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= 0093.0025.p (611 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... 520 e-148 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 72 2e-13 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 64 5e-11 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 62 1e-10 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 520 bits (1338), Expect = e-148, Method: Compositional matrix adjust. Identities = 257/313 (82%), Positives = 275/313 (87%), Gaps = 18/313 (5%) Query: 279 ARGTHQLRGKNGRRDLTSEDDAPKLHKVLADSGLGSRRDMEELIVAGRVSVNGEPAHIGQ 338 AR HQ+RGKNGRRDLT+EDDAPKLHKVLAD+GLGSRRDMEELIVAGRVSVNGEPAHIGQ Sbjct: 175 ARQPHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQ 234 Query: 339 RILPTDQVRINGKLLQRKVSKKPPRVLVYHKPAGEIVSHNDPEGRASVFDRLPNMKAAKW 398 RILPTD VRINGKL+QRKVSK+PPRVLVYHKPAGEIVSH DPEGR SVFDRLP MKA KW Sbjct: 235 RILPTDAVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKW 294 Query: 399 LAVGRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEQGMRQKLLHGVELD 458 LAVGRLD+NTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELE+GMRQKLL GVELD Sbjct: 295 LAVGRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELD 354 Query: 459 DGMAQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMSLPQG 518 DG AQFS+IADGGGEGVNKWYRVTIGEGRNREVRRMFEA+GLTVSRLIRTRYG M+LPQ Sbjct: 355 DGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT 414 Query: 519 LKRGRWEELEENAVRSLLAVCGMEKQGGA-----DAPAGKSKGNGNGNRSGNGDAQPRSN 573 L+RGRWEELEENAVR+L+A CG+EKQ G AGK +GNGNG PR N Sbjct: 415 LRRGRWEELEENAVRNLMAACGLEKQAGEGKSGNGGHAGKGQGNGNG---------PRGN 465 Query: 574 ANANPMQPRGPRR 586 A MQ +GP++ Sbjct: 466 A----MQNKGPQK 474 Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 29/42 (69%), Positives = 33/42 (78%) Query: 112 SAPQAAEAPKVIVTIGEEITAAPVLLDAPTDSARTKPARRGV 153 +AP AE PKVIVT+G+E+ A PVLLDAP D R KPARRGV Sbjct: 28 AAPAPAELPKVIVTVGDEVVAPPVLLDAPADPNRNKPARRGV 69 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 56/184 (30%), Positives = 87/184 (47%), Gaps = 25/184 (13%) Query: 364 VLVYHKP---AGEIVSHNDPEGRASVFDRLPNMKAAKWLAVGRLDFNTEGLLLFTTSGDL 420 +++ +KP + +H + + A D +PN+ A GRLD ++EGLLL T G L Sbjct: 3 LILLNKPFQVMSQFSAHPERQTLADYID-IPNVYPA-----GRLDADSEGLLLLTDDGKL 56 Query: 421 ANRLMHPRYNIEREYAVRTLGELEQGMRQKLLHGVELDDGMAQFSK---IADGGG----- 472 + + HPR + + Y + G+ KL ++L D + Q S+ I + G Sbjct: 57 QHAIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRN 116 Query: 473 -------EGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMSL-PQGLKRGRW 524 W +TI EG+NR+VRRM A+GL RL+R G SL + G W Sbjct: 117 PPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEW 176 Query: 525 EELE 528 E++ Sbjct: 177 REVD 180 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 63.5 bits (153), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 67/250 (26%), Positives = 123/250 (49%), Gaps = 37/250 (14%) Query: 302 KLHKVLADSGLGSRRDMEELIVAG-RVSVNGEPAHIGQRILPTDQVRINGKLLQRKVS-K 359 +L K +++ GL SRR+ +E I G + +G ++LP +V + +R+ S + Sbjct: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTV-----ERQASAE 60 Query: 360 KPPRV-LVYHKPAGEIVSHNDPEGRASVFDRLPNMKAAKW-----------------LAV 401 + RV ++ +KP G + + + +V L N + ++W + Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVV--LVN-EQSRWAEDQTEMRFHPRQLKSLVPA 117 Query: 402 GRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEQGMRQKLLHGVEL 457 GRLD ++ GLL+ T G +A +L+ +++EY VR G+L + ++L HG+ + Sbjct: 118 GRLDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIM 177 Query: 458 DDGMAQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMSLPQ 517 D + +K+ + + R T+ EG+ R++RRM + +GL V L R R G + L + Sbjct: 178 DGKPLRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE 233 Query: 518 GLKRGRWEEL 527 L G+W L Sbjct: 234 -LPTGQWRYL 242 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 63/229 (27%), Positives = 99/229 (43%), Gaps = 9/229 (3%) Query: 303 LHKVLADSGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDQVRINGKLLQRKVSKKPP 362 L ++L G GSR+ ELI G V +NGE R P D + + + + + Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFEEEWEYREH 63 Query: 363 RVLVYHKPAGEIVSHNDPEGRASVFDRLPNMKAAKWLA-VGRLDFNTEGLLLFTTSGDLA 421 + +KP I P V LP + + VGRLD +T GLLL + G Sbjct: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 Query: 422 NRLMHPRYNIEREYAVRTLGELEQGMRQKLLHGVELDDGMAQFSKI-ADGGGEGVNKWYR 480 + P+ ++ + YA T + + + +L GV+L D A + GE + Sbjct: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 Query: 481 VTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMSLP-QGLKRGRWEELE 528 + + +G+ +V+RM A G S L RT G + L L+ G W L+ Sbjct: 180 IVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLD 228 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 0.128 0.371 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: 1,519,765 Number of extensions: 58858 Number of successful extensions: 183 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 176 Number of HSP's successfully gapped: 6 Length of query: 611 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 520 Effective length of database: 1,188,985 Effective search space: 618272200 Effective search space used: 618272200 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 (22.0 bits) S2: 133 (55.8 bits)