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= 0225.0006.p (349 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_692358.1| cytochrome c oxidase subunit II [Oceanobacillus... 271 2e-71 sp|Q04441|COX2_BACPF Cytochrome c oxidase polypeptide II precurs... 247 3e-64 ref|ZP_00182646.1| hypothetical protein Exigu203501 [Exiguobacte... 243 4e-63 sp|Q03438|COX2_BACP3 Cytochrome c oxidase polypeptide II precurs... 234 2e-60 ref|NP_243481.1| cytochrome caa3 oxidase (subunit II) [Bacillus ... 233 4e-60 >ref|NP_692358.1| cytochrome c oxidase subunit II [Oceanobacillus iheyensis HTE831] dbj|BAC13393.1| cytochrome c oxidase subunit II (aa3 type) [Oceanobacillus iheyensis HTE831] Length = 350 Score = 271 bits (693), Expect = 2e-71, Method: Compositional matrix adjust. Identities = 146/349 (41%), Positives = 202/349 (57%), Gaps = 21/349 (6%) Query: 2 MKTWQAGKRLLPMTAALGLILAGCGREDLSVLRPQGPAAESSFDLMKLSITIMIVVLLIV 61 MK W ++ + +A+ L++AGCGRE+L+ L P+G A+ + DL+ L+ IMI V +IV Sbjct: 1 MKGWMGKSKVFFLISAMALLMAGCGRENLTALDPKGYGADRAMDLILLTTFIMIGVFIIV 60 Query: 62 FSIAAYVLVRFRRKPDQRE-MPEQVEGSFKLEXXXXXXXXXXXXXXXXXXXXXXFAAGND 120 +I LVRFR+K Q + +PEQVEG+ KLE F +D Sbjct: 61 MAIYVITLVRFRKKKGQEDYIPEQVEGNHKLEVIWTVIPIILVLVIAVPTVLGTFDLADD 120 Query: 121 HSSDKNAIKVKVTGHQYWWEFEYTDYGVTTAQDLVIPAGKDIAFELSTKDVLHSFWVPSL 180 ++D++ + ++VTG+QYWW F Y V T+QDL IP G+ + + + DV HSFW+PS+ Sbjct: 121 SNADEH-VNIEVTGNQYWWHFNYAGEEVVTSQDLYIPTGERVYLNMLSSDVTHSFWIPSI 179 Query: 181 SGKMDTNPDGTTNRFSFSAPNEGVYRGKCAELCGPSHGFMEFKVKSVSEAAFEKWVNSMK 240 SGKMD NP+ N A EGVY GKCAELCGPSH M+FKV +VS +E+WV M+ Sbjct: 180 SGKMDVNPE-NVNTMYIEAHEEGVYWGKCAELCGPSHSLMDFKVIAVSPEEYEQWVADMQ 238 Query: 241 A--PAVLPEDPALAEKFK----SQCLTCHAVGDMPDLSSAPNLTGIGSRESVAGILLNDD 294 + P +PED E + + C+ CHA+G P + PNLT G R ++AGIL Sbjct: 239 SVDPEEVPEDSVAQEGQELFEANNCMNCHAIGSSP-AAIGPNLTNFGDRSTIAGIL---- 293 Query: 295 TGVDGAPVLENLKTWLHDTAGVKPGNKMPDPKKDMGLSDEEIDGIAEFL 343 P E+L WL D VKPGNKM D LS++E + IAE+L Sbjct: 294 -----EPTKEHLVEWLTDPESVKPGNKMTDQYP--ALSEDEAESIAEYL 335 >sp|Q04441|COX2_BACPF Cytochrome c oxidase polypeptide II precursor (Cytochrome aa3 subunit 2) (Oxidase aa(3) subunit 2) pir||C45335 cytochrome-c oxidase (EC 1.9.3.1) chain II - Bacillus firmus gb|AAA22364.1| cytochrome oxidase subunit II Length = 342 Score = 247 bits (631), Expect = 3e-64, Method: Compositional matrix adjust. Identities = 137/351 (39%), Positives = 195/351 (55%), Gaps = 25/351 (7%) Query: 2 MKTWQAGKRLLPMTAALGLILAGC-GREDLSVLRPQGPAAESSFDLMKLSITIMIVVLLI 60 MK W+ R LP++ L L L GC G E+L+ L P+GP A+ +D M LSI +M +V ++ Sbjct: 1 MKLWKTASRFLPLSF-LTLFLTGCLGEENLTALDPKGPQAQWIYDNMILSIIVMALVSIV 59 Query: 61 VFSIAAYVLVRFRRKPDQREMPEQVEGSFKLEXXXXXXXXXXXXXXXXXXXXXXFAAGN- 119 VF+I +L ++RRKP E+P+QV G+ LE F + Sbjct: 60 VFAIFFIILAKYRRKPGDDEIPKQVHGNTALEITWTVIPIILLVILAVPTITGTFMFADK 119 Query: 120 --DHSSDKNAIKVKVTGHQYWWEFEYTDYGVTTAQDLVIPAGKDIAFELSTKDVLHSFWV 177 D N + +KVTGHQ+WW+F+Y + G T QD+ IP G+ + FEL +DVLHSFWV Sbjct: 120 DPDPEVGDNTVYIKVTGHQFWWQFDYENEGFTAGQDVYIPVGEKVIFELHAQDVLHSFWV 179 Query: 178 PSLSGKMDTNPDGTTNRFSFSAPNEGVYRGKCAELCGPSHGFMEFKVKSVSEAAFEKWVN 237 P+L GK+DT P G TN A GV++GKCAELCGPSH M+FK+ ++ ++ WV Sbjct: 180 PALGGKIDTVP-GITNHMWLEADEPGVFKGKCAELCGPSHALMDFKLIALERDEYDAWVE 238 Query: 238 SMKAPAVLPEDPALAEKFK-----SQCLTCHAVGDMPDLSSAPNLTGIGSRESVAGILLN 292 M A P + LA + + + C+ CHAVG ++ P T G RE +AG L N Sbjct: 239 GMSAEVEEPTE-TLANQGRQVFEENSCIGCHAVGGT-GTAAGPAFTNFGEREVIAGYLEN 296 Query: 293 DDTGVDGAPVLENLKTWLHDTAGVKPGNKMPDPKKDMGLSDEEIDGIAEFL 343 +D ENL+ W+ D +K GN MP DM S+E+++ + +L Sbjct: 297 ND---------ENLEAWIRDPQSLKQGNVMP-AYPDM--SEEDMEALIAYL 335 >ref|ZP_00182646.1| hypothetical protein Exigu203501 [Exiguobacterium sp. 255-15] Length = 335 Score = 243 bits (621), Expect = 4e-63, Method: Compositional matrix adjust. Identities = 137/345 (39%), Positives = 192/345 (55%), Gaps = 30/345 (8%) Query: 10 RLLPMTAALGLILAGCGREDLSVLRPQGPAAESSFDLMKLSITIMIVVLLIVFSIAAYVL 69 RLLP+ + L+L+GCG +LS L+P+G A+ +++KLS+ +M+ VL IV I YVL Sbjct: 4 RLLPI-GLMALLLSGCGIPELSALQPRGEGAQMQLEIIKLSLWVMLFVLAIVAVIYIYVL 62 Query: 70 VRFRRKPDQREMPEQVEGSFKLEXXXXXXXXXXXXXXXXXXXXXXFAAGNDHSSDKNAIK 129 ++FRRK +P+QVEG+ LE + + KN + Sbjct: 63 MKFRRKAGDNTVPKQVEGNHTLEIIWTVIPILLLVVLAVPTIKTTVELADAKEAKKNEV- 121 Query: 130 VKVTGHQYWWEFEYTDYGVTTAQDLVIPAGKDIAFELSTKDVLHSFWVPSLSGKMDTNPD 189 + VT + YWWEFEY D GV+T Q+LVIP GK +A L++KDV+HSFWVP+LSGK DTNP Sbjct: 122 INVTANLYWWEFEYPDKGVSTGQELVIPVGKRVAVNLTSKDVIHSFWVPALSGKTDTNP- 180 Query: 190 GTTNRFSFSAPNEGVYRGKCAELCGPSHGFMEFKVKSVSEAAFEKWVNSMKAPAVLPEDP 249 G N A G Y GKCAELCGPSH M+FKV ++ + ++ W+ MK+ A E Sbjct: 181 GLDNEMWLQAQEAGTYYGKCAELCGPSHALMDFKVIALEQDDYDAWLKDMKS-AKEAETK 239 Query: 250 ALAEK-----------FKSQCLTCHAVGDMPDLSSAPNLTGIGSRESVAGILLNDDTGVD 298 L K + CL+CH G + AP+LT G R+ +AG L +D Sbjct: 240 QLDAKNKKNWTTGEQVYAQNCLSCHGGGKV-----APSLTNFGDRQRIAGYLDHDK---- 290 Query: 299 GAPVLENLKTWLHDTAGVKPGNKMPDPKKDMGLSDEEIDGIAEFL 343 ENL+ W+ + K G KMP +D +SDEE+ +A++L Sbjct: 291 -----ENLEKWIRNPQKEKQGTKMPGFSED-KISDEELSELADYL 329 >sp|Q03438|COX2_BACP3 Cytochrome c oxidase polypeptide II precursor (Cytochrome aa3 subunit 2) (Oxidase aa(3) subunit 2) pir||JX0141 cytochrome-c oxidase (EC 1.9.3.1) chain II precursor - thermophilic bacterium PS-3 dbj|BAA03045.1| cytochrome c oxidase subunit 2 [thermophilic bacterium PS3] Length = 356 Score = 234 bits (598), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 146/356 (41%), Positives = 196/356 (55%), Gaps = 36/356 (10%) Query: 10 RLLPMTAALGLILAGCGREDLSVLRPQGPAAESSFDLMKLSITIMIVVLLIVFSIAAYVL 69 RL + + L+LAGCG+ LS L+P G A+ + LM LS +IM++V+++V I YV+ Sbjct: 9 RLFSLFGMMALLLAGCGKPFLSTLQPAGEVADMQYSLMLLSTSIMVLVIVVVAIIFVYVV 68 Query: 70 VRFRR-KPDQREMPEQVEGSFKLEXXXXXXXXXXXXXXXXXXXXXXFA-----AGNDHSS 123 +RFRR K ++ ++P+QVEGS KLE F A ND Sbjct: 69 IRFRRRKGEENKIPKQVEGSHKLEIIWTVIPIILLLILAVPTVLTTFKLADVKAMNDKKR 128 Query: 124 DKNAIKVKVTGHQYWWEFEYTDYGVTTAQDLVIPAGKDIAFELSTKDVLHSFWVPSLSGK 183 DKN + V V +QYWWEFEY DYG+ T+QDLV+P + + F L DV HSFW+P++ GK Sbjct: 129 DKNTVVVNVRANQYWWEFEYPDYGIITSQDLVVPTNEKVYFNLIASDVKHSFWIPAVGGK 188 Query: 184 MDTNPDGTTNRFSFSAPNE------GVYRGKCAELCGPSHGFMEFKVKSVSEAAFEKWVN 237 MDTN D N+F + GV+ GKCAELCGPSH M+FKV+ + F+ WV Sbjct: 189 MDTNTD-NKNQFWLVFDQKATDKAGGVFYGKCAELCGPSHALMDFKVRPLPRDQFDAWVK 247 Query: 238 SM---KAPAVLPEDPALAEK---FKSQCLTCHAVGDM----PDLSSAPNLTGIGSRESVA 287 M K P V DP E F C+ CHAV + +APNL G RE +A Sbjct: 248 KMQNAKKPVV--TDPVAKEGEAIFNKSCIGCHAVTPLDKRPAQRRTAPNLADFGDRERIA 305 Query: 288 GILLNDDTGVDGAPVLENLKTWLHDTAGVKPGNKMPDPKKDMGLSDEEIDGIAEFL 343 GIL +++ ENLK WL D VKPGNKM L++E+ID + ++L Sbjct: 306 GILEHNE---------ENLKKWLRDPNSVKPGNKMAGTYGH--LTEEQIDALTKYL 350 >ref|NP_243481.1| cytochrome caa3 oxidase (subunit II) [Bacillus halodurans] pir||G83976 cytochrome caa3 oxidase (subunit II) ctaC [imported] - Bacillus halodurans (strain C-125) dbj|BAB06334.1| cytochrome caa3 oxidase (subunit II) [Bacillus halodurans] Length = 348 Score = 233 bits (595), Expect = 4e-60, Method: Compositional matrix adjust. Identities = 135/354 (38%), Positives = 190/354 (53%), Gaps = 28/354 (7%) Query: 2 MKTWQAGKRLLPMTAALGLILAGC-GREDLSVLRPQGPAAESSFDLMKLSITIMIVVLLI 60 MK W+ R LP++ + L LAGC G +L+ L PQGP AE FD M LS+ +M V ++ Sbjct: 1 MKLWKTALRFLPLSLVV-LFLAGCMGETNLTALDPQGPQAEWLFDNMLLSLYVMAFVSIV 59 Query: 61 VFSIAAYVLVRFRRKPDQREMPEQVEGSFKLEXXXXXXXXXXXXXXXXXXXXXXFAAG-- 118 VF+I +L RFRRKP E+P+QV G+ LE F Sbjct: 60 VFAIFFIILARFRRKPGDDELPKQVHGNTALEITWTVIPIILLTILAVPTITGTFMLADV 119 Query: 119 -NDHSSDKNAIKVKVTGHQYWWEFEYTDYGVTTAQDLVIPAGKDIAFELSTKDVLHSFWV 177 D ++ + + VTGHQ+WW+F+Y D G T D+ IP G+ + FEL DV+HSFWV Sbjct: 120 EPDPEVEEETVTITVTGHQFWWQFDYED-GFTAGNDVYIPVGEKVIFELHASDVMHSFWV 178 Query: 178 PSLSGKMDTNPDGTTNRFSFSAPNEGVYRGKCAELCGPSHGFMEFKVKSVSEAAFEKWVN 237 P+L GK+DT P G TN A GVY+GKCAELCG SH M+FKV ++ ++ WV Sbjct: 179 PALGGKVDTIP-GITNHLWLEASEPGVYKGKCAELCGASHALMDFKVIALERDDYDAWVE 237 Query: 238 SMKAPAVLPE-DPALAEK----FKSQ---CLTCHAVGDMPDLSSAPNLTGIGSRESVAGI 289 M P+ D L ++ F + C+ CHAVG ++ P LT G R ++A Sbjct: 238 GMMEADAEPDTDDILVQQGYELFGADGLGCIGCHAVGG-SGTAAGPTLTNFGDRTTIANF 296 Query: 290 LLNDDTGVDGAPVLENLKTWLHDTAGVKPGNKMPDPKKDMGLSDEEIDGIAEFL 343 L N+D ENL+ W+ + +K GN MP+ ++DEE++ + +L Sbjct: 297 LENND---------ENLEEWIRNPKALKQGNDMPEFPD---VTDEEMEALIAYL 338 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 0.317 0.134 0.405 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: 509,568,129 Number of extensions: 20207560 Number of successful extensions: 59455 Number of sequences better than 1.0e-05: 4108 Number of HSP's gapped: 52857 Number of HSP's successfully gapped: 4108 Length of query: 349 Length of database: 757,237,578 Length adjustment: 126 Effective length of query: 223 Effective length of database: 415,135,104 Effective search space: 92575128192 Effective search space used: 92575128192 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: 126 (53.1 bits)