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= 0010.0165.p (465 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... 543 e-155 gi|300312306|ref|YP_003776398.1| hypothetical protein Hsero_3002... 144 2e-35 gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 102 9e-23 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 57 4e-09 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 543 bits (1399), Expect = e-155, Method: Compositional matrix adjust. Identities = 272/306 (88%), Positives = 283/306 (92%), Gaps = 1/306 (0%) Query: 1 MSRKKPLPITNGDEPVKTDLPLEDDFDDGEQAGDESVSGLEPLSFRLDDEVIGQRLDKVL 60 MSRKKPL ITNGD PV TDLP + D D GDE GLEPL+ RLDDEVIGQRLDKVL Sbjct: 1 MSRKKPLQITNGDTPVHTDLP-QADDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVL 59 Query: 61 SGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQSVPADQPYAPEAMAL 120 SGL+PEFSRSRIQQWIEDGHVTV+GAPAK KMTMLGDELVEVAPQSVP+DQPY PE MAL Sbjct: 60 SGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMAL 119 Query: 121 DILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPGLANVPRAGIVHRLDKETSG 180 DILHEDK++I+LNKPAGLVVHPAAGNWSGTLLNGLLHHCP LA VPRAGIVHRLDK+TSG Sbjct: 120 DILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHRLDKDTSG 179 Query: 181 LMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS 240 +MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS Sbjct: 180 IMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS 239 Query: 241 MRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGFALVGDALYGKQHL 300 MRAKPAVTHYRRLATGEIDRKPVSL+HCRLETGRTHQIRVHLQSLGF LVGDALYGK HL Sbjct: 240 MRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHL 299 Query: 301 ASVFPR 306 SVFPR Sbjct: 300 VSVFPR 305 Score = 73.6 bits (179), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 34/45 (75%), Positives = 39/45 (86%) Query: 411 HPTSGKFRQWAAPLPADIEALLKSANIDPALAVIPEMSEEADPVL 455 HP++GKFRQWAAPLP DI ALL+ A IDPALAVIPEMS+E D V+ Sbjct: 317 HPSTGKFRQWAAPLPEDIVALLQRAGIDPALAVIPEMSDEPDEVI 361 >gi|300312306|ref|YP_003776398.1| hypothetical protein Hsero_3002 [Herbaspirillum seropedicae SmR1] Length = 248 Score = 144 bits (363), Expect = 2e-35, Method: Compositional matrix adjust. Identities = 84/122 (68%), Positives = 99/122 (81%), Gaps = 2/122 (1%) Query: 288 ALVGDALYGKQHLAS--VFPRXARARARGAQDIIAWLGPAIGPEQFEVGAEVREAFITQQ 345 ++VG A G + LA+ + A RARGAQ+I+AWLGPAIGP FEVG EVR+AF+ QQ Sbjct: 120 SVVGAAHAGWRGLAAGVLEQTVAAMRARGAQEIMAWLGPAIGPGHFEVGGEVRQAFVAQQ 179 Query: 346 AAAQHAFRAYPGRPGKYLADIYELARQRLASMDVHDVSGGGLCTVSDPRFYSYRRDKTTG 405 AAA AFR YPGRPGKYLADIY+LARQRLA++ V +VSGGGLCTV+D RFYSYRRDKTTG Sbjct: 180 AAAAAAFRDYPGRPGKYLADIYQLARQRLAAVGVTEVSGGGLCTVADTRFYSYRRDKTTG 239 Query: 406 RL 407 R+ Sbjct: 240 RM 241 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 102 bits (253), Expect = 9e-23, Method: Compositional matrix adjust. Identities = 77/257 (29%), Positives = 122/257 (47%), Gaps = 21/257 (8%) Query: 47 LDDEVIGQRLDKVLSGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQS 106 + DE GQR+D L + +S I + + G V V+ + ++V V P Sbjct: 38 ISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVRVPPIR 97 Query: 107 VPADQPYAPEAMALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPGLANVP 166 V Q IL ED +++++KPAG+ VH +G G + A P Sbjct: 98 VAEKQETVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQ-------LRAARP 150 Query: 167 RAG---IVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTIN 222 +A +VHRLD++TSG++++AK +A T+L Q++ + ++Y LV G + Sbjct: 151 QAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVK 210 Query: 223 APMARHPRDRIKMAVSQSMRAKPAVTHY---RRLATGEIDRKPVSLVHCRLETGRTHQIR 279 P+ ++ + V +P+ T + RR +L+ L+TGRTHQIR Sbjct: 211 LPLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGD-------FALLEAELKTGRTHQIR 263 Query: 280 VHLQSLGFALVGDALYG 296 VHL S GF +VGD YG Sbjct: 264 VHLSSSGFPIVGDDKYG 280 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 54/181 (29%), Positives = 82/181 (45%), Gaps = 22/181 (12%) Query: 122 ILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPGLAN-VPRAGIVHRLDKETSG 180 ILH D +++ +KP L V P TLL L GL + VP +HRLD+ET+G Sbjct: 92 ILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRL-KKATGLQDLVP----IHRLDRETAG 146 Query: 181 LMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQS 240 ++V + A++ Q R+M + Y A+ L + P R R R++ Q Sbjct: 147 VIVFSHQPASRGKYQSMFQQRAMFKVYEAIA----PLRSDLELP--RVHRSRVEEIPEQF 200 Query: 241 MR------AKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGFALVGDAL 294 + A + TH + R + L TGR HQ+RVH+ +LG ++ D Sbjct: 201 FKMHEAEGAPNSETHISLIEA----RGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLF 256 Query: 295 Y 295 Y Sbjct: 257 Y 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 0.136 0.403 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: 1,548,357 Number of extensions: 69146 Number of successful extensions: 183 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 179 Number of HSP's successfully gapped: 5 Length of query: 465 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 376 Effective length of database: 1,198,455 Effective search space: 450619080 Effective search space used: 450619080 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: 132 (55.5 bits)