~~g~~E~~~p~~~~e~~~~D~~llDPP-R~GCa~~~L~~I~~---~kP~rivYVSCNP~T 402 (434)
T TIGR00479 345 EFLAGTLETVLPKQPWEGISPDVVLLDPP-RKGCAAEVLRTIIK---LKPKRIVYVSCNPAT 402 (434)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCEEEECCC-CCCCHHHHHHHHHH---CCCEEEEEEECCCHH
T ss_conf 13331232110144222677898888888-98745899998862---077059998448534