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= 0001.1207.p (186 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 332 1e-92 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 74 1e-14 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 69 2e-13 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 65 3e-12 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 332 bits (851), Expect = 1e-92, Method: Compositional matrix adjust. Identities = 162/186 (87%), Positives = 173/186 (93%) Query: 1 MSLILLNKPFGVMSQFSTHPQRQTLADYLDIPGIYPAGRLDADSEGLLLLTDDGKLQHAI 60 M LILLNKPF VMSQFS HP+RQTLADY+DIP +YPAGRLDADSEGLLLLTDDGKLQHAI Sbjct: 1 MPLILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 Query: 61 AHPRRKQPKTYLAQVEGLASPQALQRLRDPLDLGDFVTQPSDAKLIQEPAWLWPRNPPIR 120 AHPRRK PKTYLAQVEG SP+AL +LR PLDLGDFVTQ S A+LIQEP W+WPRNPPIR Sbjct: 61 AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120 Query: 121 QRQHLPTSWIALTISEGKNRQVRRMTAAVGLPTLRLIRIAIGPFSLATHPVMPGEWRQVD 180 QRQ+ PTSWIALTISEGKNRQVRRMTAAVGLPTLRL+RIAIGPFSLATHPVMPGEWR+VD Sbjct: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180 Query: 181 PLELEK 186 PLELE+ Sbjct: 181 PLELER 186 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 60/180 (33%), Positives = 82/180 (45%), Gaps = 20/180 (11%) Query: 4 ILLNKPFGVMSQF--STHPQRQTLA-DYLDIPGIYPAGRLDADSEGLLLLTDDGKLQHAI 60 I +NKP + S HP TL + + P GRLD D+ GLLL++DDG HA Sbjct: 66 IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 125 Query: 61 AHPRRKQPKTYLAQVEGLASPQALQRLRDPLDLGDFVTQPSDAKLIQEPAWLWPRNPPIR 120 + P+R PK Y A + + +L+ + L D EPA L R Sbjct: 126 SSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHD------------EPAPL----AATR 169 Query: 121 QRQHLPTSWIALTISEGKNRQVRRMTAAVGLPTLRLIRIAIGPFSLATHPVMPGEWRQVD 180 RQ L + + + + +GK QV+RM AA G L R AIG L + GEW +D Sbjct: 170 CRQ-LGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLD 228 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 69.3 bits (168), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 62/201 (30%), Positives = 86/201 (42%), Gaps = 42/201 (20%) Query: 4 ILLNKPFGVMS---------------QFSTHPQRQTLADY--LDIPGIYPAGRLDADSEG 46 ILLNKP G +S + S + QT + + + PAGRLD DS G Sbjct: 67 ILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDIDSVG 126 Query: 47 LLLLTDDGKLQHAIAHPRRKQPKTYLAQVE----GLASPQALQRLRDPLDLGDFVTQPSD 102 LL+LT DG++ + K YL +V+ G L+RL L + D Sbjct: 127 LLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIM--------D 178 Query: 103 AKLIQEPAWLWPRNPPIRQRQHLPTSWIALTISEGKNRQVRRMTAAVGLPTLRLIRIAIG 162 K ++ +W +R T+ EGK RQ+RRM VGL + L R+ IG Sbjct: 179 GKPLRPAKVVWQNEDQLR-----------FTLREGKKRQIRRMCDMVGLKVIGLKRVRIG 227 Query: 163 PFSLATHPVMPGEWRQVDPLE 183 L P G+WR + P E Sbjct: 228 GVKLGELPT--GQWRYLRPDE 246 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 65.1 bits (157), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 54/181 (29%), Positives = 82/181 (45%), Gaps = 19/181 (10%) Query: 3 LILLNKPFGVMSQFSTHPQRQTLADYLDI--PGIYPA-GRLDADSEGLLLLTDDGKLQHA 59 +++ +KP G + + R ++ D L G + A GRLD ++EGLLL T G L + Sbjct: 260 VLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLDYNTEGLLLFTTSGDLANR 319 Query: 60 IAHPRRKQPKTYLAQVEGLASPQALQRLRDPLDLGDFVTQPSDAKLIQEPAWLWPRNPPI 119 + HPR + Y + G Q+L ++L D P+ I + Sbjct: 320 LMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDG---PAQFSRIADGGG-------- 368 Query: 120 RQRQHLPTSWIALTISEGKNRQVRRMTAAVGLPTLRLIRIAIGPFSLATHPVMPGEWRQV 179 W +TI EG+NR+VRRM AVGL RLIR G +L + G W ++ Sbjct: 369 ----EGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTL-PQTLRRGRWEEL 423 Query: 180 D 180 + Sbjct: 424 E 424 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 0.320 0.138 0.422 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: 668,096 Number of extensions: 28543 Number of successful extensions: 76 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 74 Number of HSP's successfully gapped: 4 Length of query: 186 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 106 Effective length of database: 1,241,070 Effective search space: 131553420 Effective search space used: 131553420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 128 (53.9 bits)