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= 0001.2975.p (372 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... 612 e-176 gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 115 5e-27 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 56 6e-09 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 612 bits (1577), Expect = e-176, Method: Compositional matrix adjust. Identities = 319/362 (88%), Positives = 336/362 (92%), Gaps = 1/362 (0%) Query: 1 MSRKKPLPITNGDEPVKTDLPLEDDFDDGEQAGDDGVPGLEPLTFRLDDEVVGQRLDKVL 60 MSRKKPL ITNGD PV TDLP DDFDD + G PGLEPLT RLDDEV+GQRLDKVL Sbjct: 1 MSRKKPLQITNGDTPVHTDLPQADDFDDAHDGDEIG-PGLEPLTLRLDDEVIGQRLDKVL 59 Query: 61 SGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQSVPADQPYAPEAMAL 120 SGL+PEFSRSRIQQWIEDGHVTV+GAPAK KMTMLGDELVEVAPQSVP+DQPY PE MAL Sbjct: 60 SGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMAL 119 Query: 121 DILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVPRAGIVHRLDKETSG 180 DILHEDK++I+LNKPAGLVVHPAAGNWSGTLLNGLLHHCPALA VPRAGIVHRLDK+TSG Sbjct: 120 DILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHRLDKDTSG 179 Query: 181 LMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS 240 +MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS Sbjct: 180 IMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS 239 Query: 241 MRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGFALVGDSLYGKQHL 300 MRAKPAVTHYRRLATGEIDRKPVSL+HCRLETGRTHQIRVHLQSLGF LVGD+LYGK HL Sbjct: 240 MRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHL 299 Query: 301 APVFPRQALLAGRLGLVHPTSGKFRQWAAPLPPDIEALLQRAGIDPDLAVIPEMSEEADP 360 VFPRQALLAGRLGL+HP++GKFRQWAAPLP DI ALLQRAGIDP LAVIPEMS+E D Sbjct: 300 VSVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDE 359 Query: 361 VL 362 V+ Sbjct: 360 VI 361 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 115 bits (289), Expect = 5e-27, Method: Compositional matrix adjust. Identities = 95/321 (29%), Positives = 146/321 (45%), Gaps = 33/321 (10%) Query: 37 VPGLEPLTFRLDDEVVGQRLDKVLSGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLG 96 VP ++ LT + DE GQR+D L + +S I + + G V V+ + Sbjct: 30 VPQVQLLT--ISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAE 87 Query: 97 DELVEVAPQSVPADQPYAPEAMALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLL 156 ++V V P V Q IL ED +++++KPAG+ VH +G G + Sbjct: 88 GDVVRVPPIRVAEKQETVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQ--- 144 Query: 157 HHCPALANVPRAG---IVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG 213 A P+A +VHRLD++TSG++++AK +A T+L Q++ + ++Y LV G Sbjct: 145 ----LRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQG 200 Query: 214 -LPQLSGTINAPMARHPRDRIKMAVSQSMRAKPAVTHY---RRLATGEIDRKPVSLVHCR 269 + P+ ++ + V +P+ T + RR +L+ Sbjct: 201 DWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFG-------DFALLEAE 253 Query: 270 LETGRTHQIRVHLQSLGFALVGDSLYGKQHLAP----------VFPRQALLAGRLGLVHP 319 L+TGRTHQIRVHL S GF +VGD YG L F R L A R+ HP Sbjct: 254 LKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHP 313 Query: 320 TSGKFRQWAAPLPPDIEALLQ 340 SG A LP + + L+ Sbjct: 314 ESGDTVTLKAGLPQECASFLR 334 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust. Identities = 52/180 (28%), Positives = 79/180 (43%), Gaps = 20/180 (11%) Query: 122 ILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVPRAGIVHRLDKETSGL 181 ILH D +++ +KP L V P TLL L VP +HRLD+ET+G+ Sbjct: 92 ILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVP----IHRLDRETAGV 147 Query: 182 MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSM 241 +V + A++ Q R+M + Y A+ L + P R R R++ Q Sbjct: 148 IVFSHQPASRGKYQSMFQQRAMFKVYEAIA----PLRSDLELP--RVHRSRVEEIPEQFF 201 Query: 242 R------AKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGFALVGDSLY 295 + A + TH + R + L TGR HQ+RVH+ +LG ++ D Y Sbjct: 202 KMHEAEGAPNSETHISLIEA----RGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLFY 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 0.318 0.137 0.408 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: 1,264,625 Number of extensions: 57230 Number of successful extensions: 153 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 149 Number of HSP's successfully gapped: 3 Length of query: 372 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 285 Effective length of database: 1,207,925 Effective search space: 344258625 Effective search space used: 344258625 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 (21.7 bits) S2: 131 (55.1 bits)