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= 0037.0079.p (323 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 653 0.0 gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou... 118 5e-28 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 68 1e-12 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 653 bits (1684), Expect = 0.0, Method: Compositional matrix adjust. Identities = 320/323 (99%), Positives = 320/323 (99%) Query: 1 VQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDVVR 60 VQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRL EGDVVR Sbjct: 33 VQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVR 92 Query: 61 VPPIRVAEKQEAVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQLRAARPQA 120 VPPIRVAEKQE VVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQLRAARPQA Sbjct: 93 VPPIRVAEKQETVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQLRAARPQA 152 Query: 121 KFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLP 180 KFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLP Sbjct: 153 KFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLP 212 Query: 181 LFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFP 240 LFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFP Sbjct: 213 LFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFP 272 Query: 241 IVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAGLPQECASF 300 IVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAGLPQECASF Sbjct: 273 IVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAGLPQECASF 332 Query: 301 LRSLEGGEEGELLPYGMLAGAEG 323 LRSLEGGEEGELLPYGMLA AEG Sbjct: 333 LRSLEGGEEGELLPYGMLACAEG 355 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 118 bits (296), Expect = 5e-28, Method: Compositional matrix adjust. Identities = 96/310 (30%), Positives = 143/310 (46%), Gaps = 25/310 (8%) Query: 4 LTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDVVRVPP 63 L + DE GQR+D L + +S I + + G V VN ++ ++V V P Sbjct: 44 LRLDDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAP 103 Query: 64 IRVAEKQEAVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQ--LRAARPQAK 121 V Q IL ED L+V++KPAG+ VH +G G + L AK Sbjct: 104 QSVPSDQPYGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAK 163 Query: 122 FLE--LVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKL 179 +VHRLD+DTSG++++AK +A T+L Q++ + ++Y LV G + Sbjct: 164 VPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINA 222 Query: 180 PLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFG-------DFALLEAELKTGRTHQIRV 232 P+ ++ + V +P+ T + RR +L+ L+TGRTHQIRV Sbjct: 223 PMARHPRDRIKMAVSQSMRAKPAVTHY---RRLATGEIDRKPVSLIHCRLETGRTHQIRV 279 Query: 233 HLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAG 292 HL S GFP+VGD YG L F R L A R+ HP +G A Sbjct: 280 HLQSLGFPLVGDALYGKHHLVS----------VFPRQALLAGRLGLLHPSTGKFRQWAAP 329 Query: 293 LPQECASFLR 302 LP++ + L+ Sbjct: 330 LPEDIVALLQ 339 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 74/242 (30%), Positives = 113/242 (46%), Gaps = 21/242 (8%) Query: 17 NFLLRVCKGVPKSHIYRVLRSGEVRVNKG---RIDQTYRLVEGDVVRVPPIRVAEKQEAV 73 +FL VP+ L GEVR G + D YR GD + R + EA Sbjct: 30 SFLAERFTAVPEPVWRERLLRGEVRNQHGEALQPDTPYR--SGDCIFY--YRELPQGEAR 85 Query: 74 VPGAEFRILLEDSHLLVIDKPAGVAV-HGGSGVSYGVIEQLRAARPQAKFLELVHRLDRD 132 +P E +IL D HLLV DKP + V G V ++ +L+ A + L +HRLDR+ Sbjct: 86 IPVEE-KILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKAT-GLQDLVPIHRLDRE 143 Query: 133 TSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYS----TPD 188 T+GV++ + + ++ ++ K Y + R ++LP S P+ Sbjct: 144 TAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA-----PLRSDLELPRVHRSRVEEIPE 198 Query: 189 GERRVRVQADGQP-SHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKY 247 ++ +A+G P S T SL+ G L E TGR HQ+RVH+++ G PI+ D Y Sbjct: 199 QFFKMH-EAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLFY 257 Query: 248 GD 249 + Sbjct: 258 PE 259 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.321 0.139 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 920,201 Number of extensions: 36217 Number of successful extensions: 99 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 94 Number of HSP's successfully gapped: 3 Length of query: 323 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 238 Effective length of database: 1,217,395 Effective search space: 289740010 Effective search space used: 289740010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 131 (55.1 bits)