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= 0035.0190.p (370 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou... 743 0.0 gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 123 2e-29 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 61 2e-10 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 743 bits (1919), Expect = 0.0, Method: Compositional matrix adjust. Identities = 368/370 (99%), Positives = 369/370 (99%) Query: 1 MSRKKPLQITNGDTPVHTDLPQVDDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVLS 60 MSRKKPLQITNGDTPVHTDLPQ DDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVLS Sbjct: 1 MSRKKPLQITNGDTPVHTDLPQADDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVLS 60 Query: 61 GLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMALD 120 GLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMALD Sbjct: 61 GLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMALD 120 Query: 121 ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAQVPRAGIVHRLDKDTSGI 180 ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALA+VPRAGIVHRLDKDTSGI Sbjct: 121 ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHRLDKDTSGI 180 Query: 181 MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSM 240 MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSM Sbjct: 181 MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSM 240 Query: 241 RAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHLV 300 RAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHLV Sbjct: 241 RAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHLV 300 Query: 301 SVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDEV 360 SVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDEV Sbjct: 301 SVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDEV 360 Query: 361 ISDDDFDDDY 370 ISDDDFDDDY Sbjct: 361 ISDDDFDDDY 370 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 96/310 (30%), Positives = 143/310 (46%), Gaps = 25/310 (8%) Query: 44 LRLDDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAP 103 L + DE GQR+D L + +S I + + G V VN + ++V V P Sbjct: 36 LTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVRVPP 95 Query: 104 QSVPSDQPYGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAQ 163 V Q IL ED L+V++KPAG+ VH +G G ++ L P Q Sbjct: 96 IRVAEKQETVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYG-VIEQLRAARP---Q 151 Query: 164 VPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINA 222 +VHRLD+DTSG++++AK +A T+L Q++ + ++Y LV G + Sbjct: 152 AKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKL 211 Query: 223 PMARHPRDRIKMAVSQSMRAKPAVTHY---RRLATGEIDRKPVSLIHCRLETGRTHQIRV 279 P+ ++ + V +P+ T + RR +L+ L+TGRTHQIRV Sbjct: 212 PLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGD-------FALLEAELKTGRTHQIRV 264 Query: 280 HLQSLGFPLVGDALYGKHHLVS----------VFPRQALLAGRLGLLHPSTGKFRQWAAP 329 HL S GFP+VGD YG L F R L A R+ HP +G A Sbjct: 265 HLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAG 324 Query: 330 LPEDIVALLQ 339 LP++ + L+ Sbjct: 325 LPQECASFLR 334 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 55/185 (29%), Positives = 82/185 (44%), Gaps = 20/185 (10%) Query: 116 PMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAQVPRAGIVHRLDK 175 P+ ILH D L+V +KP L V P TLL L VP +HRLD+ Sbjct: 87 PVEEKILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVP----IHRLDR 142 Query: 176 DTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMA 235 +T+G++V + A++ Q R+M + Y A+ L + P R R R++ Sbjct: 143 ETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA----PLRSDLELP--RVHRSRVEEI 196 Query: 236 VSQSMR------AKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLV 289 Q + A + TH + R + L TGR HQ+RVH+ +LG P++ Sbjct: 197 PEQFFKMHEAEGAPNSETHISLIEA----RGALGLYRLEPVTGRRHQLRVHMAALGIPIL 252 Query: 290 GDALY 294 D Y Sbjct: 253 NDLFY 257 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 0.319 0.137 0.412 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: 1,215,876 Number of extensions: 54912 Number of successful extensions: 136 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 132 Number of HSP's successfully gapped: 3 Length of query: 370 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 283 Effective length of database: 1,207,925 Effective search space: 341842775 Effective search space used: 341842775 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 (21.7 bits) S2: 131 (55.1 bits)