BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0476.0037.p (355 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K6Q3.1 B3K6Q3_9BACI Ribosomal RNA methyltransferase RrmJ/FtsJ 452 e-125 B1DLQ5.1 B1DLQ5_9BACL Ribosomal RNA methyltransferase RrmJ/FtsJ 328 6e-88 Q2JSM9.1 Q2JSM9_SYNJA Ribosomal RNA large subunit methytransfera... 156 3e-36 Q2JK31.1 Q2JK31_SYNJB Putative uncharacterized protein 147 2e-33 A9AY54.1 A9AY54_HERA2 THUMP domain protein 144 1e-32 >B3K6Q3.1 B3K6Q3_9BACI Ribosomal RNA methyltransferase RrmJ/FtsJ Length = 358 Score = 452 bits (1162), Expect = e-125, Method: Compositional matrix adjust. Identities = 210/338 (62%), Positives = 272/338 (80%), Gaps = 2/338 (0%) Query: 20 YSRYICTANHGFAPYAQEELRRLFGAVKSTLLLPGEIFLATLEAEPEEVSRVLAGQPPIF 79 +S+++CTANHGFAPYAQEELRR+FG++KST+++PGE+FL TL + E R++ +PPIF Sbjct: 21 HSKWVCTANHGFAPYAQEELRRMFGSLKSTMMMPGEVFLMTLGSSEAEAKRLITSKPPIF 80 Query: 80 LRHIQPVQFQDQGDL--SALDRLAVYLSRRSGLEGEKVALHVRKGHSSFWPDSPGELREW 137 LRH+ PVQ++ + +AL A ++ +R + + ++ +RK +S W +SP LR+ Sbjct: 81 LRHLFPVQWEIAAESVDAALQLTADHVLKREEISQSRASIQIRKTENSSWTESPAALRDD 140 Query: 138 LQERLQDLGAEFTVQDPAWVISVYADGGALYAGVSRPEENLSSWNGGMIRFRKEDGQISR 197 LQ RL L E+TVQ P W+IS++A YAGVSRPE+NLS WNGG +RF++E+GQISR Sbjct: 141 LQLRLAPLELEYTVQAPEWIISLFAADNVWYAGVSRPEDNLSDWNGGAVRFQREEGQISR 200 Query: 198 AKFKLMEAEKEFAIPFCSFRNAVDIGASPGGWTSFLLERGLKVTAVDPALMHESLRKNPG 257 AKFKL+EAEK+F IPF +FR AVDIGA+PGGWTSFLLERGL+VTAVDPA MH SL + Sbjct: 201 AKFKLLEAEKQFGIPFDTFRKAVDIGAAPGGWTSFLLERGLQVTAVDPAKMHPSLDGHKN 260 Query: 258 LKILRKNAGDVKFQDNEFDLLVCDMSWSPKLMAKLVTGLLHSLSPGGTAIVTVKLMHKKP 317 L+++ KNA DV F+++EFDLLVCDMSWSPKLMA++VTGLLHSL GGTA+VTVKL+ KKP Sbjct: 261 LRVIHKNAADVTFREHEFDLLVCDMSWSPKLMARMVTGLLHSLETGGTAVVTVKLLTKKP 320 Query: 318 MAVIKEIIAMFESERMQIQRAKQLFHNRDEITLYMIKY 355 MA++KEI+++FE+ RMQIQ AKQLFHNRDEITLYMIKY Sbjct: 321 MALVKEIMSVFEASRMQIQGAKQLFHNRDEITLYMIKY 358 >B1DLQ5.1 B1DLQ5_9BACL Ribosomal RNA methyltransferase RrmJ/FtsJ Length = 339 Score = 328 bits (840), Expect = 6e-88, Method: Compositional matrix adjust. Identities = 174/337 (51%), Positives = 231/337 (68%), Gaps = 4/337 (1%) Query: 21 SRYICTANHGFAPYAQEELRRLFGAVKSTLLLPGEIFLATLEAEPEEVSRVLAGQPPIFL 80 SR+I TAN G++PYA EELRRL VK T L GE FL E E+V+ +A PIFL Sbjct: 2 SRWIGTANQGYSPYAIEELRRLLDGVKVTQLAAGETFLFDSELSAEDVTAAVASDKPIFL 61 Query: 81 RHIQPVQ--FQDQGDLSALDRLAVYLSR-RSGLEGEKVALHVRKGHSSFWPDSPGELREW 137 RH+QPV + +G+ L L+ + R R E ++VA+HVR+ + + +P S + + Sbjct: 62 RHLQPVDRTVEIKGNADDLQELSETIRRSRLLFEDKQVAIHVRRSNKTAFPYSASDTKAV 121 Query: 138 LQERLQDLGAEFTVQDPAWVISVYADGGALYAGVSRPEENLSSWNGGMIRFRKEDGQISR 197 L L++L AE VQ P +I++YA L+ G +PE+ LS W GG IRF++E+GQISR Sbjct: 122 LDAVLEELDAEPVVQHPDIIIAIYAAASELFIGFGKPEDMLSDWPGGAIRFQREEGQISR 181 Query: 198 AKFKLMEAEKEFAIPFCSFRNAVDIGASPGGWTSFLLERGLKVTAVDPALMHESLRKNPG 257 AKFKL+EAE+EF + + FR+AVDIGA+PGGWTS LLERGL+VTA+DP MH SL +P Sbjct: 182 AKFKLLEAEREFGLDYSMFRSAVDIGAAPGGWTSLLLERGLRVTAIDPGDMHPSLAGHPA 241 Query: 258 LKILRKNAGDVKFQDNEFDLLVCDMSWSPKLMAKLVTGLLHSLSPGGTAIVTVKLMHKKP 317 L L++NA +VKF+ FDLLVCDMSWSP M +LV L +L+P +AI+T+KLMHKKP Sbjct: 242 LTYLKRNASEVKFKPGSFDLLVCDMSWSPMQMCRLVLDLEETLAPHASAIITIKLMHKKP 301 Query: 318 MAVIKEIIAMFESERMQIQRAKQLFHNRDEITLYMIK 354 + I+E+ F S I+RAKQLFHNR+EITLY+ K Sbjct: 302 LQTIREVKERF-STAFIIKRAKQLFHNREEITLYLEK 337 >Q2JSM9.1 Q2JSM9_SYNJA Ribosomal RNA large subunit methytransferase J EC=2.1.1.- Length = 356 Score = 156 bits (394), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 103/294 (35%), Positives = 160/294 (54%), Gaps = 10/294 (3%) Query: 67 EVSRVLAGQPPIFLRHIQPVQFQDQGDLSALDRLAVYLSRRSGLEGEKVALHVRKGHSSF 126 ++++ PPIFLRHI P+ + Q D +L RL L ++ V+ Sbjct: 57 DLAQAWQANPPIFLRHICPIHQERQLDEISLLRLDQNLL---AAIDPALSFSVQTRRFGK 113 Query: 127 WPDSPGELREWLQER-LQDLGAEFTVQDPAWVISVY----ADGGALYAGVSRPEENLSSW 181 P ++ L E+ + +G+ V+DP VISV + G + G+S +NLS+W Sbjct: 114 LNVKPFQVNAALAEQVMATVGSPLQVKDPQQVISVVLLASSTGLRAWLGLSLAAQNLSTW 173 Query: 182 NGGMIRFRKEDGQISRAKFKLMEAEKEFAIPFCSFRNAVDIGASPGGWTSFLLERGLKVT 241 GG+ RFR++ QISRA+FKL+EA + F +P A+D+GA+PGGW+ L G +VT Sbjct: 174 AGGVHRFRRDPDQISRAEFKLLEAIQVFRVPLQPGGRALDLGAAPGGWSRILRLHGQQVT 233 Query: 242 AVDPALMHESLRKNPGLKILRKNA-GDVKFQDNEFDLLVCDMSWSPKLMAKLVTGLLHSL 300 AVDPA + E LR + G+ R +A + +F L++ DM + A L+ L Sbjct: 234 AVDPAELDERLRHDAGICHHRLSAQAYLARCPGQFHLILNDMRMDGRASAHLMAAFAPHL 293 Query: 301 SPGGTAIVTVKLMHKKPMAVIKEIIAMFESERMQIQRAKQLFHNRDEITLYMIK 354 P G A++T+KL H+ + V+++ + + S + RA+ LFHNR EITLY+ K Sbjct: 294 EPQGAAVMTLKLPHQHRLRVLRQTLDILGSA-FPVVRARHLFHNRSEITLYLQK 346 >Q2JK31.1 Q2JK31_SYNJB Putative uncharacterized protein Length = 315 Score = 147 bits (370), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 102/295 (34%), Positives = 156/295 (52%), Gaps = 32/295 (10%) Query: 76 PPIFLRHIQP------------VQFQDQGDLSALDRLAVYLSRRSGLEGEKVALHVRKGH 123 PPIFLRHI P V+ + G++ A A+ S ++ L GE Sbjct: 30 PPIFLRHICPIHQERRLAEGSLVELRLDGEMLAAIDPALSFSVQTRLFGEPAL------- 82 Query: 124 SSFWPDSPGELREWLQER-LQDLGAEFTVQDPAWVISVY----ADGGALYAGVSRPEENL 178 P ++ E L E+ + +G+ V+DP VISV G + G+S +NL Sbjct: 83 ------KPFQVNETLAEQVMAAVGSPLQVKDPQQVISVVILAQPMGIRAWLGLSLAAQNL 136 Query: 179 SSWNGGMIRFRKEDGQISRAKFKLMEAEKEFAIPFCSFRNAVDIGASPGGWTSFLLERGL 238 S+W GG+ RFR++ QISR++FKL+EA + F IP A+D+GA+PGGW+ L G Sbjct: 137 SNWAGGIHRFRQDPEQISRSEFKLLEAIQVFQIPLVPGGQALDLGAAPGGWSRILRLYGQ 196 Query: 239 KVTAVDPALMHESLRKNPGLKILRKNA-GDVKFQDNEFDLLVCDMSWSPKLMAKLVTGLL 297 +VTAVDPA + E L ++PG+ R +A + F L++ DM A+L+ Sbjct: 197 QVTAVDPADLDERLSQDPGICHHRLSAQAYLARGPGRFHLILNDMRMDGPASARLMVAFA 256 Query: 298 HSLSPGGTAIVTVKLMHKKPMAVIKEIIAMFESERMQIQRAKQLFHNRDEITLYM 352 L P G A++T+KL + + V+++ + + S + RA+ LFHNR E+TLY+ Sbjct: 257 PHLQPQGRAVMTLKLPRQHRLRVLRQSLEILGSA-FPLVRARHLFHNRSEVTLYL 310 >A9AY54.1 A9AY54_HERA2 THUMP domain protein Length = 354 Score = 144 bits (363), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 108/310 (34%), Positives = 158/310 (50%), Gaps = 11/310 (3%) Query: 52 LPGEIFLATLEAEPEEVSRVLAGQPPIFLRHIQPVQFQD--QGDLSALDRLA-VYLSRRS 108 L E+ L LE E L +P IF+RHI PV + +G L+RL V L+ Sbjct: 35 LAPEVALVELEQPLAEWHAFLLKRPAIFVRHIAPVHREVVLEGTPDDLERLTQVALNLAP 94 Query: 109 GLEGEK---VALHVRKGHSSFWPDSPGELREWLQERLQDL-GAEFTVQDPAWVISVYADG 164 L K V + H + E+ + L E + + G V++P V+SV Sbjct: 95 HLPARKPFAVQTRLLDEHVKL---TRFEINQALAEAVSQVSGLPLDVRNPQGVLSVALSM 151 Query: 165 GALYAGVSRPEENLSSWNGGMIRFRKEDGQISRAKFKLMEAEKEFAIPFCSFRNAVDIGA 224 Y GVS E N S+W GG RF +E GQ+SRA+FKL+EA+ F I + A+D+GA Sbjct: 152 DRAYLGVSTVEFNRSAWAGGAHRFAREQGQLSRAEFKLLEAQALFNIEWPDHGQALDLGA 211 Query: 225 SPGGWTSFLLERGLKVTAVDPALMHESLRKNPGLKILRKNAGDVKFQDNEFDLLVCDMSW 284 +PGGWT L GL V A+DPA +H SLR + G++ L+ A F ++V DM Sbjct: 212 APGGWTRILRRAGLPVVAIDPADLHPSLRYDQGVRHLQILAQRFLPTQERFTVIVNDMRI 271 Query: 285 SPKLMAKLVTGLLHSLSPGGTAIVTVKLMHKKPMAVIKEIIAMFESERMQIQRAKQLFHN 344 + A L+ ++L+ G A+VT+KL H+ + +++ + I A+QLFHN Sbjct: 272 DARDSAWLMVDSANALTNDGLAVVTLKLPHEHSAQIAYHSLSILRTAYWVIG-ARQLFHN 330 Query: 345 RDEITLYMIK 354 R E+T + K Sbjct: 331 RSEVTAVLRK 340 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.320 0.136 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 2,170,771,055 Number of extensions: 88870553 Number of successful extensions: 220637 Number of sequences better than 1.0e-05: 296 Number of HSP's gapped: 220486 Number of HSP's successfully gapped: 296 Length of query: 355 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 218 Effective length of database: 1,770,017,148 Effective search space: 385863738264 Effective search space used: 385863738264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 132 (55.5 bits)