HHsearch alignment for GI: 254780872 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=97.64  E-value=0.0002  Score=48.04  Aligned_cols=106  Identities=23%  Similarity=0.229  Sum_probs=72.3

Q ss_pred             CCHHHCCEEEECCCHHHHHHHHH---HCCCCEEEECCHHHHHHHHHHHHHCCCCC-CCC--CCCCCCCCCC---CCC---
Q ss_conf             88001628885698569999997---31981699521356778888653101121-111--2210012321---115---
Q gi|254780872|r   63 HPFKGLRILDLGCGGGLLSEPMA---QMGATVTGIDPSTKNIAIAKNHANMKNIN-IDY--RVSCAEEIAE---TDE---  130 (254)
Q Consensus        63 ~~l~g~~VLDiGCG~G~~s~~la---~~g~~V~giD~S~~~i~~Ak~~a~~~~~~-i~~--~~~~~~~l~~---~~~---  130 (254)
T Consensus       268 ~P~~~E~iLD~CAAPGGKttHI~EL~~~~g~v~a~D~~~~rl~~~~~~~~RLGl~~i~~~~~~~~~~~~~~W~~e~~ksa  347 (487)
T TIGR00563       268 DPKNEETILDACAAPGGKTTHIAELMPDQGQVVALDLHKHRLKRVKENLDRLGLTIIKVEEVDGDKAGPKEWLAEVEKSA  347 (487)
T ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCHHHH
T ss_conf             88988747731148457047677424797208988621257889999998618837887720256776654445201023


Q ss_pred             -CHHHHE----E--CCCHHCCCCH----------------HHHHHHHHHHCCCCCEEEEEC
Q ss_conf             -301300----1--2431026888----------------899888875213332157743
Q gi|254780872|r  131 -KFDIIL----N--MEVIEHVDNI----------------PYFIKTCCSLLLSNGLMFIST  168 (254)
Q Consensus       131 -~FD~V~----~--~~vleHv~d~----------------~~~l~~~~~~LkpgG~liist  168 (254)
T Consensus       348 a~fDRiLlDaPCSg~GvirR~PD~kw~~~~~diA~L~~LQ~~iL~aiaP~vK~GGtLvYsT  408 (487)
T TIGR00563       348 AQFDRILLDAPCSGTGVIRRHPDIKWLRKPADIARLAELQKEILKAIAPLVKKGGTLVYST  408 (487)
T ss_pred             HHHCEEEECCCCCCCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             3314215607877443300178755566856517899999999998856535797588861