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= 0057.0009.p (250 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DAN4.1 B1DAN4_9BACL Exonuclease RNase T and DNA polymerase III 299 1e-79 A3DCR5.1 A3DCR5_CLOTH Exonuclease, RNase T and DNA polymerase III 126 2e-27 B4BFS0.1 B4BFS0_CLOTM Exonuclease RNase T and DNA polymerase III 126 2e-27 C2WA90.1 C2WA90_BACCE Exonuclease RNase T and DNA polymerase III 104 9e-21 B2J0S1.1 B2J0S1_NOSP7 Exonuclease, RNase T and DNA polymerase III 102 2e-20 >B1DAN4.1 B1DAN4_9BACL Exonuclease RNase T and DNA polymerase III Length = 264 Score = 299 bits (766), Expect = 1e-79, Method: Compositional matrix adjust. Identities = 148/250 (59%), Positives = 184/250 (73%), Gaps = 2/250 (0%) Query: 1 VDYIILDIEFNGRKFASEHPMEVIEIGAVRLDASLQYKDEFSALIRPIYFSTLNSFIKKK 60 +DYIILDIEFNGRKFAS+ PMEVIEIGAVRL+A LQ D FS+LI+P+YFS LNSFIKKK Sbjct: 1 MDYIILDIEFNGRKFASDLPMEVIEIGAVRLNADLQQTDIFSSLIKPVYFSKLNSFIKKK 60 Query: 61 TGIPQEDIDVADRFPKVITAFRAWLDQSVDGVLLLTWGGEDMKRIIQDVRMHKMDDAYWL 120 TGIPQE+ID+A +FP+VI F WLD+ + +L TWGGED+KRI+ D RMHK+DDA+WL Sbjct: 61 TGIPQEEIDIAPKFPRVIGEFINWLDRG-EPFMLFTWGGEDLKRIVYDTRMHKLDDAFWL 119 Query: 121 AATYFDLLKGVLRARGLTNDISVEGAMALLGLEPSGSAHRALDDAKMTADIFRAVFPDLD 180 + FDLLKG LR + +TND+SVE A+A L L G+AHRALDDA MTAD+FRA+F LD Sbjct: 120 SMDTFDLLKGYLRYKNITNDVSVEAALADLNLVFEGNAHRALDDAIMTADVFRAIFEHLD 179 Query: 181 FER-SQHYVDTFSNARERKTVXXXXXXXXXXXXVPTWELVAEHYFPGEDALADPRKLAEL 239 + Q Y D ++NA+ER+ V PTWE++ + G+ AL DPRK AEL Sbjct: 180 LDTYKQKYKDLYTNAKERRMVKNAVRAMRAQKAAPTWEMLVSKHLEGKIALTDPRKEAEL 239 Query: 240 QAYFAAQLGK 249 + YF A+ K Sbjct: 240 KEYFEAEAAK 249 >A3DCR5.1 A3DCR5_CLOTH Exonuclease, RNase T and DNA polymerase III Length = 215 Score = 126 bits (317), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 72/184 (39%), Positives = 109/184 (59%), Gaps = 7/184 (3%) Query: 1 VDYIILDIEFNGRKFASEHPMEVIEIGAVRLDASLQYKDEFSALIRPIYFSTLNSFIKKK 60 ++YI+ D+E N + F S P E+IEIGA++L+ +LQ FS+ I+P YF L S +K+K Sbjct: 1 MNYIVYDLELNSKPFKSSIPNEIIEIGAIKLNENLQEIGMFSSFIKPKYFKKLFSVVKQK 60 Query: 61 TGIPQEDIDVADRFPKVITAFRAWLDQSVDGVLLLTWGGEDMKRIIQDVRMHKMDDAYWL 120 T I QE I+ AD F VI F W+ D LL++WG +D+ +I + + +++ WL Sbjct: 61 TKITQEQINSADSFRNVIKQFIRWIG---DDYLLISWGHDDVLNLILNCKFNRI-KIDWL 116 Query: 121 AATYFDLLKGVLRARGLTND--ISVEGAMALLGLEPSGSAHRALDDAKMTADIFRAVFPD 178 D+ K L + S+E A+AL+G+E + HRAL DA+ TA IF+++F Sbjct: 117 KRN-IDIQKQFSAIYHLPSGQRYSLENALALIGVEIDENLHRALTDAQYTAKIFKSIFDK 175 Query: 179 LDFE 182 LD E Sbjct: 176 LDLE 179 >B4BFS0.1 B4BFS0_CLOTM Exonuclease RNase T and DNA polymerase III Length = 215 Score = 126 bits (317), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 72/184 (39%), Positives = 109/184 (59%), Gaps = 7/184 (3%) Query: 1 VDYIILDIEFNGRKFASEHPMEVIEIGAVRLDASLQYKDEFSALIRPIYFSTLNSFIKKK 60 ++YI+ D+E N + F S P E+IEIGA++L+ +LQ FS+ I+P YF L S +K+K Sbjct: 1 MNYIVYDLELNSKPFKSSIPNEIIEIGAIKLNENLQEIGMFSSFIKPKYFKKLFSVVKQK 60 Query: 61 TGIPQEDIDVADRFPKVITAFRAWLDQSVDGVLLLTWGGEDMKRIIQDVRMHKMDDAYWL 120 T I QE I+ AD F VI F W+ D LL++WG +D+ +I + + +++ WL Sbjct: 61 TKITQEQINSADSFRNVIKQFIRWIG---DDYLLISWGHDDVLNLILNCKFNRI-KIDWL 116 Query: 121 AATYFDLLKGVLRARGLTND--ISVEGAMALLGLEPSGSAHRALDDAKMTADIFRAVFPD 178 D+ K L + S+E A+AL+G+E + HRAL DA+ TA IF+++F Sbjct: 117 KRN-IDIQKQFSAIYHLPSGQRYSLENALALIGVEIDENLHRALTDAQYTAKIFKSIFDK 175 Query: 179 LDFE 182 LD E Sbjct: 176 LDLE 179 >C2WA90.1 C2WA90_BACCE Exonuclease RNase T and DNA polymerase III Length = 281 Score = 104 bits (259), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 79/268 (29%), Positives = 127/268 (47%), Gaps = 32/268 (11%) Query: 3 YIILDIEFNGRKFASEHPMEVIEIGAVRLDAS-LQYKDEFSALIRPIYFSTLNSFIKKKT 61 YI+ D+E N R + S+ P EV++IGA++++AS ++ F++L++P + L K T Sbjct: 7 YIVFDVERNFRPYKSQDPSEVVDIGAIKVEASTMRMIGRFASLVKPT--APLTRHTTKLT 64 Query: 62 GIPQEDIDVADRFPKVITAFRAWLDQSVDGVLLLTWGGEDMKRIIQDVRMHKMDDAYWLA 121 GI ++D+ + FPKVI F L + D + +TWG ED K + QD ++H ++ Sbjct: 65 GITKQDLKEVEMFPKVIEQF---LQFTEDNCMFVTWGKEDYKFLAQDCQLHHIECPSIEN 121 Query: 122 ATYFDLLKGVLRARG--LTNDISVEGAMALLGLEPSGSAHRALDDAKMTADIFRAVFPDL 179 FDL K V +A + S++ A+ LE G HRA DAK T +IF V + Sbjct: 122 ERKFDLQKFVFQAYEELFIDTPSLKFAVEQFALEWEGKQHRAYADAKNTLNIFLKVCKEK 181 Query: 180 D----FERSQHYVDT----FSNARERKTVXXXXXXXXXXXXVP----------TWELVAE 221 D ++R++ V T + ++K +P TW + E Sbjct: 182 DIYKRYKRNEELVLTKNGVLTEKAKKKMKRWVFKELKKKEHIPFHWADFQNSKTWGNIEE 241 Query: 222 HYFPGEDALADPRKLAELQAYFAAQLGK 249 Y+ ED + LQ YF + K Sbjct: 242 RYYIHEDT------IMLLQNYFTVAVKK 263 >B2J0S1.1 B2J0S1_NOSP7 Exonuclease, RNase T and DNA polymerase III Length = 187 Score = 102 bits (255), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 58/176 (32%), Positives = 92/176 (52%), Gaps = 6/176 (3%) Query: 3 YIILDIEFNG--RKFASEHPMEVIEIGAVRLD-ASLQYKDEFSALIRPIYFSTLNSFIKK 59 Y+I+D+E +K H ME+IEIGAV L+ A+ + EF I+P+ L F K Sbjct: 9 YLIVDLEATCCDKKTIPRHEMEIIEIGAVMLNRATWEIDSEFQQFIQPVRHPQLTDFCTK 68 Query: 60 KTGIPQEDIDVADRFPKVITAFRAWLDQSVDGVLLLTWGGEDMKRIIQDVRMHKMDDAYW 119 T I Q+D+D A +F + I+ F+ W+ S + +WG D K+ IQD H AY Sbjct: 69 LTSIQQQDVDEAPKFIEAISRFKEWIC-SFPNHIFCSWGNYDKKQFIQDCAFHNF--AYP 125 Query: 120 LAATYFDLLKGVLRARGLTNDISVEGAMALLGLEPSGSAHRALDDAKMTADIFRAV 175 + + ++ + G++ + A+ LG+E G+ HR +DDA A I+R + Sbjct: 126 FTSEHINIKEEFSEYLGVSKRFGMAQALNELGIELKGTHHRGIDDAHNIASIYRQI 181 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 0.322 0.138 0.409 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: 1,366,405,531 Number of extensions: 51221939 Number of successful extensions: 115848 Number of sequences better than 1.0e-05: 280 Number of HSP's gapped: 115528 Number of HSP's successfully gapped: 280 Length of query: 250 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 118 Effective length of database: 1,817,122,223 Effective search space: 214420422314 Effective search space used: 214420422314 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 (21.9 bits) S2: 129 (54.3 bits)