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= 0001.1752.p (355 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... 667 0.0 gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou... 120 2e-28 gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 66 4e-12 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 667 bits (1721), Expect = 0.0, Method: Compositional matrix adjust. Identities = 335/354 (94%), Positives = 343/354 (96%) Query: 1 MKDLARFSRGASESAAAAPASRNATASHNLPQVQLLTISDEEAGQRIDNFLLRVCKGVPK 60 MKDLARFSRGASESA AAPASRNATAS ++PQVQLLTISDEEAGQRIDNFLLRVCKGVPK Sbjct: 1 MKDLARFSRGASESAKAAPASRNATASQSVPQVQLLTISDEEAGQRIDNFLLRVCKGVPK 60 Query: 61 SHIYRVLRSGEVRVNKGRIDQTYRLVEGDVVRVPPIRVAEKQEQVVPGAEFRILLEDSHL 120 SHIYRVLRSGEVRVNKGRIDQTYRL EGDVVRVPPIRVAEKQE VVPGAEFRILLEDSHL Sbjct: 61 SHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVRVPPIRVAEKQETVVPGAEFRILLEDSHL 120 Query: 121 LVIDKPAGVAVHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTN 180 LVIDKPAGVAVHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTN Sbjct: 121 LVIDKPAGVAVHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTN 180 Query: 181 LHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTIFSL 240 LHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHT+FSL Sbjct: 181 LHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTVFSL 240 Query: 241 LRRFGEFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFTLNKALQKADGSRIAFKR 300 LRRFG+FALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYGDF LNKALQKADG RIAFKR Sbjct: 241 LRRFGDFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKR 300 Query: 301 MFLHAWRISFRHPESGETVTLKAGLPEECARFLRSLEGGAEGDLLPHNMLAGTE 354 MFLHAWRISFRHPESG+TVTLKAGLP+ECA FLRSLEGG EG+LLP+ MLA E Sbjct: 301 MFLHAWRISFRHPESGDTVTLKAGLPQECASFLRSLEGGEEGELLPYGMLACAE 354 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 120 bits (300), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 99/310 (31%), Positives = 145/310 (46%), Gaps = 25/310 (8%) Query: 36 LTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDVVRVPP 95 L + DE GQR+D L + +S I + + G V VN ++ ++V V P Sbjct: 44 LRLDDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAP 103 Query: 96 IRVAEKQEQVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQ--LRAARPQAK 153 V Q IL ED L+V++KPAG+ VH +G G + L AK Sbjct: 104 QSVPSDQPYGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAK 163 Query: 154 FLE--LVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKL 211 +VHRLD+DTSG++++AK +A T+L Q++ + ++Y LV G + Sbjct: 164 VPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINA 222 Query: 212 PLFKYSTPDGERRVRVQADGQPSHTIFSLLRRF--GEF-----ALLEAELKTGRTHQIRV 264 P+ ++ + V +P+ T + RR GE +L+ L+TGRTHQIRV Sbjct: 223 PMARHPRDRIKMAVSQSMRAKPAVTHY---RRLATGEIDRKPVSLIHCRLETGRTHQIRV 279 Query: 265 HLSSSGFPIVGDDKYGDFTLNKALQKADGSRIAFKRMFLHAWRISFRHPESGETVTLKAG 324 HL S GFP+VGD YG L F R L A R+ HP +G+ A Sbjct: 280 HLQSLGFPLVGDALYGKHHLVS----------VFPRQALLAGRLGLLHPSTGKFRQWAAP 329 Query: 325 LPEECARFLR 334 LPE+ L+ Sbjct: 330 LPEDIVALLQ 339 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 65.9 bits (159), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 73/242 (30%), Positives = 112/242 (46%), Gaps = 21/242 (8%) Query: 49 NFLLRVCKGVPKSHIYRVLRSGEVRVNKG---RIDQTYRLVEGDVVRVPPIRVAEKQEQV 105 +FL VP+ L GEVR G + D YR GD + R + E Sbjct: 30 SFLAERFTAVPEPVWRERLLRGEVRNQHGEALQPDTPYR--SGDCIFY--YRELPQGEAR 85 Query: 106 VPGAEFRILLEDSHLLVIDKPAGVAV-HGGSGVSYGVIEQLRAARPQAKFLELVHRLDRD 164 +P E +IL D HLLV DKP + V G V ++ +L+ A + L +HRLDR+ Sbjct: 86 IPVEE-KILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKAT-GLQDLVPIHRLDRE 143 Query: 165 TSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYS----TPD 220 T+GV++ + + ++ ++ K Y + R ++LP S P+ Sbjct: 144 TAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA-----PLRSDLELPRVHRSRVEEIPE 198 Query: 221 GERRVRVQADGQP-SHTIFSLLRRFGEFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKY 279 ++ +A+G P S T SL+ G L E TGR HQ+RVH+++ G PI+ D Y Sbjct: 199 QFFKMH-EAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLFY 257 Query: 280 GD 281 + 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 0.320 0.136 0.392 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: 977,992 Number of extensions: 39083 Number of successful extensions: 108 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 103 Number of HSP's successfully gapped: 3 Length of query: 355 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 269 Effective length of database: 1,212,660 Effective search space: 326205540 Effective search space used: 326205540 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)