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= 0001.2731.p (299 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134096436|ref|YP_001101511.1| putative pseudouridylate syntha... 280 7e-77 gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate syntha... 68 5e-13 gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Hermini... 56 2e-09 gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 sy... 54 7e-09 >gi|134096436|ref|YP_001101511.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 281 Score = 280 bits (716), Expect = 7e-77, Method: Compositional matrix adjust. Identities = 140/279 (50%), Positives = 193/279 (69%), Gaps = 3/279 (1%) Query: 22 PGPWRDMLSFLAEHFTAVPAEIWRERLLRGEVRNQRGEDLRPDSAYRSGDCIFYYRELPQ 81 PG W ++ FL EHF A+P W R+ RG+V + +G + SAY+ IFY+R LP+ Sbjct: 3 PGQWLTVIDFLVEHFPAIPRSEWMTRMQRGDVLDAQGRIIHVASAYQPHSKIFYFRSLPE 62 Query: 82 GEERIPVEEKILHLDEHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVPIHRLD 141 E RIP +E +L+ D++L+ DKPHFLPV P GR++QETLLVRLK++ + L P+HR+D Sbjct: 63 -EARIPFDEVVLYQDDYLVAVDKPHFLPVTPAGRYLQETLLVRLKRSLNIDTLAPMHRID 121 Query: 142 RETAGVIVFSHQRASRGKYQSMFRERSMFKVYEAIAPLRPELQLPRVHRSRVEELPEQFF 201 R+TAG+++F+ Q +R YQ++FRERS+ K YEAIAP R +L LP V+RSR+ E F Sbjct: 122 RDTAGLVLFTIQPHTRNLYQTLFRERSVSKQYEAIAPYRADLALPTVYRSRLLE-SAAFM 180 Query: 202 KMHEAQGAPNSETHISLLEARGELGLYQLEPVTGRRHQLRVHMAALGIPILNDLFYPHAV 261 KM E +G PN+ET I L+E +G L Y+LEPV+G++HQLR HMAALG+PI+ND YP Sbjct: 181 KMEEVEGVPNAETAIDLMEVQGALARYRLEPVSGQKHQLRAHMAALGMPIVNDRIYPELY 240 Query: 262 P-VGVADDLDKPLKLLARSLFFIDPLDGSERHFVSQRSL 299 P G D +PLKLLA+++ F DP+ R F S++ L Sbjct: 241 PDEGAEQDYSQPLKLLAKTISFTDPISRQLRQFESRQHL 279 >gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 326 Score = 68.2 bits (165), Expect = 5e-13, Method: Compositional matrix adjust. Identities = 75/239 (31%), Positives = 112/239 (46%), Gaps = 19/239 (7%) Query: 30 SFLAEHFTAVPAEIWRERLLRGEVRNQRGEDLRPDSAYR--SGDCIFY--YRELPQGEER 85 +FL VP L GEVR +G R D YR GD + R + Sbjct: 34 NFLLRICKGVPKSHIYRVLRSGEVRVNKG---RIDQTYRLTEGDVVRIPPIRIAEKAPST 90 Query: 86 IPVEE-KILHLDEHLLVADKPHFLPVIPTGRFVQETLLVRLKKAT-GLQDLVPIHRLDRE 143 P E KIL D HLLV DKP + V G V ++ +L+ A + L +HRLDR+ Sbjct: 91 APGAEFKILLEDNHLLVIDKPAGVAV-HGGSGVSYGVIEQLRAARPDAKFLELVHRLDRD 149 Query: 144 TAGVIVFSHQRASRGKYQSMFR-----ERSMFKVYEAIAPLRPELQLPRVHRSRVEELPE 198 T+GV+V + +R++ R +R + V+ R ++L +H+ + E Sbjct: 150 TSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGDWKNARQHIKLA-LHKYSTAD-GE 207 Query: 199 QFFKMHEAQGAPNSETHISLLEARGELGLYQLEPVTGRRHQLRVHMAALGIPILNDLFY 257 + ++ +A G S T +L++ GE L + E TGR HQ+RVH+A+ G I D Y Sbjct: 208 RRVRV-QADGM-ESHTIFNLIQRYGEFALLEAELKTGRTHQIRVHLASSGFAIAGDDKY 264 >gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Herminiimonas arsenicoxydans] Length = 318 Score = 56.2 bits (134), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 57/211 (27%), Positives = 92/211 (43%), Gaps = 26/211 (12%) Query: 65 SAYRSGDCIFYYRELPQGEERIP--VEEKILHLDEHLLVADKPHFLPVIPTGRFVQETLL 122 + Y + Y + P+ E P ++ I + D +LV DKP L V P TLL Sbjct: 64 TVYGDEKVVIYPQPAPEDEAFKPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLL 123 Query: 123 VRL----KKATGLQDLVPIHRLDRETAGVIVFSHQRASRGKYQSMFRERSMFKVYEAIAP 178 L G+ +HRLD++T+G++V + + + R++ + Y A+ Sbjct: 124 NGLLHYLPAIAGVPRAGIVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVW 183 Query: 179 LRPELQ------LPRVHRSRVEELPEQFFKMHEAQGAPNSETH-----ISLLEAR-GELG 226 P + + R R RV+ + E A + TH +L+ R L Sbjct: 184 GTPNVSGKVDTSIGRHSRDRVK------MAVSENLTAKPALTHFQRLATGMLDGRPVSLM 237 Query: 227 LYQLEPVTGRRHQLRVHMAALGIPILNDLFY 257 + QLE TGR HQ+RVHM ++G ++ D Y Sbjct: 238 MCQLE--TGRTHQIRVHMQSIGFALVGDALY 266 >gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 synthase [Herminiimonas arsenicoxydans] Length = 223 Score = 54.3 bits (129), Expect = 7e-09, Method: Compositional matrix adjust. Identities = 47/177 (26%), Positives = 82/177 (46%), Gaps = 15/177 (8%) Query: 89 EEKILHLDEHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVPIHRLDRETAGVI 148 E +IL+ DE LL+ +KP L + +G+ V + + +HRLD T+G++ Sbjct: 16 EIEILYQDEALLLINKPSGLLSL-SGKNPLNLDSVHYRLVQQFPTALMLHRLDFGTSGLL 74 Query: 149 VFSHQRASRGKYQSMFRERSMFKVYEAIAPLR-----PELQLPRVHRSRVEELPEQFFKM 203 V + + F+ R++ K Y+A+ R +++LP + + P F K+ Sbjct: 75 VVALNKTVAADIYRQFQLRTVVKTYQAVLAGRMDSDAGDIELP------IAKDPVNFPKL 128 Query: 204 HEA-QGAPNSETHISLLEARG--ELGLYQLEPVTGRRHQLRVHMAALGIPILNDLFY 257 + +H +L+ + + P+TGR HQLR+H A +G PIL Y Sbjct: 129 KICLTTGKTASSHFQVLDRQSGPDTTRVVFTPLTGRTHQLRIHSAGVGHPILGCDLY 185 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 0.323 0.141 0.427 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: 605,376 Number of extensions: 25627 Number of successful extensions: 63 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 59 Number of HSP's successfully gapped: 4 Length of query: 299 Length of database: 1,000,347 Length adjustment: 81 Effective length of query: 218 Effective length of database: 733,452 Effective search space: 159892536 Effective search space used: 159892536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 128 (53.9 bits)