HHsearch alignment for GI: 254780313 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=98.93 E-value=2.8e-09 Score=78.61 Aligned_cols=126 Identities=18% Similarity=0.228 Sum_probs=86.4
Q ss_pred CCCCEEEEEECCCCHHHHHHHHHHCCCCCCEEEEEECCCC-----CCC-CC--CCE---EEECCCCHHHHHH---HHHHH
Q ss_conf 3796788850455306899999706878832786411213-----334-69--817---8301122079999---99973
Q gi|254780313|r 66 QSNRRIVDLGSSPGSWSQVAARITGSNANNTRVVAIDILD-----MEP-IL--GVK---FFKFDFLDLDSWE---FIRQA 131 (227)
Q Consensus 66 k~g~~VlDLGaaPGgWsQva~~~~~~~~~~~~VigVDl~~-----~~~-i~--gv~---~~~gDi~~~~~~~---~i~~~ 131 (227)
T Consensus 270 ~~~E~iLD~CAAPGGKttHI~EL~~~~---g~v~a~D~~~~rl~~~~~~~~RLGl~~i~~~~~~~~~~~~~~W~~e~~-k 345 (487)
T TIGR00563 270 KNEETILDACAAPGGKTTHIAELMPDQ---GQVVALDLHKHRLKRVKENLDRLGLTIIKVEEVDGDKAGPKEWLAEVE-K 345 (487)
T ss_pred CCCCEEEEEECCCCCHHHHHHHHCCCC---CEEEEEECCHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCH-H
T ss_conf 988747731148457047677424797---208988621257889999998618837887720256776654445201-0
Q ss_pred CCCCCCEEEECCCHHHCCC-------------CCCHHHHHHHHHHHHHHHHHHCCCCCCEEE---EEEECCCCHHHHHHH
Q ss_conf 1388748975320211022-------------210157889899988987641148774699---993059998999999
Q gi|254780313|r 132 IGGNPDLVLSDMAYPTIGH-------------RKIDHLRTMSLCEAATFFALEMLNIGGDFL---VKTFQGGTTNDILCL 195 (227)
Q Consensus 132 l~~~~DlVlSDmapn~SG~-------------~~~D~~~~~~L~~~al~~A~~~Lk~gG~fV---~K~F~G~~~~~l~~~ 195 (227)
T Consensus 346 saa~fDRiLlDa-P-CSg~GvirR~PD~kw~~~~~diA~L~~LQ~~iL~aiaP~vK~GGtLvYsTCt~~p~EN~~qI~aF 423 (487)
T TIGR00563 346 SAAQFDRILLDA-P-CSGTGVIRRHPDIKWLRKPADIARLAELQKEILKAIAPLVKKGGTLVYSTCTVLPEENEEQIEAF 423 (487)
T ss_pred HHHHHCEEEECC-C-CCCCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHH
T ss_conf 233314215607-8-77443300178755566856517899999999998856535797588861458844328999999
Q ss_pred HH
Q ss_conf 98
Q gi|254780313|r 196 LK 197 (227)
Q Consensus 196 l~ 197 (227)
T Consensus 424 L~ 425 (487)
T TIGR00563 424 LN 425 (487)
T ss_pred HH
T ss_conf 76