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= 0004.0007.p (166 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 ref|NP_690992.1| polyribonucleotide nucleotidyltransferase [Ocea... 156 1e-37 ref|NP_469595.1| polyribonucleotide nucleotidyltransferase domai... 153 2e-36 ref|NP_463749.1| polyribonucleotide nucleotidyltransferase domai... 153 2e-36 ref|NP_387944.1| similar to polyribonucleotide nucleotidyltransf... 150 1e-35 ref|NP_842629.1| S1 RNA binding domain protein [Bacillus anthrac... 148 5e-35 >ref|NP_690992.1| polyribonucleotide nucleotidyltransferase [Oceanobacillus iheyensis HTE831] dbj|BAC12027.1| polyribonucleotide nucleotidyltransferase [Oceanobacillus iheyensis HTE831] Length = 127 Score = 156 bits (395), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 88/168 (52%), Positives = 107/168 (63%), Gaps = 45/168 (26%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG+KL+GKVTGIT+FGAFV+L G TGLVHISE+ADNYVKD+N+HL + D V VKV Sbjct: 1 MSIEVGSKLQGKVTGITNFGAFVELEKGTTGLVHISEVADNYVKDINEHLTVGDEVKVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 INV+KDGKIGLSIK+A D+ Sbjct: 61 INVEKDGKIGLSIKKAKDR----------------------------------------- 79 Query: 121 XPFKPAAGK---PSFEDKMSRFLKDSEERISSIKKNTEGKRGGRGAKR 165 P + K +FE KMSRFLKDSE+R++S+KK+TE KRGGRGAKR Sbjct: 80 -PVRQKNTKERTENFESKMSRFLKDSEDRLASLKKHTESKRGGRGAKR 126 >ref|NP_469595.1| polyribonucleotide nucleotidyltransferase domain present [Listeria innocua] pir||AC1464 polyribonucleotide nucleotidyltransferase domain present [imported] - Listeria innocua (strain Clip11262) emb|CAC95483.1| polyribonucleotide nucleotidyltransferase domain present [Listeria innocua] gb|AAM74000.1| YabR-like protein [Listeria monocytogenes] Length = 142 Score = 153 bits (386), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 89/169 (52%), Positives = 107/169 (63%), Gaps = 32/169 (18%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG KL+GKVTGIT+FGAFV+L GG TGLVHISE+ADNYVKD+ND L + D VTVKV Sbjct: 1 MSIEVGNKLQGKVTGITNFGAFVELEGGKTGLVHISEVADNYVKDINDILTVGDEVTVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 +N+ DGKIGLSI++AVD+ Sbjct: 61 MNIGDDGKIGLSIRKAVDRPDRPEKSYDRKPKYSK------------------------- 95 Query: 121 XPFKPAAG--KP--SFEDKMSRFLKDSEERISSIKKNTEGKRGGRGAKR 165 KPA KP SFED MS+FLKDS+ER+++IK+ TE KRGGRGAKR Sbjct: 96 ---KPAGNYVKPAESFEDIMSKFLKDSDERLTTIKRQTESKRGGRGAKR 141 >ref|NP_463749.1| polyribonucleotide nucleotidyltransferase domain present [Listeria monocytogenes EGD-e] pir||AC1102 polyribonucleotide nucleotidyltransferase domain present [imported] - Listeria monocytogenes (strain EGD-e) emb|CAD00745.1| polyribonucleotide nucleotidyltransferase domain present [Listeria monocytogenes] Length = 142 Score = 153 bits (386), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 89/169 (52%), Positives = 107/169 (63%), Gaps = 32/169 (18%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG KL+GKVTGIT+FGAFV+L GG TGLVHISE+ADNYVKD+ND L + D VTVKV Sbjct: 1 MSIEVGNKLQGKVTGITNFGAFVELEGGKTGLVHISEVADNYVKDINDILTVGDEVTVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 +N+ DGKIGLSI++AVD+ Sbjct: 61 MNIGDDGKIGLSIRKAVDRPDRPEKSYDRKPKYNK------------------------- 95 Query: 121 XPFKPAAG--KP--SFEDKMSRFLKDSEERISSIKKNTEGKRGGRGAKR 165 KPA KP SFED MS+FLKDS+ER+++IK+ TE KRGGRGAKR Sbjct: 96 ---KPAGNYVKPAESFEDIMSKFLKDSDERLTTIKRQTESKRGGRGAKR 141 >ref|NP_387944.1| similar to polyribonucleotide nucleotidyltransferase [Bacillus subtilis] sp|P37560|YABR_BACSU Hypothetical protein yabR pir||C53380 polyribonucleotide nucleotidyltransferase homolog yabR - Bacillus subtilis gb|AAB38380.1| unknown [Bacillus subtilis] dbj|BAA05298.1| unknown [Bacillus subtilis] emb|CAB11839.1| yabR [Bacillus subtilis subsp. subtilis str. 168] Length = 128 Score = 150 bits (379), Expect = 1e-35, Method: Compositional matrix adjust. Identities = 83/157 (52%), Positives = 102/157 (64%), Gaps = 38/157 (24%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG+KL+GK+TGIT+FGAFV+L GG TGLVHISE+ADNYVKD+NDHLK+ D V VKV Sbjct: 1 MSIEVGSKLQGKITGITNFGAFVELPGGSTGLVHISEVADNYVKDINDHLKVGDQVEVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 INV+KDGKIGLSIK+A D+ Sbjct: 61 INVEKDGKIGLSIKKAKDRPQARPRND--------------------------------- 87 Query: 121 XPFKPAAGKPSFEDKMSRFLKDSEERISSIKKNTEGK 157 F+P K SFE KM++FLKDSE+R+SS+K+NTE K Sbjct: 88 --FRP---KESFEQKMNKFLKDSEDRLSSLKRNTESK 119 >ref|NP_842629.1| S1 RNA binding domain protein [Bacillus anthracis str. Ames] ref|NP_976387.1| S1 RNA binding domain protein [Bacillus cereus ATCC 10987] gb|AAP24115.1| S1 RNA binding domain protein [Bacillus anthracis str. Ames] gb|AAS38995.1| S1 RNA binding domain protein [Bacillus cereus ATCC 10987] Length = 160 Score = 148 bits (373), Expect = 5e-35, Method: Compositional matrix adjust. Identities = 80/157 (50%), Positives = 100/157 (63%), Gaps = 6/157 (3%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG+KL+GKVTGIT+FGAFV+L G+TGLVHISE+ADNYVKD+NDHLK+ D V VKV Sbjct: 1 MSIEVGSKLQGKVTGITNFGAFVELPEGLTGLVHISEVADNYVKDINDHLKVGDQVEVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 INV+KDGKIGLSIK+A ++ Sbjct: 61 INVEKDGKIGLSIKKAKEREKTEGDRPRGEYQRGGDQQRSGRPQRNRSFNRDNRGGGNDR 120 Query: 121 XPFKPAAGKPSFEDKMSRFLKDSEERISSIKKNTEGK 157 P K +FE KM+RFLKDSE+R++S+K+NTE K Sbjct: 121 AP------KETFEQKMARFLKDSEDRLTSLKRNTESK 151 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 0.314 0.135 0.372 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: 180,522,026 Number of extensions: 5838851 Number of successful extensions: 19379 Number of sequences better than 1.0e-05: 1126 Number of HSP's gapped: 19294 Number of HSP's successfully gapped: 1338 Length of query: 166 Length of database: 757,237,578 Length adjustment: 116 Effective length of query: 50 Effective length of database: 442,286,094 Effective search space: 22114304700 Effective search space used: 22114304700 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: 42 (21.9 bits) S2: 121 (51.2 bits)