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= 0015.0032.p (270 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|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 74 1e-14 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 73 3e-14 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 69 4e-13 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 417 bits (1073), Expect = e-118, Method: Compositional matrix adjust. Identities = 209/248 (84%), Positives = 232/248 (93%) Query: 23 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVERQAAAE 82 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDG VVSVLGSKVLPHQ+V+VERQA+AE Sbjct: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAE 60 Query: 83 QSKRVTILINKPTGFVSGQAEDGYKPAVALVEAATRWKEDQVDTQFHPTQLRSLVPAGRL 142 Q++RVTIL+NKP G+VSGQAEDGYKPAV LV +RW EDQ + +FHP QL+SLVPAGRL Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Query: 143 DIDSVGLLVLTQDGRIAKQLIGEDTSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGK 202 DIDSVGLLVLTQDGRIAKQLIGED++VDKEYLVRVQYT+PGKLP+SDLKRLNHGL +DGK Sbjct: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 Query: 203 ALKPAKVRWQNEDQLSFILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGDLPTGEWR 262 L+PAKV WQNEDQL F L EGKKRQIRRMC++VGLKV+GLKRVRIGGVKLG+LPTG+WR Sbjct: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 Query: 263 YLRPDEQF 270 YLRPDE+F Sbjct: 241 YLRPDEKF 248 >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 = 64/240 (26%), Positives = 99/240 (41%), Gaps = 22/240 (9%) Query: 29 LSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVERQAAAEQSKRVT 88 L + + G SR+ E IE G V ++G+VV + V + E + V Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFEEEWEYREHVY 65 Query: 89 ILINKPTGFVSGQAEDGYKPAVALVEAATRWKEDQVDTQFHPTQLRSLVPAGRLDIDSVG 148 I INKP + + + L+ W++ Q P GRLD D+ G Sbjct: 66 IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQ--------------PVGRLDHDTTG 111 Query: 149 LLVLTQDGRIAKQLIGEDTSVDKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGKA--LKP 206 LL+++ DG V K Y T + ++ + +L G+ L + L Sbjct: 112 LLLMSDDGAFIHAQSSPKRHVPKVYAA----TTAEPVTEALIAQLKAGVQLHDEPAPLAA 167 Query: 207 AKVRWQNEDQLSFILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGDLP--TGEWRYL 264 + R E+ L +L +GK Q++RM G L+R IGG++L L GEW YL Sbjct: 168 TRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYL 227 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 72.8 bits (177), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 67/254 (26%), Positives = 120/254 (47%), Gaps = 29/254 (11%) Query: 20 LSIMTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQRVSVE--- 76 L+ + +L K +++ GL SRR+ +E I G V V+G+ + G ++LP V + Sbjct: 190 LTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHI-GQRILPTDAVRINGKL 248 Query: 77 -RQAAAEQSKRVTILINKPTGFVSGQAEDGYKPAVALVEAATRWKEDQVDTQFHPTQLRS 135 ++ +++ RV + +KPA +V A + V + + Sbjct: 249 IQRKVSKRPPRVLVY---------------HKPAGEIVSHADPEGRNSVFDRLPTMKAGK 293 Query: 136 LVPAGRLDIDSVGLLVLTQDGRIAKQLIGEDTSVDKEYLVRVQYTKPGKLPDSDLKRLNH 195 + GRLD ++ GLL+ T G +A +L+ ++++EY VR G+L + ++L Sbjct: 294 WLAVGRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLS 349 Query: 196 GLSLDGKALKPAKVRWQNEDQLS----FILNEGKKRQIRRMCELVGLKVVGLKRVRIGGV 251 G+ LD + +++ + ++ + EG+ R++RRM E VGL V L R R G + Sbjct: 350 GVELDDGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAM 409 Query: 252 KLGD-LPTGEWRYL 264 L L G W L Sbjct: 410 TLPQTLRRGRWEEL 423 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 68.9 bits (167), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 58/180 (32%), Positives = 85/180 (47%), Gaps = 35/180 (19%) Query: 120 KEDQVDTQF--HPTQ--------LRSLVPAGRLDIDSVGLLVLTQDGRIAKQLIGEDTSV 169 K QV +QF HP + + ++ PAGRLD DS GLL+LT DG++ + + Sbjct: 8 KPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAIAHPRRKL 67 Query: 170 DKEYLVRVQYTKPGKLPDSDLKRLNHGLSLDGKALKPAKVR------W---------QNE 214 K YL +V+ G+ L +L L L + ++ R W Q + Sbjct: 68 PKTYLAQVE----GQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIRQRQ 123 Query: 215 DQ----LSFILNEGKKRQIRRMCELVGLKVVGLKRVRIGGVKLGDLPT--GEWRYLRPDE 268 +Q ++ ++EGK RQ+RRM VGL + L R+ IG L P GEWR + P E Sbjct: 124 NQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVDPLE 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 0.136 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: 829,100 Number of extensions: 31888 Number of successful extensions: 102 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 97 Number of HSP's successfully gapped: 4 Length of query: 270 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 186 Effective length of database: 1,222,130 Effective search space: 227316180 Effective search space used: 227316180 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: 130 (54.7 bits)