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= 0005.0124.p (343 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... 558 e-160 gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou... 108 7e-25 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 = 558 bits (1437), Expect = e-160, Method: Compositional matrix adjust. Identities = 271/336 (80%), Positives = 302/336 (89%), Gaps = 4/336 (1%) Query: 1 MKDLARFSGKTPEKPESPASTQSAPAS---PQVQLLTISEEEAGQRIDNFLLRVCKGVPK 57 MKDLARFS E ++ ++++A AS PQVQLLTIS+EEAGQRIDNFLLRVCKGVPK Sbjct: 1 MKDLARFSRGASESAKAAPASRNATASQSVPQVQLLTISDEEAGQRIDNFLLRVCKGVPK 60 Query: 58 SHIYRVLRSGEVRVNKGRIDQTYRLQDGDILRVPPIRIAEKASAAVAPGAEFKILLEDNH 117 SHIYRVLRSGEVRVNKGRIDQTYRL +GD++RVPPIR+AEK V PGAEF+ILLED+H Sbjct: 61 SHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVRVPPIRVAEKQETVV-PGAEFRILLEDSH 119 Query: 118 LLIIDKPAGVAVHGGSGVSYGVIEQLRASRPDAKFLELVHRLDRDTSGVLLLAKKRSALT 177 LL+IDKPAGVAVHGGSGVSYGVIEQLRA+RP AKFLELVHRLDRDTSGVLL+AKKRSALT Sbjct: 120 LLVIDKPAGVAVHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALT 179 Query: 178 NLHEQIRDGLTDKRYLTLIHGDWKNARQHIKLPLHKYSTAEGERRVRVQEDGQASHTVFS 237 NLH+Q+R+G TDKRY TL+ GDWKNARQH+KLPL KYST +GERRVRVQ DGQ SHTVFS Sbjct: 180 NLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTVFS 239 Query: 238 LIRRYGEFALLEAELKTGRTHQIRVHLSASGFPIVGDDKYGDFPLNKALQKADGERVAFR 297 L+RR+G+FALLEAELKTGRTHQIRVHLS+SGFPIVGDDKYGDF LNKALQKADG R+AF+ Sbjct: 240 LLRRFGDFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFK 299 Query: 298 RMFLHAHQISFTHPDSGKTVTLKAGLPPECQRFLKS 333 RMFLHA +ISF HP+SG TVTLKAGLP EC FL+S Sbjct: 300 RMFLHAWRISFRHPESGDTVTLKAGLPQECASFLRS 335 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 108 bits (270), Expect = 7e-25, Method: Compositional matrix adjust. Identities = 97/318 (30%), Positives = 147/318 (46%), Gaps = 25/318 (7%) Query: 33 LTISEEEAGQRIDNFLLRVCKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLQDGDILRVPP 92 L + +E GQR+D L + +S I + + G V VN + +++ V P Sbjct: 44 LRLDDEVIGQRLDKVLSGLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAP 103 Query: 93 IRIAEKASAAVAPGAEFKILLEDNHLLIIDKPAGVAVHGGSGVSYGVIEQ--LRASRPDA 150 + P A IL ED L++++KPAG+ VH +G G + L A Sbjct: 104 QSVPSDQPYGPEPMA-LDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALA 162 Query: 151 KFLE--LVHRLDRDTSGVLLLAKKRSALTNLHEQIRDGLTDKRYLTLIHGDWKNARQHIK 208 K +VHRLD+DTSG++++AK +A T+L Q++ ++YL L+ G I Sbjct: 163 KVPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTIN 221 Query: 209 LPLHKYSTAEGERRVRVQEDGQASHTVFSLIR-RYGEF-----ALLEAELKTGRTHQIRV 262 P+ ++ ++ V + +A V R GE +L+ L+TGRTHQIRV Sbjct: 222 APMARHP--RDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRV 279 Query: 263 HLSASGFPIVGDDKYGDFPLNKALQKADGERVAFRRMFLHAHQISFTHPDSGKTVTLKAG 322 HL + GFP+VGD YG L F R L A ++ HP +GK A Sbjct: 280 HLQSLGFPLVGDALYGKHHLVS----------VFPRQALLAGRLGLLHPSTGKFRQWAAP 329 Query: 323 LPPECQRFLKSLEGLDAA 340 LP + L+ G+D A Sbjct: 330 LPEDIVALLQR-AGIDPA 346 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 66.2 bits (160), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 72/242 (29%), Positives = 113/242 (46%), Gaps = 20/242 (8%) Query: 46 NFLLRVCKGVPKSHIYRVLRSGEVRVNKG---RIDQTYRLQDGDILRVPPIRIAEKASAA 102 +FL VP+ L GEVR G + D YR GD + R + A Sbjct: 30 SFLAERFTAVPEPVWRERLLRGEVRNQHGEALQPDTPYR--SGDCIFY--YRELPQGEAR 85 Query: 103 VAPGAEFKILLEDNHLLIIDKPAGVAV-HGGSGVSYGVIEQLRASRPDAKFLELVHRLDR 161 + E KIL D+HLL+ DKP + V G V ++ +L+ + + L +HRLDR Sbjct: 86 IP--VEEKILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKAT-GLQDLVPIHRLDR 142 Query: 162 DTSGVLLLAKKRSALTNLHEQIRDGLTDKRYLTLIHGDWKNARQHIKLP-LHKYSTAE-G 219 +T+GV++ + + ++ + +R + ++ R ++LP +H+ E Sbjct: 143 ETAGVIVFSHQPASRGKYQ-----SMFQQRAMFKVYEAIAPLRSDLELPRVHRSRVEEIP 197 Query: 220 ERRVRVQEDGQA--SHTVFSLIRRYGEFALLEAELKTGRTHQIRVHLSASGFPIVGDDKY 277 E+ ++ E A S T SLI G L E TGR HQ+RVH++A G PI+ D Y Sbjct: 198 EQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALGIPILNDLFY 257 Query: 278 GD 279 + 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 0.319 0.136 0.389 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: 956,660 Number of extensions: 36649 Number of successful extensions: 113 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 106 Number of HSP's successfully gapped: 3 Length of query: 343 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 257 Effective length of database: 1,212,660 Effective search space: 311653620 Effective search space used: 311653620 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 (21.7 bits) S2: 131 (55.1 bits)