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= 0036.0270.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... 494 e-141 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 76 2e-15 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 74 1e-14 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 65 6e-12 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 494 bits (1273), Expect = e-141, Method: Compositional matrix adjust. Identities = 245/248 (98%), Positives = 247/248 (99%) Query: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVERQASAE 60 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDG VVSVLGSKVLPHQKVTVERQASAE Sbjct: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE 60 Query: 61 QAQRVTILINKPMGYVSGQAEDGYKPAMVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 QAQRVTIL+NKPMGYVSGQAEDGYKPA+VLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Query: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK Sbjct: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 Query: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 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 = 76.3 bits (186), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 67/246 (27%), Positives = 119/246 (48%), Gaps = 29/246 (11%) Query: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVE----RQASAEQ 61 +L K +++ GL SRR+ +E I G V V+G+ + G ++LP V + ++ +++ Sbjct: 198 KLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHI-GQRILPTDAVRINGKLIQRKVSKR 256 Query: 62 AQRVTILINKPMGYVSGQAEDGYKPAMVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 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-LPT 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 = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 67/244 (27%), Positives = 102/244 (41%), Gaps = 26/244 (10%) Query: 5 VRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQK--VTVERQASAEQA 62 + L + + G SR+ E IE G V ++G+VV + P K V + E Sbjct: 4 LTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVD--DYRATPDTKDLVLTIFEEEWEYR 61 Query: 63 QRVTILINKPMGYVSGQAEDGYKPAMVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDI 122 + V I INKP + + + 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--TGQ 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 = 64.7 bits (156), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 51/157 (32%), Positives = 72/157 (45%), Gaps = 25/157 (15%) Query: 111 LKSLVPAGRLDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKR 170 + ++ PAGRLD DS GLL+LT DG++ + + K YL +V+ G+ L + Sbjct: 31 IPNVYPAGRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVE----GQPSPEALDK 86 Query: 171 LNHGL-----IMDGK------------PLRPAKVVWQNEDQ--LRFTLREGKKRQIRRMC 211 L L + G P P QN+ + T+ EGK RQ+RRM Sbjct: 87 LRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMT 146 Query: 212 DMVGLKVIGLKRVRIGGVKLGELPT--GQWRYLRPDE 246 VGL + L R+ IG L P G+WR + P E Sbjct: 147 AAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVDPLE 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 0.403 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: 814,319 Number of extensions: 33347 Number of successful extensions: 98 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 92 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)