RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780666|ref|YP_003065079.1| Fmu (Sun) domain protein [Candidatus Liberibacter asiaticus str. psy62] (445 letters) >gnl|CDD|182822 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional. Length = 427 Score = 243 bits (622), Expect = 8e-65 Identities = 137/402 (34%), Positives = 212/402 (52%), Gaps = 38/402 (9%) Query: 4 GMNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRI 63 MN R +++ + V+ + SL+ L + + +S +D+ L++ + LR LPR+ Sbjct: 1 SMNLRALAAAAILQVVDQGQSLSAALP-----ALQQKVSDKDRALLQELCYGVLRRLPRL 55 Query: 64 DAVLDFVLISSLPRKKYSLQQLLRVSVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKL 123 + ++ +L L K+ + LL V + Q+LY + +A VD VE AK K L Sbjct: 56 EWLIAQLLAKPLKGKQRIVHALLLVGLYQLLYTRIPAHAAVDETVEAAKALK-RPWAKGL 114 Query: 124 VNSILRRVSREKIELLQRIAGISII----PEWFKERLENFYGK--ERVLAISDACISPL- 176 VN++LRR RE+ ELL + + P W +RL+ Y + + +LA ++ P+ Sbjct: 115 VNAVLRRFQREQEELLAELQADPVARYNHPSWLIKRLKKAYPEQWQAILAANNQ-RPPMW 173 Query: 177 ------------YIDLTVKFDIETWAHKLNAVMLPTGGIRLKELPESIVSLPGFAEGVWW 224 Y+ L + IE + H + IRL E P + LPGFAEG Sbjct: 174 LRVNRRHHSRDAYLALLAEAGIEAFPHAVGP-----DAIRL-ETPVPVHQLPGFAEGWVS 227 Query: 225 VQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQL--IVSGAKVTALDVSKRRLEKLRCN 282 VQDA+A + L N VLD CAAPGGKTA + + A+V ALD+ +RLE++R N Sbjct: 228 VQDAAAQLAATLLAPQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVREN 287 Query: 283 LDRLHLYAEDIIEMDAFD---YCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVK 339 L RL L A +I DA D + + FD +L+DAPCS+TG IRRHPD+ W R +DI Sbjct: 288 LQRLGLKAT-VIVGDARDPAQWWDGQPFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAA 346 Query: 340 SACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVL 381 A Q ++L +KPGG ++++ CS+ +++E+ ++ L Sbjct: 347 LAALQSEILDALWPLLKPGGTLLYATCSILPEENEQQIKAFL 388 >gnl|CDD|184895 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional. Length = 444 Score = 225 bits (575), Expect = 3e-59 Identities = 135/429 (31%), Positives = 212/429 (49%), Gaps = 51/429 (11%) Query: 41 LSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQLLRVSVAQILYLD-VA 99 LS +D+ L+ +V T++ +D L + + LLR+S+ Q+LYLD V Sbjct: 36 LSDKDKALLTELVYGTIQRKLTLDYYLAPFIKKRKKLDPWVRN-LLRMSLYQLLYLDKVP 94 Query: 100 DYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIELLQRIAG----ISI---IPEWF 152 D+A V+ AVE AK+ + ++ AK VN +LR + RE + + I +SI P W Sbjct: 95 DHAAVNEAVEIAKK-RGHKGIAKFVNGVLRNILREGLPDIDEIKDPVKRLSIKYSHPVWL 153 Query: 153 KERLENFYGKERVLAISDACISPLYIDL---TVKFDIETWAHKLNAVMLPTGGIRLKE-- 207 +R + YG+E+ I ++ P + T+K +E KL G ++E Sbjct: 154 VKRWIDQYGEEKAEKILESLNEPPKASIRVNTLKISVEELIEKLEE-----EGYEVEESL 208 Query: 208 -LPE-------SIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT--- 256 PE +I F +G+ +QD S+ + +VLD CAAPGGKT Sbjct: 209 LSPEALVIEKGNIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHI 268 Query: 257 AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYC--PKKL---FDAVL 311 A+L+ + KV ALD+ + +L+ + N RL L IE A D +K FD +L Sbjct: 269 AELLKNTGKVVALDIHEHKLKLIEENAKRLGL---TNIETKALDARKVHEKFAEKFDKIL 325 Query: 312 VDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQ 371 VDAPCS G IRR PD+ + + +DI Q ++L ++K GGI+V+S C+++K+ Sbjct: 326 VDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKE 385 Query: 372 DSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMD 431 ++EEV++ L P ELVPL + + +G+++I P+ G D Sbjct: 386 ENEEVIEAFLEEHP-EFELVPLQHEKPDELVYEVK---DGYLQILPND--------YGTD 433 Query: 432 GFFAVALRR 440 GFF LR+ Sbjct: 434 GFFIAKLRK 442 >gnl|CDD|161931 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles. Length = 426 Score = 208 bits (531), Expect = 3e-54 Identities = 124/393 (31%), Positives = 195/393 (49%), Gaps = 33/393 (8%) Query: 21 KRISLTCLLDLEYGDSAFRLL-------SQRDQILVRAIVNVTLRFLPRIDAVLDFVLIS 73 + I+ L LE G S LL S +D+ L++ + LR L ++D ++ ++ Sbjct: 1 RSIAAQALEQLEQGQSLSNLLPPLQQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDR 60 Query: 74 SLPRKKYSLQQLLRVSVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSR 133 + K ++ L+ V + Q+LY + +A V VE AK K + LVN +LRR R Sbjct: 61 PMKGKPRTVHYLILVGLYQLLYTRIPAHAAVAETVEGAKAIK-RKGLKGLVNGVLRRFQR 119 Query: 134 EKIELLQ---RIAGISIIPEWFKERL-ENFYGKERVLAISDACISPLYIDLTV---KFDI 186 E+ ELL + + PEW +RL + + G+ + +I +A + L + K Sbjct: 120 EQEELLAEFNALDARYLHPEWLVKRLQKAYPGQWQ--SICEANNQRPPMWLRINRTKHSR 177 Query: 187 ETWAHKLNAV-------MLPTGGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGT 239 + W L L +RL E P ++ +LPGF EG VQDASA Sbjct: 178 DEWLALLAEAGMKGFPHDLAPDAVRL-ETPAAVHALPGFEEGWVTVQDASAQWVATWLAP 236 Query: 240 LNNLSVLDLCAAPGGKTAQL--IVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMD 297 N ++LD CAAPGGKT + + A+V ALD+ + RL+++ NL RL L + D Sbjct: 237 QNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYENLKRLGLTIK-AETKD 295 Query: 298 A-----FDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGI 352 + + FD +L+DAPCS+TG IRRHPD+ W R DI + A Q ++L Sbjct: 296 GDGRGPSQWAENEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIW 355 Query: 353 SFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSP 385 +K GG +V++ CS+ +++ E ++ L+ P Sbjct: 356 PLLKTGGTLVYATCSVLPEENSEQIKAFLQEHP 388 >gnl|CDD|184894 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional. Length = 434 Score = 193 bits (492), Expect = 9e-50 Identities = 118/387 (30%), Positives = 176/387 (45%), Gaps = 56/387 (14%) Query: 82 LQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSR--EKIEL 138 L+ LL + + Q+ Y+D + A V+ VE AK++ A +VN ILR+ R E + Sbjct: 74 LRWLLHLGLYQLRYMDRIPASAAVNTTVELAKQNGLGG-LAGVVNGILRQYLRAREAGDP 132 Query: 139 L-------QRIAGISIIPEWFKERLENFYGKERVLAISDACISPLYIDLTV---KFDIET 188 L +R+A + P+W + + G E + P +DL + + +E Sbjct: 133 LPLPEDPIERLAILHSFPDWLVKLWLEWLGLEEAEQLCKWFNQPPSLDLRINPLRTSLEE 192 Query: 189 WAHKLNAVMLPT-------GGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLN 241 L + G+RL P SI LPG+ EG W VQD SA + L Sbjct: 193 VQAALAEAGITATPIPGLPQGLRLTGNPGSIRQLPGYEEGWWTVQDRSAQLVAPLLDPQP 252 Query: 242 NLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDA 298 +LD CAAPGGKT A+L+ ++ A+D S RL+KL+ N RL L + I+ D+ Sbjct: 253 GEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADS 312 Query: 299 FDYCPKK-----LFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGIS 353 + K FD +L+DAPCS GT+ RHPD W + + I + A Q +LL Sbjct: 313 RNLLELKPQWRGYFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLAP 372 Query: 354 FVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWI 413 +KPGG +V++ C+L ++E +++ L P WK L P Sbjct: 373 LLKPGGTLVYATCTLHPAENEAQIEQFLARHP-----------DWK-------LEPPKQ- 413 Query: 414 RITPDMLEKIDGVSSGMDGFFAVALRR 440 +I P DGFF LR+ Sbjct: 414 KIWPH--------RQDGDGFFMAVLRK 432 >gnl|CDD|184897 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional. Length = 445 Score = 172 bits (438), Expect = 1e-43 Identities = 132/453 (29%), Positives = 217/453 (47%), Gaps = 52/453 (11%) Query: 23 ISLTCLLDLEYG----DSAF-RLLS-----QRDQILVRAIVNVTLRFLPRIDAVLDFVLI 72 ++L L +LE G D+ R+L + D+ L +VN LR+ ++D + I Sbjct: 7 LALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFI-----I 61 Query: 73 SSLPRKKYS-----LQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKENRHFAKLVNS 126 S L+ +LR+ V Q+L+LD V +A V+ V+ A++ K H AKLVN Sbjct: 62 SRFYHHDLEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARKYK-GEHMAKLVNG 120 Query: 127 ILRRVSREKI---------ELLQRIAGISIIPEWFKERLENFYGKERVLAI-SDACISPL 176 +LR +S E I +R++ + PEW ER YG+ER A+ S +PL Sbjct: 121 VLRNISPETISLDEWLKGMPEAERLSLLYSHPEWLLERWIARYGEERTEAMLSYNNQAPL 180 Query: 177 Y---IDLTVKFDIETWAHKLN--AVMLPTGGIRLKELPESIVSL-PGFAEGVWWVQDASA 230 + I+ +K E + +V G+ L + P G+ VQ+ + Sbjct: 181 FGFRIN-RLKTTPEKFLAAPADASVTFEKSGLPNFFLSKDFSLFEPFLKLGLVSVQNPTQ 239 Query: 231 SIPVQLFGTLNNLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNLDRLH 287 ++ L +VLDLCAAPGGK+ A+L+ + ++TA+D ++LEK+R + L Sbjct: 240 ALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALG 299 Query: 288 LYAEDIIEMDAFDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKL 347 + + IE DA + P++ DA+L+DAPC+ TG + R ++ W + + + Q +L Sbjct: 300 ITIIETIEGDARSFSPEEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAEL 359 Query: 348 LLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMAL 407 L S +KPGG++V++ CS++ +++E ++ L+ P E S Sbjct: 360 LDHAASLLKPGGVLVYATCSIEPEENELQIEAFLQRHP---EFSAEPSPGSLPEPFHEVA 416 Query: 408 SPEGWIRITPDMLEKIDGVSSGMDGFFAVALRR 440 P+G I P G G DG FA LR+ Sbjct: 417 HPKGAILTLP-------GEHEGFDGGFAQRLRK 442 >gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional. Length = 431 Score = 147 bits (372), Expect = 7e-36 Identities = 113/404 (27%), Positives = 195/404 (48%), Gaps = 37/404 (9%) Query: 1 MKSGMNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFL 60 MK+ N RL++ LL RK + + DS L +D+ + +V +R Sbjct: 1 MKT--NVRLLAYRLL----RKYEKEKFIFREDV-DSVLSFLDDKDRRFFKELVWGVVR-- 51 Query: 61 PRIDAVLDFVLISSLPRKK---YSLQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKE 116 + +LD+ I+ L +KK +++ LR+ Q+L+++ V DYA V V+ + Sbjct: 52 --KEELLDWY-INQLLKKKDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLV----K 104 Query: 117 NRHFAKLVNSILRRVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACISPL 176 N +F KLVN++LRR+ + + + P+W +F +E VL I + PL Sbjct: 105 NENFKKLVNAVLRRLR--TVPEPKELHLKYSHPKWLVNYWRSFLPEEAVLRIMEWNQEPL 162 Query: 177 YIDLTV--------KFDIETWAHKLNAVMLPTG--GIRLKELPESIVSLPGFAEGVWWVQ 226 L V + AV + +++L ++ +G+ VQ Sbjct: 163 PTMLRVNSLAITREEVIKILAEEGTEAVPGKHSPFSLIVRKLGVNMNDSRVIKDGLATVQ 222 Query: 227 DASASIPVQLFGTLNNLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNL 283 S+ I L L VLD CAAPGGKT A+L+ K+ A+D+S+ +++ + + Sbjct: 223 GESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHA 282 Query: 284 DRLHLYAEDIIEMDA--FDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSA 341 RL L + +I DA + FD +LVDAPC+S GT R HP+VL + +D K + Sbjct: 283 KRLKLSSIEIKIADAERLTEYVQDTFDRILVDAPCTSLGTARNHPEVLRRVNKEDFKKLS 342 Query: 342 CFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSP 385 Q +++ Q ++ GGI+++S C++ K+++ EVV++ + Sbjct: 343 EIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYEQK 386 >gnl|CDD|129538 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase. Length = 264 Score = 136 bits (343), Expect = 2e-32 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 18/246 (7%) Query: 201 GGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT---A 257 G + E P I S P + G++++Q+AS+ IP VLD+ AAPGGKT + Sbjct: 31 GFFEVNESPLPIGSTPEYLSGLYYIQEASSMIPPLALEPDPPERVLDMAAAPGGKTTQIS 90 Query: 258 QLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAF---DYCPKKLFDAVLVDA 314 L+ + + A + SK R + L N++R + + D PK FDA+L+DA Sbjct: 91 ALMKNEGAIVANEFSKSRTKVLIANINRCGVLNVAVTNFDGRVFGAAVPK--FDAILLDA 148 Query: 315 PCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSE 374 PCS G IR+ P +DI + + Q++L+ +KPGG++V+S CSL+ +++E Sbjct: 149 PCSGEGVIRKDPSRKKNWSEEDIQEISALQKELIDSAFDALKPGGVLVYSTCSLEPEENE 208 Query: 375 EVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFF 434 VV +L P VE +P ++ + +G +R+ P +GFF Sbjct: 209 AVVDYLLEKRPDVVEELPKGDEFFGANKGKE--EVKGALRVFPQ--------IYDCEGFF 258 Query: 435 AVALRR 440 LR+ Sbjct: 259 VAKLRK 264 >gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed. Length = 470 Score = 99.2 bits (248), Expect = 2e-21 Identities = 74/230 (32%), Positives = 120/230 (52%), Gaps = 22/230 (9%) Query: 221 GVWWVQDASASIPVQ-LFGTLN-NLSVLDLCAAPGGKTAQLIV----SGAKVTALDVSKR 274 G++++Q+AS+ +PV LF N VLD+ AAPG KT Q+ GA V A + S Sbjct: 91 GLFYIQEASSMLPVAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIV-ANEYSAS 149 Query: 275 RLEKLRCNLDRLHLYAEDIIEMDA--F-DYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWT 331 R++ L N+ R + + D F P+ FDA+L+DAPCS GT+R+ PD L Sbjct: 150 RVKVLHANISRCGVSNVALTHFDGRVFGAALPET-FDAILLDAPCSGEGTVRKDPDALKN 208 Query: 332 RDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELV 391 + ++ A QR+L+ +KPGG +V+S C+L++++++ V + + P VE Sbjct: 209 WSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNREENQAVCLWLKETYPDAVEFE 268 Query: 392 PLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFFAVALRRL 441 PL + AL+ EG++ + P + + +GFF LR+ Sbjct: 269 PLGDLF---PGAEKALTEEGFLHVFPQIYDS--------EGFFVARLRKT 307 >gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB; Provisional. Length = 207 Score = 48.7 bits (117), Expect = 3e-06 Identities = 34/107 (31%), Positives = 53/107 (49%), Gaps = 16/107 (14%) Query: 39 RLLSQRDQILVRA----IVNVTLRFLPRIDAVLDFVL----ISSLPRKKYSLQQLLRVSV 90 LL DQ VR + +R ID +LD V+ + LPR + +LR++V Sbjct: 102 ELLQLADQEEVREYALERIGAVIRNRKEIDQLLDTVMVGWQLKRLPRID---RDILRLAV 158 Query: 91 AQILYLDVADYAVVDLAVEQAKR--DKENRHFAKLVNSILRRVSREK 135 +IL+L+ ++ AVE AKR D++ R F +N +LRR+ Sbjct: 159 VEILFLNTPAAVAINEAVELAKRYSDEQGRRF---INGVLRRLQDAL 202 >gnl|CDD|162621 TIGR01951, nusB, transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10. Length = 129 Score = 38.6 bits (91), Expect = 0.003 Identities = 29/109 (26%), Positives = 49/109 (44%), Gaps = 21/109 (19%) Query: 37 AFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQL-------LRVS 89 R L + D+ +V L ID ++ L K +SL++L LR++ Sbjct: 31 EERELDEEDREYFLELVRGVLENQEEIDELISPHL------KDWSLERLDPVDRAILRLA 84 Query: 90 VAQILYLDVADYAVV-DLAVEQAKR---DKENRHFAKLVNSILRRVSRE 134 ++LY Y VV + AVE AK+ + K VN +L ++++E Sbjct: 85 AYELLYRPDVPYKVVINEAVELAKKFGDEDS----HKFVNGVLDKIAKE 129 >gnl|CDD|163311 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3. Length = 251 Score = 35.5 bits (83), Expect = 0.031 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 2/72 (2%) Query: 241 NNLSVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDA 298 L VLDL G A+VTA+D+S L R N RL L ++ D Sbjct: 87 GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARKNAARLGLDNVTFLQSDW 146 Query: 299 FDYCPKKLFDAV 310 F+ P FD + Sbjct: 147 FEPLPGGKFDLI 158 >gnl|CDD|178926 PRK00202, nusB, transcription antitermination protein NusB; Reviewed. Length = 137 Score = 33.6 bits (78), Expect = 0.11 Identities = 24/106 (22%), Positives = 50/106 (47%), Gaps = 21/106 (19%) Query: 41 LSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQL-------LRVSVAQI 93 + D R++V + +D ++ L K ++L++L LR+++ ++ Sbjct: 37 YDKADPAYFRSLVRGVVENQAELDELISPYL------KDWTLERLDPVERAILRLALYEL 90 Query: 94 LYLDVADYAVV-DLAVEQAKR---DKENRHFAKLVNSILRRVSREK 135 L+ D Y VV + A+E AK+ + K VN +L ++++E Sbjct: 91 LFRDDVPYKVVINEAIELAKKFGDEDS----HKFVNGVLDKIAKEL 132 >gnl|CDD|162639 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase. Length = 224 Score = 33.0 bits (76), Expect = 0.17 Identities = 33/143 (23%), Positives = 51/143 (35%), Gaps = 28/143 (19%) Query: 224 WVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNL 283 +++D LFG L VLD+ G + L GA VT +D S+ +E + + Sbjct: 32 YIRDTIRKNKKPLFG----LRVLDVGCGGGLLSEPLARLGANVTGIDASEENIEVAKLHA 87 Query: 284 DRLHLYAEDIIEMDAFDYC--PKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSA 341 + L + D K FD V C + H D +++ Sbjct: 88 KKDPLLKIEYRCTSVEDLAEKGAKSFDVVT----CME---VLEHVP-----DPQAFIRAC 135 Query: 342 CFQRKLLLQGISFVKPGGIVVFS 364 +KPGGI+ FS Sbjct: 136 A----------QLLKPGGILFFS 148 >gnl|CDD|183301 PRK11760, PRK11760, putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional. Length = 357 Score = 32.1 bits (74), Expect = 0.29 Identities = 15/24 (62%), Positives = 17/24 (70%) Query: 247 DLCAAPGGKTAQLIVSGAKVTALD 270 DL AAPGG T QL+ G VTA+D Sbjct: 217 DLGAAPGGWTYQLVRRGMFVTAVD 240 >gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional. Length = 223 Score = 31.6 bits (72), Expect = 0.41 Identities = 36/133 (27%), Positives = 51/133 (38%), Gaps = 19/133 (14%) Query: 245 VLDLCAAPGGKTAQLIVSGA-KVTALDVSKRRLEKLRCN--LDRLHLYAEDIIEMDAFDY 301 VLDLC G +GA VTA+D+S+R + R N L + + D+ D Sbjct: 40 VLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLAGVDV---DVRRGDWARA 96 Query: 302 CPKKLFDAVLVD---APCSSTGTIRRHPDVLWT--RDTDDIVKSACFQRKLLLQGISFVK 356 + FD V+ + P R P W D ++ C LL Sbjct: 97 VEFRPFDVVVSNPPYVPAPPDAPPSRGPARAWDAGPDGRAVLDRLCDAAPALL------A 150 Query: 357 PGG--IVVFSNCS 367 PGG ++V S S Sbjct: 151 PGGSLLLVQSELS 163 >gnl|CDD|177728 PLN00113, PLN00113, leucine-rich repeat receptor-like protein kinase; Provisional. Length = 968 Score = 30.6 bits (69), Expect = 0.92 Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%) Query: 207 ELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDL 248 ++P ++ SLP W S IP L G NNL+VLDL Sbjct: 323 KIPVALTSLPRLQVLQLWSNKFSGEIPKNL-GKHNNLTVLDL 363 >gnl|CDD|162239 TIGR01177, TIGR01177, conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea. Length = 329 Score = 30.5 bits (69), Expect = 0.93 Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 1/83 (1%) Query: 234 VQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDI 293 V L VLD GG + + GAKV D+ + + R NL+ + + Sbjct: 175 VNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIEDFFV 234 Query: 294 IEMDAFDY-CPKKLFDAVLVDAP 315 DA + DA+ D P Sbjct: 235 KRGDATKLPLSSESVDAIATDPP 257 >gnl|CDD|162871 TIGR02469, CbiT, precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. Length = 124 Score = 30.0 bits (68), Expect = 1.4 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 4/72 (5%) Query: 245 VLDLCAAPGGKT--AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYC 302 + D+ A G T A +V +V A++ + L + N R + I+E DA + Sbjct: 23 LWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIERNARRFGVSNIVIVEGDAPEAL 82 Query: 303 PKKL--FDAVLV 312 L D V + Sbjct: 83 EDSLPEPDRVFI 94 >gnl|CDD|183320 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 307 Score = 29.4 bits (67), Expect = 2.0 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 12/81 (14%) Query: 244 SVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAED---IIEMDA 298 +LDLC G A+V A+D+S L N++R L ED +IE D Sbjct: 136 RILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEINIERHGL--EDRVTLIESDL 193 Query: 299 FDYCPKKLFDAVL-----VDA 314 F P + +D ++ VDA Sbjct: 194 FAALPGRRYDLIVSNPPYVDA 214 >gnl|CDD|163564 TIGR03852, sucrose_gtfA, sucrose phosphorylase. In the forward direction, this enzyme uses phosphate to cleave sucrose into D-fructose + alpha-D-glucose 1-phosphate. Characterized representatives from Streptococcus mutans and Bifidobacterium adolescentis represent well-separated branches of a molecular phylogenetic tree. In S. mutans, the region including this gene has been associated with neighboring transporter genes and multiple sugar metabolism. Length = 470 Score = 29.3 bits (66), Expect = 2.1 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%) Query: 269 LDVSKRRLEK-LRCNLDRLHLYAEDIIEMDAFDYCPKKL 306 LDV+ ++ +R NL+ L + II +DAF Y KKL Sbjct: 160 LDVTSETTKRFIRDNLENLAEHGASIIRLDAFAYAVKKL 198 >gnl|CDD|182340 PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional. Length = 251 Score = 29.0 bits (65), Expect = 2.3 Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%) Query: 226 QDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDR 285 Q SA + + VLD PG + G++VTALD+S L + R D Sbjct: 27 QRQSADALLAMLPQRKFTHVLDAGCGPGWMSRYWRERGSQVTALDLSPPMLAQARQK-DA 85 Query: 286 LHLYAEDIIE 295 Y IE Sbjct: 86 ADHYLAGDIE 95 >gnl|CDD|185285 PRK15387, PRK15387, E3 ubiquitin-protein ligase SspH2; Provisional. Length = 788 Score = 29.0 bits (64), Expect = 2.6 Identities = 32/103 (31%), Positives = 48/103 (46%), Gaps = 21/103 (20%) Query: 189 WAHKLNAVMLPTGGIRLKELPES---IVSLPGFAEGVWWVQDASASIPVQLFG--TLNNL 243 WA+ LPT L+EL S + SLP ++P +L+ NN Sbjct: 328 WAYNNQLTSLPTLPSGLQELSVSDNQLASLP--------------TLPSELYKLWAYNN- 372 Query: 244 SVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRL 286 + L A P G +LIVSG ++T+L V L++L + +RL Sbjct: 373 RLTSLPALPSG-LKELIVSGNRLTSLPVLPSELKELMVSGNRL 414 >gnl|CDD|162684 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology. Length = 240 Score = 28.8 bits (65), Expect = 2.6 Identities = 28/146 (19%), Positives = 48/146 (32%), Gaps = 32/146 (21%) Query: 225 VQDASASIPVQLFGTLNNL---SVLDLCAAPGGKTAQLIVSGAKV--TALDVSKRRLEKL 279 +Q A + L SVLD+ G T L+ + ALD+S L + Sbjct: 15 IQREMAKRLLALLKEKGIFIPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQA 74 Query: 280 RCNL-DRLHLYAEDIIEMDAFDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIV 338 + L + + D ++ D FD ++ + + W D + Sbjct: 75 KTKLSENVQFICGDAEKLPLED----SSFDLIV----SNLA--------LQWCDDLSQAL 118 Query: 339 KSACFQRKLLLQGISFVKPGGIVVFS 364 +KPGG++ FS Sbjct: 119 SELA----------RVLKPGGLLAFS 134 >gnl|CDD|183310 PRK11779, sbcB, exonuclease I; Provisional. Length = 476 Score = 28.3 bits (64), Expect = 4.5 Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 28/88 (31%) Query: 384 SPIPVELVPLNS----AYWK----------SIDMAMALSPEGWIRITPDMLEKIDGVSSG 429 P+P++LV LN A K ID L +R PD+ EK+ V + Sbjct: 292 LPVPLKLVHLNKCPVLAPAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFAE 351 Query: 430 M--------------DGFFAVALRRLIQ 443 DGFF+ A RRL++ Sbjct: 352 AEPFAPSDDVDAQLYDGFFSDADRRLME 379 >gnl|CDD|161854 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms. Length = 861 Score = 28.1 bits (63), Expect = 4.8 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 5/45 (11%) Query: 130 RVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACIS 174 + K ++L++I ++ +PEW + R N+ + D CIS Sbjct: 427 KTKDIKDQMLEQIKKVNWVPEWGEGRFGNW-----LENRPDWCIS 466 >gnl|CDD|152360 pfam11925, DUF3443, Protein of unknown function (DUF3443). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 400 to 434 amino acids in length. This protein has two conserved sequence motifs: NPV and DNNG. Length = 369 Score = 28.1 bits (63), Expect = 5.1 Identities = 11/44 (25%), Positives = 20/44 (45%) Query: 222 VWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAK 265 V + +++IP+Q+ G + SV C++ G GA Sbjct: 99 VTIGGETASNIPIQVIGDSSTASVPSSCSSGGASENTPADLGAN 142 >gnl|CDD|184932 PRK14968, PRK14968, putative methyltransferase; Provisional. Length = 188 Score = 27.6 bits (62), Expect = 6.7 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%) Query: 244 SVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDI--IEMDAFDY 301 VL++ G +G KV +D++ +E +CN ++ + I D F+ Sbjct: 26 RVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSDLFEP 85 Query: 302 CPKKLFDAVLVDAP 315 FD +L + P Sbjct: 86 FRGDKFDVILFNPP 99 >gnl|CDD|163310 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors. Length = 284 Score = 27.5 bits (62), Expect = 7.1 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 12/81 (14%) Query: 244 SVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAED---IIEMDA 298 +LDLC G A+V A+D+S L N++R L ED +I+ D Sbjct: 124 RILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGL--EDRVTLIQSDL 181 Query: 299 FDYCPKKLFDAVL-----VDA 314 F P + +D ++ VDA Sbjct: 182 FAALPGRKYDLIVSNPPYVDA 202 >gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity. Length = 667 Score = 27.4 bits (61), Expect = 8.4 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 11/91 (12%) Query: 89 SVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIELL----QRIAG 144 +LD +D ++ R ++ L+ +K + + R+ Sbjct: 443 DRLPEDHLDRKK---LDAFFDEIFELLPER-IREITKESLKEK-LQKTKKILFNEDRLES 497 Query: 145 IS-IIPEWFKERLENFYGKERVLAIS-DACI 173 I+ I E + + E F K V+AIS AC+ Sbjct: 498 IAKDIAEHYAKFKELFKFKAMVVAISRYACV 528 >gnl|CDD|152126 pfam11690, DUF3287, Protein of unknown function (DUF3287). This eukaryotic family of proteins has no known function. Length = 144 Score = 27.3 bits (60), Expect = 8.7 Identities = 13/33 (39%), Positives = 17/33 (51%) Query: 106 LAVEQAKRDKENRHFAKLVNSILRRVSREKIEL 138 LAV+ KR E R K +N +L V+ EL Sbjct: 66 LAVQHQKRSLEKRKIRKKINRMLLIVTAISREL 98 >gnl|CDD|149353 pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 95 Score = 27.3 bits (61), Expect = 9.2 Identities = 29/120 (24%), Positives = 44/120 (36%), Gaps = 27/120 (22%) Query: 246 LDLCAAPGGKTAQLI-VSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDY-CP 303 LD+ G T L + GA+VT +D+S L R L + DA D P Sbjct: 1 LDVGCGTGLLTEALARLPGAQVTGVDLSPEMLALARKRAQEDGL---TFVVGDAEDLPFP 57 Query: 304 KKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVF 363 + FD V+ S + D + ++ ++L KPGG +V Sbjct: 58 DESFDVVV----SSLV--------LHHLPDPERALREI---ARVL-------KPGGKLVI 95 >gnl|CDD|147828 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This family consists of several Eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis. This family also plays a role in chromosome segregation. Length = 268 Score = 26.9 bits (60), Expect = 9.9 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%) Query: 107 AVEQAKRDKENRHFAKLV-NSILRRVSREKIELLQRIAGISIIPEWFKERLENFYGKERV 165 A E+A++ +E + F K V L+ ++EK ++L++I K+R G Sbjct: 133 ASEEARKQRELKKFGKQVQVEKLQERAKEKKDMLEKIKK------LKKKRKGGGEGDLFD 186 Query: 166 LAISDA 171 + DA Sbjct: 187 FLLDDA 192 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.138 0.406 Gapped Lambda K H 0.267 0.0672 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,459,791 Number of extensions: 498766 Number of successful extensions: 1079 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1040 Number of HSP's successfully gapped: 45 Length of query: 445 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 349 Effective length of database: 3,920,105 Effective search space: 1368116645 Effective search space used: 1368116645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 59 (26.6 bits)