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= 0001.3528.p (560 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... 828 0.0 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 72 1e-13 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 68 2e-12 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 66 7e-12 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 828 bits (2139), Expect = 0.0, Method: Compositional matrix adjust. Identities = 477/555 (85%), Positives = 489/555 (88%), Gaps = 23/555 (4%) Query: 17 KPKVAAAPEAAAPAPAPVAPELPKVIVTVGEEVVAPPVLLDAPVDPNRAKPARRGVRGPR 76 K K A + AAPAPA ELPKVIVTVG+EVVAPPVLLDAP DPNR KPARRGVRGPR Sbjct: 18 KAKPVEAEQIAAPAPA----ELPKVIVTVGDEVVAPPVLLDAPADPNRNKPARRGVRGPR 73 Query: 77 ALRNNRAAQRAAAGGAEAAPAQGKGEGDAVPAERHQPRGQFGKNNAHAGQAGQQG----- 131 ALRNNRAAQRAAA P GK + A P + QPRGQFGK + GQ Q G Sbjct: 74 ALRNNRAAQRAAASAEGGVP--GKADNGAAPEQ--QPRGQFGKGHGQGGQNAQNGQGQQG 129 Query: 132 KKNFDKNGKKPKAPQLGLRANEPVDDIFSYVTSEAYDRDEGAKAGGRQAHQMRGKNGRRD 191 KKNFDKNGKKPKAPQLGLRA EPVDDIFSYVTSEAYDRDE K G RQ HQMRGKNGRRD Sbjct: 130 KKNFDKNGKKPKAPQLGLRAAEPVDDIFSYVTSEAYDRDENPKGGARQPHQMRGKNGRRD 189 Query: 192 LTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLI 251 LTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLI Sbjct: 190 LTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLI 249 Query: 252 QRKVSKRPPRVLVYHKPAGEIVSHSDPEGRSSVFDRLPTMKAGKWLAVGRLDFNTEGLLL 311 QRKVSKRPPRVLVYHKPAGEIVSH+DPEGR+SVFDRLPTMKAGKWLAVGRLD+NTEGLLL Sbjct: 250 QRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLDYNTEGLLL 309 Query: 312 FTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVELDDGPAQFSRIADGGGE 371 FTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLL+GVELDDGPAQFSRIADGGGE Sbjct: 310 FTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRIADGGGE 369 Query: 372 GVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLKRGRWEELEENAVR 431 GVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTL+RGRWEELEENAVR Sbjct: 370 GVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRWEELEENAVR 429 Query: 432 NLMAACGLEKQAGEAKSGNGGHAGKGQGNGNGNGPRGNAMQNKGPQKGR------NGGNF 485 NLMAACGLEKQAGE KSGNGGHAGKGQ GNGNGPRGNAMQNKGPQKGR GGN+ Sbjct: 430 NLMAACGLEKQAGEGKSGNGGHAGKGQ--GNGNGPRGNAMQNKGPQKGRGGNYGNQGGNY 487 Query: 486 GNQGGGNYGNGGNYGGGNKGGQPKSRQPDPLQTALGFPDIGNGQRRGNRPQRGGNTAANF 545 GNQGG GG YGGGNKGGQPKSRQPDPLQTALGFPD GQRR NRPQRGGN+A NF Sbjct: 488 GNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDA--GQRRNNRPQRGGNSAPNF 545 Query: 546 MLGGLPGMNRRRGGR 560 MLGGLPGMNRRRGGR Sbjct: 546 MLGGLPGMNRRRGGR 560 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 67/229 (29%), Positives = 101/229 (44%), Gaps = 9/229 (3%) Query: 201 LHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPP 260 L ++L G GSR+ ELI G V +NGE R P D + + + + R Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFEEEWEYREH 63 Query: 261 RVLVYHKPAGEIVSHSDPEGRSSVFDRLPTMKAGKWLA-VGRLDFNTEGLLLFTTSGDLA 319 + +KP I P V LP + + VGRLD +T GLLL + G Sbjct: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 Query: 320 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVELDDGPAQFSRI-ADGGGEGVNKWYR 378 + P+ ++ + YA T + E + +L AGV+L D PA + GE + Sbjct: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 Query: 379 VTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT-LKRGRWEELE 426 + + +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 = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 48/143 (33%), Positives = 68/143 (47%), Gaps = 16/143 (11%) Query: 300 GRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVELDDGP 359 GRLD ++EGLLL T G L + + HPR + + Y + G+ KL ++L D Sbjct: 38 GRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFV 97 Query: 360 AQFSR---IADGGGEGV------------NKWYRVTIGEGRNREVRRMFEAVGLTVSRLI 404 Q S+ I + G W +TI EG+NR+VRRM AVGL RL+ Sbjct: 98 TQGSQARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLV 157 Query: 405 RTRYGAMTL-PQTLKRGRWEELE 426 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 = 66.2 bits (160), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 64/246 (26%), Positives = 114/246 (46%), Gaps = 29/246 (11%) Query: 200 KLHKVLADAGLGSRRDMEELIVAG-RVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKR 258 +L K +++ GL SRR+ +E I G + +G ++LP V + ++ +++ Sbjct: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVE----RQASAEQ 61 Query: 259 PPRVLVY---------------HKPAGEIVSHSDPEGRSSVFDRLPTMKAGKWLAVGRLD 303 RV + +KPA +V+ R + + GRLD Sbjct: 62 AQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121 Query: 304 FNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLAGVELDDGP 359 ++ GLL+ T G +A +L+ +++EY VR G+L E ++L G+ +D P Sbjct: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKP 181 Query: 360 AQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLKR 419 + +++ + + R T+ EG+ R++RRM + VGL V L R R G + L + L Sbjct: 182 LRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE-LPT 236 Query: 420 GRWEEL 425 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 0.313 0.135 0.398 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: 1,356,503 Number of extensions: 54596 Number of successful extensions: 137 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 126 Number of HSP's successfully gapped: 4 Length of query: 560 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 470 Effective length of database: 1,193,720 Effective search space: 561048400 Effective search space used: 561048400 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: 133 (55.8 bits)