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= 0001.2975.p (372 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Hermini... 422 e-119 gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate syntha... 116 2e-27 gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 sy... 88 7e-19 >gi|134095125|ref|YP_001100200.1| pseudouridine synthase [Herminiimonas arsenicoxydans] Length = 318 Score = 422 bits (1086), Expect = e-119, Method: Compositional matrix adjust. Identities = 201/303 (66%), Positives = 249/303 (82%) Query: 42 PLTFRLDDEVVGQRLDKVLSGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVE 101 P+ L V G RLDKVLS L+P++SRSR+QQWI+ GHV+VDG A+ KMT+ GDE V Sbjct: 13 PIELDLTPAVCGVRLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIARAKMTVYGDEKVV 72 Query: 102 VAPQSVPADQPYAPEAMALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPA 161 + PQ P D+ + PEAM L+I +ED +I++++KPAGLVVHPAAGNWSGTLLNGLLH+ PA Sbjct: 73 IYPQPAPEDEAFKPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLHYLPA 132 Query: 162 LANVPRAGIVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTI 221 +A VPRAGIVHRLDK+TSGLMVVAKTL A TDLVRQLQAR++KR+YLALVWG P +SG + Sbjct: 133 IAGVPRAGIVHRLDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTPNVSGKV 192 Query: 222 NAPMARHPRDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVH 281 + + RH RDR+KMAVS+++ AKPA+TH++RLATG +D +PVSL+ C+LETGRTHQIRVH Sbjct: 193 DTSIGRHSRDRVKMAVSENLTAKPALTHFQRLATGMLDGRPVSLMMCQLETGRTHQIRVH 252 Query: 282 LQSLGFALVGDSLYGKQHLAPVFPRQALLAGRLGLVHPTSGKFRQWAAPLPPDIEALLQR 341 +QS+GFALVGD+LYGKQHL VFPRQAL A RLGLVHP SG +W++ LP D L+ R Sbjct: 253 MQSIGFALVGDALYGKQHLTTVFPRQALHARRLGLVHPVSGAAVEWSSELPQDFADLIAR 312 Query: 342 AGI 344 +GI Sbjct: 313 SGI 315 >gi|134095276|ref|YP_001100351.1| 23S rRNA pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 326 Score = 116 bits (290), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 91/311 (29%), Positives = 141/311 (45%), Gaps = 31/311 (9%) Query: 47 LDDEVVGQRLDKVLSGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQS 106 + +E GQR+D L + +S I + + G V V+ + ++V + P Sbjct: 23 ISEEEAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLTEGDVVRIPPIR 82 Query: 107 VPADQPYAPEAMALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVP 166 + P IL ED +++++KPAG+ VH +G G + A + Sbjct: 83 IAEKAPSTAPGAEFKILLEDNHLLVIDKPAGVAVHGGSGVSYGVIEQLR----AARPDAK 138 Query: 167 RAGIVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINAPM 225 +VHRLD++TSG++V+AK +A T+L Q++ ++YL LV G I + Sbjct: 139 FLELVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGDWKNARQHIKLAL 198 Query: 226 ARHP------RDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIR 279 ++ R R++ +S + Y GE +L+ L+TGRTHQIR Sbjct: 199 HKYSTADGERRVRVQADGMESHTIFNLIQRY-----GEF-----ALLEAELKTGRTHQIR 248 Query: 280 VHLQSLGFALVGDSLYGKQHLAP----------VFPRQALLAGRLGLVHPTSGKFRQWAA 329 VHL S GFA+ GD YG L R L A ++ +HP SGK A Sbjct: 249 VHLASSGFAIAGDDKYGDFALNRELQKANGERVALKRMFLHAHQITFIHPESGKPVTLNA 308 Query: 330 PLPPDIEALLQ 340 PLPP+ E L+ Sbjct: 309 PLPPECERFLK 319 >gi|134095434|ref|YP_001100509.1| 23S rRNA pseudouridylate 746 synthase [Herminiimonas arsenicoxydans] Length = 223 Score = 88.2 bits (217), Expect = 7e-19, Method: Compositional matrix adjust. Identities = 67/209 (32%), Positives = 111/209 (53%), Gaps = 17/209 (8%) Query: 120 LDILHEDKSIIILNKPAGLVVHPAAGNWSG-TLLNGLLHHCPALANVPRAGIVHRLDKET 178 ++IL++D++++++NKP+GL+ + SG LN H + P A ++HRLD T Sbjct: 17 IEILYQDEALLLINKPSGLL------SLSGKNPLNLDSVHYRLVQQFPTALMLHRLDFGT 70 Query: 179 SGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINAPMARHPRDRIKMAV 237 SGL+VVA D+ RQ Q R++ + Y A++ G + +G I P+A+ P + K+ + Sbjct: 71 SGLLVVALNKTVAADIYRQFQLRTVVKTYQAVLAGRMDSDAGDIELPIAKDPVNFPKLKI 130 Query: 238 SQSMRAKPAVTHYRRLATGEIDRKP---VSLVHCRLETGRTHQIRVHLQSLGFALVGDSL 294 + K A +H++ L DR+ + V TGRTHQ+R+H +G ++G L Sbjct: 131 CLTT-GKTASSHFQVL-----DRQSGPDTTRVVFTPLTGRTHQLRIHSAGVGHPILGCDL 184 Query: 295 YGKQHLAPVFPRQALLAGRLGLVHPTSGK 323 YG + R L A + HP SG+ Sbjct: 185 YGTPESQQMADRLLLHATTVEFDHPISGE 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 0.318 0.137 0.408 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: 754,707 Number of extensions: 32695 Number of successful extensions: 106 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 101 Number of HSP's successfully gapped: 3 Length of query: 372 Length of database: 1,000,347 Length adjustment: 83 Effective length of query: 289 Effective length of database: 726,862 Effective search space: 210063118 Effective search space used: 210063118 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 129 (54.3 bits)