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= 0007.0041.p (188 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... 379 e-107 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 74 6e-15 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 69 2e-13 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 65 4e-12 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 379 bits (973), Expect = e-107, Method: Compositional matrix adjust. Identities = 187/188 (99%), Positives = 188/188 (100%) Query: 1 MPLILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 MPLILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI Sbjct: 1 MPLILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 Query: 61 AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIEEPGWMWPRNPPIR 120 AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLI+EPGWMWPRNPPIR Sbjct: 61 AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120 Query: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD Sbjct: 121 QRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVD 180 Query: 181 PLELERQG 188 PLELERQG Sbjct: 181 PLELERQG 188 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 74.3 bits (181), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 62/181 (34%), Positives = 86/181 (47%), Gaps = 22/181 (12%) Query: 4 ILLNKP--FQVMSQFSAHPERQTLA-DYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60 I +NKP + + S HP TL + +V P GRLD D+ GLLL++DDG HA Sbjct: 66 IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 125 Query: 61 AHPRRKLPKTYLAQVEGQPSPEAL-DKLRQPLDLGDFVTQGSQARLIEEPGWMWPRNPPI 119 + P+R +PK Y A +P EAL +L+ + L D EP + Sbjct: 126 SSPKRHVPKVY-AATTAEPVTEALIAQLKAGVQLHD------------EPAPL----AAT 168 Query: 120 RQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREV 179 R RQ + + + + +GK QV+RM AA G L R AIG L + GEW + Sbjct: 169 RCRQ-LGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYL 227 Query: 180 D 180 D Sbjct: 228 D 228 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 68.9 bits (167), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 48/143 (33%), Positives = 68/143 (47%), Gaps = 16/143 (11%) Query: 38 GRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFV 97 GRLD ++EGLLL T G L + + HPR + + Y + G+ KL ++L D Sbjct: 298 GRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGP 357 Query: 98 TQGSQARLIEEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLV 157 Q S R+ + G W +TI EG+NR+VRRM AVGL RL+ Sbjct: 358 AQFS--RIADGGGEGV-------------NKWYRVTIGEGRNREVRRMFEAVGLTVSRLI 402 Query: 158 RIAIGPFSLATHPVMPGEWREVD 180 R G +L + G W E++ Sbjct: 403 RTRYGAMTL-PQTLRRGRWEELE 424 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 64.7 bits (156), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 62/201 (30%), Positives = 86/201 (42%), Gaps = 42/201 (20%) Query: 4 ILLNKPFQVMS---------------QFSAHPERQTLADY--IDIPNVYPAGRLDADSEG 46 ILLNKP +S + S E QT + + ++ PAGRLD DS G Sbjct: 67 ILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDIDSVG 126 Query: 47 LLLLTDDGKLQHAIAHPRRKLPKTYLAQVE----GQPSPEALDKLRQPLDLGDFVTQGSQ 102 LL+LT DG++ + + K YL +V+ G+ L +L L + G Sbjct: 127 LLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGL-----IMDGK- 180 Query: 103 ARLIEEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIG 162 P P QN+ + T+ EGK RQ+RRM VGL + L R+ IG Sbjct: 181 -----------PLRPAKVVWQNEDQ--LRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIG 227 Query: 163 PFSLATHPVMPGEWREVDPLE 183 L P G+WR + P E Sbjct: 228 GVKLGELPT--GQWRYLRPDE 246 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 0.319 0.137 0.420 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: 669,598 Number of extensions: 29216 Number of successful extensions: 83 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 80 Number of HSP's successfully gapped: 4 Length of query: 188 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 108 Effective length of database: 1,241,070 Effective search space: 134035560 Effective search space used: 134035560 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 (21.7 bits) S2: 128 (53.9 bits)