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= 0029.0255.p (240 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... 489 e-139 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 74 1e-14 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 69 3e-13 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 62 5e-11 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 489 bits (1258), Expect = e-139, Method: Compositional matrix adjust. Identities = 237/240 (98%), Positives = 238/240 (99%) Query: 1 MAKLTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFGEEWEY 60 MAKLTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIF EEWEY Sbjct: 1 MAKLTLDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFEEEWEY 60 Query: 61 REHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGA 120 REHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGA Sbjct: 61 REHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGA 120 Query: 121 FIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENLLEI 180 FIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENLLEI Sbjct: 121 FIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENLLEI 180 Query: 181 VLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLEVLALEEGEWTYLDAEQMALLVPDAE 240 VLEQGKYHQVKRMLAAAGNHCSAL+RTAIGGLQLE LALEEGEWTYLDAEQMALLVPDAE Sbjct: 181 VLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLDAEQMALLVPDAE 240 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 62/181 (34%), Positives = 86/181 (47%), Gaps = 22/181 (12%) Query: 66 IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 125 I +NKP + + S HP TL + +V P GRLD D+ GLLL++DDG HA Sbjct: 4 ILLNKP--FQVMSQFSAHPERQTLA-DYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 Query: 126 SSPKRHVPKVY-AATTAEPVTEALIAQLKAGVQLHD------------EPAPL----AAT 168 + P+R +PK Y A +P EAL +L+ + L D EP + Sbjct: 61 AHPRRKLPKTYLAQVEGQPSPEAL-DKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPI 119 Query: 169 RCRQ-LGENLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLEVLALEEGEWTYL 227 R RQ + + + + +GK QV+RM AA G L R AIG L + GEW + Sbjct: 120 RQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREV 179 Query: 228 D 228 D Sbjct: 180 D 180 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 69.3 bits (168), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 66/229 (28%), Positives = 100/229 (43%), Gaps = 9/229 (3%) Query: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFGEEWEYREH 63 L ++L G GSR+ ELI G V +NGE R P D + + + R Sbjct: 199 LHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPP 258 Query: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 + +KP I P V LP + + VGRLD++T GLLL + G Sbjct: 259 RVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLA-VGRLDYNTEGLLLFTTSGDLA 317 Query: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 + P+ ++ + YA T + E + +L +GV+L D PA + GE + Sbjct: 318 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRI-ADGGGEGVNKWYR 376 Query: 180 IVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLEVLALEEGEWTYLD 228 + + +G+ +V+RM A G S L RT G + L L G W L+ Sbjct: 377 VTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLP-QTLRRGRWEELE 424 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 61.6 bits (148), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 51/187 (27%), Positives = 78/187 (41%), Gaps = 22/187 (11%) Query: 59 EYREHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQ--------------PVGR 104 E + V I +NKP + + + L+ EQ W + Q P GR Sbjct: 60 EQAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGR 119 Query: 105 LDHDTTGLLLMSDDGAFIHAQSSPKRHVPKVYAA----TTAEPVTEALIAQLKAGVQLHD 160 LD D+ GLL+++ DG V K Y T + E+ + +L G+ + Sbjct: 120 LDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDG 179 Query: 161 EPAPLAATRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALRRTAIGGLQLEVLALE 220 +P L + E+ L L +GK Q++RM G L+R IGG++L L Sbjct: 180 KP--LRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLG--ELP 235 Query: 221 EGEWTYL 227 G+W YL Sbjct: 236 TGQWRYL 242 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 0.135 0.402 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: 781,500 Number of extensions: 32496 Number of successful extensions: 91 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 87 Number of HSP's successfully gapped: 4 Length of query: 240 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 157 Effective length of database: 1,226,865 Effective search space: 192617805 Effective search space used: 192617805 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)