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= 0345.0006.p (252 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KHK0.1 B3KHK0_9BACI Pseudouridine synthase EC=5.4.99.- 330 7e-89 B1DFI6.1 B1DFI6_9BACL Pseudouridine synthase EC=5.4.99.- 306 1e-81 A1HLV7.1 A1HLV7_9FIRM Pseudouridine synthase EC=5.4.99.- 293 1e-77 B0A959.1 B0A959_9CLOT Pseudouridine synthase EC=5.4.99.- 283 8e-75 Q2B4L3.1 Q2B4L3_9BACI Pseudouridine synthase EC=5.4.99.- 283 8e-75 >B3KHK0.1 B3KHK0_9BACI Pseudouridine synthase EC=5.4.99.- Length = 253 Score = 330 bits (846), Expect = 7e-89, Method: Compositional matrix adjust. Identities = 171/251 (68%), Positives = 198/251 (78%), Gaps = 6/251 (2%) Query: 1 MSATGNSSKKQRIDKVLSHMGIGSRSDIRKQAKQGLIRVNGTVIKDSGFHVDPYADTIEV 60 MS G ++ QR+DKVLS++G GSR++++K+AKQG I VNGTV KD G HVDPYAD IE Sbjct: 1 MSGKGRTT--QRLDKVLSNLGFGSRAELKKKAKQGSIVVNGTVTKDPGKHVDPYADIIEF 58 Query: 61 SGEPVVYREYIYLMMNKPPGVLSATEDKRDRTVLDLLKPEYAQFEPFPVGRLDKDTVGLL 120 GE + YREY+YLM++KPPGV+SATED RDRTVLDLL EY FEPFPVGRLDKDT GLL Sbjct: 59 EGETIQYREYVYLMLHKPPGVVSATEDLRDRTVLDLLDAEYRVFEPFPVGRLDKDTEGLL 118 Query: 121 LLTNDGQLAHELLSPRKHVPKTYEATVEGEVDXXXXXXXXXGVELEDGYVTLPAQLTILG 180 LLTNDG+LAHELLSPRKH+PKTYEATVEG VD GV L+DGYVTLP +L I Sbjct: 119 LLTNDGKLAHELLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLDDGYVTLPGELAIHS 178 Query: 181 ---RERGSKTLSQISLTITEGKFHQVKRMFLAVGKKVVFLKRVSMGALKLDERLAPGACR 237 RE G + LS+ISLTI EGKFHQVKRMF AVGKKVV+LKR+SMG L+LDE L G R Sbjct: 179 HEEREDGVQ-LSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYR 237 Query: 238 ELTAEELRVLG 248 ELT +EL ++G Sbjct: 238 ELTEQELALIG 248 >B1DFI6.1 B1DFI6_9BACL Pseudouridine synthase EC=5.4.99.- Length = 249 Score = 306 bits (784), Expect = 1e-81, Method: Compositional matrix adjust. Identities = 160/242 (66%), Positives = 185/242 (76%), Gaps = 1/242 (0%) Query: 9 KKQRIDKVLSHMGIGSRSDIRKQAKQGLIRVNGTVIKDSGFHVDPYADTIEVSGEPVVYR 68 KK RIDK+LSH G G+RS+I+K KQG + V G V+KDSG VDP D + GE V+YR Sbjct: 3 KKMRIDKLLSHTGYGTRSEIKKLVKQGKVTVAGKVVKDSGQLVDPELDEVAFDGELVLYR 62 Query: 69 EYIYLMMNKPPGVLSATEDKRDRTVLDLLKPEYAQFEPFPVGRLDKDTVGLLLLTNDGQL 128 E IYLMMNKPPGV+SATED+R+RTV+DLL+ E +PFPVGRLDKDTVGLLLLTNDGQL Sbjct: 63 EVIYLMMNKPPGVISATEDRRERTVIDLLEQEDQLMDPFPVGRLDKDTVGLLLLTNDGQL 122 Query: 129 AHELLSPRKHVPKTYEATVEGEVDXXXXXXXXXGVELEDGYVTLPAQLTILGRERGSKTL 188 AHELLSPRKHVPKTYEA V+G+V GV L+DGYVT+P+ L IL ++ G + Sbjct: 123 AHELLSPRKHVPKTYEAVVQGDVGEEDQEQFKAGVTLDDGYVTMPSDLKILKKDSGEGGV 182 Query: 189 -SQISLTITEGKFHQVKRMFLAVGKKVVFLKRVSMGALKLDERLAPGACRELTAEELRVL 247 S ISLTI EGKFHQVKRMF AVGKKVVFLKR+SMG L+LD L G RELT EEL +L Sbjct: 183 TSVISLTIMEGKFHQVKRMFEAVGKKVVFLKRISMGPLELDADLEEGTYRELTDEELALL 242 Query: 248 GA 249 A Sbjct: 243 RA 244 >A1HLV7.1 A1HLV7_9FIRM Pseudouridine synthase EC=5.4.99.- Length = 245 Score = 293 bits (749), Expect = 1e-77, Method: Compositional matrix adjust. Identities = 148/241 (61%), Positives = 179/241 (74%), Gaps = 4/241 (1%) Query: 9 KKQRIDKVLSHMGIGSRSDIRKQAKQGLIRVNGTVIKDSGFHVDPYADTIEVSGEPVVYR 68 ++QR+DKVL+H+G GSR +I+K K + VNG V++D HV P+ D IEV GEP+ YR Sbjct: 5 ERQRLDKVLAHLGYGSRREIKKMVKAERVIVNGAVVRDPELHVFPWQDRIEVDGEPIHYR 64 Query: 69 EYIYLMMNKPPGVLSATEDKRDRTVLDLLKPEYAQFEPFPVGRLDKDTVGLLLLTNDGQL 128 EYIYLMMNKP GVLSATED + V+DLL+PE+ F PFPVGRLDKDT GLLLLTNDGQL Sbjct: 65 EYIYLMMNKPQGVLSATEDAAGKVVVDLLRPEHKAFAPFPVGRLDKDTEGLLLLTNDGQL 124 Query: 129 AHELLSPRKHVPKTYEATVEGEVDXXXXXXXXXGVELEDGYVTLPAQLTILGRERGSKTL 188 AH LL+P+KHVPK Y A V+G V G+ L+DGY TLPA+LTIL + + Sbjct: 125 AHRLLAPKKHVPKRYYARVKGVVTDEDKGAFQAGITLDDGYRTLPAELTIL----HAGPV 180 Query: 189 SQISLTITEGKFHQVKRMFLAVGKKVVFLKRVSMGALKLDERLAPGACRELTAEELRVLG 248 S++ L I EGKFHQVKRMF A GK V +LKR++MGAL LDE+LAPG RELTA+EL LG Sbjct: 181 SEVELVIYEGKFHQVKRMFAARGKTVTYLKRLAMGALVLDEKLAPGEYRELTADELASLG 240 Query: 249 A 249 A Sbjct: 241 A 241 >B0A959.1 B0A959_9CLOT Pseudouridine synthase EC=5.4.99.- Length = 258 Score = 283 bits (725), Expect = 8e-75, Method: Compositional matrix adjust. Identities = 146/240 (60%), Positives = 177/240 (73%), Gaps = 4/240 (1%) Query: 8 SKKQRIDKVLSHMGIGSRSDIRKQAKQGLIRVNGTVIKDSGFHVDPYADTIEVSGEPVVY 67 SKKQRIDK+LS++G GSRS+++K K GL++VNG VI + G VD D I GE V Y Sbjct: 19 SKKQRIDKILSNLGYGSRSELKKFCKNGLVKVNGKVINNPGVQVDVENDEIIFDGEKVTY 78 Query: 68 REYIYLMMNKPPGVLSATEDKRDRTVLDLLKPEYAQFEPFPVGRLDKDTVGLLLLTNDGQ 127 +E+IYLM+NKP G +SAT DKRD VLDL+ E FEPFPVGRLDKDT GLL+LTNDGQ Sbjct: 79 KEFIYLMLNKPDGYISATFDKRDPIVLDLIDKEDLVFEPFPVGRLDKDTEGLLVLTNDGQ 138 Query: 128 LAHELLSPRKHVPKTYEATVEGEVDXXXXXXXXXGVELEDGYVTLPAQLTILGRERGSKT 187 LAH +LSP+KHVPKTY A +EG V GV L+DGY T+PA+L IL S Sbjct: 139 LAHRVLSPKKHVPKTYYAKIEGIVTEEDIKAFAKGVTLDDGYETMPAELIIL----KSDE 194 Query: 188 LSQISLTITEGKFHQVKRMFLAVGKKVVFLKRVSMGALKLDERLAPGACRELTAEELRVL 247 +S+I LTI EGKFHQVKRMF +V KKV++LKR+SMG LKLDE LA G RELT EE++++ Sbjct: 195 ISEIELTIHEGKFHQVKRMFESVDKKVIYLKRLSMGKLKLDENLALGEYRELTDEEVKMI 254 >Q2B4L3.1 Q2B4L3_9BACI Pseudouridine synthase EC=5.4.99.- Length = 239 Score = 283 bits (725), Expect = 8e-75, Method: Compositional matrix adjust. Identities = 148/236 (62%), Positives = 173/236 (73%), Gaps = 4/236 (1%) Query: 12 RIDKVLSHMGIGSRSDIRKQAKQGLIRVNGTVIKDSGFHVDPYADTIEVSGEPVVYREYI 71 RIDKVL+++G GSR +++K K G + VN IKD+ HVDP D I ++GE V YRE+I Sbjct: 2 RIDKVLANLGYGSRKEVKKLLKDGSVTVNDEKIKDAKQHVDPEKDLIRINGETVEYREFI 61 Query: 72 YLMMNKPPGVLSATEDKRDRTVLDLLKPEYAQFEPFPVGRLDKDTVGLLLLTNDGQLAHE 131 YLMMNKPPGV+SATED RD TV+DLL+ E FEPFPVGRLDKDT GLLL+TNDGQLAH Sbjct: 62 YLMMNKPPGVISATEDNRDETVIDLLEAEDLIFEPFPVGRLDKDTEGLLLITNDGQLAHR 121 Query: 132 LLSPRKHVPKTYEATVEGEVDXXXXXXXXXGVELEDGYVTLPAQLTILGRERGSKTLSQI 191 LLSP+KHVPKTY A ++ EV GV L+DGY T P +L IL S S I Sbjct: 122 LLSPKKHVPKTYFAVIDQEVTEEDVTAFRKGVILDDGYATKPGELNIL----KSGERSDI 177 Query: 192 SLTITEGKFHQVKRMFLAVGKKVVFLKRVSMGALKLDERLAPGACRELTAEELRVL 247 LTITEGKFHQVKRMF AVGKKVV+L+R+SMG L+LDE L G RELT EEL+ L Sbjct: 178 ELTITEGKFHQVKRMFEAVGKKVVYLQRLSMGPLRLDETLELGEYRELTEEELQSL 233 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 0.316 0.136 0.377 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: 1,424,652,597 Number of extensions: 57920012 Number of successful extensions: 131130 Number of sequences better than 1.0e-05: 3468 Number of HSP's gapped: 124515 Number of HSP's successfully gapped: 3468 Length of query: 252 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 120 Effective length of database: 1,817,122,223 Effective search space: 218054666760 Effective search space used: 218054666760 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: 129 (54.3 bits)