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= 0169.0003.p (334 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... 412 e-116 gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 127 2e-30 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 64 2e-11 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 412 bits (1058), Expect = e-116, Method: Compositional matrix adjust. Identities = 219/344 (63%), Positives = 260/344 (75%), Gaps = 19/344 (5%) Query: 1 MSRTTPPKVVKAFATEPVEIPEGDDSLDEVVE-EFTDGAEPITLKLTDDACGVRLDKVLS 59 MSR P ++ ++P+ DD D E G EP+TL+L D+ G RLDKVLS Sbjct: 1 MSRKKPLQITNGDTPVHTDLPQADDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVLS 60 Query: 60 GLVPQYSRSRIQQWIEGGHVTVDGNPARTKMTVLGDELVVITPQAAPEDNAFQPEPMDLR 119 GL+P++SRSRIQQWIE GHVTV+G PA+ KMT+LGDELV + PQ+ P D + PEPM L Sbjct: 61 GLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMALD 120 Query: 120 IIHEDKAIMVIDKPAGLVVHPAAGNWSGTLLNGLLHHCPALAGVPRAGIVHRLDKDTSGL 179 I+HEDKA++V++KPAGLVVHPAAGNWSGTLLNGLLHHCPALA VPRAGIVHRLDKDTSG+ Sbjct: 121 ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHRLDKDTSGI 180 Query: 180 MVVAKTLAAQTDLVRQLQARTVKRQYLALVWGMPQLSGTVDAPMARRAR--------REP 231 MVVAKTLAAQTDLVRQLQAR++KRQYLALVWG+PQLSGT++APMAR R + Sbjct: 181 MVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSM 240 Query: 232 DALPXA----------LDGRAVSLMRCQLETGRTHQIRVHMQSLGFALVGDALYGKSHLM 281 A P +D + VSL+ C+LETGRTHQIRVH+QSLGF LVGDALYGK HL+ Sbjct: 241 RAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHLV 300 Query: 282 TFFPRQALQAWKLGLIHPTTGKQVEWEVGLPADFTELLERAGID 325 + FPRQAL A +LGL+HP+TGK +W LP D LL+RAGID Sbjct: 301 SVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGID 344 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 99/306 (32%), Positives = 145/306 (47%), Gaps = 37/306 (12%) Query: 43 LKLTDDACGVRLDKVLSGLVPQYSRSRIQQWIEGGHVTVD-GNPARTKMTVLGDELVVIT 101 L ++D+ G R+D L + +S I + + G V V+ G +T GD +V + Sbjct: 36 LTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLAEGD-VVRVP 94 Query: 102 PQAAPEDNAFQPEPMDLRIIHEDKAIMVIDKPAGLVVHPAAGNWSGTLLNGLLHHCPALA 161 P E + RI+ ED ++VIDKPAG+ VH +G G + A Sbjct: 95 PIRVAEKQETVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQ-------LRA 147 Query: 162 GVPRAG---IVHRLDKDTSGLMVVAKTLAAQTDLVRQLQARTVKRQYLALVWG-MPQLSG 217 P+A +VHRLD+DTSG++++AK +A T+L Q++ T ++Y LV G Sbjct: 148 ARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQ 207 Query: 218 TVDAPM--------ARRARREPDALPX----ALDGRA--VSLMRCQLETGRTHQIRVHMQ 263 V P+ RR R + D P +L R +L+ +L+TGRTHQIRVH+ Sbjct: 208 HVKLPLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLS 267 Query: 264 SLGFALVGDALYGKSHL----------MTFFPRQALQAWKLGLIHPTTGKQVEWEVGLPA 313 S GF +VGD YG L F R L AW++ HP +G V + GLP Sbjct: 268 SSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAGLPQ 327 Query: 314 DFTELL 319 + L Sbjct: 328 ECASFL 333 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 52/182 (28%), Positives = 85/182 (46%), Gaps = 26/182 (14%) Query: 115 PMDLRIIHEDKAIMVIDKPAGLVVHPAAGNWSGTLLNGLLHHCPALAGVPRAGIVHRLDK 174 P++ +I+H D ++V DKP L V P TLL L VP +HRLD+ Sbjct: 87 PVEEKILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVP----IHRLDR 142 Query: 175 DTSGLMVVAKTLAAQTDLVRQLQARTVKRQYLALVWGMPQLSGTVDAPMARRAR------ 228 +T+G++V + A++ Q R + + Y A+ L ++ P R+R Sbjct: 143 ETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA----PLRSDLELPRVHRSRVEEIPE 198 Query: 229 -----REPDALPXA------LDGR-AVSLMRCQLETGRTHQIRVHMQSLGFALVGDALYG 276 E + P + ++ R A+ L R + TGR HQ+RVHM +LG ++ D Y Sbjct: 199 QFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLFYP 258 Query: 277 KS 278 ++ Sbjct: 259 EA 260 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 0.136 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: 1,166,659 Number of extensions: 53685 Number of successful extensions: 135 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 131 Number of HSP's successfully gapped: 3 Length of query: 334 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 248 Effective length of database: 1,212,660 Effective search space: 300739680 Effective search space used: 300739680 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)