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= 0188.0034.p (205 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KLM7.1 B3KLM7_9BACI Pseudouridylate synthase EC=5.4.99.- 279 1e-73 B1DJU3.1 B1DJU3_9BACL Pseudouridylate synthase EC=5.4.99.- 222 1e-56 A4J151.1 TRUA_DESRM tRNA pseudouridine synthase A EC=5.4.99.12 157 7e-37 B7GJ99.1 TRUA_ANOFW tRNA pseudouridine synthase A EC=5.4.99.12 155 1e-36 B4BBT0.1 B4BBT0_CLOTM Pseudouridylate synthase EC=5.4.99.- 154 5e-36 >B3KLM7.1 B3KLM7_9BACI Pseudouridylate synthase EC=5.4.99.- Length = 263 Score = 279 bits (713), Expect = 1e-73, Method: Compositional matrix adjust. Identities = 132/203 (65%), Positives = 156/203 (76%) Query: 1 VHAYGQPFNFLTASKIPLERWCLALNARLPQDIVVTEAREVPLEFHSRRGAKRKTYRYTI 60 VHA Q FNF TAS IP+ERWC+ALN LP+DIVV++A EVP+EFHSR AKRKTYR+TI Sbjct: 55 VHARAQVFNFYTASPIPVERWCMALNTWLPEDIVVSDAMEVPMEFHSRHAAKRKTYRFTI 114 Query: 61 NGNRFPDPFQRRLQYHHPVKLDLPAMQQGLAHIIGTHDFTSFASRKSTKTSHVRTIFEAH 120 N N++PD F RR Q HH KLD+ AM+QGL+H+IGTHDFT+FASRKSTK SHVRTIF+A Sbjct: 115 NANQYPDLFNRRYQIHHHGKLDIAAMEQGLSHLIGTHDFTTFASRKSTKPSHVRTIFDAW 174 Query: 121 MEVDRSMCRNGTADQGVIDTYITGSGFLQHMVRIIMGTLIHVGEGKIRAEXXXXXXXXXX 180 +E D SMCR GT DQG+I TY++G+GFLQHMVRIIMGTLI VGEGK + Sbjct: 175 IEKDTSMCRPGTRDQGIIHTYVSGNGFLQHMVRIIMGTLIEVGEGKRHPDDMKVILEAQN 234 Query: 181 XXXXGPTAVAQGLALWSVEYDEA 203 GPTA+ +GL LW V+YD A Sbjct: 235 RAAAGPTAMGKGLMLWEVDYDIA 257 >B1DJU3.1 B1DJU3_9BACL Pseudouridylate synthase EC=5.4.99.- Length = 246 Score = 222 bits (566), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 110/202 (54%), Positives = 136/202 (67%), Gaps = 10/202 (4%) Query: 1 VHAYGQPFNFLTASKIPLERWCLALNARLPQDIVVTEAREVPLEFHSRRGAKRKTYRYTI 60 VHA GQ FNFLT S IP ERW +ALN RLP+DIV+ EA EVP FHSRR AKRKTYRYTI Sbjct: 55 VHANGQVFNFLTESTIPAERWAIALNTRLPKDIVILEAHEVPEAFHSRRSAKRKTYRYTI 114 Query: 61 NGNRFPDPFQRRLQYHHPVKLDLPAMQQGLAHIIGTHDFTSFASRKSTKTSHVRTIFEAH 120 + +FPD F RR +HHP L++ AMQ+GL+ ++G HDFTSF S STK HVRTI+EA+ Sbjct: 115 DMGKFPDVFYRRYAFHHPTPLNVEAMQKGLSFLVGEHDFTSFTSIHSTKPHHVRTIYEAY 174 Query: 121 MEVDRSMCRNGTADQGVIDTYITGSGFLQHMVRIIMGTLIHVGEGKIRAEXXXXXXXXXX 180 +E + M + Y+TG+GFL +M+RI+MGTL+HVG GK++ E Sbjct: 175 LEREGQM----------LHMYMTGNGFLYNMIRIVMGTLLHVGHGKLKPEDMARILEGRK 224 Query: 181 XXXXGPTAVAQGLALWSVEYDE 202 GPTA+ GL L VEY E Sbjct: 225 RSLAGPTAMPHGLMLMKVEYPE 246 >A4J151.1 TRUA_DESRM tRNA pseudouridine synthase A EC=5.4.99.12 Length = 247 Score = 157 bits (396), Expect = 7e-37, Method: Compositional matrix adjust. Identities = 87/201 (43%), Positives = 117/201 (58%), Gaps = 11/201 (5%) Query: 1 VHAYGQPFNFLTAS-KIPLERWCLALNARLPQDIVVTEAREVPLEFHSRRGAKRKTYRYT 59 VHA GQ NF + +P E+ LALN LP DI V +A EVP++FH+R A KTYRY+ Sbjct: 57 VHAQGQVVNFRSEKWPVPAEKAPLALNVLLPGDIKVVKAEEVPMDFHARFSAVAKTYRYS 116 Query: 60 INGNRFPDPFQRRLQYHHPVKLDLPAMQQGLAHIIGTHDFTSFASRKSTKTSHVRTIFEA 119 I +R PF R YH P +LD+ AMQ+G A+++GT+DF SF ++ + +RTI+ A Sbjct: 117 IYHHRVMSPFHRYYCYHEPRRLDVNAMQEGAAYLLGTYDFKSFQAQGTPVKDTIRTIYRA 176 Query: 120 HMEVDRSMCRNGTADQGVIDTYITGSGFLQHMVRIIMGTLIHVGEGKIRAEXXXXXXXXX 179 + D VI+ Y+ G+GFL +MVRII GTL+++G GKI+ E Sbjct: 177 DI----------IEDAPVINLYLRGNGFLYNMVRIITGTLLNIGFGKIKPEDMVKIIESK 226 Query: 180 XXXXXGPTAVAQGLALWSVEY 200 G TA QGL L VEY Sbjct: 227 NRTLAGTTAPPQGLCLMEVEY 247 >B7GJ99.1 TRUA_ANOFW tRNA pseudouridine synthase A EC=5.4.99.12 Length = 246 Score = 155 bits (393), Expect = 1e-36, Method: Compositional matrix adjust. Identities = 89/203 (43%), Positives = 113/203 (55%), Gaps = 15/203 (7%) Query: 1 VHAYGQPFNFLTASKIPLERWCLALNARLPQDIVVTEAREVPLEFHSRRGAKRKTYRYTI 60 VHAYGQ +F T IP ERW ALNA LP D++V EA EVP FH+R K+K YRY + Sbjct: 56 VHAYGQVIHFDTPLTIPDERWPKALNALLPDDVIVKEASEVPSSFHARFSVKKKEYRYRV 115 Query: 61 NGNRFPDPFQRRLQYHHPVKLDLPAMQQGLAHIIGTHDFTSFASRKSTKTSHVRTIFEAH 120 + F R YHHP + +PAM + L ++IGTHDFTSF S K+ VRTI+EA Sbjct: 116 WIGE-KNVFLRHYVYHHPYDVSVPAMNEALRYLIGTHDFTSFCSAKTEVDDKVRTIYEAE 174 Query: 121 M--EVDRSMCRNGTADQGVIDTYITGSGFLQHMVRIIMGTLIHVGEGKIRAEXXXXXXXX 178 + E + + R + G+GFL +MVRII+GT++ VG G+ AE Sbjct: 175 VVQEGEELIFR------------LVGNGFLYNMVRIIVGTVLEVGRGERCAEEIKTILEQ 222 Query: 179 XXXXXXGPTAVAQGLALWSVEYD 201 G TA GL LW V YD Sbjct: 223 KNRSVAGKTAPGHGLYLWHVSYD 245 >B4BBT0.1 B4BBT0_CLOTM Pseudouridylate synthase EC=5.4.99.- Length = 244 Score = 154 bits (389), Expect = 5e-36, Method: Compositional matrix adjust. Identities = 85/200 (42%), Positives = 115/200 (57%), Gaps = 10/200 (5%) Query: 1 VHAYGQPFNFLTASKIPLERWCLALNARLPQDIVVTEAREVPLEFHSRRGAKRKTYRYTI 60 VHA GQ NF+T S IP +R+ ALN LP DIV+ E++EV ++FH+R AK K YRY I Sbjct: 55 VHALGQVANFITNSGIPGDRFSYALNRMLPDDIVIKESQEVDMDFHARYKAKGKRYRYLI 114 Query: 61 NGNRFPDPFQRRLQYHHPVKLDLPAMQQGLAHIIGTHDFTSFASRKSTKTSHVRTIFEAH 120 ++FP R YH KLD +MQ+ ++ +GTHDF++F S S+ + VRTI + Sbjct: 115 YNSQFPSALLRHRTYHVSHKLDFESMQRAASYFLGTHDFSAFRSSGSSAKTSVRTITDVS 174 Query: 121 MEVDRSMCRNGTADQGVIDTYITGSGFLQHMVRIIMGTLIHVGEGKIRAEXXXXXXXXXX 180 +E + ++ I G GFL +MVRII+GTL+ VG GKIRA+ Sbjct: 175 LE----------REDKIVKFEIAGDGFLYNMVRIIVGTLMEVGIGKIRADEIPQIIESRK 224 Query: 181 XXXXGPTAVAQGLALWSVEY 200 G TA A+GL L V Y Sbjct: 225 RKRAGRTAPAEGLYLVEVYY 244 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 0.323 0.137 0.419 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: 1,146,463,343 Number of extensions: 44149551 Number of successful extensions: 70657 Number of sequences better than 1.0e-05: 1640 Number of HSP's gapped: 68603 Number of HSP's successfully gapped: 1640 Length of query: 205 Length of database: 3,060,696,203 Length adjustment: 129 Effective length of query: 76 Effective length of database: 1,845,385,268 Effective search space: 140249280368 Effective search space used: 140249280368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 128 (53.9 bits)