HHsearch alignment for GI: 254780634 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=752.61 Aligned_cols=413 Identities=26% Similarity=0.370 Sum_probs=338.1
Q ss_pred HHHHHHH-HHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-------CHHH----H--HH
Q ss_conf 9999999-9956997899999999868588955799999999999975899999705689-------6799----9--99
Q gi|254780634|r 10 AIEILKD-IRTHKKPITNSLKDWGMSHRFAGSSDRASISNIVHDVLRKYLSSAYIMDSDD-------PESL----V--YA 75 (429)
Q Consensus 10 A~eiL~~-v~~~~~~ad~~L~~~~~~~r~lgs~DR~~i~~lvyg~lR~~~~ld~il~~~~-------~r~~----~--~~ 75 (429)
T Consensus 4 A~~~l~~V~~~~~sys~~~~~~~~~~~~-ls~~dr~Ll~ELvyGv~r~~~~Ld~li~~L~~kP~~~k~~~~~r~l~L~ly 82 (487)
T TIGR00563 4 AAEALIQVLEQGQSYSNLLPDLVLKQNE-LSDQDRRLLTELVYGVLRRLRALDYLIKKLIDKPLKGKPRVVHRLLRLVLY 82 (487)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 8999999973155145678998863057-883003231112223213504578999997417888874899999999999
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHCCCCC-HHHHHHHHHCCCCCC------------CCCHHHHCCCHHHHH-HHHHHCC-H
Q ss_conf 999743889899999885433034332-046775442034336------------791235089988999-9998574-4
Q gi|254780634|r 76 VIMKDWDIPWEKMLSMLKEDLFSPPLP-KESVIKSFHSRQLEN------------APLHIQGNIPQWLQS-SFQSYFK-D 140 (429)
Q Consensus 76 ~l~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~~~~~~~~~~~------------~~~~i~~s~P~WL~~-~~~~~~g-e 140 (429)
T Consensus 83 ~~~yl~~vP~~AAv~e~V~~Ak~~g~~~l~~lVNGvLR~~qR~~~~~~~~l~~~~~~~~~~y~hP~WL~~~l~~~~~~~~ 162 (487)
T TIGR00563 83 QQLYLERVPAHAAVNEAVELAKALGLKGLKGLVNGVLRRFQREQVQSKDELLAEVRKLAEEYSHPEWLVKKLKKAYPGKW 162 (487)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHH
T ss_conf 99997507824678899899997167522367888888886035765547888987411233586899999987244755
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHC-----------------CCCCCCCC--CCCCCCCCCCCCCCCCC
Q ss_conf 899999986289861112477889989999989871-----------------88754547--54311345665444610
Q gi|254780634|r 141 TWLKEAKSLSMRAPLDLRTNTLKVNRCKLFKNLCHY-----------------GVHHSSIS--RFGLRIPATKGKSRLPN 201 (429)
Q Consensus 141 ~~~~~l~a~~~~~pl~iRvN~~k~~~~~~~~~L~~~-----------------gi~~~~~~--~~~~~l~~~~~~~~~~~ 201 (429)
T Consensus 163 ~~E~i~~~~nq~P~~~LRvN~~k~~r~~~~~~L~e~nltttamaGlPqGlrlGG~~~~~~~~~pdAv~L~~p------~~ 236 (487)
T TIGR00563 163 EAESICEANNQKPPMWLRVNQLKASREELLDLLAEENLTTTAMAGLPQGLRLGGIEGEKGDLAPDAVKLEKP------IA 236 (487)
T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCHHHHHCCCC------CH
T ss_conf 789999986777784402130034589999999885435777632765404356145566661456640465------23
Q ss_pred HHCCHHH-----CCCEEEEECCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEHHHHCCHHHHHHHHHHH
Q ss_conf 1109631-----26548984155654211236666625860134688279999998616881005524989999999998
Q gi|254780634|r 202 VMNDITF-----QRGWFEIQDEGSQIVSNLTAITNSSQILDFCAGGGGKTLALSMLLNNKGQIHAWDNNKSRMAPIVARI 276 (429)
Q Consensus 202 ~~~~~~f-----~~G~~~VQD~aSql~~~~l~~~~g~~vLD~CAapGGKt~~la~~~~~~g~i~A~D~~~~Rl~~l~~~~ 276 (429)
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 HHCCCCCCEEE--ECCCCCCC----CCC----CCCEEEECCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 75028860882--15543445----723----246789627544504444422366724967899999987899999999
Q gi|254780634|r 277 KRAGIHNVQLH--SSWESLRN----LQE----HFTTVLVDAPCSGTGTWRRRPDIKWRLSQKNLIERTEEQKKILEESAQ 346 (429)
Q Consensus 277 ~r~g~~~v~~~--~~~~~~~~----~~~----~fd~vl~DaPCSg~G~~rr~Pe~~w~~~~~~~~~~~~lQ~~iL~~a~~ 346 (429)
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 HHCCCCEEEEEECCCCHHHCHHHHHHHHHHCCCCEE-----EE-C--CCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf 608983899977588824299989999985799799-----41-4--300222345555555567698499804479862
Q gi|254780634|r 347 FVRPEGYLVYITCSILPEENIQQINYFLSKNPHFSI-----DS-I--IDDWNQLYDLKNHPSLFIENGCCVLTPFLTNTD 418 (429)
Q Consensus 347 ~lk~gG~lvYsTCS~~~~Ene~vv~~fL~~~~~~~~-----~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~d 418 (429)
T Consensus 397 ~vK~GGtLvYsTCt~~p~EN~~qI~aFL~~~A~~e~cetGt~dW~sepPdlsfE~~~P~~~~~~~~~g~lq~LP~~~~~D 476 (487)
T TIGR00563 397 LVKKGGTLVYSTCTVLPEENEEQIEAFLNATADQEHCETGTEDWLSEPPDLSFEKRLPEKVTESVRSGGLQILPHAEEGD 476 (487)
T ss_pred HHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 53579758886145884432899999976535578751587433578887410023778889862236301068887877
Q ss_pred EEEEEEEEECC
Q ss_conf 15899996269
Q gi|254780634|r 419 GFFFCRLKRHT 429 (429)
Q Consensus 419 Gff~a~l~k~~ 429 (429)
T Consensus 477 GFFiA~L~Kka 487 (487)
T TIGR00563 477 GFFIAKLKKKA 487 (487)
T ss_pred CEEEEEEECCC
T ss_conf 41552110379