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= 0007.0134.p (184 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... 330 6e-92 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 78 5e-16 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 70 8e-14 gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 68 4e-13 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 330 bits (845), Expect = 6e-92, Method: Compositional matrix adjust. Identities = 161/183 (87%), Positives = 170/183 (92%) Query: 1 LILFNKPFGVMSQFSAHPERQTLADYLDLPDIYPAGRLDADSEGLLLLTDDGKLQHAIAH 60 LIL NKPF VMSQFSAHPERQTLADY+D+P++YPAGRLDADSEGLLLLTDDGKLQHAIAH Sbjct: 3 LILLNKPFQVMSQFSAHPERQTLADYIDIPNVYPAGRLDADSEGLLLLTDDGKLQHAIAH 62 Query: 61 PRRKQPKTYLAQVEGLATPEALQRLRNPLDLGDFVTQPGEARLIQEPAWMWPRTPPIRQR 120 PRRK PKTYLAQVEG +PEAL +LR PLDLGDFVTQ +ARLIQEP WMWPR PPIRQR Sbjct: 63 PRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIRQR 122 Query: 121 ANQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPLMPGEWREVDPQ 180 NQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHP+MPGEWREVDP Sbjct: 123 QNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWREVDPL 182 Query: 181 ELD 183 EL+ Sbjct: 183 ELE 185 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 77.8 bits (190), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 61/185 (32%), Positives = 83/185 (44%), Gaps = 22/185 (11%) Query: 2 ILFNKPFGVMSQF--SAHPERQTLA-DYLDLPDIYPAGRLDADSEGLLLLTDDGKLQHAI 58 I NKP + S HP TL + D+ P GRLD D+ GLLL++DDG HA Sbjct: 66 IAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIHAQ 125 Query: 59 AHPRRKQPKTYLAQVEGLATPEALQRLRNPLDLGDFVTQPGEARLIQEPAWMWPRTPPIR 118 + P+R PK Y A T + +L+ + L D EPA P Sbjct: 126 SSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHD------------EPA------PLAA 167 Query: 119 QRANQ-PTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPLMPGEWREV 177 R Q + + + + +GK QV+RM AA G L R AIG L L GEW + Sbjct: 168 TRCRQLGENLLEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYL 227 Query: 178 DPQEL 182 D +++ Sbjct: 228 DAEQM 232 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 70.5 bits (171), Expect = 8e-14, Method: Compositional matrix adjust. Identities = 62/201 (30%), Positives = 85/201 (42%), Gaps = 42/201 (20%) Query: 2 ILFNKPFGVMS---------------QFSAHPERQTLADY--LDLPDIYPAGRLDADSEG 44 IL NKP G +S + S E QT + L + PAGRLD DS G Sbjct: 67 ILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDIDSVG 126 Query: 45 LLLLTDDGKLQHAIAHPRRKQPKTYLAQVE----GLATPEALQRLRNPLDLGDFVTQPGE 100 LL+LT DG++ + K YL +V+ G L+RL + L + +P + Sbjct: 127 LLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKPLRPAK 186 Query: 101 ARLIQEPAWMWPRTPPIRQRANQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIG 160 +W +R T+ EGK RQ+RRM VGL + L R+ IG Sbjct: 187 V--------VWQNEDQLR-----------FTLREGKKRQIRRMCDMVGLKVIGLKRVRIG 227 Query: 161 PFSLATHPLMPGEWREVDPQE 181 L P G+WR + P E Sbjct: 228 GVKLGELP--TGQWRYLRPDE 246 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 68.2 bits (165), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 54/183 (29%), Positives = 83/183 (45%), Gaps = 23/183 (12%) Query: 1 LILFNKPFGVMSQFSAHPERQTLADYLDLPDIYPA-----GRLDADSEGLLLLTDDGKLQ 55 +++++KP G + + R ++ D L P + GRLD ++EGLLL T G L Sbjct: 260 VLVYHKPAGEIVSHADPEGRNSVFDRL--PTMKAGKWLAVGRLDYNTEGLLLFTTSGDLA 317 Query: 56 HAIAHPRRKQPKTYLAQVEGLATPEALQRLRNPLDLGDFVTQPGEARLIQEPAWMWPRTP 115 + + HPR + Y + G Q+L + ++L D P + I + Sbjct: 318 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDG---PAQFSRIADGG------- 367 Query: 116 PIRQRANQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPLMPGEWR 175 W +TI EG+NR+VRRM AVGL RL+R G +L L G W Sbjct: 368 -----GEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTL-PQTLRRGRWE 421 Query: 176 EVD 178 E++ Sbjct: 422 ELE 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 0.137 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: 679,968 Number of extensions: 29422 Number of successful extensions: 94 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 91 Number of HSP's successfully gapped: 4 Length of query: 184 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 104 Effective length of database: 1,241,070 Effective search space: 129071280 Effective search space used: 129071280 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: 127 (53.5 bits)