>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=96.61  E-value=0.024  Score=34.54  Aligned_cols=101  Identities=17%  Similarity=0.306  Sum_probs=74.5

Q ss_pred             HHHEEECCCCCC-CEEEEECCCCCHHHHHHHHCC---CEEEEECCCHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHH
Q ss_conf             442011147788-338860246423588885068---5699844758899999997886089964999768999989886
Q gi|254781000|r  199 LEWVLAATKGIQ-GDLLELYCGNGNFSLVLARHF---DRVLAVEIAKPSVEAARYNIAANHVNNVKIVRMSSKEFTQAMR  274 (371)
Q Consensus       199 ~~~v~~~~~~~~-~~vlDLycG~G~fsl~La~~~---~~V~gvE~~~~ai~~A~~Na~~N~i~n~~f~~~~a~~~~~~~~  274 (371)
T Consensus       260 aq~va~~L~P~~~E~iLD~CAAPGGKttHI~EL~~~~g~v~a~D~~~~rl~~~~~~~~RLGl~~i~~~~~~~~~~~----  335 (487)
T TIGR00563       260 AQWVATLLDPKNEETILDACAAPGGKTTHIAELMPDQGQVVALDLHKHRLKRVKENLDRLGLTIIKVEEVDGDKAG----  335 (487)
T ss_pred             HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHCCEEEEEEEECCCCCC----
T ss_conf             9999997388988747731148457047677424797208988621257889999998618837887720256776----


Q ss_pred             HCCCCCCCCCCHHCCCCCCEEEECCCCCCHHH
Q ss_conf             23322223210101478779998697026348
Q gi|254781000|r  275 REREFNRLKDIDIHSYRFKTIFVDPPRSGLDD  306 (371)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~d~vilDPPR~G~~~  306 (371)
T Consensus       336 ---~~~W~~e~~ksaa~fDRiLlDaPCSg~Gv  364 (487)
T TIGR00563       336 ---PKEWLAEVEKSAAQFDRILLDAPCSGTGV  364 (487)
T ss_pred             ---CCCCCCCCHHHHHHHCEEEECCCCCCCCC
T ss_conf             ---65444520102333142156078774433