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/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate syntha... 513 e-147 gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Hermini... 123 2e-29 gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 sy... 84 1e-17 >gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 326 Score = 513 bits (1320), Expect = e-147, Method: Compositional matrix adjust. Identities = 246/301 (81%), Positives = 270/301 (89%) Query: 37 TISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDVVRVPPI 96 TIS+EEAGQRIDNFLLR+CKGVPKSHIYRVLRSGEVRVNKGRIDQTYRL EGDVVR+PPI Sbjct: 22 TISEEEAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLTEGDVVRIPPI 81 Query: 97 RVAEKQEQVVPGAEFRILLEDSHLLVIDKPAGVAVHGGSGVSYGVIEQLRAARPQAKFLE 156 R+AEK PGAEF+ILLED+HLLVIDKPAGVAVHGGSGVSYGVIEQLRAARP AKFLE Sbjct: 82 RIAEKAPSTAPGAEFKILLEDNHLLVIDKPAGVAVHGGSGVSYGVIEQLRAARPDAKFLE 141 Query: 157 LVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKY 216 LVHRLDRDTSGVL++AKKRSALTNLH+Q+R G DKRY LV GDWKNARQH+KL L KY Sbjct: 142 LVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGDWKNARQHIKLALHKY 201 Query: 217 STPDGERRVRVQADGQPSHTIFSLLRRFGEFALLEAELKTGRTHQIRVHLSSSGFPIVGD 276 ST DGERRVRVQADG SHTIF+L++R+GEFALLEAELKTGRTHQIRVHL+SSGF I GD Sbjct: 202 STADGERRVRVQADGMESHTIFNLIQRYGEFALLEAELKTGRTHQIRVHLASSGFAIAGD 261 Query: 277 DKYGDFTLNKALQKADGSRIAFKRMFLHAWRISFRHPESGETVTLKAGLPEECARFLRSL 336 DKYGDF LN+ LQKA+G R+A KRMFLHA +I+F HPESG+ VTL A LP EC RFL+SL Sbjct: 262 DKYGDFALNRELQKANGERVALKRMFLHAHQITFIHPESGKPVTLNAPLPPECERFLKSL 321 Query: 337 E 337 + Sbjct: 322 K 322 >gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Herminiimonas arsenicoxydans] Length = 318 Score = 123 bits (308), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 102/317 (32%), Positives = 155/317 (48%), Gaps = 28/317 (8%) Query: 29 NLPQVQLLTISDEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEG 88 ++P ++L ++ G R+D L + +S + + + +G V V+ G I + V G Sbjct: 10 DVPPIEL-DLTPAVCGVRLDKVLSTLVPQYSRSRLQQWIDAGHVSVD-GEIARAKMTVYG 67 Query: 89 DVVRVPPIRVAEKQEQVVPGA-EFRILLEDSHLLVIDKPAGVAVHGGSG-----VSYGVI 142 D V + A + E P A + I ED+ +LVIDKPAG+ VH +G + G++ Sbjct: 68 DEKVVIYPQPAPEDEAFKPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLL 127 Query: 143 EQLRA--ARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQG 200 L A P+A +VHRLD+DTSG++++AK A T+L Q++ T + Y LV G Sbjct: 128 HYLPAIAGVPRAG---IVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWG 184 Query: 201 DWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTIFSLLRRFG----EFALLEAELKT 256 N V + ++S + V +P+ T F L +L+ +L+T Sbjct: 185 T-PNVSGKVDTSIGRHSRDRVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLET 243 Query: 257 GRTHQIRVHLSSSGFPIVGDDKYGDFTLNKALQKADGSRIAFKRMFLHAWRISFRHPESG 316 GRTHQIRVH+ S GF +VGD YG L F R LHA R+ HP SG Sbjct: 244 GRTHQIRVHMQSIGFALVGDALYGKQHLTT----------VFPRQALHARRLGLVHPVSG 293 Query: 317 ETVTLKAGLPEECARFL 333 V + LP++ A + Sbjct: 294 AAVEWSSELPQDFADLI 310 >gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 synthase [Herminiimonas arsenicoxydans] Length = 223 Score = 83.6 bits (205), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 65/217 (29%), Positives = 108/217 (49%), Gaps = 28/217 (12%) Query: 110 EFRILLEDSHLLVIDKPAGVAVHGG------SGVSYGVIEQLRAARPQAKFLELVHRLDR 163 E IL +D LL+I+KP+G+ G V Y +++Q A ++HRLD Sbjct: 16 EIEILYQDEALLLINKPSGLLSLSGKNPLNLDSVHYRLVQQFPTAL-------MLHRLDF 68 Query: 164 DTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGER 223 TSG+L++A ++ +++ Q + T K Y ++ G + ++LP+ K P Sbjct: 69 GTSGLLVVALNKTVAADIYRQFQLRTVVKTYQAVLAGRMDSDAGDIELPIAK--DPVNFP 126 Query: 224 RVRVQ-ADGQPSHTIFSLLRRFG--EFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYG 280 ++++ G+ + + F +L R + + TGRTHQ+R+H + G PI+G D YG Sbjct: 127 KLKICLTTGKTASSHFQVLDRQSGPDTTRVVFTPLTGRTHQLRIHSAGVGHPILGCDLYG 186 Query: 281 DFTLNKALQKADGSRIAFKRMFLHAWRISFRHPESGE 317 ++ Q AD R+ LHA + F HP SGE Sbjct: 187 T---PESQQMAD-------RLLLHATTVEFDHPISGE 213 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 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: 3295 Number of Hits to DB: 596,161 Number of extensions: 23390 Number of successful extensions: 67 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 61 Number of HSP's successfully gapped: 3 Length of query: 355 Length of database: 1,000,347 Length adjustment: 83 Effective length of query: 272 Effective length of database: 726,862 Effective search space: 197706464 Effective search space used: 197706464 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: 129 (54.3 bits)