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= 0027.0112.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... 495 e-141 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 74 1e-14 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 70 2e-13 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 67 1e-12 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 495 bits (1275), Expect = e-141, Method: Compositional matrix adjust. Identities = 247/248 (99%), Positives = 247/248 (99%) Query: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE 60 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE Sbjct: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE 60 Query: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Query: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK Sbjct: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 Query: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPPGQWR 240 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELP GQWR Sbjct: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 Query: 241 YLRPDEKF 248 YLRPDEKF Sbjct: 241 YLRPDEKF 248 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 29/246 (11%) Query: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVE----RQASAEQ 61 +L K +++ GL SRR+ +E I G V V+G + G ++LP V + ++ +++ Sbjct: 198 KLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHI-GQRILPTDAVRINGKLIQRKVSKR 256 Query: 62 AQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121 RV + +KPA +V+ + R + + GRLD Sbjct: 257 PPRVLVY---------------HKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLD 301 Query: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKP 181 ++ GLL+ T G +A +L+ +++EY VR G+L E ++L G+ +D P Sbjct: 302 YNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLSGVELDDGP 357 Query: 182 LRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE-LPP 236 + +++ + + R T+ EG+ R++RRM + VGL V L R R G + L + L Sbjct: 358 AQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRR 417 Query: 237 GQWRYL 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 = 70.1 bits (170), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 66/244 (27%), Positives = 101/244 (41%), Gaps = 26/244 (10%) Query: 5 VRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQK--VTVERQASAEQA 62 + L + + G SR+ E IE G V ++G VV + P K V + E Sbjct: 4 LTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVD--DYRATPDTKDLVLTIFEEEWEYR 61 Query: 63 QRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDI 122 + V I +NKP + + + L+ EQ W + Q P GRLD Sbjct: 62 EHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQ--------------PVGRLDH 107 Query: 123 DSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKP- 181 D+ GLL+++ DG V K Y T + E+ + +L G+ + +P Sbjct: 108 DTTGLLLMSDDGAFIHAQSSPKRHVPKVYAA----TTAEPVTEALIAQLKAGVQLHDEPA 163 Query: 182 -LRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELP--PGQ 238 L + E+ L L +GK Q++RM G L+R IGG++L L G+ Sbjct: 164 PLAATRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGE 223 Query: 239 WRYL 242 W YL Sbjct: 224 WTYL 227 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 67.4 bits (163), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 63/201 (31%), Positives = 87/201 (43%), Gaps = 42/201 (20%) Query: 67 ILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDIDSVG 126 ILLNKP +S + S E QT + + ++ PAGRLD DS G Sbjct: 4 ILLNKPFQVMS---------------QFSAHPERQTLADY--IDIPNVYPAGRLDADSEG 46 Query: 127 LLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGL-----IMDGK- 180 LL+LT DG++ + + K YL +V+ G+ L +L L + G Sbjct: 47 LLLLTDDGKLQHAIAHPRRKLPKTYLAQVE----GQPSPEALDKLRQPLDLGDFVTQGSQ 102 Query: 181 -----------PLRPAKVVWQNEDQ--LRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIG 227 P P QN+ + T+ EGK RQ+RRM VGL + L R+ IG Sbjct: 103 ARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIG 162 Query: 228 GVKLGELP--PGQWRYLRPDE 246 L P PG+WR + 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 0.319 0.137 0.405 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: 762,241 Number of extensions: 29986 Number of successful extensions: 81 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 77 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 129 (54.3 bits)