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= 0007.0026.p (375 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat... 407 e-115 gi|300312001|ref|YP_003776093.1| HipA-like protein [Herbaspirill... 93 4e-20 gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou... 72 1e-13 gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou... 66 5e-12 >gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 407 bits (1046), Expect = e-115, Method: Compositional matrix adjust. Identities = 201/301 (66%), Positives = 228/301 (75%), Gaps = 3/301 (0%) Query: 76 MRPTAPLPLKDGVAPSYLWLQDAAGVWNNMLDFLTARFPGVTEEAWRQRMARGEVVNQDG 135 MRPT LP+++G++PSYLWLQ G W ML FL RF V E WR+R+ RGEV NQ G Sbjct: 1 MRPTPTLPMREGLSPSYLWLQ--PGPWRTMLSFLAERFTAVPEPVWRERLLRGEVRNQHG 58 Query: 136 VALAPDSAYRRGDCLFYYRDLEGGEAPIPFTEQILHQDAHLLVVDKPHFVPVIPTGRFLH 195 AL PD+ YR GDC+FYYR+L GEA IP E+ILH D HLLV DKPHF+PVIPTGRF+ Sbjct: 59 EALQPDTPYRSGDCIFYYRELPQGEARIPVEEKILHLDDHLLVADKPHFLPVIPTGRFVQ 118 Query: 196 ESLLVRLKKKTGLADLTPIHRLDRETAGVIIFSHNPASRGAYQAMFQQRTMDKTYEALAG 255 E+LLVRLKK TGL DL PIHRLDRETAGVI+FSH PASRG YQ+MFQQR M K YEA+A Sbjct: 119 ETLLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAP 178 Query: 256 LLEGRSFPFTHRSRMVD-ADKFFLMREEEGAPNSETHVDLIERRGALGLYRLNPVTGRKH 314 L P HRSR+ + ++FF M E EGAPNSETH+ LIE RGALGLYRL PVTGR+H Sbjct: 179 LRSDLELPRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRH 238 Query: 315 QLRVHMAALGIPIVNDNFYPHVVPAGTADNYDAPLKLLARSIAFTDPLSGDVRYFESLRT 374 QLRVHMAALGIPI+ND FYP VP G AD+ D PLKLLARS+ F DPL G R+F S R Sbjct: 239 QLRVHMAALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERN 298 Query: 375 L 375 L Sbjct: 299 L 299 >gi|300312001|ref|YP_003776093.1| HipA-like protein [Herbaspirillum seropedicae SmR1] Length = 446 Score = 92.8 bits (229), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 41/59 (69%), Positives = 49/59 (83%) Query: 1 VLRELANIWRIPEPKLQMVLVDTVERAMQSWPELLRSLPLNDTQRSRIKAHLDNNPSVI 59 +LR+LAN+WRIPEPKLQ VLVDTVERAM WP L+ SLPL D QR+R+ +HLD N SV+ Sbjct: 370 ILRQLANLWRIPEPKLQAVLVDTVERAMTQWPALIASLPLTDAQRTRLLSHLDANASVL 428 >gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudouridine synthase C [Herbaspirillum seropedicae SmR1] Length = 355 Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 88/285 (30%), Positives = 122/285 (42%), Gaps = 40/285 (14%) Query: 107 DFLTARFPGVTEEAWRQRMARGEV-VNQDGVALAPDSAYR--RGDCLFY--YRDLEGGEA 161 +FL GV + + + GEV VN+ + D YR GD + R E E Sbjct: 49 NFLLRVCKGVPKSHIYRVLRSGEVRVNKGRI----DQTYRLAEGDVVRVPPIRVAEKQET 104 Query: 162 PIPFTE-QILHQDAHLLVVDKPHFVPVIPTGRFLHESLLVRLKKKTGLAD-LTPIHRLDR 219 +P E +IL +D+HLLV+DKP V V G + ++ +L+ A L +HRLDR Sbjct: 105 VVPGAEFRILLEDSHLLVIDKPAGVAV-HGGSGVSYGVIEQLRAARPQAKFLELVHRLDR 163 Query: 220 ETAGVIIFSHNPASRGAYQAMFQQRTMDKTYEALAGL------------LEGRSFPFTHR 267 +T+GV++ + ++ ++ T DK Y L L S P R Sbjct: 164 DTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYSTPDGER 223 Query: 268 SRMVDADKFFLMREEEGAPNSETHVDLIERRGALGLYRLNPVTGRKHQLRVHMAALGIPI 327 V AD G P S T L+ R G L TGR HQ+RVH+++ G PI Sbjct: 224 RVRVQAD---------GQP-SHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFPI 273 Query: 328 VNDNFYPHVV---PAGTADNYDAPLK---LLARSIAFTDPLSGDV 366 V D+ Y AD K L A I+F P SGD Sbjct: 274 VGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDT 318 >gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudouridine synthase D [Herbaspirillum seropedicae SmR1] Length = 370 Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 60/189 (31%), Positives = 86/189 (45%), Gaps = 23/189 (12%) Query: 161 APIPFTEQILHQDAHLLVVDKPHFVPVIPTGRFLHESLLVRLKKKTGLADLTP----IHR 216 P P ILH+D L+V++KP + V P +LL L P +HR Sbjct: 113 GPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHR 172 Query: 217 LDRETAGVIIFSHNPASRGAYQAMFQQRTMDKTYEALA-GL--LEGR-SFPFTHRSRMVD 272 LD++T+G+++ + A++ Q R+M + Y AL GL L G + P R D Sbjct: 173 LDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPR--D 230 Query: 273 ADKFFLMREEEGAPNSETHVDLIERRGALGLYRLNPV--------TGRKHQLRVHMAALG 324 K + + P + TH RR A G PV TGR HQ+RVH+ +LG Sbjct: 231 RIKMAVSQSMRAKP-AVTHY----RRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLG 285 Query: 325 IPIVNDNFY 333 P+V D Y Sbjct: 286 FPLVGDALY 294 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 0.322 0.138 0.423 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: 1,306,026 Number of extensions: 59553 Number of successful extensions: 143 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 139 Number of HSP's successfully gapped: 4 Length of query: 375 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 288 Effective length of database: 1,207,925 Effective search space: 347882400 Effective search space used: 347882400 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 (21.9 bits) S2: 131 (55.1 bits)