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= 0541.0072.p (379 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CAC1266 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 197 2e-50 BS_yjbO [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 174 3e-43 lin0968 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 171 2e-42 BS_yhcT [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 170 4e-42 BS_ylyB [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 168 1e-41 >CAC1266 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 299 Score = 197 bits (502), Expect = 2e-50, Method: Compositional matrix adjust. Identities = 115/313 (36%), Positives = 172/313 (54%), Gaps = 43/313 (13%) Query: 7 SPITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGDTV 66 + + Y V + + ++ L++ S +L+ E+ + +NG+ V +S RV GD + Sbjct: 4 NKLVYLVEKKYENFKIRDYLKQVHGFSTRLIRGAAFGER-LFVNGKTVRLSYRVLEGDKI 62 Query: 67 QIRMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQ 126 ++ + + S+++ P+ + I+YED ++V+NK A MIVHPT + TL+NG++YY+ + Sbjct: 63 EVDVNKPESQNVDPEKMDLNIVYEDSDIIVLNKPANMIVHPTKNYQHGTLSNGLLYYFRE 122 Query: 127 KGEQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGD 186 KGE R V+RLD +TSG++++AKN +SH ++ M T K Y A V G + L G Sbjct: 123 KGENCIVRLVNRLDMDTSGLVLVAKNQFSHMALARDMKLDTFKKEYIAVVRGNLSSLKGT 182 Query: 187 IDGPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSSIG 246 ID PI ++ EP RR + G S+T +EV E Y A KV+L LE+GRTHQIRVH+SSIG Sbjct: 183 IDKPIYKEEEEPIRRTIDDRGQESITHFEVVERYKNADKVKLVLETGRTHQIRVHLSSIG 242 Query: 247 CPLIGDGMYRHPLYSKAGLPAGEPGARVPERAQLERVAELDAKERVQLERIAELDASISR 306 P+IGD +Y GE +EL I R Sbjct: 243 NPIIGDSLY------------GEE-------------SEL-----------------IKR 260 Query: 307 QALHAVRLSFQHP 319 QALHA +L F HP Sbjct: 261 QALHAFKLQFPHP 273 >BS_yjbO [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 150 Score = 174 bits (440), Expect = 3e-43, Method: Compositional matrix adjust. Identities = 0/299 (0%), Positives = 0/299 (0%), Gaps = 43/299 (14%) Query: 30 MDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGDTVQIRM-EQETSEDILPQPLPFEIL 88 + S +++ ++R G + + Sbjct: 10 TLMCWNTRSNWWRISVNFSPKSSQIHHALRTVAGRFAVKSIDYFWHDSCNASKRFHIWES 69 Query: 89 YEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQKGEQFRFRPVHRLDQETSGVLV 148 E L V+ ++V G + V+ Sbjct: 70 IMLELLFVIGFFVMLMVTGVSLLGIIAALVVATAIMFLGGMLALMIKLLPWLLLAIAVVW 129 Query: 149 IAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGDIDGPIDRDPAEPHRRIVTPDGY 208 Sbjct: 130 189 Query: 209 PSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSSIGCPLIGDGMYRHPLYSKAGLPAG 268 Sbjct: 190 ------------- 236 Query: 269 EPGARVPERAQLERVAELDAKERVQLERIAELDASISRQALHAVRLSFQHPVLRTELVF 327 Sbjct: 237 ----------------------------- 266 >lin0968 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 200 Score = 171 bits (433), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 0/249 (0%), Positives = 0/249 (0%), Gaps = 3/249 (1%) Query: 9 ITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQG-IMLNGERVYISVRVNTGDTVQ 67 + + I++ R R+ + + + + Sbjct: 3 DKFGEGRDPYLYPGLDIMRNR-LNIRQQQRLEQAAYEMTALRAATIELGPLVRGLPHLRT 61 Query: 68 IRMEQETSED-ILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQ 126 I + Q +I D + G+ Sbjct: 62 IHRQLYQDIFDWAGQLREVDIYQGDTPFCHFAYIEKEGNALMQDLEEEGYLVGLEKAKFV 121 Query: 127 KGEQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGD 186 + + ++ L G + + + I AW + GD Sbjct: 122 ERLAHYYCEINVLHPFRVGSGLAQRIFFEQLAIHAGYQLSWQGIEKEAWNQANQSGAMGD 181 Query: 187 IDGPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSSIG 246 Sbjct: 182 241 Query: 247 CPLIGDGMY 255 Sbjct: 242 250 >BS_yhcT [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 302 Score = 170 bits (430), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 91/245 (37%), Positives = 144/245 (58%), Gaps = 3/245 (1%) Query: 13 VPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGDTVQIRMEQ 72 + +DG L ++L+ + S+ ++ M+ Q I +N E V ++ V GD V I +++ Sbjct: 12 INEKQDGQWLFSVLKTALKASKPVIQDW-MSHQQIKVNHESVLNNMIVKKGDRVFIDLQE 70 Query: 73 ETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQKGEQFR 132 + ++P+ +IL+ED H+L++NK AG+ HP T TLAN + Y++ GE + Sbjct: 71 SEASSVIPEYGELDILFEDNHMLIINKPAGIATHPNEDGQTGTLANLIAYHYQINGETCK 130 Query: 133 FRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGDIDGPID 192 R VHRLDQ+TSG +V AK+ +H + +Q+ T+ + Y A G G I+ PI Sbjct: 131 VRHVHRLDQDTSGAIVFAKHRLAHAILDQQLEKKTLKRTYTAIAEGKLRTKKGTINPPIG 190 Query: 193 RDPAEPHRRIVTPDGYPSLTRYEV--KEVYPGAAKVELKLESGRTHQIRVHMSSIGCPLI 250 RD + P RR V+P G ++T ++V + VEL+LE+GRTHQIRVH++S+G PL Sbjct: 191 RDRSHPTRRRVSPGGQTAVTHFKVMASNAKERLSLVELELETGRTHQIRVHLASLGHPLT 250 Query: 251 GDGMY 255 GD +Y Sbjct: 251 GDSLY 255 >BS_ylyB [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 273 Score = 168 bits (426), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 88/212 (41%), Positives = 130/212 (61%), Gaps = 3/212 (1%) Query: 47 IMLNGERVYISVRVNTGDTVQIRMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVH 106 +++NG V + ++ GD V + + + + D+L +P+ +I YED+ +LVVNK GM+VH Sbjct: 42 VVVNGSAVKANYKIQPGDQVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVH 101 Query: 107 PTHGHYTDTLANGVVYYWAQ-KGEQFRFRP--VHRLDQETSGVLVIAKNPYSHQHISEQM 163 P GH T TL NG++ + G RP VHR+D++TSG+L++AKN +H+ + Q+ Sbjct: 102 PAPGHLTGTLVNGLMAHCTDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQL 161 Query: 164 IAGTVDKRYNAWVHGVPAVLSGDIDGPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGA 223 + TV ++Y A VHG+ + G ID PI RD + VT DG ++T + V E + Sbjct: 162 VNKTVTRKYTAVVHGLISHDDGTIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLEGFQDF 221 Query: 224 AKVELKLESGRTHQIRVHMSSIGCPLIGDGMY 255 VE +LE+GRTHQIRVHM IG PL GD Y Sbjct: 222 TLVECQLETGRTHQIRVHMKYIGFPLAGDPKY 253 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.317 0.135 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 28,303,651 Number of extensions: 1133845 Number of successful extensions: 2802 Number of sequences better than 1.0e-05: 141 Number of HSP's gapped: 2543 Number of HSP's successfully gapped: 141 Length of query: 379 Length of database: 38,378,431 Length adjustment: 108 Effective length of query: 271 Effective length of database: 25,922,359 Effective search space: 7024959289 Effective search space used: 7024959289 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: 117 (49.7 bits)