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= 0008.0081.p (403 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 690 0.0 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 70 2e-13 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 69 7e-13 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 65 1e-11 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 690 bits (1780), Expect = 0.0, Method: Compositional matrix adjust. Identities = 371/403 (92%), Positives = 378/403 (93%), Gaps = 2/403 (0%) Query: 1 VTSEAYDRDEGAKAGGRQPHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIV 60 VTSEAYDRDE K G RQPHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIV Sbjct: 160 VTSEAYDRDENPKGGARQPHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIV 219 Query: 61 AGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPPRVLVYHKPSGEIVSHADPEGR 120 AGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPPRVLVYHKP+GEIVSHADPEGR Sbjct: 220 AGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGR 279 Query: 121 SSVFDRLPTMKAGKWLAVGRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGEL 180 +SVFDRLPTMKAGKWLAVGRLD+NTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGEL Sbjct: 280 NSVFDRLPTMKAGKWLAVGRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGEL 339 Query: 181 EEGMRQKLLSGVELDDGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVS 240 EEGMRQKLLSGVELDDGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVS Sbjct: 340 EEGMRQKLLSGVELDDGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVS 399 Query: 241 RLIRTRYGAMTLPQTLKRGRWEELEENAVRNLMAACGLEKQAGEAKSGNGGNAGQASRGQ 300 RLIRTRYGAMTLPQTL+RGRWEELEENAVRNLMAACGLEKQAGE KSGNGG+AG+ +G Sbjct: 400 RLIRTRYGAMTLPQTLRRGRWEELEENAVRNLMAACGLEKQAGEGKSGNGGHAGKG-QGN 458 Query: 301 GNGPRGNAMQNKGPQKGRQGGNFGQGGNGGNGGNYGNGGGYGGGGGNKGGQPKSRQPDPL 360 GNGPRGNAMQNKGPQKGR G QGGN GN G G G GGGNKGGQPKSRQPDPL Sbjct: 459 GNGPRGNAMQNKGPQKGRGGNYGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPL 518 Query: 361 QTALGFPDAGNQRRGNRPQRGGNSAPNFMLGGLPGMNRRRGGR 403 QTALGFPDAG QRR NRPQRGGNSAPNFMLGGLPGMNRRRGGR Sbjct: 519 QTALGFPDAG-QRRNNRPQRGGNSAPNFMLGGLPGMNRRRGGR 560 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 66/229 (28%), Positives = 101/229 (44%), Gaps = 9/229 (3%) Query: 40 LHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPP 99 L ++L G GSR+ ELI G V +NGE R P D + + + + R Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFEEEWEYREH 63 Query: 100 RVLVYHKPSGEIVSHADPEGRSSVFDRLPTMKAGKWLA-VGRLDFNTEGLLLFTTSGDLA 158 + +KP I P V LP + + VGRLD +T GLLL + G Sbjct: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 Query: 159 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRI-ADGGGEGVNKWYR 217 + P+ ++ + YA T + E + +L +GV+L D PA + GE + Sbjct: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 Query: 218 VTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQ-TLKRGRWEELE 265 + + +G+ +V+RM A G S L RT G + L L+ G W L+ Sbjct: 180 IVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLD 228 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 68.9 bits (167), Expect = 7e-13, Method: Compositional matrix adjust. Identities = 48/143 (33%), Positives = 68/143 (47%), Gaps = 16/143 (11%) Query: 139 GRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGP 198 GRLD ++EGLLL T G L + + HPR + + Y + G+ KL ++L D Sbjct: 38 GRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFV 97 Query: 199 AQFSR---IADGGGEGV------------NKWYRVTIGEGRNREVRRMFEAVGLTVSRLI 243 Q S+ I + G W +TI EG+NR+VRRM AVGL RL+ Sbjct: 98 TQGSQARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLV 157 Query: 244 RTRYGAMTL-PQTLKRGRWEELE 265 R G +L + G W E++ Sbjct: 158 RIAIGPFSLATHPVMPGEWREVD 180 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 63/246 (25%), Positives = 114/246 (46%), Gaps = 29/246 (11%) Query: 39 KLHKVLADAGLGSRRDMEELIVAG-RVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKR 97 +L K +++ GL SRR+ +E I G + +G ++LP V + ++ +++ Sbjct: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVE----RQASAEQ 61 Query: 98 PPRVLVY---------------HKPSGEIVSHADPEGRSSVFDRLPTMKAGKWLAVGRLD 142 RV + +KP+ +V+ R + + GRLD Sbjct: 62 AQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121 Query: 143 FNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLSGVELDDGP 198 ++ GLL+ T G +A +L+ +++EY VR G+L E ++L G+ +D P Sbjct: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKP 181 Query: 199 AQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLKR 258 + +++ + + R T+ EG+ R++RRM + VGL V L R R G + L + L Sbjct: 182 LRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE-LPT 236 Query: 259 GRWEEL 264 G+W L Sbjct: 237 GQWRYL 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 0.314 0.137 0.407 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: 1,254,910 Number of extensions: 53753 Number of successful extensions: 170 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 5 Length of query: 403 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 316 Effective length of database: 1,207,925 Effective search space: 381704300 Effective search space used: 381704300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 132 (55.5 bits)