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= 0009.0244.p (217 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 342 2e-95 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 75 5e-15 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 65 4e-12 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 60 2e-10 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 342 bits (876), Expect = 2e-95, Method: Compositional matrix adjust. Identities = 163/194 (84%), Positives = 176/194 (90%) Query: 23 PDTEGLAFTLFDEEWVYREHVYIALNKPANFECSRKPSHHPGVLTILPEQFSWRDVQPVG 82 PDT+ L T+F+EEW YREHVYIA+NKP N ECSRKPSHHPGVLT+LPEQF+WRDVQPVG Sbjct: 44 PDTKDLVLTIFEEEWEYREHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVG 103 Query: 83 RLDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATTHDAVTDELIAQLLGGVQLHDEPA 142 RLDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATT + VT+ LIAQL GVQLHDEPA Sbjct: 104 RLDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPA 163 Query: 143 PLAAVTCRKLDAHLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLDALELEEGE 202 PLAA CR+L +LLEIVLEQGKYHQVKRMLAAAGNHCSAL+RTAIGGLQL+AL LEEGE Sbjct: 164 PLAATRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGE 223 Query: 203 WCYLDAEQLGLLVP 216 W YLDAEQ+ LLVP Sbjct: 224 WTYLDAEQMALLVP 237 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 74.7 bits (182), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 60/184 (32%), Positives = 85/184 (46%), Gaps = 20/184 (10%) Query: 45 IALNKPANFECSRKPSHHPGVLTILPEQFSWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 104 I LNKP F+ + S HP T L + +V P GRLD D+ GLLL++DDG HA Sbjct: 4 ILLNKP--FQVMSQFSAHPERQT-LADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 Query: 105 SSPKRHVPKVYAATTHDAVTDELIAQLLGGVQLHD------------EPA---PLAAVTC 149 + P+R +PK Y A + E + +L + L D EP P Sbjct: 61 AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120 Query: 150 RKLD--AHLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLDALELEEGEWCYLD 207 ++ + + + + +GK QV+RM AA G L R AIG L + GEW +D Sbjct: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180 Query: 208 AEQL 211 +L Sbjct: 181 PLEL 184 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 65.5 bits (158), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 51/184 (27%), Positives = 77/184 (41%), Gaps = 22/184 (11%) Query: 41 EHVYIALNKPANFECSRKPSHHPGVLTILPEQFSWRDVQ--------------PVGRLDH 86 + V I LNKP + + + + ++ EQ W + Q P GRLD Sbjct: 63 QRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDI 122 Query: 87 DTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATTHDAVTDEL----IAQLLGGVQLHDEPA 142 D+ GLL+++ DG V K Y +L + +L G+ + +P Sbjct: 123 DSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKPL 182 Query: 143 PLAAVTCRKLDAHLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLDALELEEGE 202 A V + D L L +GK Q++RM G L+R IGG++L EL G+ Sbjct: 183 RPAKVVWQNEDQ--LRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLG--ELPTGQ 238 Query: 203 WCYL 206 W YL Sbjct: 239 WRYL 242 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 60.1 bits (144), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 39/129 (30%), Positives = 63/129 (48%), Gaps = 3/129 (2%) Query: 81 VGRLDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAATTHDAVTDELIAQLLGGVQLHDE 140 VGRLD++T GLLL + G + P+ ++ + YA T + + + +LL GV+L D Sbjct: 297 VGRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDG 356 Query: 141 PAPLAAVTCRKLDA--HLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLDALEL 198 PA + + + + + +G+ +V+RM A G S L RT G + L L Sbjct: 357 PAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT-L 415 Query: 199 EEGEWCYLD 207 G W L+ Sbjct: 416 RRGRWEELE 424 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 0.321 0.137 0.429 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: 689,052 Number of extensions: 28610 Number of successful extensions: 64 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 63 Number of HSP's successfully gapped: 4 Length of query: 217 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 136 Effective length of database: 1,236,335 Effective search space: 168141560 Effective search space used: 168141560 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 (21.9 bits) S2: 128 (53.9 bits)