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= 0586.0007.p (304 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KIH2.1 B3KIH2_9BACI tRNA pseudouridine synthase B 411 e-113 B1DM49.1 B1DM49_9BACL tRNA pseudouridine synthase B 347 6e-94 C0ZF47.1 C0ZF47_BREBN tRNA pseudouridine synthase B EC=4.2.1.70 258 5e-67 Q2B0A8.1 Q2B0A8_9BACI TRNA pseudouridine 55 synthase 257 1e-66 A5ZWK3.1 A5ZWK3_9FIRM Putative uncharacterized protein 252 3e-65 >B3KIH2.1 B3KIH2_9BACI tRNA pseudouridine synthase B Length = 303 Score = 411 bits (1057), Expect = e-113, Method: Compositional matrix adjust. Identities = 205/303 (67%), Positives = 243/303 (80%), Gaps = 1/303 (0%) Query: 1 MSELTGVLAVYKPAGFTSHDVVAKARRILGMKRIGHTGTLDPQVTGVLPLCLGRATRVVE 60 M++L G+LAV+KPAG+TSHDVVAK R ++ +KRIGHTGTLDP+VTGVLPLCLGRATRVVE Sbjct: 1 MTQLEGILAVHKPAGWTSHDVVAKVRGMVRLKRIGHTGTLDPEVTGVLPLCLGRATRVVE 60 Query: 61 YIQELPKEYVATLRLGLSSDTEDLTGTITETVDEVHVTEAEVLAVLKSFQGVISQVPPMY 120 Y+QELPKEY A LRLG S+DTED+TG + ET DEV VT E L L+SF+G ISQVPPMY Sbjct: 61 YLQELPKEYHAVLRLGYSTDTEDITGNVVETADEVRVTRDEALEALQSFRGQISQVPPMY 120 Query: 121 SAVKVDGKRLYELAREGKTVERKSREVEIYEIEMTGMIWNGNHPDVTFRVLCSKGTYIRT 180 SAVK++GKRLYELAREGKTVERKSR V I+EIEMT G + +++FRVLCSKGTYIRT Sbjct: 121 SAVKINGKRLYELAREGKTVERKSRTVTIHEIEMTDFDAEGEYTEISFRVLCSKGTYIRT 180 Query: 181 LCVDIGRALGLPGVMVKLERTMSAGISASHCLTLEQIAEYKEAGTLEAHLIAADEAVSHL 240 LCVDIGR LGLP VMVKL RT+SAGI+ + CLTLEQI ++ + TL+ LI D+A+ HL Sbjct: 181 LCVDIGRKLGLPSVMVKLVRTISAGITEAQCLTLEQIEQFMKDETLQTRLIPVDQAIHHL 240 Query: 241 PRHTVMDGKKKAALQGQRLSLRHVAPEVQHNGHFRLYDEQGGFLGIYV-LEETGAIAPVK 299 +HTV + K +AAL+GQRLS R V P V + RLYD + FLGIY EETGAI PVK Sbjct: 241 AKHTVSEEKAEAALKGQRLSSRAVEPAVDSSEPIRLYDIKENFLGIYKRQEETGAIVPVK 300 Query: 300 VFA 302 VF+ Sbjct: 301 VFS 303 >B1DM49.1 B1DM49_9BACL tRNA pseudouridine synthase B Length = 300 Score = 347 bits (891), Expect = 6e-94, Method: Compositional matrix adjust. Identities = 170/300 (56%), Positives = 218/300 (72%), Gaps = 1/300 (0%) Query: 4 LTGVLAVYKPAGFTSHDVVAKARRILGMKRIGHTGTLDPQVTGVLPLCLGRATRVVEYIQ 63 + G++AV+KPAG+TSHDVVAK RRI+ MKRIGH GTLDP VTGVLPLCLGR+TRVVEY+Q Sbjct: 1 MDGIIAVWKPAGWTSHDVVAKVRRIVRMKRIGHAGTLDPMVTGVLPLCLGRSTRVVEYLQ 60 Query: 64 ELPKEYVATLRLGLSSDTEDLTGTITETVDEVHVTEAEVLAVLKSFQGVISQVPPMYSAV 123 E PK Y A ++LG ++DTEDLTGT+ E + VT +VL VL+SF G I QVPPM+SAV Sbjct: 61 ERPKAYEAVIQLGTATDTEDLTGTVLEEQTGIIVTREQVLQVLQSFVGEIDQVPPMFSAV 120 Query: 124 KVDGKRLYELAREGKTVERKSREVEIYEIEMTGMIWNGNHPDVTFRVLCSKGTYIRTLCV 183 KVDGKRLYELAREGKTVERKSR+V I++I++ + + + P F V+CSKGTYIRTLCV Sbjct: 121 KVDGKRLYELAREGKTVERKSRKVTIHQIDLLNVDLDADKPRFAFSVICSKGTYIRTLCV 180 Query: 184 DIGRALGLPGVMVKLERTMSAGISASHCLTLEQIAEYKEAGTLEAHLIAADEAVSHLPRH 243 DIGRALG+P M +L RTMS GI+ C+TLE++ E + AG LE ++ AD A+ HL R Sbjct: 181 DIGRALGVPAAMAELTRTMSGGITREQCVTLEELEELQAAGKLEEKMLPADIAIDHLQRV 240 Query: 244 TVMDGKKKAALQGQRLSLRHVAPEVQHNGHFRLYDEQGGFLGIY-VLEETGAIAPVKVFA 302 + AL+GQ++ +A + RLY E F+GI+ ++ A+ PVKVF+ Sbjct: 241 QANAAVTEMALRGQKIPYNRMAASFDSSSLVRLYGENDAFIGIFEADDQASALKPVKVFS 300 >C0ZF47.1 C0ZF47_BREBN tRNA pseudouridine synthase B EC=4.2.1.70 Length = 308 Score = 258 bits (659), Expect = 5e-67, Method: Compositional matrix adjust. Identities = 132/270 (48%), Positives = 177/270 (65%), Gaps = 3/270 (1%) Query: 1 MSELTGVLAVYKPAGFTSHDVVAKARRILGMKRIGHTGTLDPQVTGVLPLCLGRATRVVE 60 MS + GVL + KPAG TSHD VA+ RR+ G K++GHTGTLDP VTGVLP+C+G ATR+VE Sbjct: 1 MSNVNGVLVIDKPAGMTSHDCVARIRRLYGTKKVGHTGTLDPDVTGVLPICVGHATRLVE 60 Query: 61 YIQELPKEYVATLRLGLSSDTEDLTGTITET--VDEVHVTEAEVLAVLKSFQGVISQVPP 118 Y+QELPK Y +RLG ++ TED +G + E VD +T + A+ +SF G + QVPP Sbjct: 61 YLQELPKRYDVVMRLGSTTTTEDASGEVVEQAGVDAAWITTERIQALFESFLGEMEQVPP 120 Query: 119 MYSAVKVDGKRLYELAREGKTVERKSREVEIYEIEMTGMIWNGNHPDVTFRVLCSKGTYI 178 M+SAVKV+GKRLY+LAREG +ER++R+V +YE+ + + +G+ DV F CSKGTY+ Sbjct: 121 MFSAVKVNGKRLYDLAREGTVIERQARKVTLYELTLHKISVDGDTVDVAFTCTCSKGTYM 180 Query: 179 RTLCVDIGRALGLPGVMVKLERTMSAGISASHCLTLEQIAEYKEAG-TLEAHLIAADEAV 237 RTLCVD+GRALG P M L R S + L+QI E +G + HL++ +A+ Sbjct: 181 RTLCVDLGRALGYPAHMKLLRRIKSGPFQEQEAIPLQQIEEQAASGEDISRHLVSIPQAI 240 Query: 238 SHLPRHTVMDGKKKAALQGQRLSLRHVAPE 267 S LP V + KA G +L V E Sbjct: 241 SFLPSFQVKPERIKAVRNGLATALPGVTAE 270 >Q2B0A8.1 Q2B0A8_9BACI TRNA pseudouridine 55 synthase Length = 307 Score = 257 bits (656), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 144/306 (47%), Positives = 189/306 (61%), Gaps = 11/306 (3%) Query: 3 ELTGVLAVYKPAGFTSHDVVAKARRILGMKRIGHTGTLDPQVTGVLPLCLGRATRVVEYI 62 E+ G++ ++KP G TSHD V K R+IL MKRIGHTGTLDP VTGVLP+C+GRAT+V EYI Sbjct: 2 EMEGIIPLFKPKGMTSHDCVFKLRKILRMKRIGHTGTLDPDVTGVLPICIGRATKVAEYI 61 Query: 63 QELPKEYVATLRLGLSSDTEDLTG-TITETVDEVHVTEAEVLAVLKSFQGVISQVPPMYS 121 + K Y + LG S+ TED +G I E VT A+V+ VL++ +G I+Q PPMYS Sbjct: 62 TDAGKAYEGEVTLGFSTSTEDASGEKIEEKPVAGRVTRAQVIDVLENLKGEITQTPPMYS 121 Query: 122 AVKVDGKRLYELAREGKTVERKSREVEIYEIEMTG--MIWNGNHPDVTFRVLCSKGTYIR 179 AVKV+GKRLYE AR+G VER +R+V IY IE+ + G +P FRV CSKGTYIR Sbjct: 122 AVKVNGKRLYEYARKGIEVERPTRKVSIYSIELLSEEQEFEGPNPSFRFRVECSKGTYIR 181 Query: 180 TLCVDIGRALGLPGVMVKLERTMSAGISASHCLTLEQIAEYKEAGTLEAHLIAADEAVSH 239 TL V IG ALG P M LER SA + CLT + I +E+G L A + +E +SH Sbjct: 182 TLAVMIGEALGYPAHMSGLERIRSASFAKEECLTFKDIEALQESGELAAKIRPLEEGISH 241 Query: 240 LPRHTVMDGKKKAALQGQRLSLRHVAPEV--QHNGHFRLYDEQGGFLGIYV--LEETGAI 295 LP++T+ D + G L++ P+ + G + E G L IY+ + G + Sbjct: 242 LPKYTISDTVAEKVKNGALLNI----PDFLEKETGPIVVQTEAGTALAIYLHHPAKPGLM 297 Query: 296 APVKVF 301 P KV Sbjct: 298 KPSKVL 303 >A5ZWK3.1 A5ZWK3_9FIRM Putative uncharacterized protein Length = 294 Score = 252 bits (643), Expect = 3e-65, Method: Compositional matrix adjust. Identities = 146/299 (48%), Positives = 183/299 (61%), Gaps = 7/299 (2%) Query: 4 LTGVLAVYKPAGFTSHDVVAKARRILGMKRIGHTGTLDPQVTGVLPLCLGRATRVVEYIQ 63 + GVL + K G+TS DVVAK R IL MK+IGHTGTLDP+ GVLP+ LG+AT++V+ + Sbjct: 1 MDGVLNIRKEKGYTSFDVVAKLRGILHMKKIGHTGTLDPEAEGVLPVVLGKATKLVDLLT 60 Query: 64 ELPKEYVATLRLGLSSDTEDLTGTITETVDEVHVTEAEVLAVLKSFQGVISQVPPMYSAV 123 E K Y A L LGL +DT+D+TGT+ E V VTE EV V++SF G Q+PPMYSA+ Sbjct: 61 EKQKTYEALLHLGLETDTQDMTGTVLEE-KPVEVTEEEVRTVIRSFLGEQQQIPPMYSAL 119 Query: 124 KVDGKRLYELAREGKTVERKSREVEIYEIEMTGMIWNGNHPDVTFRVLCSKGTYIRTLCV 183 KVDGK+LYELAREGKTVERK R V+ YEIE+ + P V F V CSKGTYIRTLC Sbjct: 120 KVDGKKLYELAREGKTVERKPRAVQFYEIEIKKI----ELPYVRFSVTCSKGTYIRTLCH 175 Query: 184 DIGRALGLPGVMVKLERTMSAGISASHCLTLEQIAEYKEAGTLEAHLIAADEAVSHLPRH 243 DIG+ LG G M +L RT S +TL Q+ E GT+ +I+ +A+ P Sbjct: 176 DIGQKLGCGGCMEELLRTRSGNFVWEDSMTLAQVEEAVRNGTIGDRVISIGQALKDYPEI 235 Query: 244 TVMDGKKKAALQGQRLSLRHVAPEVQHNGHFRLYDEQGGFLGIYVLEETGA-IAPVKVF 301 + G L+ R V E G R+ D QGGF GIY +E P K+F Sbjct: 236 FCTREGDRLLENGNALAERFVRGE-HKEGWVRMCDSQGGFKGIYQWDEVKKRYQPQKMF 293 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.319 0.135 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,740,079,437 Number of extensions: 69639093 Number of successful extensions: 186511 Number of sequences better than 1.0e-05: 1892 Number of HSP's gapped: 182850 Number of HSP's successfully gapped: 1892 Length of query: 304 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 169 Effective length of database: 1,788,859,178 Effective search space: 302317201082 Effective search space used: 302317201082 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: 131 (55.1 bits)