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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KB50.1 B3KB50_9BACI Pseudouridine synthase EC=5.4.99.- 447 e-124 B1D7C3.1 B1D7C3_9BACL Pseudouridine synthase EC=5.4.99.- 331 7e-89 A6TSZ4.1 A6TSZ4_ALKMQ Pseudouridine synthase EC=5.4.99.- 212 6e-53 Q97JK8.1 Q97JK8_CLOAB Pseudouridine synthase EC=5.4.99.- 197 1e-48 A8MF48.1 A8MF48_ALKOO Pseudouridine synthase EC=5.4.99.- 197 1e-48 >B3KB50.1 B3KB50_9BACI Pseudouridine synthase EC=5.4.99.- Length = 354 Score = 447 bits (1150), Expect = e-124, Method: Compositional matrix adjust. Identities = 228/325 (70%), Positives = 252/325 (77%), Gaps = 11/325 (3%) Query: 5 YYSPITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGD 64 YY PI Y VP EDG LLKTILQKRM VSRKLLSRLK+TEQGIMLNG RVYISV+V GD Sbjct: 4 YYPPIRYVVPSHEDGMLLKTILQKRMGVSRKLLSRLKLTEQGIMLNGTRVYISVKVQAGD 63 Query: 65 TVQIRMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYW 124 V+IRMEQE S D+LPQP+ ILYEDEHLLV+NK AG+IVHPTHGHYTDTLANGVV+YW Sbjct: 64 LVEIRMEQERSNDMLPQPMELHILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHYW 123 Query: 125 AQKGEQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLS 184 +KG +RFR VHRLDQETSGVLVIAKN Y HQH+SEQMIAGTVDKRY A+VHG P+ + Sbjct: 124 QEKGWNYRFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSSQT 183 Query: 185 GDIDGPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSS 244 GDIDGPIDRDP EPHRRIVTP+GYPSLTRY V E YP A+ VELKLE+GRTHQIRVHM S Sbjct: 184 GDIDGPIDRDPLEPHRRIVTPEGYPSLTRYRVCETYPSASLVELKLETGRTHQIRVHMLS 243 Query: 245 IGCPLIGDGMYRHPLYSKAGLPAGEPGARVPERAQLER--VAELDAKERVQLERIAELDA 302 IGCPLIGD MYRHP+YS+ GL P A PER + V LD I LD Sbjct: 244 IGCPLIGDQMYRHPVYSEQGL---LPDA--PERDEDSNGAVGSLDPLAAT----IMRLDG 294 Query: 303 SISRQALHAVRLSFQHPVLRTELVF 327 + RQALHA L+ HP+ +VF Sbjct: 295 YMDRQALHAASLTLMHPIEGKTMVF 319 >B1D7C3.1 B1D7C3_9BACL Pseudouridine synthase EC=5.4.99.- Length = 316 Score = 331 bits (849), Expect = 7e-89, Method: Compositional matrix adjust. Identities = 166/321 (51%), Positives = 217/321 (67%), Gaps = 37/321 (11%) Query: 4 GYYSPITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTG 63 GYY + +V G ++T+L++++ VSR LLSRLK+TE GI +NG R Y + +V G Sbjct: 8 GYYKALAVEVGADMAGKDVRTVLERKLGVSRSLLSRLKLTEYGITVNGVRAYTTAKVTEG 67 Query: 64 DTVQIRMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYY 123 D+V IRME+E SEDILPQ LP I++ED++LLVVNK AG+IVHPT GHYT+TLANG+V++ Sbjct: 68 DSVAIRMEEEISEDILPQDLPLSIVFEDDYLLVVNKPAGIIVHPTKGHYTNTLANGIVHH 127 Query: 124 WAQKGEQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVL 183 W +GE+ RFRPVHRLD++TSG++VIAKNPY HQ +SEQ+ AGT+ K Y A+V+G P+ Sbjct: 128 WQVRGERVRFRPVHRLDEDTSGLVVIAKNPYIHQQLSEQLQAGTIMKIYCAYVYGTPSPA 187 Query: 184 SGDIDGPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPG--AAKVELKLESGRTHQIRVH 241 G + PIDR+P +PH RIVTP+GYPS+T Y+ V+ G A+KV LKLE+GRTHQIRVH Sbjct: 188 DGTVGAPIDRNPEDPHVRIVTPEGYPSVTHYKTAAVFGGGQASKVRLKLETGRTHQIRVH 247 Query: 242 MSSIGCPLIGDGMYRHPLYSKAGLPAGEPGARVPERAQLERVAELDAKERVQLERIAELD 301 M IGCPLIGDGMY GL G ++ E + Sbjct: 248 MKHIGCPLIGDGMY--------GLQTG---------------------------KVDEWE 272 Query: 302 ASISRQALHAVRLSFQHPVLR 322 + RQALHA L HP+ + Sbjct: 273 TAAGRQALHAETLGLTHPMTK 293 >A6TSZ4.1 A6TSZ4_ALKMQ Pseudouridine synthase EC=5.4.99.- Length = 308 Score = 212 bits (539), Expect = 6e-53, Method: Compositional matrix adjust. Identities = 110/247 (44%), Positives = 160/247 (64%), Gaps = 2/247 (0%) Query: 9 ITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGDTVQI 68 ITY+V +D LK L+ R+D+S +LL++LK +++ I++NG+ ++ GD ++I Sbjct: 12 ITYEVEAEDDQQPLKETLKNRLDLSSRLLTKLKKSKR-ILINGQYAKYHELLSEGDWIKI 70 Query: 69 RMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQKG 128 M +E S+ PQ +PF ++YED ++V+NK G++ HPT H DT+AN Y +KG Sbjct: 71 DMTEEASQ-FEPQEIPFNVVYEDIDVIVINKEPGIVSHPTKSHPKDTIANAAQNYLEKKG 129 Query: 129 EQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGDID 188 R R V+RLD +TSG+LVIAKNPY+H +S+QM A + K+Y A+V GV G+ID Sbjct: 130 VACRIRFVNRLDMDTSGLLVIAKNPYTHHIMSQQMKANEITKKYVAFVKGVVVANEGEID 189 Query: 189 GPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSSIGCP 248 G I R E +R+V G SLT++ V E Y A +E+ L +GRTHQIRVHM SIG P Sbjct: 190 GAIYRSSDETIKRVVDDRGQQSLTKFTVLERYADATMLEVSLLTGRTHQIRVHMESIGHP 249 Query: 249 LIGDGMY 255 ++GD +Y Sbjct: 250 MLGDHLY 256 >Q97JK8.1 Q97JK8_CLOAB Pseudouridine synthase EC=5.4.99.- Length = 299 Score = 197 bits (502), Expect = 1e-48, 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 >A8MF48.1 A8MF48_ALKOO Pseudouridine synthase EC=5.4.99.- Length = 305 Score = 197 bits (501), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 108/247 (43%), Positives = 152/247 (61%), Gaps = 2/247 (0%) Query: 9 ITYQVPPSEDGWLLKTILQKRMDVSRKLLSRLKMTEQGIMLNGERVYISVRVNTGDTVQI 68 I Y+ + G LK IL+ ++D S +LL+R+K + I +NGE + +N GD ++I Sbjct: 12 IIYEAENDDAGKELKKILKNKLDFSSRLLARVKRG-KTIFVNGEYLKYHETINAGDEIKI 70 Query: 69 RMEQETSEDILPQPLPFEILYEDEHLLVVNKAAGMIVHPTHGHYTDTLANGVVYYWAQKG 128 ME E + L Q +PFE +YED L++VNK G++ HPT H T+ANG Y KG Sbjct: 71 VMEDEPNHFTL-QDVPFEAVYEDVDLILVNKEPGIVTHPTKSHPDWTIANGAALYLKSKG 129 Query: 129 EQFRFRPVHRLDQETSGVLVIAKNPYSHQHISEQMIAGTVDKRYNAWVHGVPAVLSGDID 188 + R V+RLD +TSG+L+IAKN Y+H +SEQM ++K+Y A+V GV G I+ Sbjct: 130 IDCKVRFVNRLDMDTSGLLIIAKNAYAHHVLSEQMQEDRIEKKYIAFVWGVIKEDEGRIE 189 Query: 189 GPIDRDPAEPHRRIVTPDGYPSLTRYEVKEVYPGAAKVELKLESGRTHQIRVHMSSIGCP 248 PI R + +R+V G S+T ++V E Y A VE+KL +GRTHQIRVHM +G P Sbjct: 190 APIYRTTMDSIKRVVDERGQESITEFKVLERYKNATMVEVKLLTGRTHQIRVHMEHLGHP 249 Query: 249 LIGDGMY 255 LIGD +Y Sbjct: 250 LIGDTLY 256 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 0.135 0.396 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: 2,246,792,993 Number of extensions: 93580141 Number of successful extensions: 225504 Number of sequences better than 1.0e-05: 4756 Number of HSP's gapped: 217040 Number of HSP's successfully gapped: 4765 Length of query: 379 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 242 Effective length of database: 1,770,017,148 Effective search space: 428344149816 Effective search space used: 428344149816 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: 132 (55.5 bits)