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= 0023.0011.p (248 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 417 e-118 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 74 1e-14 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 73 3e-14 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 70 2e-13 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 417 bits (1071), Expect = e-118, Method: Compositional matrix adjust. Identities = 209/248 (84%), Positives = 232/248 (93%) Query: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVERQAAAE 60 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDG VVSVLGSKVLPHQ+V+VERQA+AE Sbjct: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE 60 Query: 61 QSKRVTILINKPMGFVSGQAEDGYKPAVALVESATRWKEDHVDTQFHPTQLRSLVPAGRL 120 Q++RVTIL+NKPMG+VSGQAEDGYKPAV LV +RW ED + +FHP QL+SLVPAGRL Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Query: 121 DIDSVGLLVLTQDGRIAKQLIGEDSSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGK 180 DIDSVGLLVLTQDGRIAKQLIGEDS+VDKEYLVRVQYT+PGKLP+SDLKRLNHGL +DGK Sbjct: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 Query: 181 ALKPAKVRWQNDDQLSFILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGDLPTGEWR 240 L+PAKV WQN+DQL F L EGKKRQIRRMC++VGLKV+GLKRVRIGGVKLG+LPTG+WR Sbjct: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 Query: 241 YLRPDEQF 248 YLRPDE+F Sbjct: 241 YLRPDEKF 248 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 66/246 (26%), Positives = 117/246 (47%), Gaps = 29/246 (11%) Query: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVE----RQAAAEQ 61 +L K +++ GL SRR+ +E I G V V+G+ + G ++LP V + ++ +++ Sbjct: 198 KLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHI-GQRILPTDAVRINGKLIQRKVSKR 256 Query: 62 SKRVTILINKPMGFVSGQAEDGYKPAVALVESATRWKEDHVDTQFHPTQLRSLVPAGRLD 121 RV + +KPA +V A + V + + + GRLD Sbjct: 257 PPRVLVY---------------HKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLD 301 Query: 122 IDSVGLLVLTQDGRIAKQLIGEDSSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGKA 181 ++ GLL+ T G +A +L+ ++++EY VR G+L + ++L G+ LD Sbjct: 302 YNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLSGVELDDGP 357 Query: 182 LKPAKVRWQNDDQLS----FILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGD-LPT 236 + +++ + ++ + EG+ R++RRM E VGL V L R R G + L L Sbjct: 358 AQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRR 417 Query: 237 GEWRYL 242 G W L Sbjct: 418 GRWEEL 423 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 72.8 bits (177), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 63/242 (26%), Positives = 99/242 (40%), Gaps = 22/242 (9%) Query: 5 VRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVERQAAAEQSKR 64 + L + + G SR+ E IE G V ++G+VV + V + E + Sbjct: 4 LTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFEEEWEYREH 63 Query: 65 VTILINKPMGFVSGQAEDGYKPAVALVESATRWKEDHVDTQFHPTQLRSLVPAGRLDIDS 124 V I INKP + + + L+ W R + P GRLD D+ Sbjct: 64 VYIAINKPPNIECSRKPSHHPGVLTLLPEQFTW--------------RDVQPVGRLDHDT 109 Query: 125 VGLLVLTQDGRIAKQLIGEDSSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSL--DGKAL 182 GLL+++ DG V K Y T + ++ + +L G+ L + L Sbjct: 110 TGLLLMSDDGAFIHAQSSPKRHVPKVYAA----TTAEPVTEALIAQLKAGVQLHDEPAPL 165 Query: 183 KPAKVRWQNDDQLSFILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGDLP--TGEWR 240 + R ++ L +L +GK Q++RM G L+R IGG++L L GEW Sbjct: 166 AATRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWT 225 Query: 241 YL 242 YL Sbjct: 226 YL 227 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 70.1 bits (170), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 59/201 (29%), Positives = 89/201 (44%), Gaps = 42/201 (20%) Query: 67 ILINKPMGFVSGQAEDGYKPAVALVESATRWKEDHVDTQFHPTQLRSLVPAGRLDIDSVG 126 IL+NKP +S + + +A D++D + ++ PAGRLD DS G Sbjct: 4 ILLNKPFQVMSQFSAHPERQTLA----------DYID-------IPNVYPAGRLDADSEG 46 Query: 127 LLVLTQDGRIAKQLIGEDSSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGKALKPAK 186 LL+LT DG++ + + K YL +V+ G+ L +L L L + ++ Sbjct: 47 LLLLTDDGKLQHAIAHPRRKLPKTYLAQVE----GQPSPEALDKLRQPLDLGDFVTQGSQ 102 Query: 187 VR------W-------------QNDDQLSFILNEGKKRQIRRMCELVGLKVVGLKRVRIG 227 R W Q ++ ++EGK RQ+RRM VGL + L R+ IG Sbjct: 103 ARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIG 162 Query: 228 GVKLGDLPT--GEWRYLRPDE 246 L P GEWR + P E Sbjct: 163 PFSLATHPVMPGEWREVDPLE 183 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 0.318 0.136 0.399 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: 765,002 Number of extensions: 28991 Number of successful extensions: 96 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 91 Number of HSP's successfully gapped: 4 Length of query: 248 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 165 Effective length of database: 1,226,865 Effective search space: 202432725 Effective search space used: 202432725 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)