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= 0010.0024.p (668 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... 647 0.0 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 70 8e-13 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 64 3e-11 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 64 3e-11 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 647 bits (1670), Expect = 0.0, Method: Compositional matrix adjust. Identities = 386/581 (66%), Positives = 433/581 (74%), Gaps = 49/581 (8%) Query: 93 RAKKVVADADTAPAPAPVAESASPAAEAPKVIVTIGEEITAAPVLLDAPTDSARTKPARR 152 +AK V A+ APAPA E PKVIVT+G+E+ A PVLLDAP D R KPARR Sbjct: 18 KAKPVEAEQIAAPAPA----------ELPKVIVTVGDEVVAPPVLLDAPADPNRNKPARR 67 Query: 153 GVRGPRALRNNRAAQRAAEAGEG----EPHHAVAGDEQPLSVDANAPVPVADQAMAESRR 208 GVRGPRALRNNRAAQRAA + EG + + A ++QP Q + Sbjct: 68 GVRGPRALRNNRAAQRAAASAEGGVPGKADNGAAPEQQPRG-----------QFGKGHGQ 116 Query: 209 DGQGQDRNRQQKGKKPFVKGGK-PKAPQLGLRSHDAGDDVFSFVTSDAYDKEDGARSGAR 267 GQ + Q+GKK F K GK PKAPQLGLR+ + DD+FS+VTS+AYD+++ + GAR Sbjct: 117 GGQNAQNGQGQQGKKNFDKNGKKPKAPQLGLRAAEPVDDIFSYVTSEAYDRDENPKGGAR 176 Query: 268 GTHQLRGKNGRRDLTSEDDAPKLHKVLADSGLGSRRDMEELIVAGRVSVNGEPAHIGQRI 327 HQ+RGKNGRRDLT+EDDAPKLHKVLAD+GLGSRRDMEELIVAGRVSVNGEPAHIGQRI Sbjct: 177 QPHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRI 236 Query: 328 LPTDQVRINGKLLQRKVSKKPPRVLVYHKPAGEIVSHNDPEGRPSVFDRLPNMKAAKWLA 387 LPTD VRINGKL+QRKVSK+PPRVLVYHKPAGEIVSH DPEGR SVFDRLP MKA KWLA Sbjct: 237 LPTDAVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLA 296 Query: 388 VGRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEQGMRQKLLHGVELDDG 447 VGRLD+NTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELE+GMRQKLL GVELDDG Sbjct: 297 VGRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDG 356 Query: 448 VAQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMTLPQGLK 507 AQFS+IADGGGEGVNKWYRVTIGEGRNREVRRMFEA+GLTVSRLIRTRYG MTLPQ L+ Sbjct: 357 PAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLR 416 Query: 508 RGRWEELEENAVRTLLTVCGLEKPGGAEAPSGKSKGGNSGNRNGNGDNRNGNVNGDSQPR 567 RGRWEELEENAVR L+ CGLEK G E SG GG++G GNG+ PR Sbjct: 417 RGRWEELEENAVRNLMAACGLEKQAG-EGKSG--NGGHAGKGQGNGNG----------PR 463 Query: 568 SNANANPMQPRGPRRDQQPSWQGQGQGPRQGQGSRQGQGQGQGQGGRPQGNKPRQPDPLQ 627 NA MQ +GP++ + ++ QG G+ QG G G G + K RQPDPLQ Sbjct: 464 GNA----MQNKGPQKGRGGNYGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQ 519 Query: 628 TALGFPDAGQRRHNRPQRNGGS------GGMPGQGMGAGGQ 662 TALGFPDAGQRR+NRPQR G S GG+PG GG+ Sbjct: 520 TALGFPDAGQRRNNRPQRGGNSAPNFMLGGLPGMNRRRGGR 560 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 69.7 bits (169), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 51/158 (32%), Positives = 75/158 (47%), Gaps = 21/158 (13%) Query: 374 FDRLPNMKAAKWLAVGRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEQG 433 + +PN+ A GRLD ++EGLLL T G L + + HPR + + Y + G+ Sbjct: 28 YIDIPNVYPA-----GRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVEGQPSPE 82 Query: 434 MRQKLLHGVELDDGVAQFSK---IADGGGEG------------VNKWYRVTIGEGRNREV 478 KL ++L D V Q S+ I + G W +TI EG+NR+V Sbjct: 83 ALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQV 142 Query: 479 RRMFEAIGLTVSRLIRTRYGVMTL-PQGLKRGRWEELE 515 RRM A+GL RL+R G +L + G W E++ Sbjct: 143 RRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 68/250 (27%), Positives = 124/250 (49%), Gaps = 37/250 (14%) Query: 289 KLHKVLADSGLGSRRDMEELIVAG-RVSVNGEPAHIGQRILPTDQVRINGKLLQRKVS-K 346 +L K +++ GL SRR+ +E I G + +G ++LP +V + +R+ S + Sbjct: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTV-----ERQASAE 60 Query: 347 KPPRV-LVYHKPAGEIVSHNDPEGRPSVFDRLPNMKAAKW-----------------LAV 388 + RV ++ +KP G + + +P+V L N + ++W + Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVV--LVN-EQSRWAEDQTEMRFHPRQLKSLVPA 117 Query: 389 GRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEQGMRQKLLHGVEL 444 GRLD ++ GLL+ T G +A +L+ +++EY VR G+L + ++L HG+ + Sbjct: 118 GRLDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIM 177 Query: 445 DDGVAQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMTLPQ 504 D + +K+ + + R T+ EG+ R++RRM + +GL V L R R G + L + Sbjct: 178 DGKPLRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE 233 Query: 505 GLKRGRWEEL 514 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 = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 65/237 (27%), Positives = 103/237 (43%), Gaps = 9/237 (3%) Query: 290 LHKVLADSGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDQVRINGKLLQRKVSKKPP 349 L ++L G GSR+ ELI G V +NGE R P D + + + + + Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFEEEWEYREH 63 Query: 350 RVLVYHKPAGEIVSHNDPEGRPSVFDRLPNMKAAKWLA-VGRLDFNTEGLLLFTTSGDLA 408 + +KP I P P V LP + + VGRLD +T GLLL + G Sbjct: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 Query: 409 NRLMHPRYNIEREYAVRTLGELEQGMRQKLLHGVELDDGVAQFSKI-ADGGGEGVNKWYR 467 + P+ ++ + YA T + + + +L GV+L D A + GE + Sbjct: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 Query: 468 VTIGEGRNREVRRMFEAIGLTVSRLIRTRYGVMTL-PQGLKRGRWEELEENAVRTLL 523 + + +G+ +V+RM A G S L RT G + L L+ G W L+ + L+ Sbjct: 180 IVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLDAEQMALLV 236 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 0.311 0.131 0.381 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: 1,475,342 Number of extensions: 55202 Number of successful extensions: 171 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 169 Number of HSP's successfully gapped: 4 Length of query: 668 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 576 Effective length of database: 1,184,250 Effective search space: 682128000 Effective search space used: 682128000 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 (21.8 bits) S2: 134 (56.2 bits)