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= 0541.0095.p (124 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_523212.1| PUTATIVE CYTOCHROME C OXIDASE POLYPEPTIDE II OX... 60 1e-08 ref|NP_242894.1| BH2028~unknown [Bacillus halodurans] >gi|254901... 60 1e-08 ref|NP_925110.1| cytochrome c oxidase subunit II [Gloeobacter vi... 59 2e-08 ref|NP_770425.1| cytochrome C oxidase [Bradyrhizobium japonicum]... 57 2e-07 ref|NP_386622.1| PROBABLE ALTERNATIVE CYTOCHROME C OXIDASE POLYP... 55 5e-07 >ref|NP_523212.1| PUTATIVE CYTOCHROME C OXIDASE POLYPEPTIDE II OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum] emb|CAD18804.1| PUTATIVE CYTOCHROME C OXIDASE POLYPEPTIDE II OXIDOREDUCTASE PROTEIN [Ralstonia solanacearum] Length = 125 Score = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust. Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 3/84 (3%) Query: 43 ISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLD---GKDSSQVIVPEEA 99 + A ++F LK+GVPV + G +P+ ++R D G+ + + PE Sbjct: 41 VHARKFTFTPDHITLKRGVPVVFELTGQDILMGFSIPDFSVRADVVPGQTARLALTPERT 100 Query: 100 GTFEMTCAIMCGSGHSSMSAKVIV 123 GTFE C I CG+GH +M+ ++V Sbjct: 101 GTFEFLCDIFCGTGHETMNGTLVV 124 >ref|NP_242894.1| BH2028~unknown [Bacillus halodurans] pir||D83903 hypothetical protein BH2028 [imported] - Bacillus halodurans (strain C-125) dbj|BAB05747.1| BH2028~unknown [Bacillus halodurans] Length = 143 Score = 60.1 bits (144), Expect = 1e-08, Method: Compositional matrix adjust. Identities = 30/85 (35%), Positives = 50/85 (58%), Gaps = 3/85 (3%) Query: 41 LIISATNYSFDQKEYHLKKGVPVNIVFKNESGNHGILVPELNLRLDGKDSSQVIVPEEAG 100 L I A N+SFDQ++Y + G V I F+N G+H ++ N+ L + V ++AG Sbjct: 58 LHIQADNFSFDQEQYEVPLGATVEITFENVEGHHEAVIEGYNVSL-SEGEPVTFVADQAG 116 Query: 101 TFEMTCAIMCG--SGHSSMSAKVIV 123 FE+ C+++CG H +M +K++V Sbjct: 117 EFELACSVVCGPIDDHENMVSKLVV 141 >ref|NP_925110.1| cytochrome c oxidase subunit II [Gloeobacter violaceus] dbj|BAC90105.1| cytochrome c oxidase subunit II [Gloeobacter violaceus PCC 7421] Length = 308 Score = 59.3 bits (142), Expect = 2e-08, Method: Compositional matrix adjust. Identities = 36/109 (33%), Positives = 51/109 (46%), Gaps = 8/109 (7%) Query: 24 ASNKDGAAETGLTADEELIISATNYSF-----DQKEYHLKKGVPVNIVFKNESGNHGILV 78 A+N D AA L E + A +S+ E HL G PV + K+ H V Sbjct: 143 ATNPDPAAPPPLIIAVEAVQYAWIFSYPGSETQVSELHLPIGRPVRMDMKSNDVIHAFWV 202 Query: 79 PELNLRLD---GKDSSQVIVPEEAGTFEMTCAIMCGSGHSSMSAKVIVE 124 PE L+ D G+ + P +AG +++ CA +CG+ H M VIVE Sbjct: 203 PEFRLKQDVIPGRTTQVSFTPTKAGKYQLRCAELCGAYHGGMVVDVIVE 251 >ref|NP_770425.1| cytochrome C oxidase [Bradyrhizobium japonicum] sp|P98053|COXM_BRAJA Alternative cytochrome c oxidase polypeptide II (Cytochrome BB3 subunit 2) (Oxidase BB(3) subunit 2) pir||B48364 cytochrome-c oxidase (EC 1.9.3.1) chain II - Bradyrhizobium japonicum emb|CAA48547.1| cytochrome-c oxidase [Bradyrhizobium japonicum] dbj|BAC49050.1| cytochrome C oxidase [Bradyrhizobium japonicum USDA 110] Length = 277 Score = 56.6 bits (135), Expect = 2e-07, Method: Compositional matrix adjust. Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%) Query: 54 EYHLKKGVPVNIVFKNESGNHGILVPELNLRLD---GKDSSQVIVPEEAGTFEMTCAIMC 110 + HL G PV ++ ++ H VPE ++D G + I P GTF++ CA +C Sbjct: 170 DLHLPIGKPVKVLLRSVDVLHDFYVPEFRAKMDMVPGMVTYFWIRPIRTGTFDVLCAELC 229 Query: 111 GSGHSSMSAKVIVE 124 G+ H M AKVIVE Sbjct: 230 GAAHYQMRAKVIVE 243 >ref|NP_386622.1| PROBABLE ALTERNATIVE CYTOCHROME C OXIDASE POLYPEPTIDE II TRANSMEMBRANE PROTEIN [Sinorhizobium meliloti] emb|CAC47095.1| PROBABLE ALTERNATIVE CYTOCHROME C OXIDASE POLYPEPTIDE II TRANSMEMBRANE PROTEIN [Sinorhizobium meliloti] Length = 314 Score = 55.1 bits (131), Expect = 5e-07, Method: Compositional matrix adjust. Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 3/74 (4%) Query: 54 EYHLKKGVPVNIVFKNESGNHGILVPELNLRLD---GKDSSQVIVPEEAGTFEMTCAIMC 110 E HL G PV ++ ++ H VPE ++D G + + P GTFE+ CA +C Sbjct: 170 ELHLPVGKPVKMLLRSVDVLHDFYVPEFRAKMDMVPGMITYFWLTPTRTGTFEILCAELC 229 Query: 111 GSGHSSMSAKVIVE 124 G GH M V+V+ Sbjct: 230 GVGHPQMRGTVVVD 243 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 0.312 0.130 0.366 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: 148,584,658 Number of extensions: 5726695 Number of successful extensions: 13884 Number of sequences better than 1.0e-05: 6 Number of HSP's gapped: 13993 Number of HSP's successfully gapped: 6 Length of query: 124 Length of database: 757,237,578 Length adjustment: 88 Effective length of query: 36 Effective length of database: 518,308,866 Effective search space: 18659119176 Effective search space used: 18659119176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 120 (50.8 bits)