HHsearch alignment for GI: 254780666 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=100.00  E-value=0  Score=791.97  Aligned_cols=422  Identities=33%  Similarity=0.457  Sum_probs=349.0

Q ss_pred             HHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf             999999999999559988-9999998511232168988999999999999960899999999984288100488999999
Q gi|254780666|r    8 RLVSSHLLSCVMRKRISL-TCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQLL   86 (445)
Q Consensus         8 R~~A~~iL~~v~~~~~~~-~~~l~~~~~~~~~~~L~~~Dr~~~~~Lv~gvlR~~~~ld~il~~~~~~~~~~~~~~~~~iL   86 (445)
T Consensus         1 R~~A~~~l~~V~~~~~sys~~~~~~~~~~---~~ls~~dr~Ll~ELvyGv~r~~~~Ld~li~~L~~kP~~~k~~~~~r~l   77 (487)
T TIGR00563         1 RDIAAEALIQVLEQGQSYSNLLPDLVLKQ---NELSDQDRRLLTELVYGVLRRLRALDYLIKKLIDKPLKGKPRVVHRLL   77 (487)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             95789999999731551456789988630---578830032311122232135045789999974178888748999999


Q ss_pred             HHHHHHHHHC-CCCCCCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCC-------CHHHHHHHCCCHHHHH-HHH
Q ss_conf             9999999986-899733256225877522587554444431022110011110-------0000123129978999-988
Q gi|254780666|r   87 RVSVAQILYL-DVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIEL-------LQRIAGISIIPEWFKE-RLE  157 (445)
Q Consensus        87 r~a~~ell~~-~~p~~a~vneaVelak~~~~~~~~~~~vNAVLR~~~r~~~~~-------~~~l~~~~s~P~Wl~~-~~~  157 (445)
T Consensus        78 ~L~ly~~~yl~~vP~~AAv~e~V~~Ak~~-g~~~l~~lVNGvLR~~qR~~~~~~~~l~~~~~~~~~~y~hP~WL~~~l~~  156 (487)
T TIGR00563        78 RLVLYQQLYLERVPAHAAVNEAVELAKAL-GLKGLKGLVNGVLRRFQREQVQSKDELLAEVRKLAEEYSHPEWLVKKLKK  156 (487)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             99999999975078246788998999971-67522367888888886035765547888987411233586899999987


Q ss_pred             HCCCHHHHHHHHHHHCCCCCEEEEE---CCCHHHHHHHHHHHHC-------CCCCCEECC----------------CCCC
Q ss_conf             4126799999999614698366761---5998999986432102-------356611104----------------5678
Q gi|254780666|r  158 NFYGKERVLAISDACISPLYIDLTV---KFDIETWAHKLNAVML-------PTGGIRLKE----------------LPES  211 (445)
Q Consensus       158 ~~~G~~~~~~l~~~~~~p~~l~i~~---k~~~~~~~~~L~~~~~-------~~~~~~~~~----------------~~~~  211 (445)
T Consensus       157 ~~~~~~~~E~i~~~~nq~P~~~LRvN~~k~~r~~~~~~L~e~nltttamaGlPqGlrlGG~~~~~~~~~pdAv~L~~p~~  236 (487)
T TIGR00563       157 AYPGKWEAESICEANNQKPPMWLRVNQLKASREELLDLLAEENLTTTAMAGLPQGLRLGGIEGEKGDLAPDAVKLEKPIA  236 (487)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCHHHHHCCCCCH
T ss_conf             24475578999998677778440213003458999999988543577763276540435614556666145664046523


Q ss_pred             HHHCHHH-----HHCCCEECCCCCCCCCCCCCCCCCCCEECCCCCCCCCEEEE---CCCCCCHHHHHCCHHHHHHHHHHH
Q ss_conf             5558501-----10010134632123222356321331003556447000010---256841000105967987765443
Q gi|254780666|r  212 IVSLPGF-----AEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQL---IVSGAKVTALDVSKRRLEKLRCNL  283 (445)
Q Consensus       212 i~~~~~f-----~eG~~~VQD~aSql~~~~l~~~~g~~VLD~CAAPGGKT~~l---~~~~~~i~A~D~~~~Rl~~l~~~~  283 (445)
T Consensus       237 ~~~lp~fnGevseeGwvTvQD~Saq~va~~L~P~~~E~iLD~CAAPGGKttHI~EL~~~~g~v~a~D~~~~rl~~~~~~~  316 (487)
T TIGR00563       237 VTKLPGFNGEVSEEGWVTVQDASAQWVATLLDPKNEETILDACAAPGGKTTHIAELMPDQGQVVALDLHKHRLKRVKENL  316 (487)
T ss_pred             HHHCCCCCCCCCCCCCEEHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf             44377978723168532132168999999738898874773114845704767742479720898862125788999999


Q ss_pred             HCCCCCCEEEEECCCC--CCC---CC-C----CCCEEEECCCCCCCCHHHCCCHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2048874177207744--577---43-4----476689616742110011011033328866778899999999999998
Q gi|254780666|r  284 DRLHLYAEDIIEMDAF--DYC---PK-K----LFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGIS  353 (445)
Q Consensus       284 ~R~g~~~~~~~~~D~~--~~~---~~-~----~fD~iLlDaPCSg~Gt~rr~Pd~~w~~~~~~l~~l~~~Q~~iL~~a~~  353 (445)
T Consensus       317 ~RLGl~~i~~~~~~~~~~~~~~W~~e~~ksaa~fDRiLlDaPCSg~GvirR~PD~kw~~~~~diA~L~~LQ~~iL~aiaP  396 (487)
T TIGR00563       317 DRLGLTIIKVEEVDGDKAGPKEWLAEVEKSAAQFDRILLDAPCSGTGVIRRHPDIKWLRKPADIARLAELQKEILKAIAP  396 (487)
T ss_pred             HHHCCEEEEEEEECCCCCCCCCCCCCCHHHHHHHCEEEECCCCCCCCCEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             86188378877202567766544452010233314215607877443300178755566856517899999999998856


Q ss_pred             HCCCCCEEEEEECCCCHHHCHHHHHHHH-----HHC-----CCCEEEC-CCCCCCCCCCCCCCCCCCCCEEEECCCCCCC
Q ss_conf             6089828999774788343999899999-----968-----8741781-3763233556643455868808988763235
Q gi|254780666|r  354 FVKPGGIVVFSNCSLDKQDSEEVVQKVL-----RSS-----PIPVELV-PLNSAYWKSIDMAMALSPEGWIRITPDMLEK  422 (445)
Q Consensus       354 ~lk~gG~lvYsTCSi~~eEne~vV~~fL-----~~~-----~~~~~~~-~~~~~~~~~~~~~~~~~~~g~~r~~P~~~~~  422 (445)
T Consensus       397 ~vK~GGtLvYsTCt~~p~EN~~qI~aFL~~~A~~e~cetGt~dW~sepPdlsfE~~~P~~~-~~~~~~g~lq~LP~~---  472 (487)
T TIGR00563       397 LVKKGGTLVYSTCTVLPEENEEQIEAFLNATADQEHCETGTEDWLSEPPDLSFEKRLPEKV-TESVRSGGLQILPHA---  472 (487)
T ss_pred             HHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCC-CCCCCCCCCCCCCCC---
T ss_conf             5357975888614588443289999997653557875158743357888741002377888-986223630106888---


Q ss_pred             CCCCCCCCCEEEEEEEEECC
Q ss_conf             57778886314667654127
Q gi|254780666|r  423 IDGVSSGMDGFFAVALRRLI  442 (445)
Q Consensus       423 ~~~~~~g~DGFF~A~l~k~~  442 (445)
T Consensus       473 -----~~~DGFFiA~L~Kka  487 (487)
T TIGR00563       473 -----EEGDGFFIAKLKKKA  487 (487)
T ss_pred             -----CCCCCEEEEEEECCC
T ss_conf             -----787741552110379