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= 0349.0013.p (166 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|ZP_00060351.1| COG0564: Pseudouridylate synthases, 23S RNA-s... 194 9e-49 ref|ZP_00099063.1| COG0564: Pseudouridylate synthases, 23S RNA-s... 149 3e-35 ref|NP_812683.1| ribosomal large subunit pseudouridine synthase ... 135 3e-31 gb|EAD81786.1| unknown [environmental sequence] 128 4e-29 gb|EAB62107.1| unknown [environmental sequence] 122 4e-27 >ref|ZP_00060351.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Clostridium thermocellum ATCC 27405] Length = 243 Score = 194 bits (492), Expect = 9e-49, Method: Compositional matrix adjust. Identities = 93/158 (58%), Positives = 117/158 (74%) Query: 1 MIFAKTSKAASRLSESVRSHSFHKVYLTVVHGKPPAAQGRLVHTLLKDAKTNTVTIVRKG 60 M+FAKTSKAASRLS+ VR+ F KVYL VVHG +GRL + LLKD + NTV++V++ Sbjct: 85 MVFAKTSKAASRLSDQVRTRQFKKVYLAVVHGILDKLEGRLENYLLKDTRNNTVSVVKED 144 Query: 61 TPGGKEAILDYTVIGSAEGYSLLKIDLLTGRSHQIRVQLSGIRCPLYGDQKYGAAVNKPG 120 TPGGK A+LDY V G G+SL+K+ L TGR HQIRVQL+ I PLYGDQKYG VNKPG Sbjct: 145 TPGGKLAVLDYKVEGIYNGFSLVKVSLHTGRPHQIRVQLANIGHPLYGDQKYGHGVNKPG 204 Query: 121 QQIALWSAVVGFPHPVTKEEIELISLPPQTHPWSLWSQ 158 QQIALWS+ + F HPV K+E+ PP+ PW+ +++ Sbjct: 205 QQIALWSSEIAFVHPVLKQEMIFSCEPPEVEPWTWFNR 242 >ref|ZP_00099063.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Desulfitobacterium hafniense] Length = 241 Score = 149 bits (375), Expect = 3e-35, Method: Compositional matrix adjust. Identities = 76/164 (46%), Positives = 103/164 (62%), Gaps = 9/164 (5%) Query: 1 MIFAKTSKAASRLSESVRSHSFHKVYLTVVHGKPPAAQGRLVHTLLKDAKTNTVTIVRKG 60 M+FAKTSK+A+RLSE +R+ F K YL ++ G+P + L+H L+KD K+N V+ V+KG Sbjct: 76 MVFAKTSKSAARLSEQIRNREFTKTYLALIQGQPAKQKNTLIHYLVKDEKSNKVSAVKKG 135 Query: 61 TPGGKEAILDYTVIGSAEGYSLLKIDLLTGRSHQIRVQLSGIRCPLYGDQKYGAAVN--- 117 G KEAILDY V+ S SL+K++L TGR HQIRVQ + + PLYGD KYG V Sbjct: 136 AKGAKEAILDYEVVHSQSDLSLVKVNLRTGRPHQIRVQFAHLGHPLYGDYKYGKIVKTSK 195 Query: 118 ----KPGQQIALWSAVVGFPHPVTKEEIELISLPPQTHPWSLWS 157 KP + LWS + HP++K +I S P Q PW+ + Sbjct: 196 TSLTKP--HLGLWSYEISCLHPISKGQIHFKSYPHQHKPWNQFD 237 >ref|NP_812683.1| ribosomal large subunit pseudouridine synthase D [Bacteroides thetaiotaomicron VPI-5482] gb|AAO78877.1| ribosomal large subunit pseudouridine synthase D [Bacteroides thetaiotaomicron VPI-5482] Length = 223 Score = 135 bits (340), Expect = 3e-31, Method: Compositional matrix adjust. Identities = 71/153 (46%), Positives = 93/153 (60%) Query: 1 MIFAKTSKAASRLSESVRSHSFHKVYLTVVHGKPPAAQGRLVHTLLKDAKTNTVTIVRKG 60 +IFAKTSKA +RL+E R+ K Y VV P +G LVH L ++ K N K Sbjct: 65 VIFAKTSKALTRLNEMFRTSEVKKTYWAVVKNAPKEPEGELVHYLARNEKQNKSFAYDKE 124 Query: 61 TPGGKEAILDYTVIGSAEGYSLLKIDLLTGRSHQIRVQLSGIRCPLYGDQKYGAAVNKPG 120 P K+AIL+Y +IG +E Y LL++DL TGR HQIR QL+ + CP+ GD KYGA + P Sbjct: 125 VPNSKKAILNYRLIGHSENYYLLEVDLKTGRHHQIRCQLAKMGCPIKGDLKYGAPRSNPD 184 Query: 121 QQIALWSAVVGFPHPVTKEEIELISLPPQTHPW 153 I L + V F HPV+KE IEL + P+ + W Sbjct: 185 GSICLHARKVRFIHPVSKELIELEAPLPEGNLW 217 >gb|EAD81786.1| unknown [environmental sequence] Length = 219 Score = 128 bits (322), Expect = 4e-29, Method: Compositional matrix adjust. Identities = 64/155 (41%), Positives = 91/155 (58%) Query: 1 MIFAKTSKAASRLSESVRSHSFHKVYLTVVHGKPPAAQGRLVHTLLKDAKTNTVTIVRKG 60 +IF+KTSK+ +R++E ++ K+Y + KP +L + L K+ K N +V + Sbjct: 65 LIFSKTSKSLTRMNELQKNRKIKKIYYAITEKKPKKDSNKLTNFLKKNQKKNKSFVVDES 124 Query: 61 TPGGKEAILDYTVIGSAEGYSLLKIDLLTGRSHQIRVQLSGIRCPLYGDQKYGAAVNKPG 120 K+A+L+Y VI E Y LL+I L TGR HQIR QLS I CP+ GD KYGA Sbjct: 125 DVKSKKAVLNYKVIKQLENYFLLEIILETGRHHQIRCQLSNIGCPIKGDVKYGAKRPNKD 184 Query: 121 QQIALWSAVVGFPHPVTKEEIELISLPPQTHPWSL 155 + I L S + F HPVTK+E+ + + PP T+ W L Sbjct: 185 RSICLHSNKIEFIHPVTKKELTITAQPPNTNIWLL 219 >gb|EAB62107.1| unknown [environmental sequence] Length = 171 Score = 122 bits (305), Expect = 4e-27, Method: Compositional matrix adjust. Identities = 62/155 (40%), Positives = 89/155 (57%) Query: 1 MIFAKTSKAASRLSESVRSHSFHKVYLTVVHGKPPAAQGRLVHTLLKDAKTNTVTIVRKG 60 +IF+KTSK+ +R++E ++ K Y + KP +L + L K+ N +V + Sbjct: 17 LIFSKTSKSLTRMNELQKNRKIKKTYYAITEKKPKKDSNKLTNFLKKNQTKNKSFVVDES 76 Query: 61 TPGGKEAILDYTVIGSAEGYSLLKIDLLTGRSHQIRVQLSGIRCPLYGDQKYGAAVNKPG 120 K+A+L+Y VI E Y LL+I L TGR HQIR QLS I CP+ GD KYGA Sbjct: 77 DVKSKKAVLNYKVIKKLENYFLLEIILETGRHHQIRCQLSHIGCPIKGDVKYGAKRPNKD 136 Query: 121 QQIALWSAVVGFPHPVTKEEIELISLPPQTHPWSL 155 + I L S + F HPVTK+E+ + + PP ++ W L Sbjct: 137 RSICLHSNKIEFIHPVTKKELTITAQPPNSNIWLL 171 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 0.318 0.133 0.397 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: 248,535,599 Number of extensions: 9645068 Number of successful extensions: 22781 Number of sequences better than 1.0e-05: 651 Number of HSP's gapped: 22617 Number of HSP's successfully gapped: 651 Length of query: 166 Length of database: 757,237,578 Length adjustment: 116 Effective length of query: 50 Effective length of database: 442,286,094 Effective search space: 22114304700 Effective search space used: 22114304700 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 (21.7 bits) S2: 121 (51.2 bits)