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= 0225.0008.p (208 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_243479.1| cytochrome caa3 oxidase (subunit III) [Bacillus... 202 3e-51 sp|Q03439|COX3_BACP3 CYTOCHROME C OXIDASE POLYPEPTIDE III (CYTOC... 193 2e-48 dbj|BAA11113.1| cytochrome c oxidase subunit III [Geobacillus st... 192 3e-48 sp|Q04442|COX3_BACPF Cytochrome c oxidase polypeptide III (Cytoc... 190 2e-47 ref|NP_389374.1| cytochrome caa3 oxidase (subunit III) [Bacillus... 182 4e-45 >ref|NP_243479.1| cytochrome caa3 oxidase (subunit III) [Bacillus halodurans] pir||E83976 cytochrome caa3 oxidase (subunit III) ctaE [imported] - Bacillus halodurans (strain C-125) dbj|BAB06332.1| cytochrome caa3 oxidase (subunit III) [Bacillus halodurans] Length = 206 Score = 202 bits (514), Expect = 3e-51, Method: Compositional matrix adjust. Identities = 99/205 (48%), Positives = 129/205 (62%), Gaps = 1/205 (0%) Query: 4 AHAESAAGNLPHEPEKATLEGRNKVLAFWLFLGGESVXXXXXXXXXXXXRNQTNEGPSAN 63 H +++ G LP PE+ATLEG+NK L FW FLGGE++ R+ T +GP Sbjct: 3 GHVDTSKG-LPSHPERATLEGKNKFLGFWFFLGGETILFATFFGTYLGLRSGTADGPLPQ 61 Query: 64 DLFHLPXXXXXXXXXXXXXXXXXXXIQAMHRGKVAVLRNWLLVTVFLGLCFLVLEIYEFS 123 D+F LP + AM + K ++ W+ +TV LGL FL EIYEF Sbjct: 62 DIFALPLVFIMTMLLLTSSLTSVIAMAAMKKNKFGAMKLWMWITVLLGLGFLGFEIYEFY 121 Query: 124 VYVRHEEFGMTTSAFSSAFYTLVGFHGAHVAFGILWISVLIGQLARKGLTVVTAPKIYVS 183 YV H E G +TSAF+S+FY+LVG HGAHVAFG+ WI L+ + R G+T+ APK YV+ Sbjct: 122 EYVHHYELGFSTSAFASSFYSLVGLHGAHVAFGLSWIITLLIRYNRSGITLTNAPKFYVA 181 Query: 184 AMYWHFIDVVWVFIFTVVYLLGKVG 208 ++YWHFIDVVWVFIFTVVYL+G +G Sbjct: 182 SLYWHFIDVVWVFIFTVVYLMGVLG 206 >sp|Q03439|COX3_BACP3 CYTOCHROME C OXIDASE POLYPEPTIDE III (CYTOCHROME AA3 SUBUNIT 3) (OXIDASE AA(3) SUBUNIT 3) pir||JX0142 cytochrome-c oxidase (EC 1.9.3.1) chain III - thermophilic bacterium PS-3 dbj|BAA03047.1| cytochtome c oxidase subunit 3 [thermophilic bacterium PS3] Length = 207 Score = 193 bits (491), Expect = 2e-48, Method: Compositional matrix adjust. Identities = 105/207 (50%), Positives = 129/207 (62%), Gaps = 4/207 (1%) Query: 5 HAES--AAGNLPHEPEK-ATLEGRNKVLAFWLFLGGESVXXXXXXXXXXXXRNQTNEGPS 61 HAE A P PE+ ATLEG+NK L FWLFLGGE+V +++TN GPS Sbjct: 2 HAEEKLTAETFPAAPERNATLEGKNKFLGFWLFLGGETVLFASLFATYLALKDKTNGGPS 61 Query: 62 ANDLFHLPXXXXXXXXXXXXXXXXXXXIQAMHRGKVAVLRNWLLVTVFLGLCFLVLEIYE 121 A +LF +P I M ++ W +TV LG FL LEIYE Sbjct: 62 AEELFQMPVVFMATMLLLTSSLTSVYAIYHMKNFDFKKMQLWFGITVLLGAGFLGLEIYE 121 Query: 122 FSVYVRHEEFGMTTSAFSSAFYTLVGFHGAHVAFGILWISVLIGQLARKGLTVVTAPKIY 181 F+ YV HE TTSAF+SAFYTLVG HG+HVAFG+LWI L+ + A++GL + APK Y Sbjct: 122 FNEYV-HEGHKFTTSAFASAFYTLVGTHGSHVAFGLLWILTLMIRNAKRGLNLYNAPKFY 180 Query: 182 VSAMYWHFIDVVWVFIFTVVYLLGKVG 208 V+++YWHFIDVVWVFIFTVVYL+G VG Sbjct: 181 VASLYWHFIDVVWVFIFTVVYLMGMVG 207 >dbj|BAA11113.1| cytochrome c oxidase subunit III [Geobacillus stearothermophilus] Length = 206 Score = 192 bits (489), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 100/197 (50%), Positives = 122/197 (61%), Gaps = 1/197 (0%) Query: 12 NLPHEPEKATLEGRNKVLAFWLFLGGESVXXXXXXXXXXXXRNQTNEGPSANDLFHLPXX 71 P PE+ATLEG+NK L FWLFLGGE+V +++TN GPS +LF +P Sbjct: 11 TFPAAPERATLEGKNKFLGFWLFLGGETVLFASLFATYLALKDKTNGGPSGEELFQMPIV 70 Query: 72 XXXXXXXXXXXXXXXXXIQAMHRGKVAVLRNWLLVTVFLGLCFLVLEIYEFSVYVRHEEF 131 I M ++ W +TV LG FL LEIYEF YV HE Sbjct: 71 FMATMLLLTSSLTSVYAIYHMKNFDFQKMQLWFGITVLLGAGFLALEIYEFYEYV-HEGH 129 Query: 132 GMTTSAFSSAFYTLVGFHGAHVAFGILWISVLIGQLARKGLTVVTAPKIYVSAMYWHFID 191 T+SAF SAFYTLVG HGAHVAFG+LWI L+ + A++GL + APK YV+++YWHFID Sbjct: 130 KFTSSAFGSAFYTLVGTHGAHVAFGLLWILTLMIRNAKRGLNLYNAPKFYVASLYWHFID 189 Query: 192 VVWVFIFTVVYLLGKVG 208 VVWVFIFTVVYL+G VG Sbjct: 190 VVWVFIFTVVYLMGMVG 206 >sp|Q04442|COX3_BACPF Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3) pir||E45335 cytochrome-c oxidase (EC 1.9.3.1) chain III - Bacillus firmus gb|AAA22366.1| cytochrome oxidase subunit III Length = 206 Score = 190 bits (482), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 97/205 (47%), Positives = 123/205 (60%) Query: 4 AHAESAAGNLPHEPEKATLEGRNKVLAFWLFLGGESVXXXXXXXXXXXXRNQTNEGPSAN 63 A A + LP PE+ATLEG+NK L FW FLGGE++ R T +GP++ Sbjct: 2 AGAVDTSKGLPSHPERATLEGKNKFLGFWFFLGGETILFATFFGTFLGLRGGTADGPTSA 61 Query: 64 DLFHLPXXXXXXXXXXXXXXXXXXXIQAMHRGKVAVLRNWLLVTVFLGLCFLVLEIYEFS 123 DL L + AM + + W+ +TV LGL FL EIYEF Sbjct: 62 DLVALDLVFIMTMLLLTSSLTSVLAMFAMKKNNFKAMMIWMWITVVLGLAFLGFEIYEFH 121 Query: 124 VYVRHEEFGMTTSAFSSAFYTLVGFHGAHVAFGILWISVLIGQLARKGLTVVTAPKIYVS 183 YV +FG +TSAF+SAFY+LVG HGAHVAFG+ WI VL+ + + G+T+ APK YV+ Sbjct: 122 HYVVDYQFGFSTSAFASAFYSLVGLHGAHVAFGLSWIIVLLIRYRKSGITLTNAPKFYVA 181 Query: 184 AMYWHFIDVVWVFIFTVVYLLGKVG 208 +YWHFIDVVWVFIFTVVYL+G G Sbjct: 182 GLYWHFIDVVWVFIFTVVYLMGVGG 206 >ref|NP_389374.1| cytochrome caa3 oxidase (subunit III) [Bacillus subtilis] sp|P24012|COX3_BACSU Cytochrome c oxidase polypeptide III (Cytochrome aa3 subunit 3) (Caa-3605 subunit 3) (Oxidase aa(3) subunit 3) pir||F69609 cytochrome-c oxidase (EC 1.9.3.1) chain III - Bacillus subtilis emb|CAB11344.1| cytochrome c oxidase subunit III, aa3 type [Bacillus subtilis] emb|CAB13364.1| cytochrome caa3 oxidase (subunit III) [Bacillus subtilis subsp. subtilis str. 168] Length = 207 Score = 182 bits (463), Expect = 4e-45, Method: Compositional matrix adjust. Identities = 94/199 (47%), Positives = 117/199 (58%) Query: 10 AGNLPHEPEKATLEGRNKVLAFWLFLGGESVXXXXXXXXXXXXRNQTNEGPSANDLFHLP 69 A P PEK TLEG+NK L FWLFLGGE+V RN P ++F + Sbjct: 9 AETFPASPEKVTLEGKNKFLGFWLFLGGETVLFASLFATFLALRNSNAGDPPTTEMFDVT 68 Query: 70 XXXXXXXXXXXXXXXXXXXIQAMHRGKVAVLRNWLLVTVFLGLCFLVLEIYEFSVYVRHE 129 + M ++ WL +T+ LG FL LEIYEF Y Sbjct: 69 LVFIATMLLLTSSLTSVYAMYHMKNFSFGKMQLWLGITILLGAGFLGLEIYEFKHYTHEF 128 Query: 130 EFGMTTSAFSSAFYTLVGFHGAHVAFGILWISVLIGQLARKGLTVVTAPKIYVSAMYWHF 189 F +T+SA SAFYTLVG HGAHVAFG++WIS L+ + A++GL + TAPK YV+++YWHF Sbjct: 129 GFTITSSALGSAFYTLVGTHGAHVAFGLMWISTLMIRNAKRGLNLYTAPKFYVASLYWHF 188 Query: 190 IDVVWVFIFTVVYLLGKVG 208 IDVVWVFIFTVVYL+G VG Sbjct: 189 IDVVWVFIFTVVYLMGMVG 207 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 0.327 0.140 0.442 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: 257,189,266 Number of extensions: 8194469 Number of successful extensions: 25356 Number of sequences better than 1.0e-05: 1496 Number of HSP's gapped: 23934 Number of HSP's successfully gapped: 1496 Length of query: 208 Length of database: 757,237,578 Length adjustment: 120 Effective length of query: 88 Effective length of database: 431,425,698 Effective search space: 37965461424 Effective search space used: 37965461424 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: 123 (52.0 bits)