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= 0118.0003.p (116 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value pir||A44914 tRNA nucleotidyltransferase (EC 2.7.7.56) - Bacillus... 122 3e-27 ref|NP_390715.1| ribonuclease PH [Bacillus subtilis] >gi|133188|... 122 3e-27 ref|NP_563170.1| ribonuclease PH [Clostridium perfringens] >gi|2... 120 8e-27 ref|NP_658509.1| RNase_PH, 3' exoribonuclease family [Bacillus a... 118 4e-26 ref|NP_834204.1| Ribonuclease PH [Bacillus cereus ATCC 14579] >g... 117 7e-26 >pir||A44914 tRNA nucleotidyltransferase (EC 2.7.7.56) - Bacillus subtilis Length = 245 Score = 122 bits (305), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 64/102 (62%), Positives = 78/102 (76%), Gaps = 1/102 (0%) Query: 1 MAFAVNKIALQHKLSVFPITDYLAAISVGVVGDE-TLLDLNYEEDSKAKVDMNVVMTGGG 59 MA A+ K+ + PITD+LAAISVG+ ++ LLDLNYEEDS A+VDMNV+MTG G Sbjct: 137 MAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSG 196 Query: 60 AFVEVQGTGEERPFTRQELDQLLGLGEKGIYELIAVQKEVLG 101 FVE+QGTGEE F+R++L+ LLGL EKGI ELI QKEVLG Sbjct: 197 RFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG 238 >ref|NP_390715.1| ribonuclease PH [Bacillus subtilis] sp|P28619|RNPH_BACSU Ribonuclease PH (RNase PH) (tRNA nucleotidyltransferase) gb|AAA22705.1| RNase PH emb|CAA99554.1| RNase PH [Bacillus subtilis] emb|CAB14797.1| ribonuclease PH [Bacillus subtilis subsp. subtilis str. 168] Length = 245 Score = 122 bits (305), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 64/102 (62%), Positives = 78/102 (76%), Gaps = 1/102 (0%) Query: 1 MAFAVNKIALQHKLSVFPITDYLAAISVGVVGDE-TLLDLNYEEDSKAKVDMNVVMTGGG 59 MA A+ K+ + PITD+LAAISVG+ ++ LLDLNYEEDS A+VDMNV+MTG G Sbjct: 137 MAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSG 196 Query: 60 AFVEVQGTGEERPFTRQELDQLLGLGEKGIYELIAVQKEVLG 101 FVE+QGTGEE F+R++L+ LLGL EKGI ELI QKEVLG Sbjct: 197 RFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG 238 >ref|NP_563170.1| ribonuclease PH [Clostridium perfringens] sp|Q8XI67|RNPH_CLOPE Ribonuclease PH (RNase PH) (tRNA nucleotidyltransferase) dbj|BAB81960.1| ribonuclease PH [Clostridium perfringens str. 13] Length = 248 Score = 120 bits (302), Expect = 8e-27, Method: Compositional matrix adjust. Identities = 58/108 (53%), Positives = 79/108 (73%) Query: 4 AVNKIALQHKLSVFPITDYLAAISVGVVGDETLLDLNYEEDSKAKVDMNVVMTGGGAFVE 63 AVNK+ + +V+PI +++A+SVG+VG+E +LDL YEED AKVDMNVVMT G F+E Sbjct: 140 AVNKLHQKKPFNVYPIRHFVSAVSVGIVGEEKILDLCYEEDHVAKVDMNVVMTEEGEFIE 199 Query: 64 VQGTGEERPFTRQELDQLLGLGEKGIYELIAVQKEVLGAIALKIPAGQ 111 +QGTGE PF+R+ELD+LL L EKG ++I QK+ L +L I G+ Sbjct: 200 IQGTGEAGPFSRKELDELLNLAEKGAKQMIQAQKDALKTDSLWIGTGR 247 >ref|NP_658509.1| RNase_PH, 3' exoribonuclease family [Bacillus anthracis A2012] ref|NP_846927.1| ribonuclease PH [Bacillus anthracis str. Ames] gb|AAP28413.1| ribonuclease PH [Bacillus anthracis str. Ames] Length = 245 Score = 118 bits (296), Expect = 4e-26, Method: Compositional matrix adjust. Identities = 61/108 (56%), Positives = 77/108 (71%), Gaps = 1/108 (0%) Query: 1 MAFAVNKIALQHKLSVFPITDYLAAISVGVVGDE-TLLDLNYEEDSKAKVDMNVVMTGGG 59 M A K+ K+S P+ DYLAA SVG+V ++ +LDLNY EDSKA VDMNV+MTG G Sbjct: 137 MVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYAEDSKADVDMNVIMTGKG 196 Query: 60 AFVEVQGTGEERPFTRQELDQLLGLGEKGIYELIAVQKEVLGAIALKI 107 FVEVQGTGEE F+R +L++LL E+GI++LI +QKE LG I I Sbjct: 197 QFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDIQKEALGDIVSHI 244 >ref|NP_834204.1| Ribonuclease PH [Bacillus cereus ATCC 14579] ref|NP_980879.1| ribonuclease PH [Bacillus cereus ATCC 10987] gb|AAP11405.1| Ribonuclease PH [Bacillus cereus ATCC 14579] gb|AAS43487.1| ribonuclease PH [Bacillus cereus ATCC 10987] Length = 245 Score = 117 bits (293), Expect = 7e-26, Method: Compositional matrix adjust. Identities = 61/108 (56%), Positives = 77/108 (71%), Gaps = 1/108 (0%) Query: 1 MAFAVNKIALQHKLSVFPITDYLAAISVGVVGDE-TLLDLNYEEDSKAKVDMNVVMTGGG 59 M A K+ K+S P+ DYLAA SVG+V ++ +LDLNY EDSKA VDMNV+MTG G Sbjct: 137 MVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYAEDSKADVDMNVIMTGKG 196 Query: 60 AFVEVQGTGEERPFTRQELDQLLGLGEKGIYELIAVQKEVLGAIALKI 107 FVEVQGTGEE F+R +L++LL E+GI++LI +QKE LG I I Sbjct: 197 QFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDMQKEALGDIVSHI 244 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.316 0.137 0.370 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 165,614,120 Number of extensions: 6582163 Number of successful extensions: 16933 Number of sequences better than 1.0e-05: 275 Number of HSP's gapped: 16950 Number of HSP's successfully gapped: 275 Length of query: 116 Length of database: 757,237,578 Length adjustment: 81 Effective length of query: 35 Effective length of database: 537,314,559 Effective search space: 18806009565 Effective search space used: 18806009565 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: 120 (50.8 bits)