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