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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KL16.1 B3KL16_9BACI Pseudouridine synthase, RluA family EC=3.2... 352 5e-95 B1DDS6.1 B1DDS6_9BACL Pseudouridine synthase, RluA family EC=3.2... 228 1e-57 C3BHL1.1 C3BHL1_9BACI Pseudouridine synthase 211 8e-53 C3B0Y6.1 C3B0Y6_BACMY Pseudouridine synthase 211 8e-53 C3AJ33.1 C3AJ33_BACMY Pseudouridine synthase 211 8e-53 >B3KL16.1 B3KL16_9BACI Pseudouridine synthase, RluA family EC=3.2.1.17 Length = 302 Score = 352 bits (902), Expect = 5e-95, Method: Compositional matrix adjust. Identities = 167/255 (65%), Positives = 200/255 (78%) Query: 10 VTGGGAWTRRGEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGIQWKG 69 ++ GG+W++RGEWLE+ PG+ + + + A KWLL TVGMP KL+ +L E GIQW+G Sbjct: 1 MSYGGSWSKRGEWLEMTPGKALLGQPDRDEAAAKWLLETVGMPEKLYRKLHHEQGIQWRG 60 Query: 70 DRLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHVVAAH 129 DRLRL LFPYRE GIEP WQEL+VL+EDDFCLVV+KPAG+AVHPD E TL+HVVAA+ Sbjct: 61 DRLRLVLFPYREYGIEPRWQELQVLYEDDFCLVVNKPAGLAVHPDNESRETTLNHVVAAY 120 Query: 130 YSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGVVPPE 189 Y G AVRH+HRLDKDTTGPVLYAKNEYAQL LDE MR K + R+YAAIV+G V E Sbjct: 121 YEAEGIHAAVRHIHRLDKDTTGPVLYAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQE 180 Query: 190 LKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLRSGTVLKVQLETGRTHQIRVHLS 249 LK ID PIG+DR+HA+RRRVS GQ A+T I+ E ++L ++LETGRTHQIRVHLS Sbjct: 181 LKRIDLPIGKDRYHASRRRVSLTGQAAITHILSAEAYPKASLLHIRLETGRTHQIRVHLS 240 Query: 250 HLGHPLYGDTLYGGP 264 H+GHPL GD LYGGP Sbjct: 241 HMGHPLLGDVLYGGP 255 >B1DDS6.1 B1DDS6_9BACL Pseudouridine synthase, RluA family EC=3.2.1.17 Length = 332 Score = 228 bits (580), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 130/279 (46%), Positives = 166/279 (59%), Gaps = 31/279 (11%) Query: 16 WTRRGEWLEVMPGRVI-------TAAGE-------PEAA-----IDKWLLATVGMPVKLH 56 + R G+WL ++P + TA+G+ PEA + +WLLA P K Sbjct: 6 YRREGQWLSLLPADLAGEAAGKDTASGQQTEQLSIPEAGSHPHLVRQWLLACSLFPAKWI 65 Query: 57 ERLRREGGIQWKGDRLRLALFP---------YRE---AGIEPAWQELEVLFEDDFCLVVH 104 RL GGI W+G+R+RL FP YR+ +G Q EVL+EDDF LV++ Sbjct: 66 NRLFSVGGIGWEGERIRLLAFPPVDPVSDSLYRKVKSSGHSLLEQTTEVLYEDDFSLVLN 125 Query: 105 KPAGMAVHPDGSGTEVTLDHVVAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLA 164 KPAGM VH SG TLD A G VRH+HRLD DT+GPVLY+KN+ AQ Sbjct: 126 KPAGMPVHESHSGQTGTLDEAAARWLLEQGDPLPVRHIHRLDDDTSGPVLYSKNDLAQWV 185 Query: 165 LDEDMRAKAVSRLYAAIVEGVVPPELKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDRE 224 LDE MR K + R Y A+V+G V ++APIG+DRHH++RRRV+PGG A+T Sbjct: 186 LDEAMREKRIDRRYLAVVQGKVKKSSGTVNAPIGKDRHHSSRRRVTPGGDLAITHYETIR 245 Query: 225 VLRSGTVLKVQLETGRTHQIRVHLSHLGHPLYGDTLYGG 263 T++++QLETGRTHQIRVH+SHLGHPL GD LYGG Sbjct: 246 AFSDATLVRLQLETGRTHQIRVHMSHLGHPLLGDKLYGG 284 >C3BHL1.1 C3BHL1_9BACI Pseudouridine synthase Length = 307 Score = 211 bits (538), Expect = 8e-53, Method: Compositional matrix adjust. Identities = 121/272 (44%), Positives = 162/272 (59%), Gaps = 19/272 (6%) Query: 18 RRGEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGI-------QW--- 67 R+GEW E+ A +ID L G+P KL +LR E GI +W Sbjct: 5 RKGEWCEI-----TVPAKWSGISIDSLLKEEWGVPKKLLHQLRMEKGIIVNGERKRWSEP 59 Query: 68 --KGDRLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHV 125 +GD+L++ +F E G++P + +LEV+FEDD L+V+KPA M HP G TL ++ Sbjct: 60 LAEGDKLQVHMFIQEEYGVQPEFGDLEVIFEDDHVLIVNKPAHMDTHPSSKGGTGTLANL 119 Query: 126 VAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGV 185 VA H + G T VRH+HRLDKDTTG V++AK+ A +D + + + R Y A+VEG Sbjct: 120 VAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGAIMDRLLMERNIKRTYLALVEGK 179 Query: 186 VPPELKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLRSG--TVLKVQLETGRTHQ 243 V + +IDA IGRDRHHA RRRVS G AVT + + T++ +QLETG+THQ Sbjct: 180 VKKKQGIIDAAIGRDRHHATRRRVSLKGDQAVTHYRVEKYFKHQDVTLVTLQLETGKTHQ 239 Query: 244 IRVHLSHLGHPLYGDTLYGGPPWSAAGQRSHS 275 IRVH+SH GHPL GDTLYGG + Q H+ Sbjct: 240 IRVHMSHSGHPLIGDTLYGGQSTYMSSQALHA 271 >C3B0Y6.1 C3B0Y6_BACMY Pseudouridine synthase Length = 307 Score = 211 bits (538), Expect = 8e-53, Method: Compositional matrix adjust. Identities = 121/272 (44%), Positives = 162/272 (59%), Gaps = 19/272 (6%) Query: 18 RRGEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGI-------QW--- 67 R+GEW E+ A +ID L G+P KL +LR E GI +W Sbjct: 5 RKGEWCEI-----TVPAKWSGISIDSLLKEEWGVPKKLLHQLRMEKGIIVNGERKRWSEP 59 Query: 68 --KGDRLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHV 125 +GD+L++ +F E G++P + +LEV+FEDD L+V+KPA M HP G TL ++ Sbjct: 60 LAEGDKLQVHMFIQEEYGVQPEFGDLEVIFEDDHVLIVNKPAHMDTHPSSKGGTGTLANL 119 Query: 126 VAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGV 185 VA H + G T VRH+HRLDKDTTG V++AK+ A +D + + + R Y A+VEG Sbjct: 120 VAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGAIMDRLLMERNIKRTYLALVEGK 179 Query: 186 VPPELKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLRSG--TVLKVQLETGRTHQ 243 V + +IDA IGRDRHHA RRRVS G AVT + + T++ +QLETG+THQ Sbjct: 180 VKKKQGIIDAAIGRDRHHATRRRVSLKGDQAVTHYRVEKYFKHQDVTLVTLQLETGKTHQ 239 Query: 244 IRVHLSHLGHPLYGDTLYGGPPWSAAGQRSHS 275 IRVH+SH GHPL GDTLYGG + Q H+ Sbjct: 240 IRVHMSHSGHPLIGDTLYGGQSTYMSSQALHA 271 >C3AJ33.1 C3AJ33_BACMY Pseudouridine synthase Length = 307 Score = 211 bits (538), Expect = 8e-53, Method: Compositional matrix adjust. Identities = 121/272 (44%), Positives = 162/272 (59%), Gaps = 19/272 (6%) Query: 18 RRGEWLEVMPGRVITAAGEPEAAIDKWLLATVGMPVKLHERLRREGGI-------QW--- 67 R+GEW E+ A +ID L G+P KL +LR E GI +W Sbjct: 5 RKGEWCEI-----TVPAKWSGISIDSLLKEEWGVPKKLLHQLRMEKGIIVNGERKRWSEP 59 Query: 68 --KGDRLRLALFPYREAGIEPAWQELEVLFEDDFCLVVHKPAGMAVHPDGSGTEVTLDHV 125 +GD+L++ +F E G++P + +LEV+FEDD L+V+KPA M HP G TL ++ Sbjct: 60 LAEGDKLQVHMFIQEEYGVQPEFGDLEVIFEDDHVLIVNKPAHMDTHPSSKGGTGTLANL 119 Query: 126 VAAHYSVSGGGTAVRHLHRLDKDTTGPVLYAKNEYAQLALDEDMRAKAVSRLYAAIVEGV 185 VA H + G T VRH+HRLDKDTTG V++AK+ A +D + + + R Y A+VEG Sbjct: 120 VAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGAIMDRLLMERNIKRTYLALVEGK 179 Query: 186 VPPELKVIDAPIGRDRHHAARRRVSPGGQTAVTRIMDREVLRSG--TVLKVQLETGRTHQ 243 V + +IDA IGRDRHHA RRRVS G AVT + + T++ +QLETG+THQ Sbjct: 180 VKKKQGIIDAAIGRDRHHATRRRVSLKGDQAVTHYRVEKYFKHQDVTLVTLQLETGKTHQ 239 Query: 244 IRVHLSHLGHPLYGDTLYGGPPWSAAGQRSHS 275 IRVH+SH GHPL GDTLYGG + Q H+ Sbjct: 240 IRVHMSHSGHPLIGDTLYGGQSTYMSSQALHA 271 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 0.317 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: 9421015 Number of Hits to DB: 2,574,325,560 Number of extensions: 124728737 Number of successful extensions: 363260 Number of sequences better than 1.0e-05: 4687 Number of HSP's gapped: 355310 Number of HSP's successfully gapped: 4689 Length of query: 365 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 228 Effective length of database: 1,770,017,148 Effective search space: 403563909744 Effective search space used: 403563909744 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: 132 (55.5 bits)