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: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_691770.1| hypothetical protein OB0849 [Oceanobacillus ihe... 339 5e-92 ref|NP_809555.1| RNA pseudouridylate synthase [Bacteroides theta... 262 7e-69 ref|NP_969610.1| Pseudouridylate synthase, 23S RNA-specific [Bde... 178 1e-43 ref|NP_782220.1| ribosomal large subunit pseudouridine synthase ... 169 1e-40 ref|NP_785347.1| pseudouridylate synthase [Lactobacillus plantar... 165 1e-39 >ref|NP_691770.1| hypothetical protein OB0849 [Oceanobacillus iheyensis HTE831] dbj|BAC12805.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831] Length = 303 Score = 339 bits (870), Expect = 5e-92, Method: Compositional matrix adjust. Identities = 163/284 (57%), Positives = 218/284 (76%), Gaps = 2/284 (0%) Query: 34 SYTVAEPAELLAFLLKTITSRGRNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLE 93 +Y V E +LL FLLK + +R RNS+KS+L+RGQVSV+ TKHNF L+ G TV I Sbjct: 17 TYEVEETEQLLPFLLKVMDNRSRNSVKSILTRGQVSVDDHIETKHNFMLNKGSTVRILKN 76 Query: 94 KP-VQAKEMTGLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQSNPHNRV 152 K +Q G++I+YEDDD+IVI+KE+GLLSIAT ++ + TA QLM +V+Q +P NRV Sbjct: 77 KAAIQQDVFVGMSIMYEDDDIIVIEKESGLLSIATEKERKHTALHQLMHYVKQQHPANRV 136 Query: 153 FVVHRLDRDTSGVMMFAKSEQLQQTLQNTWKETVKERSYVALVEGVVKKPEGTISSWLKE 212 +VVHRLD+DTSGVMMFAK+E++++ LQN WK+ VKER+YVALVEG V K +G I SWLKE Sbjct: 137 YVVHRLDKDTSGVMMFAKNERVKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIVSWLKE 196 Query: 213 TSTLKMYSSPHEGDGLHAVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGD 272 ++T KMYSS + DG A T Y+++Q N +SLLE+ LETGRKNQIRVHM ++GHP+VGD Sbjct: 197 SATRKMYSSRVKNDGQRAATRYRVLQTNNRYSLLELQLETGRKNQIRVHMEELGHPVVGD 256 Query: 273 KKYGAETKAV-GRLGLHARLLSFVHPSSGELLTFESAIPKTFLK 315 K+YG++ ++V GRLGLHA++LSF HP + +L+ F S +P F + Sbjct: 257 KRYGSKGRSVIGRLGLHAKILSFYHPVTNKLMLFRSDVPNAFFQ 300 >ref|NP_809555.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron VPI-5482] gb|AAO75749.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron VPI-5482] Length = 306 Score = 262 bits (670), Expect = 7e-69, Method: Compositional matrix adjust. Identities = 138/284 (48%), Positives = 183/284 (64%), Gaps = 3/284 (1%) Query: 34 SYTVAEPAELLAFLLKTITSRGRNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLE 93 +Y V EP EL+ FL + R +KS+LS+ V V+ T+ NF L PG V I E Sbjct: 19 NYAVKEPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMKVQISKE 78 Query: 94 KPVQAKEMTGLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQSNPHNRVF 153 K + L IVYED +IV++K GLLS+ T E TAY L E+V++S +RVF Sbjct: 79 KGKKEFHNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVF 138 Query: 154 VVHRLDRDTSGVMMFAKSEQLQQTLQNTWKETVKERSYVALVEGVVKKPEGTISSWLKET 213 +VHRLDRDTSG+MMFAK E+ Q+TL++ W E V +R YVA+VEG ++K T+ SWL + Sbjct: 139 IVHRLDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGTMEKDYDTVVSWLTD- 197 Query: 214 STLKMYSSPHEGDGLHAVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGDK 273 TL + SS ++ G ++THYK I+ +SLLE+ LETGRKNQIRVHM D+GHPI+GD Sbjct: 198 KTLYVSSSDYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIRVHMQDLGHPIIGDG 257 Query: 274 KYGAET--KAVGRLGLHARLLSFVHPSSGELLTFESAIPKTFLK 315 +YG E +GRL LHA L F HP +G+L+ FE+ P F K Sbjct: 258 RYGGEESLNPIGRLALHAFKLCFYHPVTGDLMEFETPYPGEFKK 301 >ref|NP_969610.1| Pseudouridylate synthase, 23S RNA-specific [Bdellovibrio bacteriovorus HD100] emb|CAE80603.1| Pseudouridylate synthase, 23S RNA-specific [Bdellovibrio bacteriovorus] Length = 230 Score = 178 bits (452), Expect = 1e-43, Method: Compositional matrix adjust. Identities = 93/213 (43%), Positives = 140/213 (65%), Gaps = 4/213 (1%) Query: 103 GLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVRQSNPHNR--VFVVHRLDR 160 G I++ED D+IV K AG+L++A D + T + L +VR+ NP + V+VVHRLD+ Sbjct: 12 GFEILHEDLDVIVGNKAAGVLTVAAKWDRDNTVHNLLNLYVRKGNPRSNKCVYVVHRLDQ 71 Query: 161 DTSGVMMFAKSEQLQQTLQNTWKETVKERSYVALVEGVVKKPEGTISSWLKETSTLKMYS 220 T+GV++FAK+EQ+Q L++ WK T+K +Y A+V G + K GTI+S+L+E ++S Sbjct: 72 ATTGVLIFAKTEQVQHFLKDDWKSTIK--TYYAIVHGKMPKKSGTITSYLEEDENYVVHS 129 Query: 221 SPHEGDGLHAVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGDKKYGAETK 280 S G A+T Y++++ FSLL+++L TG+KNQIRVH++ GHPIVGD KYG T Sbjct: 130 SKDSDKGKLAITEYEVLKETEKFSLLKINLLTGKKNQIRVHLAGEGHPIVGDPKYGKPTT 189 Query: 281 AVGRLGLHARLLSFVHPSSGELLTFESAIPKTF 313 + L LH+ L F HP S + +T ++ +P F Sbjct: 190 NLKELRLHSASLEFTHPHSKKRITIKAPVPNYF 222 >ref|NP_782220.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] gb|AAO36157.1| ribosomal large subunit pseudouridine synthase D [Clostridium tetani E88] Length = 307 Score = 169 bits (427), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 108/295 (36%), Positives = 166/295 (56%), Gaps = 13/295 (4%) Query: 32 VKSYTVAEPAE---LLAFLLKTITSRGRNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTV 88 ++ + V E E L F+++ + + R+ IK + + VN + + K N+++ G V Sbjct: 5 IEKFLVKEEFENERLDLFIVENLKDKSRSFIKKLSDDKGIMVNDE-IKKVNYKVKCGDIV 63 Query: 89 TIDLEKP---VQAKEMTGLTIVYEDDDLIVIQKEAGLLSIATGEDNELTAYRQLMEHVR- 144 + L K KE L I+YED+D+IVI K G++ + + T L+ H + Sbjct: 64 KVLLPKEEGIYLEKENMDLNILYEDEDIIVINKPQGMVVHPGVGNTKGTLVNGLLAHCKS 123 Query: 145 --QSNPHNRVFVVHRLDRDTSGVMMFAKSEQLQQTLQNTWKETVKERSYVALVEGVVKKP 202 N R +VHR+D+DTSG+++ AK+ + + L N K+ R Y+AL EGV+K+ Sbjct: 124 LSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSMLRVYMALTEGVIKED 183 Query: 203 EGTISSWLKETSTLKMYSSPHEGDGLHAVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHM 262 GTI L + ++ + + +G AVTHYK+I + SL+E LETGR +QIRVHM Sbjct: 184 MGTIDKDLGRNPSDRIKFAVVD-EGKRAVTHYKVINRYNNNSLIECRLETGRTHQIRVHM 242 Query: 263 SDIGHPIVGDKKYGAETKAVGRLG--LHARLLSFVHPSSGELLTFESAIPKTFLK 315 S IGHPIVGD YG + + G LHA+ L F+HP++GE + F+S IP+ F K Sbjct: 243 SYIGHPIVGDPTYGYKRQKFKLKGQMLHAKKLGFIHPTNGEYMEFDSEIPEEFKK 297 >ref|NP_785347.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1] emb|CAD64195.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1] Length = 307 Score = 165 bits (417), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 102/266 (38%), Positives = 155/266 (58%), Gaps = 12/266 (4%) Query: 56 RNSIKSMLSRGQVSVNGKAVTKHNFQLHPGQTVTIDLEKPVQA---KEMTGLTIVYEDDD 112 R+ + ++ QV+VNG+ + + + PG + + + Q E L IVYEDDD Sbjct: 32 RSQVDKLIKTDQVTVNGQ-LEASKYHVKPGDEIVVAAQTVQQTTIEPENIPLDIVYEDDD 90 Query: 113 LIVIQKEAGLL-SIATGEDNELTAYRQLMEHVRQS--NPHNRVFVVHRLDRDTSGVMMFA 169 ++V+ K G++ A G N T L+ H S N R +VHR+D+DTSG++M A Sbjct: 91 VLVVNKPQGMVVHPAPGHPNH-TLVNALLYHSPLSTINGEFRPGIVHRIDKDTSGLLMVA 149 Query: 170 KSEQLQQTLQNTWKETVKERSYVALVEGVVKKPEGTISSWLKETSTLKMYSSPHEGDGLH 229 K+++ Q+L K R YVALV GV+K+ GTI++ L + + + + G Sbjct: 150 KNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTINAPLGRSPKDRKKQAIVK-TGRP 208 Query: 230 AVTHYKLIQGNRHFSLLEVHLETGRKNQIRVHMSDIGHPIVGDKKYGAE--TKAVGRLGL 287 AVTH+K+++ +H++L+ LETGR +QIRVH+ IGHP+VGD YG + K G+ L Sbjct: 209 AVTHFKVLKRYQHYTLISCRLETGRTHQIRVHLQSIGHPLVGDPLYGPKKTIKGHGQF-L 267 Query: 288 HARLLSFVHPSSGELLTFESAIPKTF 313 HA+LL F HP +G+LLTFE+ +P F Sbjct: 268 HAKLLGFKHPVTGDLLTFEAPLPPIF 293 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 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: 2715099 Number of Hits to DB: 434,107,476 Number of extensions: 17096730 Number of successful extensions: 45604 Number of sequences better than 1.0e-05: 1292 Number of HSP's gapped: 43305 Number of HSP's successfully gapped: 1294 Length of query: 323 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 197 Effective length of database: 415,135,104 Effective search space: 81781615488 Effective search space used: 81781615488 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: 126 (53.1 bits)