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= 0176.0003.p (365 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_388802.1| similar to hypothetical proteins [Bacillus subt... 203 7e-51 ref|NP_831075.1| Ribosomal large subunit pseudouridine synthase ... 201 2e-50 ref|NP_655191.1| PseudoU_synth_2, RNA pseudouridylate synthase [... 201 2e-50 ref|NP_977726.1| ribosomal large subunit pseudouridine synthase,... 197 2e-49 ref|NP_465768.1| similar to putative ribosomal large subunit pse... 161 2e-38 >ref|NP_388802.1| similar to hypothetical proteins [Bacillus subtilis] sp|P54604|YHCT_BACSU Hypothetical pseudouridine synthase yhcT (Pseudouridylate synthase) (Uracil hydrolyase) pir||H69823 conserved hypothetical protein yhcT - Bacillus subtilis emb|CAA65704.1| hypothetical protein [Bacillus subtilis] emb|CAB12749.1| yhcT [Bacillus subtilis subsp. subtilis str. 168] Length = 302 Score = 203 bits (516), Expect = 7e-51, Method: Compositional matrix adjust. Identities = 120/338 (35%), Positives = 174/338 (51%), Gaps = 61/338 (18%) Query: 20 GEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGIQWKGDRLRLALFPY 79 G+WL + + TA + I W+ +K++ I KGDR+ + L Sbjct: 18 GQWLFSV---LKTALKASKPVIQDWM---SHQQIKVNHESVLNNMIVKKGDRVFIDLQES 71 Query: 80 REAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHVVAAHYSVSGGGTAV 139 + + P + EL++LFED+ L+++KPAG+A HP+ G TL +++A HY ++G V Sbjct: 72 EASSVIPEYGELDILFEDNHMLIINKPAGIATHPNEDGQTGTLANLIAYHYQINGETCKV 131 Query: 140 RHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGVVPPELKVIDAPIGR 199 RH+HRLD+DT+G +++AK+ A LD+ + K + R Y AI EG + + I+ PIGR Sbjct: 132 RHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTINPPIGR 191 Query: 200 DRHHAARRRVSPGGQTAVT--RIMDREVLRSGTVLKVQLETGRTHQIRVHLSHLGHPLYG 257 DR H RRRVSPGGQTAVT ++M ++++++LETGRTHQIRVHL+ LGHPL G Sbjct: 192 DRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHLASLGHPLTG 251 Query: 258 DTLYGGPPWSAAGQRSHSGGPTISESAWSTGVGRLDRESPGRTGGGTGDSPARPGTGPAG 317 D+LYGG G Sbjct: 252 DSLYGG-----------------------------------------------------G 258 Query: 318 SRGPDRQALHGELLAFSHPWTREQLEIADPWPEDMLRL 355 S+ +RQALH + HP T E + P+P DM L Sbjct: 259 SKLLNRQALHANKVQAVHPITDELIVAEAPFPADMKNL 296 >ref|NP_831075.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 14579] gb|AAP08276.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus ATCC 14579] Length = 307 Score = 201 bits (511), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 113/267 (42%), Positives = 159/267 (59%), Gaps = 9/267 (3%) Query: 18 RRGEWLEVM-----PGRVITAAGEPEAAIDKWLLATVGMP--VKLHERLRREGGIQWKGD 70 ++GEW E+ G I + + E I K LL + M V ++ RR + + D Sbjct: 5 KKGEWCEITVPAKWNGISIESVLKVEWEIPKKLLHQLRMEKGVTVNGEQRRWNELLKEND 64 Query: 71 RLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHVVAAHY 130 +L++ +F E G++P + EL V++EDD L+V+KP M HP G TL ++VA H+ Sbjct: 65 KLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDTHPAEKGGTGTLANLVAFHF 124 Query: 131 SVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGVVPPEL 190 + G T VRH+HRLDKDTTG V++AK+ A +D + + + R YAA+VEG V + Sbjct: 125 QMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLLMERKIKRTYAALVEGKVKKKQ 184 Query: 191 KVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLR--SGTVLKVQLETGRTHQIRVHL 248 IDA IGRDRHHA RRR+SP G A+T + + + T + +QLETGRTHQIRVH+ Sbjct: 185 GKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQNTTFVTLQLETGRTHQIRVHM 244 Query: 249 SHLGHPLYGDTLYGGPPWSAAGQRSHS 275 SH G+PL GD LYGG + Q H+ Sbjct: 245 SHNGNPLVGDVLYGGQTKYMSSQALHA 271 >ref|NP_655191.1| PseudoU_synth_2, RNA pseudouridylate synthase [Bacillus anthracis A2012] Length = 307 Score = 201 bits (511), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 116/267 (43%), Positives = 160/267 (59%), Gaps = 9/267 (3%) Query: 18 RRGEWLEVM-----PGRVITAAGEPEAAIDKWLLATVGMP--VKLHERLRREGGIQWKGD 70 ++GEW E+ G I + + E I K LL + M V ++ RR + +GD Sbjct: 5 KKGEWCEMTVPAKWNGISIESLLKIEWEIPKKLLHQLRMEKGVTVNGEQRRWNELLKEGD 64 Query: 71 RLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHVVAAHY 130 +L++ +F E +EP + EL+V++EDD L+V+KP M HP G TL ++VA HY Sbjct: 65 KLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANLVAFHY 124 Query: 131 SVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGVVPPEL 190 + G T VRH+HRLDKDTTG V++AK+ A +D + + + R YAA+VEG V + Sbjct: 125 QMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGKVKKKQ 184 Query: 191 KVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLR--SGTVLKVQLETGRTHQIRVHL 248 IDA IGRDRHHA RRRVSP G A+T E + + T + +QLETGRTHQIRVH+ Sbjct: 185 GTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQNVTFVTLQLETGRTHQIRVHM 244 Query: 249 SHLGHPLYGDTLYGGPPWSAAGQRSHS 275 S+ G+PL GD LYGG + Q H+ Sbjct: 245 SYNGNPLVGDVLYGGQTKYMSRQALHA 271 >ref|NP_977726.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus ATCC 10987] gb|AAS40334.1| ribosomal large subunit pseudouridine synthase, RluD subfamily [Bacillus cereus ATCC 10987] Length = 307 Score = 197 bits (502), Expect = 2e-49, Method: Compositional matrix adjust. Identities = 113/272 (41%), Positives = 159/272 (58%), Gaps = 19/272 (6%) Query: 18 RRGEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGIQWKGD------- 70 ++GEW E+ A +I+ L +P KL +LR E G+ G+ Sbjct: 5 KKGEWCEI-----TVPAKWNGISIESLLKIEWEIPKKLLHQLRMEKGVTVNGEQRRWNEL 59 Query: 71 -----RLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHV 125 +L++ +F E G+EP + EL+V++EDD L+V+KP M HP G TL ++ Sbjct: 60 LKEDEKLQVHMFMEEEYGVEPEYGELDVVYEDDHVLIVNKPEKMDTHPAEKGGMGTLANL 119 Query: 126 VAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGV 185 VA H+ + G T VRH+HRLDKDTTG V++AK+ A +D + + + R YAA+VEG Sbjct: 120 VAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLLMERKIKRTYAALVEGK 179 Query: 186 VPPELKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLR--SGTVLKVQLETGRTHQ 243 V + IDA IGRDRHHA RRRVSP G A+T + + + T++ +QLETGRTHQ Sbjct: 180 VKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQNVTLVTLQLETGRTHQ 239 Query: 244 IRVHLSHLGHPLYGDTLYGGPPWSAAGQRSHS 275 IRVH+S+ G+PL GD LYGG + Q H+ Sbjct: 240 IRVHMSYNGNPLVGDILYGGGTKYMSRQALHA 271 >ref|NP_465768.1| similar to putative ribosomal large subunit pseudouridine synthase [Listeria monocytogenes EGD-e] pir||AD1355 probable ribosomal large chain pseudouridine synthase homolog lmo2244 [imported] - Listeria monocytogenes (strain EGD-e) emb|CAD00322.1| lmo2244 [Listeria monocytogenes] Length = 289 Score = 161 bits (408), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 85/202 (42%), Positives = 128/202 (63%), Gaps = 6/202 (2%) Query: 67 WKGDRLRLALFPYREAGIEPAWQ-ELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHV 125 + G L L +F + + P ++ +LE+++EDDF LVV+KP M HP+ S T + Sbjct: 56 FVGASLSLPIFLHDKI---PVYEYDLEIIYEDDFLLVVNKPVDMKTHPNDSYETDTCANA 112 Query: 126 VAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGV 185 V + +G +HRLD+ T+G VL+AKN+ A L M +A+ R Y A V+G Sbjct: 113 VQYYLEKTGQDANALAVHRLDQTTSGLVLFAKNKLAIAGLSWQMENRAIHRTYLAAVDGT 172 Query: 186 VPPELKVIDAPIGRDRHHAARRRVSPGGQTAVT--RIMDREVLRSGTVLKVQLETGRTHQ 243 ++ I+ PIG DRHH +RR++SP GQ AVT ++++ + ++ ++++ Q+ETGRTHQ Sbjct: 173 WGLVMQTINKPIGEDRHHGSRRQISPYGQPAVTHVKVLENDNEKNTSLVECQIETGRTHQ 232 Query: 244 IRVHLSHLGHPLYGDTLYGGPP 265 IRVHLS +GHP+ GDTLYGG P Sbjct: 233 IRVHLSGIGHPIIGDTLYGGSP 254 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.317 0.136 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 621,761,753 Number of extensions: 29437702 Number of successful extensions: 85051 Number of sequences better than 1.0e-05: 1134 Number of HSP's gapped: 83497 Number of HSP's successfully gapped: 1134 Length of query: 365 Length of database: 757,237,578 Length adjustment: 127 Effective length of query: 238 Effective length of database: 412,420,005 Effective search space: 98155961190 Effective search space used: 98155961190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 126 (53.1 bits)