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/707/707 3697 sequences; 1,221,021 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|152981261|ref|YP_001353083.1| ribosomal large subunit pseudou... 435 e-123 gi|152981207|ref|YP_001353037.1| ribosomal large subunit pseudou... 125 4e-30 gi|152981434|ref|YP_001352926.1| pseudouridylate synthases, 23S ... 91 8e-20 >gi|152981261|ref|YP_001353083.1| ribosomal large subunit pseudouridine synthase D [Janthinobacterium sp. Marseille] Length = 342 Score = 435 bits (1119), Expect = e-123, Method: Compositional matrix adjust. Identities = 213/332 (64%), Positives = 262/332 (78%), Gaps = 1/332 (0%) Query: 13 DEPVKTDLPLEDDFDDGEQAGDDGVPGLEPLTFRLDDEVVGQRLDKVLSGLMPEFSRSRI 72 D P+ E D + G GDD L P+ L+ +V G RLDKVLS L+P++SRSR+ Sbjct: 9 DTPILNKTMPESDLE-GVDDGDDLALELPPIELDLNPDVCGVRLDKVLSTLVPQYSRSRL 67 Query: 73 QQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQSVPADQPYAPEAMALDILHEDKSIIIL 132 QQWI+ GHV+VDG A+ KMT+ GDE V + PQ P D+ + PEAM L I+HED ++++ Sbjct: 68 QQWIDGGHVSVDGEVARAKMTVYGDEKVVIYPQPAPEDEAFKPEAMDLAIVHEDAEMLVI 127 Query: 133 NKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVPRAGIVHRLDKETSGLMVVAKTLAAQT 192 NKPAGLVVHPAAGNWSGTLLNGLLH+ P+++ VPRAGIVHRLDK+TSGLMVVAKTL A T Sbjct: 128 NKPAGLVVHPAAGNWSGTLLNGLLHYLPSISGVPRAGIVHRLDKDTSGLMVVAKTLIAHT 187 Query: 193 DLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMAVSQSMRAKPAVTHYRR 252 DLVRQLQAR++KR+YLALVWG P ++G I+A + RH RDRIKMAVS+++ AKPAVTH++R Sbjct: 188 DLVRQLQARTVKREYLALVWGTPNITGKIDASIGRHARDRIKMAVSENLTAKPAVTHFQR 247 Query: 253 LATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGFALVGDSLYGKQHLAPVFPRQALLAG 312 LATG +D +PVSL+ CRLETGRTHQIRVH+QS+GFALVGD LYGKQHL VFPRQAL A Sbjct: 248 LATGMLDGRPVSLMLCRLETGRTHQIRVHMQSIGFALVGDGLYGKQHLTTVFPRQALHAR 307 Query: 313 RLGLVHPTSGKFRQWAAPLPPDIEALLQRAGI 344 RLGL+HP SG+ +W++ LP D L+ RAGI Sbjct: 308 RLGLIHPVSGEAVEWSSELPQDFAELIARAGI 339 >gi|152981207|ref|YP_001353037.1| ribosomal large subunit pseudouridine synthase C [Janthinobacterium sp. Marseille] Length = 339 Score = 125 bits (314), Expect = 4e-30, Method: Compositional matrix adjust. Identities = 93/308 (30%), Positives = 144/308 (46%), Gaps = 25/308 (8%) Query: 47 LDDEVVGQRLDKVLSGLMPEFSRSRIQQWIEDGHVTVDGAPAKGKMTMLGDELVEVAPQS 106 ++DE GQR+D L + +S I + + G V V+ ++ ++V + P Sbjct: 36 INDEDAGQRIDNFLLRICKGVPKSHIYRVLRSGEVRVNKGRIDQTYRLVEGDIVRIPPIR 95 Query: 107 VPADQPYAPEAMALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVP 166 + P IL ED +++++KPAG+ VH +G G + A + Sbjct: 96 IAEKAPSTAPGAEFKILLEDNHLLVIDKPAGVAVHGGSGVSYGVIEQLR----AARPDAK 151 Query: 167 RAGIVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINAPM 225 +VHRLD++TSG++V+AK +A T+L Q++ ++YL LV G I P+ Sbjct: 152 FLELVHRLDRDTSGVLVLAKKRSALTNLHEQIRGGEPDKRYLVLVHGDWKNARQHIKLPL 211 Query: 226 ARH--PRDRIKMAV-SQSMRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHL 282 ++ P ++ V + M + +R P SL+ L+TGRTHQIRVHL Sbjct: 212 HKYTTPEGERRVRVQADGMESHTVFNLIQRYG-------PFSLLEAELKTGRTHQIRVHL 264 Query: 283 QSLGFALVGDSLYGKQHLAP----------VFPRQALLAGRLGLVHPTSGKFRQWAAPLP 332 S GFA+ GD YG L R L A ++ +HP SGK APLP Sbjct: 265 ASSGFAIAGDDKYGDFALNRDLQKADGERVALKRMFLHAHQITFIHPESGKPVTLNAPLP 324 Query: 333 PDIEALLQ 340 P+ E L+ Sbjct: 325 PECERFLK 332 >gi|152981434|ref|YP_001352926.1| pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp. Marseille] Length = 223 Score = 91.3 bits (225), Expect = 8e-20, Method: Compositional matrix adjust. Identities = 70/223 (31%), Positives = 118/223 (52%), Gaps = 11/223 (4%) Query: 110 DQPYAPEAM-ALDILHEDKSIIILNKPAGLVVHPAAGNWSGTLLNGLLHHCPALANVPRA 168 D AP + ++I+++D++I+++NKP+GL+ + L+ + H + P+A Sbjct: 6 DTFVAPTCVDEIEIIYQDEAILLINKPSGLLTLSGKNPLN---LDSVHHRL--VQQFPQA 60 Query: 169 GIVHRLDKETSGLMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINAPMAR 227 ++HRLD TSGL+VVA A ++ RQ Q R++ + Y A++ G + + G I P+A+ Sbjct: 61 LMIHRLDLGTSGLLVVALNKAVAANINRQFQLRTVAKTYQAVLAGQVAEDHGKITLPIAK 120 Query: 228 HPRDRIKMAVSQSMRAKPAVTHYRRLATGEIDRKPVSLVHCRLETGRTHQIRVHLQSLGF 287 P + K+ + + K A +HY L ++D ++ TGRTHQ+R+H +G Sbjct: 121 DPLNFPKLKICLA-SGKAASSHYEVLDR-QVDADTTRVLFTP-HTGRTHQLRIHSAGIGH 177 Query: 288 ALVGDSLYGKQHLAPVFPRQALLAGRLGLVHPTSG-KFRQWAA 329 ++G LYG R L A L HP SG +FR +A Sbjct: 178 PILGCDLYGTAESEQGAERLLLHATTLEFDHPLSGARFRGVSA 220 Database: BlastDatabases/707/707 Posted date: Apr 13, 2011 12:58 PM Number of letters in database: 1,221,021 Number of sequences in database: 3697 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: 3697 Number of Hits to DB: 921,227 Number of extensions: 40133 Number of successful extensions: 122 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 117 Number of HSP's successfully gapped: 3 Length of query: 372 Length of database: 1,221,021 Length adjustment: 85 Effective length of query: 287 Effective length of database: 906,776 Effective search space: 260244712 Effective search space used: 260244712 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: 130 (54.7 bits)