HHsearch alignment for GI: 254780875 and conserved domain: TIGR00563

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase B; InterPro: IPR004573 This family consists of bacterial sequences related to Escherichia coli rsmB, an rRNA SAM-dependent methyltransferase. All, are likely to be functionally equivalent and based on comparison of core motifs would appear to belong to a larger superfamily of S-adenosyl-methionine (AdoMet)-dependent RNA m5C methyltransferases . In E. coli, originally, the reading frame, encoding this protein, was interpreted as two reading frames, fmu and fmv. It has since been renamed, rsmB (Alternate Gene Symbols: rrmB, sun, fmu, fmv, yhdB). The recombinant protein, commonly referred to as Fmu, has been demonstrated to methylate only C967 of the 16S ribosomal RNA and to produce only m5C at that position. . The structure of the E. coli protein (Fmu) has been determined . Fmu contains three subdomains which share structural homology to DNA m5C methyltransferases and two RNA binding protein families. The N-terminal sequence of Fmu shares homology to another (noncatalytic) RNA binding protein, e.g. the ribosomal RNA antiterminator protein NusB (IPR011605 from INTERPRO). The catalytic lobe of Fmu, N1 domain, comprises the conserved core identified in all of the putative RNA m5C MTase sequences. Although the N1 domain is structurally homologous to known RNA binding proteins, there is no clear sequence motif that defines its role in RNA binding and recognition. At the functional centre of the catalytic lobe is the MTase domain of Fmu (residues 232-429), which adopts a fold typical of known AdoMet-dependent methyltransferases. In spite of the lack of a conserved RNA binding motif in the N1 domain, the close association of the N1 and MTase domains suggest that any RNA bound in the active site of the MTase domain is likely to interact with the N1 domain. ; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing.
Probab=96.79  E-value=0.003  Score=41.84  Aligned_cols=142  Identities=18%  Similarity=0.252  Sum_probs=92.6

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHCCCCCCCC
Q ss_conf             4620512235655531012332110124686056642142112331222233-321001333222002444201100012
Q gi|254780875|r   69 SDTFEPRPETELLVDSALAFSLPRIEKRDVVRILDLGTGTGAVCLALLKESP-FFKGVGVDISCKALEIAKSNAVTNGVS  147 (264)
Q Consensus        69 ~~vLIPRpeTE~lv~~~l~~~~~~~~~~~~~~vLDlG~GsG~i~i~la~~~~-~~~v~~~Dis~~al~~A~~N~~~~~~~  147 (264)
T Consensus       250 eGwvTvQD~Saq~va~~L-------~P~~~E~iLD~CAAPGGKttHI~EL~~~~g~v~a~D~~~~rl~~~~~~~~RLGl~  322 (487)
T TIGR00563       250 EGWVTVQDASAQWVATLL-------DPKNEETILDACAAPGGKTTHIAELMPDQGQVVALDLHKHRLKRVKENLDRLGLT  322 (487)
T ss_pred             CCCEEHHHHHHHHHHHHH-------CCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHCCE
T ss_conf             853213216899999973-------8898874773114845704767742479720898862125788999999861883


Q ss_pred             -CCCCCCCCC------CCCCCC---CHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC----CCCHHHHHHHH
Q ss_conf             -222222222------222221---0023332011333210012211111235754332101123----21025689999
Q gi|254780875|r  148 -ERFDTLQSD------WFSSVE---GLFDVIVSNPPYIESVIVDCLGLEVRDFDPRISLDGGIDG----LSHYRTIADGV  213 (264)
Q Consensus       148 -~~i~~~~~d------~~~~~~---~~fD~IvsNPPYI~~~~~~~l~~~v~~~EP~~AL~gg~dG----l~~~~~ii~~~  213 (264)
T Consensus       323 ~i~~~~~~~~~~~~~~W~~e~~ksaa~fDRiLlDaPCSg~Gvi--------rR~PD~kw~~~~~diA~L~~LQ~~iL~ai  394 (487)
T TIGR00563       323 IIKVEEVDGDKAGPKEWLAEVEKSAAQFDRILLDAPCSGTGVI--------RRHPDIKWLRKPADIARLAELQKEILKAI  394 (487)
T ss_pred             EEEEEEECCCCCCCCCCCCCCHHHHHHHCEEEECCCCCCCCCE--------EECCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             7887720256776654445201023331421560787744330--------01787555668565178999999999988


Q ss_pred             HHHCCCCCEEEE
Q ss_conf             985378878999
Q gi|254780875|r  214 SRHLNKDGLCSV  225 (264)
Q Consensus       214 ~~~L~~~G~l~l  225 (264)
T Consensus       395 aP~vK~GGtLvY  406 (487)
T TIGR00563       395 APLVKKGGTLVY  406 (487)
T ss_pred             HHHHCCCCEEEE
T ss_conf             565357975888