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= 0247.0021.p (252 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH1576 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase... 271 8e-73 BS_ypuL [J] COG1187 16S rRNA uridine-516 pseudouridylate synthas... 261 6e-70 SA1324 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase... 247 1e-65 lin2063 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthas... 239 4e-63 CAC1851 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthas... 233 2e-61 >BH1576 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases Length = 242 Score = 271 bits (693), Expect = 8e-73, Method: Compositional matrix adjust. Identities = 135/238 (56%), Positives = 173/238 (72%), Gaps = 1/238 (0%) Query: 1 MERLQKILAQAGVASRRKCEEMILAGKVEVNGELVTTLGTKVDPATDIIKVAGRLIRGEN 60 MERLQK++AQAG+ASRRK E++IL GKV+VNG++V LG KV+P D I+V G + E Sbjct: 1 MERLQKVIAQAGIASRRKAEQLILEGKVKVNGQVVKELGIKVNPNQDDIEVEGVPVEKEE 60 Query: 61 KIYIMFNKPKGVITSASDDKGRKVVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAN 120 +Y + KP GVI+S DDKGRKVVTD+L+ I++RVYPVGRLDYDT GLLLLTNDGEFAN Sbjct: 61 PVYFLLYKPTGVISSVKDDKGRKVVTDFLE-IEQRVYPVGRLDYDTSGLLLLTNDGEFAN 119 Query: 121 LLTHPKHHVPKTYLATVKGVPHGTALDKLKAGIKLEDGMTAPAEVEYKDVDEENKESVIS 180 LL HP+H + K Y+A VKG+P L L G+KLEDG TAPA+V+ VD + +++ Sbjct: 120 LLMHPRHKIEKVYVAKVKGIPTRDQLKLLARGVKLEDGPTAPAKVKMLSVDRRKQTAIVK 179 Query: 181 ITIHEGRNRQVRRMFEAISHPVIRLKRISFGDILLQNLKRGSYRHLTKDEINHLQQIA 238 +TIHEGRNRQVRRMFE I V++LKR F + L + G R L E+ HL+++A Sbjct: 180 LTIHEGRNRQVRRMFETIGCEVMKLKREQFAFLDLSGMNPGDVRPLKPIEVKHLRELA 237 >BS_ypuL [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases Length = 229 Score = 261 bits (667), Expect = 6e-70, Method: Compositional matrix adjust. Identities = 131/226 (57%), Positives = 168/226 (74%), Gaps = 1/226 (0%) Query: 1 MERLQKILAQAGVASRRKCEEMILAGKVEVNGELVTTLGTKVDPATDIIKVAGRLIRGEN 60 MERLQK++A AGVASR K EE+I GKV+VNG++VT LG KV +D I+V G + E Sbjct: 1 MERLQKVIAHAGVASRSKAEELIKEGKVKVNGKVVTELGVKVT-GSDQIEVNGLKVEREE 59 Query: 61 KIYIMFNKPKGVITSASDDKGRKVVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAN 120 +Y + KP+GVI++A DDKGRKVVTD+ K I +R+YP+GRLDYDT GLLLLTNDGEFAN Sbjct: 60 PVYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFAN 119 Query: 121 LLTHPKHHVPKTYLATVKGVPHGTALDKLKAGIKLEDGMTAPAEVEYKDVDEENKESVIS 180 L HPK+ + KTY+A VKG+P L KL+ GI+LE+G TAPA+ + +D++ + S+I Sbjct: 120 KLMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQ 179 Query: 181 ITIHEGRNRQVRRMFEAISHPVIRLKRISFGDILLQNLKRGSYRHL 226 +TIHEGRNRQVRRMFEAI H VI+LKR + + L+ L G R L Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 225 >SA1324 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases Length = 245 Score = 247 bits (630), Expect = 1e-65, Method: Compositional matrix adjust. Identities = 132/241 (54%), Positives = 169/241 (70%), Gaps = 1/241 (0%) Query: 1 MERLQKILAQAGVASRRKCEEMILAGKVEVNGELVTTLGTKVDPATDIIKVAGRLIRGEN 60 +ERLQK +A +G SRRK E +I GKV+VNG VT LGTKV P+ D I+V G I E+ Sbjct: 5 LERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPS-DTIEVEGIKIELED 63 Query: 61 KIYIMFNKPKGVITSASDDKGRKVVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAN 120 KIYI+F+KP VITS SDD+GR VVTDY K I+ R+YPVGRLDYDT GLLLLTNDGEF N Sbjct: 64 KIYILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTN 123 Query: 121 LLTHPKHHVPKTYLATVKGVPHGTALDKLKAGIKLEDGMTAPAEVEYKDVDEENKESVIS 180 L+THP++ + K Y+A +KG + L+ GI+LEDGMT PAEV+ K D++ +++ Sbjct: 124 LMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVE 183 Query: 181 ITIHEGRNRQVRRMFEAISHPVIRLKRISFGDILLQNLKRGSYRHLTKDEINHLQQIAKA 240 ITI EGRNRQVRRMFE H V +L RI +G + + L G R LT E+ ++ +A+ Sbjct: 184 ITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVKVMRHLAEH 243 Query: 241 G 241 G Sbjct: 244 G 244 >lin2063 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases Length = 182 Score = 239 bits (609), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 0/241 (0%), Positives = 0/241 (0%), Gaps = 1/241 (0%) Query: 1 MERLQKILAQAGVASRRKCEEMILAGKVEVNGELVTTLGTKVDPATDIIKVAGRLIRGEN 60 M+ IL A E+ ++ ++ + Sbjct: 1 MQTEHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAK-GQLLVTRRALSKKAWP 59 Query: 61 KIYIMFNKPKGVITSASDDKGRKVVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAN 120 ++ + +++D + L + + E Sbjct: 60 GVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCP 119 Query: 121 LLTHPKHHVPKTYLATVKGVPHGTALDKLKAGIKLEDGMTAPAEVEYKDVDEENKESVIS 180 + + V D L + ++ + + + S + Sbjct: 120 VFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 179 Query: 181 ITIHEGRNRQVRRMFEAISHPVIRLKRISFGDILLQNLKRGSYRHLTKDEINHLQQIAKA 240 Sbjct: 180 239 Query: 241 G 241 Sbjct: 240 240 >CAC1851 [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases Length = 236 Score = 233 bits (594), Expect = 2e-61, Method: Compositional matrix adjust. Identities = 125/237 (52%), Positives = 164/237 (69%), Gaps = 4/237 (1%) Query: 2 ERLQKILAQAGVASRRKCEEMILAGKVEVNGELVTTLGTKVDPATDIIKVAGRLIRGENK 61 ERLQK +A+ GVASRRKCE+MI G+V+VNG +VT LG KVD D I++ + I+ E+K Sbjct: 3 ERLQKYMAECGVASRRKCEKMIQDGRVKVNGTIVTELGFKVDYKKDTIELDNKEIKLEDK 62 Query: 62 -IYIMFNKPKGVITSASDDKGRKVVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDGEFAN 120 +Y + NKPKG +T+ASD +GRK V D L KERV+PVGRLD++T GLL++TNDGE N Sbjct: 63 KVYAILNKPKGYLTAASDYRGRKTVIDLL-NFKERVFPVGRLDFNTTGLLIVTNDGEIFN 121 Query: 121 LLTHPKHHVPKTYLATVKGVPHGTALDKLKAGIKLEDGMTAPAEVEYKDVDEENKESVIS 180 + HP+ +V K YLATVKG P LD L+ GI + +T AEV D +N S++ Sbjct: 122 RIMHPRQNVNKCYLATVKGKPQFKHLDALRKGIDIGGYITKEAEVSVVSFDGKN--SILK 179 Query: 181 ITIHEGRNRQVRRMFEAISHPVIRLKRISFGDILLQNLKRGSYRHLTKDEINHLQQI 237 I IHEG+ RQVRRM A+ PV LKRIS G+I L +LK G+ R L K+EI +L+ + Sbjct: 180 IVIHEGKKRQVRRMCAAVGFPVEELKRISIGNIKLGDLKEGNVRMLNKEEIEYLRSL 236 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.317 0.136 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 18,657,976 Number of extensions: 787919 Number of successful extensions: 3248 Number of sequences better than 1.0e-05: 98 Number of HSP's gapped: 3070 Number of HSP's successfully gapped: 98 Length of query: 252 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 148 Effective length of database: 26,383,695 Effective search space: 3904786860 Effective search space used: 3904786860 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 114 (48.5 bits)