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= 0025.0079.p (332 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptid... 498 e-142 gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ... 225 4e-60 gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid... 181 8e-47 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 498 bits (1282), Expect = e-142, Method: Compositional matrix adjust. Identities = 268/290 (92%), Positives = 269/290 (92%), Gaps = 19/290 (6%) Query: 35 WRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG 94 WRRW+FATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG Sbjct: 32 WRRWLFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG 91 Query: 95 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGAT 154 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGAT Sbjct: 92 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGAT 151 Query: 155 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC 214 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC Sbjct: 152 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC 211 Query: 215 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAA-------------------XYI 255 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAA YI Sbjct: 212 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYI 271 Query: 256 MILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVWAHHMFTTG 305 MILPAFGIVSQIIPAFARK LFGYASMVYATASIAILSFIVWAHHMFTTG Sbjct: 272 MILPAFGIVSQIIPAFARKPLFGYASMVYATASIAILSFIVWAHHMFTTG 321 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 225 bits (574), Expect = 4e-60, Method: Compositional matrix adjust. Identities = 126/296 (42%), Positives = 173/296 (58%), Gaps = 26/296 (8%) Query: 35 WRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAE---LFQPGLQFFRPEFFNQLTT 91 WR W + +HK IG +Y+ + MLL G A+++RA+ F F P ++Q+ T Sbjct: 55 WRDWFTSIDHKRIGIMYIVLAIVMLLRGFADAVMMRAQQAIAFGDNAGFLPPHHYDQVFT 114 Query: 92 MHGLVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPG 151 HG++M+F MP G N+++PLQIGA D+AF +NNFSFW+ ALL+ S V G Sbjct: 115 AHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGALLVMASLFV-G 173 Query: 152 GATAAGWTLYAPLSTQM---GPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLM 208 GW Y PLS + G+D I+A+ + G +++ IN++VTI+ MRAPGM +M Sbjct: 174 EFARTGWLAYPPLSGILYSPDVGVDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMM 233 Query: 209 KMPMFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFN------------------ 250 KMP+F WT L T L++A PVL + M DR FGT+FF Sbjct: 234 KMPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLIWIWG 293 Query: 251 -AAXYIMILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVWAHHMFTTG 305 YI++LPAFGI S+I+ F+ K+LFGY SMVYAT I ILS++VW HH FT G Sbjct: 294 HPEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMG 349 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 181 bits (459), Expect = 8e-47, Method: Compositional matrix adjust. Identities = 108/309 (34%), Positives = 165/309 (53%), Gaps = 24/309 (7%) Query: 25 DHGHHDHPHGWRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPE 84 + D P W W+ A NHK I ++ +F L GG+LAL +R +L +P + Sbjct: 14 EQTWSDPPGLWG-WLCAVNHKAIARRFMVTTFVFFLLGGMLALAMRLQLARPDAELIGAR 72 Query: 85 FFNQLTTMHGLVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLA 144 +NQL TMHG M+F +P A +++PL IGA +AF R+N F++W+ LLL Sbjct: 73 LYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFLFGGLLLY 132 Query: 145 GSFLVPGGATAAGWTLYAPLSTQ---MGPGMDMGIFAMHIMGASSIMGSINIIVTILNMR 201 G+FL G GW Y PL+ G G+D+ + S+++ +I II T++ +R Sbjct: 133 GAFLA-GSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIITTVMKLR 191 Query: 202 APGMTLMKMPMFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFN----------- 250 APGM+L +MP+F W L+T+ +++ MP + A T +TDR T F++ Sbjct: 192 APGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYSHQNGGDALLWQ 251 Query: 251 --------AAXYIMILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVWAHHMF 302 Y++ LP G++S IIP FAR+ + GY +MV A + A L+F +W HHMF Sbjct: 252 HLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGLWVHHMF 311 Query: 303 TTGXHDAHR 311 T +A + Sbjct: 312 ATTLPEAGK 320 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.331 0.140 0.464 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 871,292 Number of extensions: 33071 Number of successful extensions: 153 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 146 Number of HSP's successfully gapped: 3 Length of query: 332 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 246 Effective length of database: 1,212,660 Effective search space: 298314360 Effective search space used: 298314360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 131 (55.1 bits)