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= 0231.0032.p (323 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CAC2114 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 163 3e-40 SMc00647 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 162 5e-40 mlr3740 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 157 2e-38 BMEI0377 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 154 1e-37 AGc4432 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific 147 2e-35 >CAC2114 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 305 Score = 163 bits (413), Expect = 3e-40, Method: Compositional matrix adjust. Identities = 101/285 (35%), Positives = 160/285 (56%), Gaps = 10/285 (3%) Query: 39 EPAELLAFLLKTITSRGRNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLEKPVQA 98 E + +L + + R+ I+ ++ + +V VNGKAV K N++L V ++ + Sbjct: 13 ENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAV-KSNYKLKSRDNVEFEIPDNEEL 71 Query: 99 K---EMTGLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQSNPHNRVF-- 153 K E L IVYED D++V+ K G++ + T L+ H + + N V Sbjct: 72 KIEAENIPLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGTLVNALLYHCKDLSGINGVLRP 131 Query: 154 -VVHRLDRDTSGVMMFAKSEQLQQTLQNTWKETVKERSYVALVEGVVKKPEGTISSWLKE 212 +VHR+D+DTSG+++ AK++ + L N KE R Y A+VEG++K+ EGT+ L Sbjct: 132 GIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVYRAVVEGIIKEDEGTVDKPLAR 191 Query: 213 TSTLKMYSSPHEGDGLHAVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGD 272 ++ + +G G +AVTHYK+++ R+ +L+E LETGR +QIRVHM+ IGH +VGD Sbjct: 192 HPVERVKIAVVKG-GRNAVTHYKVLERYRNSTLIECKLETGRTHQIRVHMAYIGHALVGD 250 Query: 273 KKYGAETKAVGRLG--LHARLLSFVHPSSGELLTFESAIPKTFLK 315 YG + + G LHA+ L F+HP+ G+ + FE P F K Sbjct: 251 PLYGYKKQRFNLEGQMLHAQKLGFIHPTKGKYMEFEREAPSHFQK 295 >SMc00647 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 343 Score = 162 bits (411), Expect = 5e-40, Method: Compositional matrix adjust. Identities = 110/304 (36%), Positives = 159/304 (52%), Gaps = 36/304 (11%) Query: 43 LLAFLLKTITSR-GRNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDL---EKPVQA 98 L AFL + + RN IKS++ +G VS+NG VT+ ++HPG + I L E P Sbjct: 25 LDAFLTEALAGEFSRNRIKSLIEQGAVSINGATVTEPKRKVHPGDSFRIALPEPEDPEPK 84 Query: 99 KEMTGLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQS----NPHNRVFV 154 E L ++YED DLIV+ K AGL+ + T L+ H S R + Sbjct: 85 GEAIPLDVLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVKRPGI 144 Query: 155 VHRLDRDTSGVMMFAKSEQLQQTLQNTWKETVK----ERSYVALVEGVVKKPEGTISSWL 210 VHRLD+DTSGVM+ AK++ + L + + + + ER+Y A+V G ++ +G I + L Sbjct: 145 VHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVWGRPRQLKGKIDAPL 204 Query: 211 KETS--TLKMYSSPHEGDGLHAVTHYKLIQ-------GNRHFSLLEVHLETGRKNQIRVH 261 T + D A+THY++++ G S +E HLETGR +QIRVH Sbjct: 205 GRAGDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSLASTVECHLETGRTHQIRVH 264 Query: 262 MSDIGHPIVGDKKYGA--ETKA-------------VGRLGLHARLLSFVHPSSGELLTFE 306 M+ IGHP++GD YGA TKA R LHA +L F HP++GE + FE Sbjct: 265 MAHIGHPLIGDPDYGAAFRTKANLLPEPARAAVNRFPRQALHAFMLQFEHPATGETMHFE 324 Query: 307 SAIP 310 + +P Sbjct: 325 TPVP 328 >mlr3740 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 200 Score = 157 bits (398), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 0/293 (0%), Positives = 0/293 (0%), Gaps = 35/293 (11%) Query: 56 RNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLEKPVQAK---EMTGLTIVYEDDD 112 R + + +++ A + + + + Q + D Sbjct: 27 RQQQRLEQAAYEMTALRAATIELGPLVRGLPHLRTIHRQLYQDIFDWAGQLREVDIYQGD 86 Query: 113 LIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQS----NPHNRVFVVHRLDRDTSGVMMF 168 + + + + V R SG+ Sbjct: 87 TPFCHFAYIEKEGNALMQDLEEEGYLVGLEKAKFVERLAHYYCEINVLHPFRVGSGLAQR 146 Query: 169 AKSEQLQQTLQNTWKETVK----ERSYVALVEGVVKKPEGTISSWLKETSTLKMYSSPHE 224 EQL Sbjct: 147 IFFEQLAIHAGYQLSWQGIEKEA 206 Query: 225 G--DGLHAVTHY----KLIQGNRHF---SLLEVHLETGRKNQIRVHMSDIGHPIVGDKKY 275 Sbjct: 207 266 Query: 276 G---------------AETKAVGRLGLHARLLSFVHPSSGELLTFESAIPKTF 313 Sbjct: 267 319 >BMEI0377 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 347 Score = 154 bits (390), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 103/294 (35%), Positives = 157/294 (53%), Gaps = 36/294 (12%) Query: 56 RNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLEKPVQAK---EMTGLTIVYEDDD 112 R+ ++S+++ G V+++G + +L G + I L +P A+ E L I+YEDDD Sbjct: 42 RSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIVLPEPEPAEPQGENIPLDILYEDDD 101 Query: 113 LIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQS----NPHNRVFVVHRLDRDTSGVMMF 168 LIVI K AGL+ + T L+ S R +VHRLD+DTSGVM+ Sbjct: 102 LIVINKPAGLVVHPGNGNWTGTLVNALIYQCGDSLSGIGGIRRPGIVHRLDKDTSGVMVV 161 Query: 169 AKSEQLQQTLQNTWKETVK----ERSYVALVEGVVKKPEGTISSWLKET---STLKMYSS 221 AK+++ + L + + + ER+Y+ALV G+ ++P+GT+ ++L + T + Sbjct: 162 AKNDRAHRHLSEQFADHGRTGDLERAYLALVWGMTERPQGTVDAYLGRSHRDRTKQAVVH 221 Query: 222 PHEGDGLHAVTHYKLIQ-------GNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGDKK 274 D HA+THY ++ SL+E LETGR +QIRVHM+ IGHP+VGD Sbjct: 222 EEREDARHAITHYATVEKFSPREDATALASLVECRLETGRTHQIRVHMAHIGHPLVGDMD 281 Query: 275 YGA--ETKA-------------VGRLGLHARLLSFVHPSSGELLTFESAIPKTF 313 YG+ +TKA R LHA LL+F HP + EL+ FE+ +P+ Sbjct: 282 YGSAYKTKANKLPEPLKEAVQGFHRQALHAWLLAFTHPITEELMRFEAPLPEDM 335 >AGc4432 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific Length = 340 Score = 147 bits (372), Expect = 2e-35, Method: Compositional matrix adjust. Identities = 101/293 (34%), Positives = 157/293 (53%), Gaps = 35/293 (11%) Query: 56 RNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTI---DLEKPVQAKEMTGLTIVYEDDD 112 R+ +K+++ +G V +NG+ VT+ ++HPG V I + E PV E L + YED+D Sbjct: 39 RSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRVEIVMPEPEDPVPQGEDIPLDVEYEDED 98 Query: 113 LIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQS----NPHNRVFVVHRLDRDTSGVMMF 168 LIV+ K AGL+ + T L+ H S R +VHRLD++TSGVM+ Sbjct: 99 LIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVKRPGIVHRLDKETSGVMVV 158 Query: 169 AKSEQLQQTLQNTWKETVK----ERSYVALVEGVVKKPEGTISSWLKETS--TLKMYSSP 222 AK++ + L + + + ER+Y A+V G + GT+ + L + T + + Sbjct: 159 AKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRPRTLRGTVDAALGRGTDRTKRAVKNE 218 Query: 223 HEGDGLHAVTHYKLIQ-------GNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGDKKY 275 D A+THY++++ + S++E LETGR +QIRVHM+ IGHP++GD +Y Sbjct: 219 DSFDAREAITHYEVMERFHEKPDASCLASMVECRLETGRTHQIRVHMAHIGHPLIGDPEY 278 Query: 276 GA--ETKA-------------VGRLGLHARLLSFVHPSSGELLTFESAIPKTF 313 GA TKA R LHA LL+F HP +GE++ FE+ +P+ Sbjct: 279 GAAFRTKANLLDEPARSTVNRFPRQALHAYLLAFEHPRTGEVMEFETDMPEDM 331 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 0.315 0.130 0.367 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: 22,049,538 Number of extensions: 878800 Number of successful extensions: 2036 Number of sequences better than 1.0e-05: 146 Number of HSP's gapped: 1691 Number of HSP's successfully gapped: 147 Length of query: 323 Length of database: 38,378,431 Length adjustment: 107 Effective length of query: 216 Effective length of database: 26,037,693 Effective search space: 5624141688 Effective search space used: 5624141688 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: 116 (49.3 bits)