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= 0044.0012.p (467 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_cydA [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 603 e-172 VC1844 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 320 4e-87 VCA0872 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 307 2e-83 STM0740 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 296 5e-80 cydA [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 289 6e-78 >BS_cydA [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 Length = 468 Score = 603 bits (1556), Expect = e-172, Method: Compositional matrix adjust. Identities = 288/469 (61%), Positives = 366/469 (78%), Gaps = 4/469 (0%) Query: 1 MDTVMLSRIQFASTTIFHYFFVPVSIGLALLIAIMETMYVRKGNDEYKRMAQFWGKLFLI 60 M ++L+RIQFASTT+FH+ FVP+SIGL ++A+MET+Y+ K N+ Y +MA+FWG LFLI Sbjct: 1 MSELVLARIQFASTTLFHFLFVPMSIGLVFMVALMETLYLVKKNELYLKMAKFWGHLFLI 60 Query: 61 NFAVGVVTGILQEFQFGMNWSDYSRFVGDVFGXXXXXXXXXXXXXXSTFIGIWIFGWDKV 120 NFAVGVVTGILQEFQFG+NWSDYSRFVGDVFG S FIG+WIFGWD++ Sbjct: 61 NFAVGVVTGILQEFQFGLNWSDYSRFVGDVFGAPLAIEALLAFFMESIFIGLWIFGWDRL 120 Query: 121 SKRVHLLSIWLVALGTMLSAFWILLANSFMQHPVGFAVNNGRAEMNDIWALVTNGQLLVE 180 K++H L IWLV+ GT++S+FWIL ANSFMQ PVGF + NGRAEMND AL+TN QL VE Sbjct: 121 PKKIHALCIWLVSFGTIMSSFWILTANSFMQEPVGFTIKNGRAEMNDFGALITNPQLWVE 180 Query: 181 FPHTVLAAYATGAFLVTGISAYKLLKKQDVSFFRKSFEIAAIVGIISSFGVAIAGHAQAQ 240 FPH + A ATGAF + G+SA+KLLKK++V FF++SF++A IVG+ + GV ++GH QA+ Sbjct: 181 FPHVIFGALATGAFFIAGVSAFKLLKKKEVPFFKQSFKLAMIVGLCAGLGVGLSGHMQAE 240 Query: 241 YLVETQPMKMAASEGLWDDSGDPAAWTVIANIDPDNKISTHEVKIPYMLSFLSYSKFSGS 300 +L+E+QPMKMAASEGLW+DSGDPAAWT A ID N+ S++E+K+PY LS+L+Y KFSGS Sbjct: 241 HLMESQPMKMAASEGLWEDSGDPAAWTAFATIDTKNEKSSNEIKVPYALSYLAYQKFSGS 300 Query: 301 VKGMNTLQAEYEQAYGPGDYIPPVRTTFWSFRIMVAAGSLMILLGVYAIYLMWRKKMERP 360 VKGM TLQAEYE+ YG GDYIPPV+TTFWSFRIMV AG +MIL + ++L RKK+E Sbjct: 301 VKGMKTLQAEYEKIYGKGDYIPPVKTTFWSFRIMVGAGVVMILAALGGLWLNRRKKLEN- 359 Query: 361 NTWFMRFMFWGLLLPPIANTSGWIMTEMGRQPWTVFGLMTTEDSVSPNITSGQVLFSVIS 420 + W++R M + P +AN++GWIMTE+GRQPWTV GLMTT SVSPN+T+G +LFS+I+ Sbjct: 360 SKWYLRIMIALISFPFLANSAGWIMTEIGRQPWTVMGLMTTAQSVSPNVTAGSLLFSIIA 419 Query: 421 FTAIYAILGLVLVGLFIKVIKKGPYAMDNDHG--ESHDPYNKEGSHAFS 467 F +Y ILG +LV LFI+ IKKG DN H S DP+++E H S Sbjct: 420 FGVMYMILGALLVFLFIREIKKGA-EHDNHHDVPVSTDPFSQEVYHGIS 467 >VC1844 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 Length = 541 Score = 320 bits (819), Expect = 4e-87, Method: Compositional matrix adjust. Identities = 188/507 (37%), Positives = 271/507 (53%), Gaps = 60/507 (11%) Query: 1 MDTVMLSRIQFASTTIFHYFFVPVSIGLALLIAIMETMYVRKGNDEYKRMAQFWGKLFLI 60 +D V LSR+QFA T ++H+ FVP+++G+A L+AIME++YV YK M +FWGKLF I Sbjct: 15 IDVVDLSRLQFALTAMYHFLFVPLTLGMAFLLAIMESLYVMTDKQIYKDMTKFWGKLFGI 74 Query: 61 NFAVGVVTGILQEFQFGMNWSDYSRFVGDVFGXXXXXXXXXXXXXXSTFIGIWIFGWDKV 120 NFA+GV TG+ EFQFG NWS YS +VGD+FG STF+G++ FGWD++ Sbjct: 75 NFALGVATGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEALVAFFLESTFVGLFFFGWDRL 134 Query: 121 SKRVHLLSIWLVALGTMLSAFWILLANSFMQHPVG--FAVNNGRAEMNDIWALVTNGQLL 178 SKR HL+ WLVALG+ SA WIL+AN +MQ+PVG F R EM +V N Sbjct: 135 SKRQHLVVTWLVALGSNFSALWILVANGWMQNPVGSEFNFETMRMEMVSFADVVLNPVAQ 194 Query: 179 VEFPHTVLAAYATGAFLVTGISAYKLLKKQDVSFFRKSFEIAAIVGIISSFGVAIAGHAQ 238 V+F HTV A Y TGA + GISAY LLK +DV+F R+SF IAA G+ S V + G Sbjct: 195 VKFVHTVAAGYTTGAMFILGISAYYLLKGRDVAFARRSFAIAASFGMASVLSVIVLGDES 254 Query: 239 AQYLVETQPMKMAASEGLWDDSGDPAAWTVIANIDPDNKISTHEVKIPYMLSFLSYSKFS 298 L E Q +K+AA E W PAA+T+ + + + + +KIP+ L ++ Sbjct: 255 GYELGEVQRVKLAAIESEWHTEPAPAAFTLFGIPNQEEMRTDYAIKIPFALGIIATRSLD 314 Query: 299 GSVKGMNTL-----------------------------------QAEYEQAYG------- 316 V G+ L + +++ YG Sbjct: 315 EQVVGLRDLRDEHVERIRTGIYAYDLLERLRAGEKTPENMAAFDEVKHDLGYGLLLKRYT 374 Query: 317 --------------PGDYIPPVRTTFWSFRIMVAAGSLMILLGVYAIYLMWRKKMERPNT 362 D IP V FWSFRIMVA G +M+++ A R+K+E+ Sbjct: 375 DKVTDATEEQIQAAADDSIPTVWPLFWSFRIMVACGFIMLVVFGAAFIQTCRQKIEQKK- 433 Query: 363 WFMRFMFWGLLLPPIANTSGWIMTEMGRQPWTVFGLMTTEDSVSPNITSGQVLFSVISFT 422 W ++ + + LP IA +GW + E GRQPW V G + + + +++G+++ S+++ Sbjct: 434 WVLKAALFSIPLPWIAVETGWFVAEYGRQPWAV-GEILPVNVAASALSAGEIITSMLAIL 492 Query: 423 AIYAILGLVLVGLFIKVIKKGPYAMDN 449 A+Y I + V L +K +KGP ++ Sbjct: 493 ALYTIFLIAEVYLMVKFTRKGPSSLKT 519 >VCA0872 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 Length = 530 Score = 307 bits (787), Expect = 2e-83, Method: Compositional matrix adjust. Identities = 181/507 (35%), Positives = 264/507 (52%), Gaps = 60/507 (11%) Query: 1 MDTVMLSRIQFASTTIFHYFFVPVSIGLALLIAIMETMYVRKGNDEYKRMAQFWGKLFLI 60 +D V LSR+QFA T +FH+ FVP++IG++ L+AIME++YV G Y+ M +FWGKLF I Sbjct: 6 IDVVELSRLQFALTAMFHFLFVPLTIGMSCLLAIMESIYVLTGKQIYQDMTRFWGKLFGI 65 Query: 61 NFAVGVVTGILQEFQFGMNWSDYSRFVGDVFGXXXXXXXXXXXXXXSTFIGIWIFGWDKV 120 NFA+GV TG+ EFQFG NWS YS +VGD+FG STF+G++ FGW ++ Sbjct: 66 NFALGVTTGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEALVAFFLESTFVGLFFFGWSRL 125 Query: 121 SKRVHLLSIWLVALGTMLSAFWILLANSFMQHPVG--FAVNNGRAEMNDIWALVTNGQLL 178 SKR HLL WLVALG+ SA WIL+AN +MQ+PVG F R EM +V N Sbjct: 126 SKRQHLLITWLVALGSSFSALWILVANGWMQNPVGAEFNYQTMRMEMTSFAEVVLNPVAQ 185 Query: 179 VEFPHTVLAAYATGAFLVTGISAYKLLKKQDVSFFRKSFEIAAIVGIISSFGVAIAGHAQ 238 V+F HTV +AY GA + G+S+Y LL+ +D+ F R+SF IAA G+ + V + G Sbjct: 186 VKFLHTVASAYTCGAMFILGVSSYYLLQGRDIEFARRSFAIAATFGMAAIISVIVLGDES 245 Query: 239 AQYLVETQPMKMAASEGLWDDSGDPAAWTVIANIDPDNKISTHEVKIPYMLSFLSYSKFS 298 L + Q +K+AA E W PAA+T+ + + + +KIPY++ ++ F Sbjct: 246 GYKLGDVQKVKLAAIEAEWHTEPAPAAFTLFGLPNQKEGKTDYAIKIPYLMGLIATRSFD 305 Query: 299 GSVKGMNTL------------------------------QAEYEQ-----AYG------- 316 V G++ L Q ++EQ YG Sbjct: 306 EQVTGLHDLRHEHLLRIRNGMVAYQLLERLQAGDASVETQRKFEQTKHDLGYGLLLKRYT 365 Query: 317 --------------PGDYIPPVRTTFWSFRIMVAAGSLMILLGVYAIYLMWRKKMERPNT 362 D +P V FWSFRIMV G +M+ + A+ R+++ Sbjct: 366 DTITDANEAQIQQAADDSMPTVWPLFWSFRIMVGCGFIMLFVFGAALLQTCRQRITH-KP 424 Query: 363 WFMRFMFWGLLLPPIANTSGWIMTEMGRQPWTVFGLMTTEDSVSPNITSGQVLFSVISFT 422 W ++ W + LP IA +GW + E GRQPW + ++ +VS T ++ S+ Sbjct: 425 WVLKAALWSIPLPWIAIEAGWFVAEYGRQPWAIGEVLPVTVAVSSQ-TFENLITSLAIIL 483 Query: 423 AIYAILGLVLVGLFIKVIKKGPYAMDN 449 ++Y + V L + V +KGP ++ Sbjct: 484 SLYTVFIFVESYLIVTVARKGPSSLKT 510 >STM0740 [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 Length = 522 Score = 296 bits (758), Expect = 5e-80, Method: Compositional matrix adjust. Identities = 181/513 (35%), Positives = 267/513 (52%), Gaps = 62/513 (12%) Query: 1 MDTVMLSRIQFASTTIFHYFFVPVSIGLALLIAIMETMYVRKGNDEYKRMAQFWGKLFLI 60 +D V LSR+QFA T ++H+ FVP+++G+A L+AIMET+YV G YK M +FWGKLF I Sbjct: 2 LDIVELSRLQFALTAMYHFLFVPLTLGMAFLLAIMETVYVLSGKQIYKDMTKFWGKLFGI 61 Query: 61 NFAVGVVTGILQEFQFGMNWSDYSRFVGDVFGXXXXXXXXXXXXXXSTFIGIWIFGWDKV 120 NFA+GV TG+ EFQFG NWS YS +VGD+FG STF+G++ FGWD++ Sbjct: 62 NFALGVATGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRL 121 Query: 121 SKRVHLLSIWLVALGTMLSAFWILLANSFMQHPVG--FAVNNGRAEMNDIWALVTNGQLL 178 SK H+ WLVALG+ LSA WIL+AN +MQ+P+ F R EM LV N Sbjct: 122 SKVQHMCVTWLVALGSNLSALWILVANGWMQNPIAADFNFETMRMEMVSFSELVLNPVAQ 181 Query: 179 VEFPHTVLAAYATGAFLVTGISAYKLLKKQDVSFFRKSFEIAAIVGIISSFGVAIAGHAQ 238 V+F HTV + Y TGA + GISAY +LK +D +F ++SF IAA G+ + V + G Sbjct: 182 VKFVHTVASGYVTGAMFILGISAYYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLGDES 241 Query: 239 AQYLVETQPMKMAASEGLWDDSGDPAAWTVIANIDPDNKISTHEVKIPYMLSFLSYSKFS 298 + + Q K+AA E W+ PA++T+ D D + + ++IPY L ++ Sbjct: 242 GYEMGDVQKTKLAAIEAEWETQPAPASFTLFGIPDQDKQENHLAIQIPYALGIIATRSVD 301 Query: 299 GSVKGMNTLQAEYEQ-------AY--------GPGD----------------------YI 321 V G+ L ++E+ AY G D Y Sbjct: 302 TPVIGLKDLMVQHEERIRNGMKAYELLEQLRAGSTDQAVRDQFNSMKKDLGYGLLLKRYT 361 Query: 322 PPVRTT-------------------FWSFRIMVAAGSLMILLGVYAIYLMWRKKMERPNT 362 P V +++FRIMVA G L++ + + + + R ++ Sbjct: 362 PNVTDATEAQIQQATKDSIPRVAPLYFAFRIMVACGFLLLAIIALSFWSVIRNRIGE-KK 420 Query: 363 WFMRFMFWGLLLPPIANTSGWIMTEMGRQPWTVFGLMTTEDSVSPNITSGQVLFSVISFT 422 W +R +G+ LP IA +GW + E GRQPW + ++ T + S ++T G +LFS+ Sbjct: 421 WLLRAALYGIPLPWIAVEAGWFVAEYGRQPWAIGEVLPTAVANS-SLTVGDLLFSMFLIC 479 Query: 423 AIYAILGLVLVGLFIKVIKKGPYAMDNDHGESH 455 +Y + + + L K + GP ++ G H Sbjct: 480 GLYTLFLVAELFLMFKFARLGPSSLKT--GRYH 510 >cydA [C] COG1271 Cytochrome bd-type quinol oxidase, subunit 1 Length = 523 Score = 289 bits (740), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 176/513 (34%), Positives = 264/513 (51%), Gaps = 62/513 (12%) Query: 1 MDTVMLSRIQFASTTIFHYFFVPVSIGLALLIAIMETMYVRKGNDEYKRMAQFWGKLFLI 60 +D V LSR+QFA T ++H+ FVP+++G+A L+AIMET+YV G YK M +FWGKLF I Sbjct: 3 LDIVELSRLQFALTAMYHFLFVPLTLGMAFLLAIMETVYVLSGKQIYKDMTKFWGKLFGI 62 Query: 61 NFAVGVVTGILQEFQFGMNWSDYSRFVGDVFGXXXXXXXXXXXXXXSTFIGIWIFGWDKV 120 NFA+GV TG+ EFQFG NWS YS +VGD+FG STF+G++ FGWD++ Sbjct: 63 NFALGVATGLTMEFQFGTNWSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRL 122 Query: 121 SKRVHLLSIWLVALGTMLSAFWILLANSFMQHPVG--FAVNNGRAEMNDIWALVTNGQLL 178 K H+ WLVALG+ LSA WIL+AN +MQ+P+ F R EM LV N Sbjct: 123 GKVQHMCVTWLVALGSNLSALWILVANGWMQNPIASDFNFETMRMEMVSFSELVLNPVAQ 182 Query: 179 VEFPHTVLAAYATGAFLVTGISAYKLLKKQDVSFFRKSFEIAAIVGIISSFGVAIAGHAQ 238 V+F HTV + Y TGA + GISA+ +LK +D +F ++SF IAA G+ + V + G Sbjct: 183 VKFVHTVASGYVTGAMFILGISAWYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLGDES 242 Query: 239 AQYLVETQPMKMAASEGLWDDSGDPAAWTVIANIDPDNKISTHEVKIPYMLSFLSYSKFS 298 + + Q K+AA E W+ PAA+T+ D + + + ++IPY L ++ Sbjct: 243 GYEMGDVQKTKLAAIEAEWETQPAPAAFTLFGIPDQEEETNKFAIQIPYALGIIATRSVD 302 Query: 299 GSVKGMNTLQAEYEQ-------AYG------PGDYIPPVRTTFWSFR------------- 332 V G+ L ++E+ AY G VR F S + Sbjct: 303 TPVIGLKELMVQHEERIRNGMKAYSLLEQLRSGSTDQAVRDQFNSMKKDLGYGLLLKRYT 362 Query: 333 ------------------------------IMVAAGSLMILLGVYAIYLMWRKKMERPNT 362 IMVA G L++ + + + + R ++ Sbjct: 363 PNVADATEAQIQQATKDSIPRVAPLYFAFRIMVACGFLLLAIIALSFWSVIRNRIGE-KK 421 Query: 363 WFMRFMFWGLLLPPIANTSGWIMTEMGRQPWTVFGLMTTEDSVSPNITSGQVLFSVISFT 422 W +R +G+ LP IA +GW + E GRQPW + ++ T + S ++T+G ++FS++ Sbjct: 422 WLLRAALYGIPLPWIAVEAGWFVAEYGRQPWAIGEVLPTAVANS-SLTAGDLIFSMVLIC 480 Query: 423 AIYAILGLVLVGLFIKVIKKGPYAMDNDHGESH 455 +Y + + + L K + GP ++ G H Sbjct: 481 GLYTLFLVAELFLMFKFARLGPSSLKT--GRYH 511 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.325 0.138 0.434 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 33,543,954 Number of extensions: 1326024 Number of successful extensions: 5037 Number of sequences better than 1.0e-05: 30 Number of HSP's gapped: 4942 Number of HSP's successfully gapped: 44 Length of query: 467 Length of database: 38,378,431 Length adjustment: 110 Effective length of query: 357 Effective length of database: 25,691,691 Effective search space: 9171933687 Effective search space used: 9171933687 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 118 (50.1 bits)