BLASTP 2.2.26 [Sep-21-2011]
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= psy2379
(585 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FFT|A Chain A, The Structure Of Ubiquinol Oxidase From Escherichia Coli
pdb|1FFT|F Chain F, The Structure Of Ubiquinol Oxidase From Escherichia Coli
Length = 663
Score = 778 bits (2010), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 372/583 (63%), Positives = 454/583 (77%), Gaps = 1/583 (0%)
Query: 1 MLFRGFTDAVMMRLQQAISFGSSFGYLPPEHYNQIFTAHGVIMIFFVAMPLVTGIINFIV 60
ML RGF DA+MMR QQA++ G+LPP HY+QIFTAHGVIMIFFVAMP V G++N +V
Sbjct: 68 MLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVV 127
Query: 61 PLQIGARDVAFPFLNNLSFWMTSGGAILVMISLFIGEFASTGWLGYPPLSGIAQSPGVGV 120
PLQIGARDVAFPFLNNLSFW T G ILV +SL +GEFA TGWL YPPLSGI SPGVGV
Sbjct: 128 PLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGV 187
Query: 121 DYYIWSLQIAGIGTLLSGINMIATIIKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLT 180
DY+IWSLQ++GIGT L+GIN TI+KMRAPGM + MP+FTW +LC N+LI+A+FP+LT
Sbjct: 188 DYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILT 247
Query: 181 SVLFLSTLDRYIGTHFFTNDLGGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSS 240
+ L TLDRY+GTHFFTND+GGN+MMY+NLIW WGHPEVYIL+LPVFG+FSE+ +TFS
Sbjct: 248 VTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSR 307
Query: 241 KRLFGYSSMVYATVVITLLSYIVWLHHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWL 300
KRLFGY+S+V+ATV IT+LS+IVWLHHFFTMG+GANVNAFFGITTMII+IPTG KIFNWL
Sbjct: 308 KRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWL 367
Query: 301 FTMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGG 360
FTMY+GRI F +LWTIGF++TF +GGM GV+LAVP A+F+LHNSLFL+AHFHNVIIGG
Sbjct: 368 FTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGG 427
Query: 361 VLFGLMSGINYWFPKAFGYKLEPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFE 420
V+FG +G+ YW+PKAFG+KL WGK +FWFW+IGF+VAFMPLY LGFMG+TRR+S
Sbjct: 428 VVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQI 487
Query: 421 DISLQIWFQIAAFGTLLIAMGILSFIIQLIVSYRKRHTLIDITGDPWNGRTLEWSTSSPP 480
D IAA G +LIA+GIL +IQ+ VS R R D+TGDPW GRTLEW+TSSPP
Sbjct: 488 DPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPP 547
Query: 481 PVYNFAFIPLIHQSDSWWYMXXXXXXXXX-XXXQDILMPKNTNIGILISIFSLIMGFALV 539
P YNFA +P +H+ D++W M ++I MPKN+ GI+I+ FS I GFA++
Sbjct: 548 PFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMI 607
Query: 540 WHMWXXXXXXXXXXXXXXXYNTFNYKRNYYISSEEITCIEKKR 582
WH+W +F+ +YY+ EI +E +
Sbjct: 608 WHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQH 650
>pdb|1M56|A Chain A, Structure Of Cytochrome C Oxidase From Rhodobactor
Sphaeroides (Wild Type)
pdb|1M56|G Chain G, Structure Of Cytochrome C Oxidase From Rhodobactor
Sphaeroides (Wild Type)
pdb|2GSM|A Chain A, Catalytic Core (Subunits I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides
pdb|2GSM|C Chain C, Catalytic Core (Subunits I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides
pdb|3DTU|A Chain A, Catalytic Core Subunits (i And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides Complexed With Deoxycholic
Acid
pdb|3DTU|C Chain C, Catalytic Core Subunits (i And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides Complexed With Deoxycholic
Acid
pdb|3FYE|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State
pdb|3FYE|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State
pdb|3FYI|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State Bound
With Cyanide
pdb|3FYI|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides In The Reduced State Bound
With Cyanide
Length = 566
Score = 327 bits (837), Expect = 1e-89, Method: Compositional matrix adjust.
Identities = 179/474 (37%), Positives = 275/474 (58%), Gaps = 16/474 (3%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HG++M+FFV +P L G N+ +PL IGA D+AFP +NNLS+W+ G L +
Sbjct: 95 WNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAV 154
Query: 91 ISLFI----GEFAST-GWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SLF G+ S GW+ YPPLS G D I+++ ++G ++L INMI T
Sbjct: 155 ASLFAPGGNGQLGSGIGWVLYPPLS--TSESGYSTDLAIFAVHLSGASSILGAINMITTF 212
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM + +P+F W+ T LI+ A PVL + + DR GT FF GG+
Sbjct: 213 LNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDP 272
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI+VLP FGI S V++TF+ K +FGY MVYA V I +L ++VW
Sbjct: 273 VLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWA 332
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G ++F + TM+I++PTG KIF+W+ TM+ G I + P+LW +GF+ F
Sbjct: 333 HHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFT 392
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ G++L+ + + H++ ++VAHFH V+ G +FG+ +GI +W K G + +
Sbjct: 393 VGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWA 452
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
GK FW +G + F P + LG G+ RR + + + W +++ G L
Sbjct: 453 GKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPE-AFATWNFVSSLGAFLSFA--SFL 509
Query: 446 IIQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNFAFIPLIHQSDSW 497
++ Y + WN TLEW+ +SPPP + F +P + + W
Sbjct: 510 FFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLP---KREDW 560
>pdb|1M57|A Chain A, Structure Of Cytochrome C Oxidase From Rhodobacter
Sphaeroides (Eq(I-286) Mutant))
pdb|1M57|G Chain G, Structure Of Cytochrome C Oxidase From Rhodobacter
Sphaeroides (Eq(I-286) Mutant))
Length = 566
Score = 325 bits (834), Expect = 3e-89, Method: Compositional matrix adjust.
Identities = 178/474 (37%), Positives = 275/474 (58%), Gaps = 16/474 (3%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HG++M+FFV +P L G N+ +PL IGA D+AFP +NNLS+W+ G L +
Sbjct: 95 WNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAV 154
Query: 91 ISLFI----GEFAST-GWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SLF G+ S GW+ YPPLS G D I+++ ++G ++L INMI T
Sbjct: 155 ASLFAPGGNGQLGSGIGWVLYPPLS--TSESGYSTDLAIFAVHLSGASSILGAINMITTF 212
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM + +P+F W+ T LI+ A PVL + + DR GT FF GG+
Sbjct: 213 LNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDP 272
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHP+VYI+VLP FGI S V++TF+ K +FGY MVYA V I +L ++VW
Sbjct: 273 VLYQHILWFFGHPQVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWA 332
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G ++F + TM+I++PTG KIF+W+ TM+ G I + P+LW +GF+ F
Sbjct: 333 HHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFT 392
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ G++L+ + + H++ ++VAHFH V+ G +FG+ +GI +W K G + +
Sbjct: 393 VGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWA 452
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
GK FW +G + F P + LG G+ RR + + + W +++ G L
Sbjct: 453 GKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPE-AFATWNFVSSLGAFLSFA--SFL 509
Query: 446 IIQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNFAFIPLIHQSDSW 497
++ Y + WN TLEW+ +SPPP + F +P + + W
Sbjct: 510 FFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTFEQLP---KREDW 560
>pdb|1V54|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V54|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V55|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|1V55|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|2DYR|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYR|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYS|A Chain A, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2DYS|N Chain N, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2EIJ|A Chain A, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIJ|N Chain N, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIK|A Chain A, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIK|N Chain N, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIL|A Chain A, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIL|N Chain N, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIM|A Chain A, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIM|N Chain N, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIN|A Chain A, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIN|N Chain N, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2ZXW|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|2ZXW|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|3ABL|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABL|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABM|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABM|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABK|A Chain A, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3ABK|N Chain N, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3AG1|A Chain A, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG1|N Chain N, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG2|A Chain A, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG2|N Chain N, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG3|A Chain A, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG3|N Chain N, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG4|A Chain A, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
F Reduced State At 100 K
pdb|3AG4|N Chain N, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
F Reduced State At 100 K
pdb|3ASN|A Chain A, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASN|N Chain N, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASO|A Chain A, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
pdb|3ASO|N Chain N, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
Length = 514
Score = 322 bits (824), Expect = 5e-88, Method: Compositional matrix adjust.
Identities = 181/458 (39%), Positives = 276/458 (60%), Gaps = 10/458 (2%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
YN + TAH +MIFF+ MP ++ G N++VPL IGA D+AFP +NN+SFW+ +L++
Sbjct: 54 YNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113
Query: 91 ISLFIGEFASTGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATIIKMRA 150
S + A TGW YPPL+G G VD I+SL +AG+ ++L IN I TII M+
Sbjct: 114 ASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKP 173
Query: 151 PGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNIMMYVN 210
P M P+F W+ + T +L++ + PVL + + + DR + T FF GG+ ++Y +
Sbjct: 174 PAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQH 233
Query: 211 LIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRL-FGYSSMVYATVVITLLSYIVWLHHFF 269
L W +GHPEVYIL+LP FG+ S +V+ +S K+ FGY MV+A + I L +IVW HH F
Sbjct: 234 LFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMF 293
Query: 270 TMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFVIGGM 329
T+G + A+F TMII+IPTG K+F+WL T++ G I++ ++W +GF+ F +GG+
Sbjct: 294 TVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGL 353
Query: 330 AGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFWGKCS 389
G++LA + + +LH++ ++VAHFH V+ G +F +M G +WFP GY L W K
Sbjct: 354 TGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIH 413
Query: 390 FWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTL--LIAMGILSFII 447
F +G + F P + LG G+ RR S + D + +W I++ G+ L A+ ++ FII
Sbjct: 414 FAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPD-AYTMWNTISSMGSFISLTAVMLMVFII 472
Query: 448 QLIVSYRKRHTLIDITGDPWNGRTLEWSTSSPPPVYNF 485
+ ++ +D+T LEW PPP + F
Sbjct: 473 WEAFASKREVLTVDLT-----TTNLEWLNGCPPPYHTF 505
>pdb|1OCC|A Chain A, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|1OCC|N Chain N, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|2OCC|A Chain A, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2OCC|N Chain N, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1OCO|A Chain A, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
State
pdb|1OCO|N Chain N, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
State
pdb|1OCR|A Chain A, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCR|N Chain N, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCZ|A Chain A, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|1OCZ|N Chain N, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|2Y69|A Chain A, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
pdb|2Y69|N Chain N, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
pdb|2YBB|L Chain L, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
Length = 514
Score = 322 bits (824), Expect = 5e-88, Method: Compositional matrix adjust.
Identities = 181/458 (39%), Positives = 276/458 (60%), Gaps = 10/458 (2%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
YN + TAH +MIFF+ MP ++ G N++VPL IGA D+AFP +NN+SFW+ +L++
Sbjct: 54 YNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113
Query: 91 ISLFIGEFASTGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATIIKMRA 150
S + A TGW YPPL+G G VD I+SL +AG+ ++L IN I TII M+
Sbjct: 114 ASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKP 173
Query: 151 PGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNIMMYVN 210
P M P+F W+ + T +L++ + PVL + + + DR + T FF GG+ ++Y +
Sbjct: 174 PAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQH 233
Query: 211 LIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRL-FGYSSMVYATVVITLLSYIVWLHHFF 269
L W +GHPEVYIL+LP FG+ S +V+ +S K+ FGY MV+A + I L +IVW HH F
Sbjct: 234 LFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMF 293
Query: 270 TMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFVIGGM 329
T+G + A+F TMII+IPTG K+F+WL T++ G I++ ++W +GF+ F +GG+
Sbjct: 294 TVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGL 353
Query: 330 AGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFWGKCS 389
G++LA + + +LH++ ++VAHFH V+ G +F +M G +WFP GY L W K
Sbjct: 354 TGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIH 413
Query: 390 FWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTL--LIAMGILSFII 447
F +G + F P + LG G+ RR S + D + +W I++ G+ L A+ ++ FII
Sbjct: 414 FAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPD-AYTMWNTISSMGSFISLTAVMLMVFII 472
Query: 448 QLIVSYRKRHTLIDITGDPWNGRTLEWSTSSPPPVYNF 485
+ ++ +D+T LEW PPP + F
Sbjct: 473 WEAFASKREVLTVDLT-----TTNLEWLNGCPPPYHTF 505
>pdb|1AR1|A Chain A, Structure At 2.7 Angstrom Resolution Of The Paracoccus
Denitrificans Two-Subunit Cytochrome C Oxidase Complexed
With An Antibody Fv Fragment
pdb|3HB3|A Chain A, High Resolution Crystal Structure Of Paracoccus
Denitrificans Cytochrome C Oxidase
Length = 558
Score = 321 bits (823), Expect = 7e-88, Method: Compositional matrix adjust.
Identities = 182/475 (38%), Positives = 274/475 (57%), Gaps = 18/475 (3%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HGV+M+FFV +P L G N+ +PL IGA D+AFP LNNLS+WM G L +
Sbjct: 87 WNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGV 146
Query: 91 ISLFI----GEFAS-TGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SL + S GW+ YPPLS G +D I+++ ++G ++L IN+I T
Sbjct: 147 ASLLAPGGNDQMGSGVGWVLYPPLS--TTEAGYSMDLAIFAVHVSGASSILGAINIITTF 204
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM L +P+F W+ T LI+ + PVL + + +DR GT FF GG+
Sbjct: 205 LNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDP 264
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI++LP FGI S V+STF+ K +FGY MV A I +L ++VW
Sbjct: 265 VLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWA 324
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G A+F + TM I++PTG K+F+W+ TM+ G I F+ P+LW GF+ F
Sbjct: 325 HHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFT 384
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ GV+L+ + + H++ ++VAHFH V+ G +FG+ +G+ YW K G + +
Sbjct: 385 VGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWA 444
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
G+ FW IG + F P + LG G+ RR + + W I++ G + L F
Sbjct: 445 GQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYP-VEFAYWNNISSIGAYISFASFLFF 503
Query: 446 I-IQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNFAFIPLIHQSDSW 497
I I + + + + WN TLEW+ SPPP + F +P + + W
Sbjct: 504 IGIVFYTLFAGKRVNVP---NYWNEHADTLEWTLPSPPPEHTFETLP---KREDW 552
>pdb|1QLE|A Chain A, Cryo-structure Of The Paracoccus Denitrificans
Four-subunit Cytochrome C Oxidase In The Completely
Oxidized State Complexed With An Antibody Fv Fragment
Length = 538
Score = 321 bits (822), Expect = 8e-88, Method: Compositional matrix adjust.
Identities = 182/473 (38%), Positives = 272/473 (57%), Gaps = 15/473 (3%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HGV+M+FFV +P L G N+ +PL IGA D+AFP LNNLS+WM G L +
Sbjct: 71 WNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGV 130
Query: 91 ISLFI----GEFAS-TGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SL + S GW+ YPPLS G +D I+++ ++G ++L IN+I T
Sbjct: 131 ASLLAPGGNDQMGSGVGWVLYPPLS--TTEAGYSMDLAIFAVHVSGASSILGAINIITTF 188
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM L +P+F W+ T LI+ + PVL + + +DR GT FF GG+
Sbjct: 189 LNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDP 248
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI++LP FGI S V+STF+ K +FGY MV A I +L ++VW
Sbjct: 249 VLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWA 308
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G A+F + TM I++PTG K+F+W+ TM+ G I F+ P+LW GF+ F
Sbjct: 309 HHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFT 368
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ GV+L+ + + H++ ++VAHFH V+ G +FG+ +G+ YW K G + +
Sbjct: 369 VGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWA 428
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
G+ FW IG + F P + LG G+ RR + + W I++ G + L F
Sbjct: 429 GQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYP-VEFAYWNNISSIGAYISFASFLFF 487
Query: 446 I-IQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNFAFIPLIHQSD 495
I I + + + + WN TLEW+ SPPP + F +P D
Sbjct: 488 IGIVFYTLFAGKRVNVP---NYWNEHADTLEWTLPSPPPEHTFETLPKREDWD 537
>pdb|3OMI|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMI|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMN|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
pdb|3OMN|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
Length = 535
Score = 320 bits (821), Expect = 1e-87, Method: Compositional matrix adjust.
Identities = 176/462 (38%), Positives = 269/462 (58%), Gaps = 13/462 (2%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HG++M+FFV +P L G N+ +PL IGA +AFP +NNLS+W+ G L +
Sbjct: 79 WNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPAMAFPRMNNLSYWLYVAGTSLAV 138
Query: 91 ISLFI----GEFAS-TGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SLF G+ S GW+ YPPLS G D I+++ ++G ++L INMI T
Sbjct: 139 ASLFAPGGNGQLGSGIGWVLYPPLS--TSESGYSTDLAIFAVHLSGASSILGAINMITTF 196
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM + +P+F W+ T LI+ A PVL + + DR GT FF GG+
Sbjct: 197 LNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDP 256
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI+VLP FGI S V++TF+ K +FGY MVYA V I +L ++VW
Sbjct: 257 VLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWA 316
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G ++F + TM+I++PTG KIF+W+ TM+ G I + P+LW +GF+ F
Sbjct: 317 HHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFT 376
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ G++L+ + + H++ ++VAHFH V+ G +FG+ +GI +W K G + +
Sbjct: 377 VGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWA 436
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
GK FW +G + F P + LG G+ RR + + + W +++ G L
Sbjct: 437 GKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPE-AFATWNFVSSLGAFLSFA--SFL 493
Query: 446 IIQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNF 485
++ Y + WN TLEW+ +SPPP + F
Sbjct: 494 FFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 535
>pdb|3OM3|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OM3|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OMA|A Chain A, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
pdb|3OMA|C Chain C, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
Length = 535
Score = 320 bits (820), Expect = 1e-87, Method: Compositional matrix adjust.
Identities = 176/462 (38%), Positives = 269/462 (58%), Gaps = 13/462 (2%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HG++M+FFV +P L G N+ +PL IGA D+AFP +NNLS+W+ G L +
Sbjct: 79 WNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAV 138
Query: 91 ISLFI----GEFAS-TGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SLF G+ S GW+ YPPLS G D I+++ ++G ++L INMI T
Sbjct: 139 ASLFAPGGNGQLGSGIGWVLYPPLS--TSESGYSTDLAIFAVHLSGASSILGAINMITTF 196
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM + +P+F W+ T LI+ A PVL + + DR GT FF GG+
Sbjct: 197 LNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDP 256
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI+VLP FGI S V++TF+ K +FGY MVYA V I +L ++VW
Sbjct: 257 VLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWA 316
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G ++F + TM+I++PTG IF+W+ TM+ G I + P+LW +GF+ F
Sbjct: 317 HHMYTAGLSLTQQSYFMMATMVIAVPTGIMIFSWIATMWGGSIELKTPMLWALGFLFLFT 376
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ G++L+ + + H++ ++VAHFH V+ G +FG+ +GI +W K G + +
Sbjct: 377 VGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWA 436
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
GK FW +G + F P + LG G+ RR + + + W +++ G L
Sbjct: 437 GKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPE-AFATWNFVSSLGAFLSFA--SFL 493
Query: 446 IIQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNF 485
++ Y + WN TLEW+ +SPPP + F
Sbjct: 494 FFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 535
>pdb|3EHB|A Chain A, A D-Pathway Mutation Decouples The Paracoccus
Denitrificans Cytochrome C Oxidase By Altering The Side
Chain Orientation Of A Distant, Conserved Glutamate
Length = 558
Score = 320 bits (819), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 181/475 (38%), Positives = 274/475 (57%), Gaps = 18/475 (3%)
Query: 32 YNQIFTAHGVIMIFFVAMP-LVTGIINFIVPLQIGARDVAFPFLNNLSFWMTSGGAILVM 90
+N + T HGV+M+FFV +P L G N+ +PL IGA D+AFP L+NLS+WM G L +
Sbjct: 87 WNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLDNLSYWMYVCGVALGV 146
Query: 91 ISLFI----GEFAS-TGWLGYPPLSGIAQSPGVGVDYYIWSLQIAGIGTLLSGINMIATI 145
SL + S GW+ YPPLS G +D I+++ ++G ++L IN+I T
Sbjct: 147 ASLLAPGGNDQMGSGVGWVLYPPLS--TTEAGYSMDLAIFAVHVSGASSILGAINIITTF 204
Query: 146 IKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLSTLDRYIGTHFFTNDLGGNI 205
+ MRAPGM L +P+F W+ T LI+ + PVL + + +DR GT FF GG+
Sbjct: 205 LNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDP 264
Query: 206 MMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSYIVWL 265
++Y +++W +GHPEVYI++LP FGI S V+STF+ K +FGY MV A I +L ++VW
Sbjct: 265 VLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWA 324
Query: 266 HHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRGRIRFEVPILWTIGFMITFV 325
HH +T G A+F + TM I++PTG K+F+W+ TM+ G I F+ P+LW GF+ F
Sbjct: 325 HHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFT 384
Query: 326 IGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKLEPFW 385
+GG+ GV+L+ + + H++ ++VAHFH V+ G +FG+ +G+ YW K G + +
Sbjct: 385 VGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWA 444
Query: 386 GKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQIWFQIAAFGTLLIAMGILSF 445
G+ FW IG + F P + LG G+ RR + + W I++ G + L F
Sbjct: 445 GQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYP-VEFAYWNNISSIGAYISFASFLFF 503
Query: 446 I-IQLIVSYRKRHTLIDITGDPWN--GRTLEWSTSSPPPVYNFAFIPLIHQSDSW 497
I I + + + + WN TLEW+ SPPP + F +P + + W
Sbjct: 504 IGIVFYTLFAGKRVNVP---NYWNEHADTLEWTLPSPPPEHTFETLP---KREDW 552
>pdb|2YEV|A Chain A, Structure Of Caa3-Type Cytochrome Oxidase
pdb|2YEV|D Chain D, Structure Of Caa3-Type Cytochrome Oxidase
Length = 791
Score = 316 bits (809), Expect = 3e-86, Method: Compositional matrix adjust.
Identities = 180/482 (37%), Positives = 284/482 (58%), Gaps = 15/482 (3%)
Query: 9 AVMMRLQQAISFGSSFGYLPPEHYNQIFTAHGVIMIFF-VAMPLVTGIINFIVPLQIGAR 67
++++R Q A+ +L E YNQI T HG M+FF + +TG NF+VPL +GAR
Sbjct: 46 SLLIRTQLAVPNNQ---FLTGEQYNQILTLHGATMLFFFIIQAGLTGFGNFVVPLMLGAR 102
Query: 68 DVAFPFLNNLSFWMTSGGAILVMISLFI-GEFASTGWLGYPPLSGIAQSPGVGVDYYIWS 126
DVA P +N S+W G +L ++S F G S GW Y P S ++S GVD+Y+ +
Sbjct: 103 DVALPRVNAFSYWAFLGAIVLALMSYFFPGGAPSVGWTFYYPFSAQSES---GVDFYLAA 159
Query: 127 LQIAGIGTLLSGINMIATIIKMRAPGMKLMNMPIFTWTALCTNILIVAAFPVLTSVLFLS 186
+ + G +LL N +ATI +RA GM L MPI+ W+ ++L + + LT+ L
Sbjct: 160 ILLLGFSSLLGNANFVATIYNLRAQGMSLWKMPIYVWSVFAASVLNLFSLAGLTAATLLV 219
Query: 187 TLDRYIGTHFFTNDLGGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGY 246
L+R IG +F +GG+ +++ W + HP VY+++LP GI +EV STF+ K LFGY
Sbjct: 220 LLERKIGLSWFNPAVGGDPVLFQQFFWFYSHPTVYVMLLPYLGILAEVASTFARKPLFGY 279
Query: 247 SSMVYATVVITLLSYIVWLHHFFTMGSGANVNAFFGITTMIISIPTGAKIFNWLFTMYRG 306
MV+A + I +L +VW HH FT+G F T +I++PTG K+FN + T++ G
Sbjct: 280 RQMVWAQMGIVVLGTMVWAHHMFTVGESTLFQIAFAFFTALIAVPTGVKLFNIIGTLWGG 339
Query: 307 RIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGVLFGLM 366
+++ + P+ W +GF+ F++GG+ GV+L++ ++ H+S F+VAHFHNV++ G FG
Sbjct: 340 KLQMKTPLYWVLGFIFNFLLGGITGVMLSMTPLDYQFHDSYFVVAHFHNVLMAGSGFGAF 399
Query: 367 SGINYWFPKAFGYKLEPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRMSHFEDISLQI 426
+G+ YW+PK G + G+ FW +L+G+ + F+P Y LG++G+ RR + + +
Sbjct: 400 AGLYYWWPKMTGRMYDERLGRLHFWLFLVGYLLTFLPQYALGYLGMPRRYYTY-NADIAG 458
Query: 427 WFQ---IAAFGTLLIAMGILSFIIQLIVSYRKRHTLIDITGDPWNGRTLEWSTSSPPPVY 483
W + ++ G ++ +G L +I + S R D +PW G TLEW T+SPP +
Sbjct: 459 WPELNLLSTIGAYILGLGGLVWIYTMWKSLRSGPKAPD---NPWGGYTLEWLTASPPKAH 515
Query: 484 NF 485
NF
Sbjct: 516 NF 517
>pdb|4GP8|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant
Y133w+t231f From Thermus Thermophilus
Length = 568
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 106/491 (21%), Positives = 194/491 (39%), Gaps = 74/491 (15%)
Query: 16 QAISFGSSFGY------LP-PEHYNQIFTAHGVIMIFFVAMPLVTGIINFIVPLQIGARD 68
QA+++G+ Y LP + Y Q T HGV+ I+ ++ ++ R
Sbjct: 48 QALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRP 107
Query: 69 VAFPFLNNLSFWMTSGGAILVMISLFIGEFASTGWLGYPPLSGIAQSPGVGVDYYIWSLQ 128
L LS+WM G ++ + L E A+ W YPPL G W+
Sbjct: 108 NMG--LMWLSWWMAFIGLVVAALPLLANE-ATVLWTFYPPLKGH------------WAFY 152
Query: 129 IAGIGTLLSGINMIATII------KMRAPGMKLMNMPIFTWTALCTNIL--IVAAFPVLT 180
+ +LS I ++ K PG P+ T+ A+ ++ + + VL
Sbjct: 153 LGASVFVLSTWVSIYIVLDLWRRWKAANPGKV---TPLVTYMAVVFWLMWFLASLGLVLE 209
Query: 181 SVLFLSTLDRYIGTHFFTNDLGGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSS 240
+VLFL F G + ++ L W +GHP VY +LP + I ++ +
Sbjct: 210 AVLFLLPWS-------FGLVEGVDPLVARTLFWWFGHPIVYFWLLPAYAIIYTILPKQAG 262
Query: 241 KRLFGYSSMVYATVVITLLSYIVWLHH-FFTMGSGANVNAFFGITTMIISIPT------- 292
+L A ++ LLS V HH F G + T+ +++P+
Sbjct: 263 GKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTV 322
Query: 293 ------------GAKIFNWLFTMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAAN 340
G +F W+ + F P+L +G F+ GG G++ A +
Sbjct: 323 AASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLD 378
Query: 341 FLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGF 397
+++HN+ ++ HFH + V M + + P G + + G W W +G
Sbjct: 379 YVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGM 438
Query: 398 YVAFMPLYILGFMGVTRRM------SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLI 450
+ + L+ G + V RR + ++ + F + A LL+A+ + + + ++
Sbjct: 439 MIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVL 498
Query: 451 VSYRKRHTLID 461
+S ++ L +
Sbjct: 499 LSRERKPELAE 509
>pdb|4GP5|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant
Y133w From Thermus Thermophilus
Length = 568
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 106/491 (21%), Positives = 193/491 (39%), Gaps = 74/491 (15%)
Query: 16 QAISFGSSFGY------LP-PEHYNQIFTAHGVIMIFFVAMPLVTGIINFIVPLQIGARD 68
QA+++G+ Y LP + Y Q T HGV+ I+ ++ ++ R
Sbjct: 48 QALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRP 107
Query: 69 VAFPFLNNLSFWMTSGGAILVMISLFIGEFASTGWLGYPPLSGIAQSPGVGVDYYIWSLQ 128
L LS+WM G ++ + L E A+ W YPPL G W+
Sbjct: 108 NMG--LMWLSWWMAFIGLVVAALPLLANE-ATVLWTFYPPLKGH------------WAFY 152
Query: 129 IAGIGTLLSGINMIATII------KMRAPGMKLMNMPIFTWTALCTNIL--IVAAFPVLT 180
+ +LS I ++ K PG P+ T+ A+ ++ + + VL
Sbjct: 153 LGASVFVLSTWVSIYIVLDLWRRWKAANPGKV---TPLVTYMAVVFWLMWFLASLGLVLE 209
Query: 181 SVLFLSTLDRYIGTHFFTNDLGGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSS 240
+VLFL F G + ++ L W GHP VY +LP + I ++ +
Sbjct: 210 AVLFLLPWS-------FGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAG 262
Query: 241 KRLFGYSSMVYATVVITLLSYIVWLHH-FFTMGSGANVNAFFGITTMIISIPT------- 292
+L A ++ LLS V HH F G + T+ +++P+
Sbjct: 263 GKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTV 322
Query: 293 ------------GAKIFNWLFTMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAAN 340
G +F W+ + F P+L +G F+ GG G++ A +
Sbjct: 323 AASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLD 378
Query: 341 FLLHNSLFLVAHFHNVIIGGVLFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGF 397
+++HN+ ++ HFH + V M + + P G + + G W W +G
Sbjct: 379 YVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGM 438
Query: 398 YVAFMPLYILGFMGVTRRM------SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLI 450
+ + L+ G + V RR + ++ + F + A LL+A+ + + + ++
Sbjct: 439 MIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVL 498
Query: 451 VSYRKRHTLID 461
+S ++ L +
Sbjct: 499 LSRERKPELAE 509
>pdb|2QPD|A Chain A, An Unexpected Outcome Of Surface-Engineering An Integral
Membrane Protein: Improved Crystallization Of Cytochrome
Ba3 Oxidase From Thermus Thermophilus
pdb|2QPE|A Chain A, An Unexpected Outcome Of Surface-Engineering An Integral
Membrane Protein: Improved Crystallization Of Cytochrome
Ba3 Oxidase From Thermus Thermophilus
pdb|3BVD|A Chain A, Structure Of Surface-Engineered Cytochrome Ba3 Oxidase
From Thermus Thermophilus Under Xenon Pressure, 100psi
5min
pdb|3QJS|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
pdb|3QJT|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
Length = 568
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 61/290 (21%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + RL A ++ LLS
Sbjct: 224 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGRLVSDPMARLAFLLFLLLST 283
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 284 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 343
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 344 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 399
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 400 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 459
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 460 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 509
>pdb|3EH3|A Chain A, Structure Of The Reduced Form Of Cytochrome Ba3 Oxidase
From Thermus Thermophilus
pdb|3EH4|A Chain A, Structure Of The Reduced Form Of Cytochrome Ba3 Oxidase
From Thermus Thermophilus
pdb|3EH5|A Chain A, Structure Of The Reduced Form Of Cytochrome Ba3 Oxidase
From Thermus Thermophilus
Length = 618
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 65/294 (22%), Positives = 115/294 (39%), Gaps = 35/294 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + RL A ++ LLS
Sbjct: 274 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGRLVSDPMARLAFLLFLLLST 333
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 334 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 393
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 394 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 449
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 450 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 509
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSFIIQLIVSYRKRHTLIDITGDP 466
+ ++ + F + A LL+A+ L FI L R ++ P
Sbjct: 510 AQVPDAYPHAAVPMVFNVLAGIVLLVAL--LLFIYGLFSVLLSRERKPELAEAP 561
>pdb|4FAA|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant
A120f+a204f From Thermus Thermophilus
Length = 568
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 64/294 (21%), Positives = 115/294 (39%), Gaps = 35/294 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 224 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 283
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 284 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 343
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 344 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 399
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 400 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 459
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSFIIQLIVSYRKRHTLIDITGDP 466
+ ++ + F + A LL+A+ L FI L R ++ P
Sbjct: 460 AQVPDAYPHAAVPMVFNVLAGIVLLVAL--LLFIYGLFSVLLSRERKPELAEAP 511
>pdb|4FA7|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant
A204f From Thermus Thermophilus
Length = 568
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 64/294 (21%), Positives = 115/294 (39%), Gaps = 35/294 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 224 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 283
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 284 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 343
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 344 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 399
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 400 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 459
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSFIIQLIVSYRKRHTLIDITGDP 466
+ ++ + F + A LL+A+ L FI L R ++ P
Sbjct: 460 AQVPDAYPHAAVPMVFNVLAGIVLLVAL--LLFIYGLFSVLLSRERKPELAEAP 511
>pdb|1XME|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase From
Thermus Thermophilus
pdb|3QJQ|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
pdb|3QJR|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
pdb|3QJU|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
pdb|3QJV|A Chain A, The Structure Of And Photolytic Induced Changes Of Carbon
Monoxide Binding To The Cytochrome Ba3-Oxidase From
Thermus Thermophilus
pdb|3S33|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
10s After Xe Depressurization
pdb|3S38|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
30s After Xe Depressurization
pdb|3S39|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
60s After Xe Depressurization
pdb|3S3A|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
120s After Xe Depressurization
pdb|3S3B|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
240s After Xe Depressurization
pdb|3S3C|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
360s After Xe Depressurization
pdb|3S3D|A Chain A, Structure Of Thermus Thermophilus Cytochrome Ba3 Oxidase
480s After Xe Depressurization
Length = 568
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 60/290 (20%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 224 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 283
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 284 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 343
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 344 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 399
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 400 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 459
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 460 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 509
>pdb|1EHK|A Chain A, Crystal Structure Of The Aberrant Ba3-Cytochrome-C Oxidase
From Thermus Thermophilus
Length = 562
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 60/290 (20%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 218 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 277
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 278 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 337
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 338 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 393
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 394 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 453
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 454 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 503
>pdb|3S8F|A Chain A, 1.8 A Structure Of Ba3 Cytochrome C Oxidase From Thermus
Thermophilus In Lipid Environment
Length = 569
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 60/290 (20%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 225 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 284
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 285 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 344
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 345 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 400
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 401 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 460
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 461 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 510
>pdb|4GP4|A Chain A, Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant
Y133f From Thermus Thermophilus
Length = 568
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 60/290 (20%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 224 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 283
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 284 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 343
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 344 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 399
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 400 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 459
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 460 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 509
>pdb|3S8G|A Chain A, 1.8 A Structure Of Ba3 Cytochrome C Oxidase Mutant (A120f)
From Thermus Thermophilus In Lipid Environment
Length = 569
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 60/290 (20%), Positives = 118/290 (40%), Gaps = 34/290 (11%)
Query: 202 GGNIMMYVNLIWIWGHPEVYILVLPVFGIFSEVVSTFSSKRLFGYSSMVYATVVITLLSY 261
G + ++ L W GHP VY +LP + I ++ + +L A ++ LLS
Sbjct: 225 GVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLST 284
Query: 262 IVWLHH-FFTMGSGANVNAFFGITTMIISIPT-------------------GAKIFNWLF 301
V HH F G + T+ +++P+ G +F W+
Sbjct: 285 PVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIR 344
Query: 302 TMYRGRIRFEVPILWTIGFMITFVIGGMAGVILAVPAANFLLHNSLFLVAHFHNVIIGGV 361
+ F P+L +G F+ GG G++ A ++++HN+ ++ HFH + V
Sbjct: 345 ALPWDNPAFVAPVLGLLG----FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLV 400
Query: 362 LFGLMSGINYWFPKAFGYKL---EPFWGKCSFWFWLIGFYVAFMPLYILGFMGVTRRM-- 416
M + + P G + + G W W +G + + L+ G + V RR
Sbjct: 401 TLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYI 460
Query: 417 ----SHFEDISLQIWFQIAAFGTLLIAMGILSF-IIQLIVSYRKRHTLID 461
+ ++ + F + A LL+A+ + + + +++S ++ L +
Sbjct: 461 AQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAE 510
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.332 0.145 0.478
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,765,986
Number of Sequences: 62578
Number of extensions: 659414
Number of successful extensions: 1367
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1266
Number of HSP's gapped (non-prelim): 41
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 54 (25.4 bits)