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= 0002.0534.p (744 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... 554 e-158 gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptid... 382 e-107 gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase ... 260 3e-70 gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptid... 225 9e-60 gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptid... 78 3e-15 >gi|300313446|ref|YP_003777538.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 539 Score = 554 bits (1427), Expect = e-158, Method: Compositional matrix adjust. Identities = 288/291 (98%), Positives = 289/291 (99%) Query: 32 WRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG 91 WRRW+FATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG Sbjct: 32 WRRWLFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQFFRPEFFNQLTTMHG 91 Query: 92 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLASSFLVPGGAT 151 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLA SFLVPGGAT Sbjct: 92 LVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLAGSFLVPGGAT 151 Query: 152 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC 211 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC Sbjct: 152 AAGWTLYAPLSTQMGPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLMKMPMFC 211 Query: 212 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYI 271 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYI Sbjct: 212 WTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFGHPEVYI 271 Query: 272 MILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVWAHHMFTTGM 322 MILPAFGIVSQIIPAFARK LFGYASMVYATASIAILSFIVWAHHMFTTGM Sbjct: 272 MILPAFGIVSQIIPAFARKPLFGYASMVYATASIAILSFIVWAHHMFTTGM 322 Score = 412 bits (1058), Expect = e-116, Method: Compositional matrix adjust. Identities = 198/209 (94%), Positives = 203/209 (97%) Query: 536 LNGTMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDI 595 + TMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDI Sbjct: 331 MYATMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDI 390 Query: 596 QMQDTYYVVAHFHYVLVAGSLFALFAGFYYWGPKWTGFMYNEWRGKFHFWASLITFNVTF 655 QMQDTYYVVAHFHYVLVAGSLFALFAG+YYWGPKWTGFMYNEWRGKFHFWASLITFN+TF Sbjct: 391 QMQDTYYVVAHFHYVLVAGSLFALFAGYYYWGPKWTGFMYNEWRGKFHFWASLITFNITF 450 Query: 656 FPMHFLGLAGMPRRYADYPAQFTDFNMVASIGALGFGLSQVYFLFFVVIPSIKGGVKAEA 715 FPMHFLGLAGMPRRYADYPAQFTDFNM+ASIGA GFGLSQVYFLFFVVIPSIKGG +AEA Sbjct: 451 FPMHFLGLAGMPRRYADYPAQFTDFNMIASIGAFGFGLSQVYFLFFVVIPSIKGGKQAEA 510 Query: 716 KPWEGAEGLEWTVPSPAPFHTFETPPTVK 744 KPWEGAEGLEWTVPSPAPFHTFE PP VK Sbjct: 511 KPWEGAEGLEWTVPSPAPFHTFEEPPVVK 539 >gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 386 Score = 382 bits (980), Expect = e-107, Method: Compositional matrix adjust. Identities = 196/227 (86%), Positives = 205/227 (90%), Gaps = 1/227 (0%) Query: 320 TGMQWKWGYDYLKGEGEGISFLSNLATPREQITDASLKKNDNYLLEVDNPVVVPVNKKVR 379 TGMQWKWGYDYLKGEGEGISFLSNLATPREQ+TD SLKKNDNYL+EVDNPVVVPVNKKVR Sbjct: 136 TGMQWKWGYDYLKGEGEGISFLSNLATPREQVTDPSLKKNDNYLIEVDNPVVVPVNKKVR 195 Query: 380 IITTANDVIHSWTIPAFGVKQDAIPGFVRDTWFKAEKIGTYRGQCVELCGKDHAFMPIVV 439 I+TTANDVIHSWTIPAFGVKQDAIPGFVRDTWF+AEKIGTYRGQCVELCGKDHAFMPIVV Sbjct: 196 IVTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQCVELCGKDHAFMPIVV 255 Query: 440 NVVSDADYKTWVDGKKKEMAAKADDPTKVWTIDELKQRGEKVYTSNCVVCHQANGKGVPG 499 NVVS+ DYK WVDGKKKEMAAKADDP K WT+DELKQRGEKVY +NCV CHQANGKGVPG Sbjct: 256 NVVSEDDYKQWVDGKKKEMAAKADDPNKTWTVDELKQRGEKVYAANCVTCHQANGKGVPG 315 Query: 500 AFPALDGDPVVNGPKAAQIAVVLNGKNAXAAQIAVVLNGTMLIAVPT 546 AFPALDG PVVNGPK QI +VLNGKNA VLN T + AV T Sbjct: 316 AFPALDGSPVVNGPKDGQIHLVLNGKNAMPPWKG-VLNDTEIAAVIT 361 >gi|300311778|ref|YP_003775870.1| cytochrome o ubiquinol oxidase subunit I protein [Herbaspirillum seropedicae SmR1] Length = 667 Score = 260 bits (664), Expect = 3e-70, Method: Compositional matrix adjust. Identities = 136/296 (45%), Positives = 189/296 (63%), Gaps = 7/296 (2%) Query: 32 WRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAE---LFQPGLQFFRPEFFNQLTT 88 WR W + +HK IG +Y+ + MLL G A+++RA+ F F P ++Q+ T Sbjct: 55 WRDWFTSIDHKRIGIMYIVLAIVMLLRGFADAVMMRAQQAIAFGDNAGFLPPHHYDQVFT 114 Query: 89 MHGLVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPAALLLASSFLVPG 148 HG++M+F MP G N+++PLQIGA D+AF +NNFSFW+ ALL+ +S V G Sbjct: 115 AHGVIMIFFVAMPLVTGLMNYVVPLQIGARDVAFPFLNNFSFWMTTFGALLVMASLFV-G 173 Query: 149 GATAAGWTLYAPLSTQM---GPGMDMGIFAMHIMGASSIMGSINIIVTILNMRAPGMTLM 205 GW Y PLS + G+D I+A+ + G +++ IN++VTI+ MRAPGM +M Sbjct: 174 EFARTGWLAYPPLSGILYSPDVGVDYYIWALQVAGVGTLLSGINLVVTIVKMRAPGMNMM 233 Query: 206 KMPMFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGDPVMYQHIFWFFG 265 KMP+F WT L T L++A PVL + M DR FGT+FF GG+ +MY ++ W +G Sbjct: 234 KMPVFTWTSLCTNVLIVAAFPVLTAVLAMLSLDRVFGTNFFTNDMGGNAMMYVNLIWIWG 293 Query: 266 HPEVYIMILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVWAHHMFTTG 321 HPEVYI++LPAFGI S+I+ F+ K+LFGY SMVYAT I ILS++VW HH FT G Sbjct: 294 HPEVYILVLPAFGIFSEIVSTFSGKRLFGYTSMVYATVVITILSYLVWLHHFFTMG 349 Score = 157 bits (397), Expect = 3e-39, Method: Compositional matrix adjust. Identities = 87/209 (41%), Positives = 125/209 (59%), Gaps = 6/209 (2%) Query: 539 TMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQMQ 598 TM+I++PTG KIFNW+ TM+RG + FE PML+++GF+ F +GG TG++LAV P D + Sbjct: 362 TMIISIPTGAKIFNWLFTMYRGRIRFEVPMLWTIGFMVTFVIGGMTGVLLAVPPADFVLH 421 Query: 599 DTYYVVAHFHYVLVAGSLFALFAGFYYWGPKWTGFMYNEWRGKFHFWASLITFNVTFFPM 658 ++ +++AHFH V++ G +F +FAG +W PK GF NE+ GK FW L+ F + F P+ Sbjct: 422 NSLFLIAHFHNVIIGGVVFGMFAGINFWFPKAFGFKLNEFWGKCSFWFWLVGFYLAFMPL 481 Query: 659 HFLGLAGMPRRYA--DYPAQFTDFNMVASIGA--LGFGLSQVYFLFFVVIPSIKGGVKAE 714 + LGL G+ RR + D P+ F +VA+IGA + G+ V I K Sbjct: 482 YVLGLMGVTRRMSHFDDPSLQIWF-VVAAIGAGLIALGIGSFIIQIAVSIRDRKKLADVT 540 Query: 715 AKPWEGAEGLEWTVPSPAPFHTFETPPTV 743 PW G LEW+ SP P + F P V Sbjct: 541 GDPWNG-RTLEWSTSSPPPAYNFAFTPVV 568 >gi|300311626|ref|YP_003775718.1| cytochrome c oxidase polypeptide I transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 633 Score = 225 bits (574), Expect = 9e-60, Method: Compositional matrix adjust. Identities = 119/309 (38%), Positives = 179/309 (57%), Gaps = 4/309 (1%) Query: 17 DHGAHSHDDHDHPHGWRRWIFATNHKDIGTLYLWFSFTMLLSGGVLALLIRAELFQPGLQ 76 + P G W+ A NHK I ++ +F L GG+LAL +R +L +P + Sbjct: 8 EEARRLEQTWSDPPGLWGWLCAVNHKAIARRFMVTTFVFFLLGGMLALAMRLQLARPDAE 67 Query: 77 FFRPEFFNQLTTMHGLVMVFGAIMPAFVGFANWMIPLQIGASDMAFARMNNFSFWLLPPA 136 +NQL TMHG M+F +P A +++PL IGA +AF R+N F++W+ Sbjct: 68 LIGARLYNQLFTMHGTTMMFLFAVPVMQAVAAYLLPLMIGARSVAFPRLNAFAYWIFLFG 127 Query: 137 ALLLASSFLVPGGATAAGWTLYAPLSTQ---MGPGMDMGIFAMHIMGASSIMGSINIIVT 193 LLL +FL G GW Y PL+ G G+D+ + S+++ +I II T Sbjct: 128 GLLLYGAFLA-GSGPDVGWFAYVPLALNPYASGKGVDIWAQMITFTELSALIEAIVIITT 186 Query: 194 ILNMRAPGMTLMKMPMFCWTWLITAYLLIAVMPVLAGAITMTLTDRHFGTSFFNAAGGGD 253 ++ +RAPGM+L +MP+F W L+T+ +++ MP + A T +TDR T F++ GGD Sbjct: 187 VMKLRAPGMSLRRMPLFAWAMLVTSVMVLFAMPAVMLASTGLITDRLVNTQFYSHQNGGD 246 Query: 254 PVMYQHIFWFFGHPEVYIMILPAFGIVSQIIPAFARKQLFGYASMVYATASIAILSFIVW 313 +++QH+FWFFGHPEVY++ LP G++S IIP FAR+ + GY +MV A + A L+F +W Sbjct: 247 ALLWQHLFWFFGHPEVYLIFLPPLGMISTIIPTFARRSMVGYPAMVLALIATAFLAFGLW 306 Query: 314 AHHMFTTGM 322 HHMF T + Sbjct: 307 VHHMFATTL 315 Score = 202 bits (515), Expect = 6e-53, Method: Compositional matrix adjust. Identities = 106/208 (50%), Positives = 138/208 (66%), Gaps = 4/208 (1%) Query: 538 GTMLIAVPTGVKIFNWIATMWRGSMTFETPMLFSVGFIFVFTMGGFTGLILAVTPIDIQM 597 ++LIA+PT ++IF WI+T+W G F+TP+LF + F F+ MGG TGL+LA P+D+Q+ Sbjct: 326 ASLLIALPTALQIFCWISTIWLGRPVFKTPLLFVLAFFFILVMGGLTGLMLASVPLDLQL 385 Query: 598 QDTYYVVAHFHYVLVAGSLFALFAGFYYWGPKWTGFMYNEWRGKFHFWASLITFNVTFFP 657 DTY+VVAH HYVL+ G++F LF GFYYW PK+TG M +E G+++FW + FNV FFP Sbjct: 386 HDTYFVVAHLHYVLLGGAIFPLFGGFYYWFPKFTGRMLDERLGRWNFWLFFVGFNVCFFP 445 Query: 658 MHFLGLAGMPRRYADYPAQ--FTDFNMVASIGALGFGLSQVYFLFFVVIPSIKGGVKAEA 715 MH LGL GM RR Y AQ + N+ A+IGA GLS + FL VV S+ G A Sbjct: 446 MHVLGLQGMTRRVYTYAAQMGWEGLNLTATIGAFLIGLSVLLFLLNVV-HSLWRGAAAGD 504 Query: 716 KPWEGAEGLEWTVPSPAPFHTFETPPTV 743 PW GA LEW++PSP P F P V Sbjct: 505 NPW-GAATLEWSLPSPPPAGNFLEVPVV 531 >gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 77.8 bits (190), Expect = 3e-15, Method: Compositional matrix adjust. Identities = 37/87 (42%), Positives = 49/87 (56%) Query: 368 NPVVVPVNKKVRIITTANDVIHSWTIPAFGVKQDAIPGFVRDTWFKAEKIGTYRGQCVEL 427 N + +PV + V I + DVIHS +P K D IPG +A++ GTYRGQC E Sbjct: 155 NELHLPVGRAVIIDLDSEDVIHSLWLPNLHGKLDLIPGKPAQLRLRADQAGTYRGQCAEF 214 Query: 428 CGKDHAFMPIVVNVVSDADYKTWVDGK 454 CG +HA M ++V S ADY W G+ Sbjct: 215 CGLEHARMALLVTAESPADYARWASGQ 241 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 0.326 0.140 0.459 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: 2,343,501 Number of extensions: 98957 Number of successful extensions: 371 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 364 Number of HSP's successfully gapped: 8 Length of query: 744 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 652 Effective length of database: 1,184,250 Effective search space: 772131000 Effective search space used: 772131000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 134 (56.2 bits)