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= 0264.0021.p (324 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KGB0.1 B3KGB0_9BACI Pseudouridine synthase EC=5.4.99.- 483 e-135 B1DKL6.1 B1DKL6_9BACL Pseudouridine synthase EC=5.4.99.- 437 e-121 A7Z4G6.1 A7Z4G6_BACA2 Pseudouridine synthase EC=5.4.99.- 374 e-102 Q9K9V3.1 Q9K9V3_BACHD Pseudouridine synthase EC=5.4.99.- 374 e-102 Q45480.3 YLYB_BACSU Uncharacterized RNA pseudouridine synthase y... 372 e-101 >B3KGB0.1 B3KGB0_9BACI Pseudouridine synthase EC=5.4.99.- Length = 324 Score = 483 bits (1244), Expect = e-135, Method: Compositional matrix adjust. Identities = 223/306 (72%), Positives = 265/306 (86%) Query: 19 EERDVTEWTVAGENARERIDKYITESWEDDISRSQVQLWISGGHVTVNGAPVKANYKLAE 78 +E + +EWTV + A+ RIDKY+TE+ +D+SRSQVQLWI+ GHV+VN P+K+NYK+++ Sbjct: 19 QETEASEWTVDADAAKTRIDKYLTENLGEDVSRSQVQLWIADGHVSVNDGPIKSNYKVSQ 78 Query: 79 GDXXXXXXXXXXXTDLIAEDIPLEVVYEDSDVIVVNKPRGMVVHPAVGHPSGTLVNALMY 138 GD ++I EDIPLE+ +ED DVIVVNKPRGMVVHPA GH SGTLVNALM+ Sbjct: 79 GDRIVLKVPEPSAVEIIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNALMF 138 Query: 139 HCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKNDASHASLAAQLKEHSVTRRYIAVVHGN 198 HCKDLSGINGE+RPGIVHRIDKDT+GLIMAAKND +HASLAAQLKEHSV RRY+A+VHGN Sbjct: 139 HCKDLSGINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGN 198 Query: 199 LSHDQGTVDAPIGRDPHDRKLYTVTEKNSKRSVTHFTVLERFGDCTLLELQLETGRTHQI 258 +SHDQGT+DAPIGRD DRKLYTVT++NSK +VTHFTV+ERFGD +LLEL+LETGRTHQI Sbjct: 199 ISHDQGTIDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQI 258 Query: 259 RVHMKFIGHPLVGDPIYGRSKGTTMNGQALHAAVLGFVHPSTGEYMEYSAPIPADMEEVL 318 RVHMK+IGHPLVGDP+YG+SKG +NGQALHAAVLGFVHPSTGEY E+SAP+P+DM E+L Sbjct: 259 RVHMKYIGHPLVGDPVYGKSKGIKLNGQALHAAVLGFVHPSTGEYKEFSAPMPSDMNELL 318 Query: 319 FALRSR 324 LR R Sbjct: 319 TILRGR 324 >B1DKL6.1 B1DKL6_9BACL Pseudouridine synthase EC=5.4.99.- Length = 315 Score = 437 bits (1125), Expect = e-121, Method: Compositional matrix adjust. Identities = 211/313 (67%), Positives = 251/313 (80%), Gaps = 2/313 (0%) Query: 14 SGAFEEERDVTEWTVAGENARERIDKYITESW-EDDISRSQVQLWISGGHVTVNGAPVKA 72 S F E ++ E+ A E A ERIDK++T+S ED ISR+QVQ WI G V VN VK Sbjct: 3 SNLFSENEELLEFEAAPEQAGERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVKP 62 Query: 73 NYKLAEGDXXXXXXXXXXXTDLIAEDIPLEVVYEDSDVIVVNKPRGMVVHPAVGHPSGTL 132 NYKL+ GD ++AEDIPL++VYED+DVIV+NKPRGMVVHPA GH SGT+ Sbjct: 63 NYKLSSGDHVGIRVPEPEDAAIVAEDIPLDIVYEDADVIVINKPRGMVVHPAPGHSSGTV 122 Query: 133 VNALMYHCKDLSGINGEIRPGIVHRIDKDTSGLIMAAKNDASHASLAAQLKEHSVTRRYI 192 VNALMYHCKDLSGING +RPGIVHRIDKDTSGL+MAAKND +H SLA QLK+HSV+R+YI Sbjct: 123 VNALMYHCKDLSGINGVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYI 182 Query: 193 AVVHGNLSHDQGTVDAPIGRDPHDRKLYTVTEKNSKRSVTHFTVLERFG-DCTLLELQLE 251 A+VHGNL HDQGT+DAPIGRD +DRKL+TVT++NSK +VTHF VLER D T++ELQLE Sbjct: 183 ALVHGNLPHDQGTIDAPIGRDQNDRKLFTVTDRNSKHAVTHFAVLERIADDYTIVELQLE 242 Query: 252 TGRTHQIRVHMKFIGHPLVGDPIYGRSKGTTMNGQALHAAVLGFVHPSTGEYMEYSAPIP 311 TGRTHQIRVHMK+IG+PL GDP+YGR+K + GQALHAAVLGF HP TGE++E+ APIP Sbjct: 243 TGRTHQIRVHMKYIGYPLAGDPMYGRNKTVALKGQALHAAVLGFKHPRTGEFLEFEAPIP 302 Query: 312 ADMEEVLFALRSR 324 ADME V+ +LR R Sbjct: 303 ADMEHVINSLRLR 315 >A7Z4G6.1 A7Z4G6_BACA2 Pseudouridine synthase EC=5.4.99.- Length = 304 Score = 374 bits (961), Expect = e-102, Method: Compositional matrix adjust. Identities = 184/299 (61%), Positives = 221/299 (73%), Gaps = 1/299 (0%) Query: 25 EWTVAGENARERIDKYITESWEDDISRSQVQLWISGGHVTVNGAPVKANYKLAEGDXXXX 84 E TV E ERIDK++ + E+ SR+QVQ W+ G V+VNG VKANYK+ GD Sbjct: 5 EITVQPEQKSERIDKFLASTGEN-WSRTQVQQWVKEGLVSVNGKSVKANYKMQPGDQVNV 63 Query: 85 XXXXXXXTDLIAEDIPLEVVYEDSDVIVVNKPRGMVVHPAVGHPSGTLVNALMYHCKDLS 144 D++AE + L++ YED DV+VVNKPRGMVVHPA GH +GTLVN LM HC DLS Sbjct: 64 TIPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHCNDLS 123 Query: 145 GINGEIRPGIVHRIDKDTSGLIMAAKNDASHASLAAQLKEHSVTRRYIAVVHGNLSHDQG 204 GING +RPGIVHRIDKDTSGL+M AKND +H SL QL +VTR+Y AVVHG +SHD G Sbjct: 124 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVISHDDG 183 Query: 205 TVDAPIGRDPHDRKLYTVTEKNSKRSVTHFTVLERFGDCTLLELQLETGRTHQIRVHMKF 264 T+DAPIGRD DR+ TVT ++SK +VTHF VLERF D TL+E +LETGRTHQIRVHMK+ Sbjct: 184 TIDAPIGRDKKDRQSMTVTRESSKNAVTHFHVLERFQDFTLVECRLETGRTHQIRVHMKY 243 Query: 265 IGHPLVGDPIYGRSKGTTMNGQALHAAVLGFVHPSTGEYMEYSAPIPADMEEVLFALRS 323 IG PL GDP YG K NGQALHA +LGF HP TGEYME+ AP+P DM++++ LR+ Sbjct: 244 IGFPLAGDPKYGPRKTIDFNGQALHAGILGFDHPRTGEYMEFEAPLPEDMKKLIEDLRN 302 >Q9K9V3.1 Q9K9V3_BACHD Pseudouridine synthase EC=5.4.99.- Length = 305 Score = 374 bits (959), Expect = e-102, Method: Compositional matrix adjust. Identities = 176/298 (59%), Positives = 221/298 (74%), Gaps = 1/298 (0%) Query: 26 WTVAGENARERIDKYITESWEDDISRSQVQLWISGGHVTVNGAPVKANYKLAEGDXXXXX 85 WT++ + ERIDK++T E+ SR+QVQ WI GHV +NG +K+NYK+ GD Sbjct: 7 WTISEQQQGERIDKFLTAQGEE-WSRTQVQQWIKDGHVLINGRTIKSNYKVETGDTLELF 65 Query: 86 XXXXXXTDLIAEDIPLEVVYEDSDVIVVNKPRGMVVHPAVGHPSGTLVNALMYHCKDLSG 145 +++ E+IP+E++YED DV VVNKPRGMVVHPA GH +GTLVNALMYHC DLS Sbjct: 66 VPEPEVLEVVPENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMYHCNDLSS 125 Query: 146 INGEIRPGIVHRIDKDTSGLIMAAKNDASHASLAAQLKEHSVTRRYIAVVHGNLSHDQGT 205 ING +RPGIVHRIDKDTSGL+M AKND +H SL QLK + R Y A+VHGN+ HD GT Sbjct: 126 INGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGT 185 Query: 206 VDAPIGRDPHDRKLYTVTEKNSKRSVTHFTVLERFGDCTLLELQLETGRTHQIRVHMKFI 265 +DAPIGRD DR+ TVTE+NS+ +VTHFTVLERFGD T +E QLETGRTHQIRVH K+I Sbjct: 186 IDAPIGRDKVDRQSMTVTEENSRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYI 245 Query: 266 GHPLVGDPIYGRSKGTTMNGQALHAAVLGFVHPSTGEYMEYSAPIPADMEEVLFALRS 323 G PL GDP YG K +++GQALHA LGF HP TGE+M + +P +M++++ L++ Sbjct: 246 GFPLAGDPKYGPKKTLSIDGQALHAQKLGFEHPRTGEFMRFKVEMPEEMKKLIRQLQN 303 >Q45480.3 YLYB_BACSU Uncharacterized RNA pseudouridine synthase ylyB EC=5.4.99.- Length = 303 Score = 372 bits (956), Expect = e-101, Method: Compositional matrix adjust. Identities = 185/297 (62%), Positives = 218/297 (73%), Gaps = 2/297 (0%) Query: 27 TVAGENARERIDKYITESWEDDISRSQVQLWISGGHVTVNGAPVKANYKLAEGDXXXXXX 86 T + E ERIDK++ S E+D SR+QVQ W+ G V VNG+ VKANYK+ GD Sbjct: 7 TASEEQKSERIDKFLA-STENDWSRTQVQQWVKDGQVVVNGSAVKANYKIQPGDQVTVTV 65 Query: 87 XXXXXTDLIAEDIPLEVVYEDSDVIVVNKPRGMVVHPAVGHPSGTLVNALMYHCKDLSGI 146 D++AE + L++ YED DV+VVNKPRGMVVHPA GH +GTLVN LM HC DLSGI Sbjct: 66 PEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCTDLSGI 125 Query: 147 NGEIRPGIVHRIDKDTSGLIMAAKNDASHASLAAQLKEHSVTRRYIAVVHGNLSHDQGTV 206 NG +RPGIVHRIDKDTSGL+M AKND +H SL QL +VTR+Y AVVHG +SHD GT+ Sbjct: 126 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTI 185 Query: 207 DAPIGRDPHDRKLYTVTEKNSKRSVTHFTVLERFGDCTLLELQLETGRTHQIRVHMKFIG 266 DAPIGRD DR+ TVT ++ K +VTHF VLERF D TL+E QLETGRTHQIRVHMK+IG Sbjct: 186 DAPIGRDKKDRQSMTVT-RDGKNAVTHFHVLERFQDFTLVECQLETGRTHQIRVHMKYIG 244 Query: 267 HPLVGDPIYGRSKGTTMNGQALHAAVLGFVHPSTGEYMEYSAPIPADMEEVLFALRS 323 PL GDP YG K NGQALHA VLGF HP TGEY+E+ AP+P DM E++ LR Sbjct: 245 FPLAGDPKYGPRKTIDFNGQALHAGVLGFDHPRTGEYVEFEAPLPEDMAELIENLRK 301 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 0.134 0.393 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: 1,946,179,148 Number of extensions: 80276090 Number of successful extensions: 188335 Number of sequences better than 1.0e-05: 4904 Number of HSP's gapped: 175275 Number of HSP's successfully gapped: 4911 Length of query: 324 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 188 Effective length of database: 1,779,438,163 Effective search space: 334534374644 Effective search space used: 334534374644 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: 131 (55.1 bits)