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Conserved domains on  [gi|313877314|gb|ADR82395|]
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cytochrome oxidase subunit I, partial (mitochondrion) [Zeugodacus cucurbitae]

Protein Classification

heme-copper oxidase family protein( domain architecture ID 14)

heme-copper oxidase family protein may catalyze the transfer of electrons from an electron donor onto molecular oxygen

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Heme_Cu_Oxidase_I super family cl00275
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-201 2.29e-145

Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily.


The actual alignment was detected with superfamily member MTH00153:

Pssm-ID: 469701  Cd Length: 511  Bit Score: 413.88  E-value: 2.29e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00153 311 AVPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGG 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00153 391 FIHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFII 470

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00153 471 WESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-201 2.29e-145

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 413.88  E-value: 2.29e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00153 311 AVPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGG 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00153 391 FIHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFII 470

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00153 471 WESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-184 5.84e-112

Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, may play a role in assembly or oxygen delivery to the active site. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme (heme a3) and a copper ion (CuB). It also contains a low-spin heme (heme a), believed to participate in the transfer of electrons to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are transferred from cytochrome c (the electron donor) to heme a via the CuA binuclear site in subunit II, and directly from heme a to the binuclear center.


Pssm-ID: 238833  Cd Length: 488  Bit Score: 328.29  E-value: 5.84e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:cd01663  304 AVPTGIKVFSWLATMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAG 383

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:cd01663  384 FYYWFPKITGLSYNETLGKIHFWLMFIGVNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIV 463

                        170       180
                 ....*....|....*....|....*
gi 313877314 161 WESLVTQRQVIY-PMQLSSSIEWLQ 184
Cdd:cd01663  464 WESFVSGRKVIFnVGEGSTSLEWTL 488
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-200 6.74e-71

Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];


Pssm-ID: 440605  Cd Length: 535  Bit Score: 224.24  E-value: 6.74e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:COG0843  314 AVPTGVKVFNWIATMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAG 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLF 158
Cdd:COG0843  394 LYYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFPMHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLI 473

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 313877314 159 IIWESLVTQRQV-IYPMQlSSSIEWLQNTPPAEHSYSELPLLT 200
Cdd:COG0843  474 NLVVSLRKGPKAgGNPWG-ARTLEWATPSPPPLYNFASIPVVR 515
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-193 1.12e-67

cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) of cytochrome c oxidases of bacterial origin. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits I-III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit II and heme a of subunit I to the bimetallic center formed by heme a3 and copper B. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. In the bacilli an apparent split (paralogism) has created a sister clade (TIGR02882) encoding subunits (QoxA) of the aa3-type quinone oxidase complex which reacts directly with quinones, bypassing the interaction with soluble cytochrome c. This model attempts to exclude these sequences, placing them between the trusted and noise cutoffs. These families, as well as archaeal and eukaryotic cytochrome c subunit I's are included within the superfamily model, pfam00115. [Energy metabolism, Electron transport]


Pssm-ID: 213748  Cd Length: 499  Bit Score: 214.78  E-value: 1.12e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314    1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:TIGR02891 305 AVPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAA 384

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDA--YTTWNVVSTIGSSISLLGILFFLF 158
Cdd:TIGR02891 385 IYYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFPMHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLW 464

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 313877314  159 IIWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSY 193
Cdd:TIGR02891 465 NLIWSLRKGPKAGANPWGATTLEWTTSSPPPAHNF 499
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-148 3.92e-46

Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members.


Pssm-ID: 459678  Cd Length: 432  Bit Score: 157.35  E-value: 3.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314    1 AVPTGIKIFSWLATLHGTQLN-YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMA 79
Cdd:pfam00115 280 AVPSGVKVFNWLATLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFG 359

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 313877314   80 GFVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYS----DYPDAYTTWNVVSTIGSSI 148
Cdd:pfam00115 360 GIYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFFPMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-201 2.29e-145

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 413.88  E-value: 2.29e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00153 311 AVPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGG 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00153 391 FIHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFII 470

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00153 471 WESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-184 5.84e-112

Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, may play a role in assembly or oxygen delivery to the active site. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme (heme a3) and a copper ion (CuB). It also contains a low-spin heme (heme a), believed to participate in the transfer of electrons to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are transferred from cytochrome c (the electron donor) to heme a via the CuA binuclear site in subunit II, and directly from heme a to the binuclear center.


Pssm-ID: 238833  Cd Length: 488  Bit Score: 328.29  E-value: 5.84e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:cd01663  304 AVPTGIKVFSWLATMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAG 383

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:cd01663  384 FYYWFPKITGLSYNETLGKIHFWLMFIGVNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIV 463

                        170       180
                 ....*....|....*....|....*
gi 313877314 161 WESLVTQRQVIY-PMQLSSSIEWLQ 184
Cdd:cd01663  464 WESFVSGRKVIFnVGEGSTSLEWTL 488
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-201 9.15e-111

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 325.91  E-value: 9.15e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00142 311 AVPTGIKVFSWLATLHGSKVKYEPPMLWALGFIFLFTVGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFALFAG 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00142 391 FIHWFPLFTGLTLNPRWLKAHFYTMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSSLGSMISFIAVLMFVFIV 470

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00142 471 WESFVSQRLVMWSSHLSTSLEWSHRLPPDFHTYDELPILVV 511
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-199 3.11e-110

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 324.71  E-value: 3.11e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00167 313 AVPTGIKVFSWLATLHGGKIKWETPMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00167 393 FTHWFPLFTGLTLNETWTKIHFFVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNVVSSIGSLISLVAVILFLFII 472

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLL 199
Cdd:MTH00167 473 WEAFSSKRKLLPVELTSTNVEWLHGCPPPHHTWEEPPFV 511
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-197 4.37e-110

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 324.24  E-value: 4.37e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00223 310 AVPTGIKVFSWLATIYGSKIKYEAPMLWALGFIFLFTVGGLTGIILSNSSLDIMLHDTYYVVAHFHYVLSMGAVFALFAG 389

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00223 390 FNHWFPLFTGVTLHRRWAKAHFFLMFLGVNLTFFPQHFLGLAGMPRRYSDYPDCYTKWNQVSSFGSMISFVSVLFFMFIV 469

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELP 197
Cdd:MTH00223 470 WEAFVSQRSVVWSGHLSTSLEWDNLLPADFHNNSETG 506
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-201 7.03e-110

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 323.97  E-value: 7.03e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00116 313 AIPTGIKVFSWLATLHGGTIKWDPPMLWALGFIFLFTIGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00116 393 FTHWFPLFTGYTLHQTWTKAQFGVMFTGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTISSIGSLISMTAVIMLMFII 472

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00116 473 WEAFSSKRKVLQPELTTTNIEWIHGCPPPYHTFEEPAFVQV 513
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-198 8.55e-97

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 290.58  E-value: 8.55e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00037 313 AVPTGIKVFSWMATLQGSNLRWETPLLWALGFVFLFTIGGLTGIVLANSSIDVVLHDTYYVVAHFHYVLSMGAVFAIFAG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00037 393 FTHWFPLFSGVSLHPLWSKVHFFLMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSTISLVATLFFLFLI 472

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNT-PPAEHSYSELPL 198
Cdd:MTH00037 473 WEAFASQREVISPEFSSSSLEWQYSSfPPSHHTFDETPS 511
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-195 2.33e-96

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 289.09  E-value: 2.33e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00103 313 AIPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00103 393 FVHWFPLFSGYTLNDTWAKIHFTIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSSMGSFISLTAVMLMIFMI 472

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 195
Cdd:MTH00103 473 WEAFASKREVLTVELTTTNLEWLHGCPPPYHTFEE 507
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-201 3.66e-94

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 283.76  E-value: 3.66e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00077 313 AIPTGVKVFSWLATMHGGAIKWDAAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00077 393 FVHWFPLFSGYTLHSTWSKIHFGVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMMMFII 472

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 201
Cdd:MTH00077 473 WEAFSSKREVLTTELTSTNIEWLHGCPPPYHTFEEPSFVQT 513
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-195 1.56e-92

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 279.50  E-value: 1.56e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00183 313 AIPTGVKVFSWLATLHGGSIKWETPLLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAA 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00183 393 FVHWFPLFSGYTLHSTWTKIHFGVMFVGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMFLFIL 472

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 195
Cdd:MTH00183 473 WEAFAAKREVLSVELTSTNVEWLHGCPPPYHTFEE 507
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-200 1.89e-92

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 279.09  E-value: 1.89e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00007 310 AVPTGIKVFSWLATIHGSPIKYETPMLWALGFIFLFTTGGLTGIVLSNSSLDIILHDTYYVVAHFHYVLSMGAVFAIFAA 389

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00007 390 FNHWFPLFTGLTLHDRWAKAHFFLMFLGVNLTFFPQHFLGLSGMPRRYSDYPDAYTKWNVVSSFGSMLSFVALLLFIFIL 469

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLT 200
Cdd:MTH00007 470 WEAFSAQRGVIASPHMSSSLEWQDTLPLDFHNLPETGIIT 509
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-199 8.20e-80

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 247.04  E-value: 8.20e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00182 315 AVPTGIKVFSWLATIYGGTLRLDTPMLWAMGFVFLFTLGGLTGVVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIFGG 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00182 395 FYYWFGKITGYCYNELYGKIHFWLMFIGVNLTFFPQHFLGLAGFPRRYSDFADAFAGWNLVSSLGSIISIVGVVWFIYII 474

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 313877314 161 WESLVTQRQVI----YPMQLSSSIEWLQNTPPAEHSYSELPLL 199
Cdd:MTH00182 475 YDAYVREEKFIgwkeGTGESWASLEWVHSSPPLFHTYNELPFV 517
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-195 1.40e-78

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 243.43  E-value: 1.40e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00079 313 AVPTGVKVFSWLATLFGMKMKFQPLLLWVLGFIFLFTIGGLTGVILSNSSLDIILHDTYYVVSHFHYVLSLGAVFGIFTG 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00079 393 ISLWWPFMTGIVYDKLMMSAVFFLMFVGVNLTFFPLHFAGLHGMPRKYLDYPDVYSVWNVISSYGSMISVFALFLFIYVL 472

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 313877314 161 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 195
Cdd:MTH00079 473 LESFFSYRLVLHDNYINSSPEYSLSSYVFGHSYQS 507
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-199 2.25e-76

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 238.19  E-value: 2.25e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:MTH00184 315 AVPTGIKIFSWIATIFGGSLRLDTPMLWAIGFVFLFTMGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFAIFGG 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:MTH00184 395 FYYWFGKITGYCYNEVYGKIHFWLMFIGVNLTFFPQHFLGLAGLPRRYSDFHDSFAGWNQISSLGSVISIVGVVWFIYIV 474

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 313877314 161 WESLVTQRQVIYPMQLS---SSIEWLQNTPPAEHSYSELPLL 199
Cdd:MTH00184 475 YDAYVREIKFVGWVEDSghyPSLEWAQTSPPAHHTYNELPYV 516
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-164 1.04e-74

Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily.


Pssm-ID: 238461  Cd Length: 463  Bit Score: 232.04  E-value: 1.04e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:cd00919  300 AVPTGIKVFNWLATLWGGRIRFDPPMLFALGFLFLFTIGGLTGVVLANVPLDIVLHDTYYVVAHFHYVLSGGVVFAIFAG 379

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 160
Cdd:cd00919  380 LYYWFPKMTGRMLSEKLGKIHFWLWFIGFNLTFFPMHFLGLLGMPRRYADYPDGFAPWNFISSVGAFILGLGLLLFLGNL 459


                 ....
gi 313877314 161 WESL 164
Cdd:cd00919  460 FLSL 463
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-200 6.74e-71

Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];


Pssm-ID: 440605  Cd Length: 535  Bit Score: 224.24  E-value: 6.74e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:COG0843  314 AVPTGVKVFNWIATMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAG 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLF 158
Cdd:COG0843  394 LYYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFPMHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLI 473

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 313877314 159 IIWESLVTQRQV-IYPMQlSSSIEWLQNTPPAEHSYSELPLLT 200
Cdd:COG0843  474 NLVVSLRKGPKAgGNPWG-ARTLEWATPSPPPLYNFASIPVVR 515
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-193 1.12e-67

cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) of cytochrome c oxidases of bacterial origin. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits I-III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit II and heme a of subunit I to the bimetallic center formed by heme a3 and copper B. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. In the bacilli an apparent split (paralogism) has created a sister clade (TIGR02882) encoding subunits (QoxA) of the aa3-type quinone oxidase complex which reacts directly with quinones, bypassing the interaction with soluble cytochrome c. This model attempts to exclude these sequences, placing them between the trusted and noise cutoffs. These families, as well as archaeal and eukaryotic cytochrome c subunit I's are included within the superfamily model, pfam00115. [Energy metabolism, Electron transport]


Pssm-ID: 213748  Cd Length: 499  Bit Score: 214.78  E-value: 1.12e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314    1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:TIGR02891 305 AVPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAA 384

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDA--YTTWNVVSTIGSSISLLGILFFLF 158
Cdd:TIGR02891 385 IYYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFPMHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLW 464

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 313877314  159 IIWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSY 193
Cdd:TIGR02891 465 NLIWSLRKGPKAGANPWGATTLEWTTSSPPPAHNF 499
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 1-193 2.52e-61

Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits in ubiquinol oxidase varies from two to five. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons from ubiquinol to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from ubiquinol on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. It is generally believed that the channels contain water molecules that act as 'proton wires' to transfer the protons. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are believed to be transferred directly from ubiquinol (the electron donor) to the low-spin heme, and directly from the low-spin heme to the binuclear center.


Pssm-ID: 238832  Cd Length: 501  Bit Score: 198.57  E-value: 2.52e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:cd01662  306 AVPTGVKIFNWLFTMWRGRIRFETPMLWAIGFLVTFVIGGLTGVMLASPPADFQVHDTYFVVAHFHYVLIGGVVFPLFAG 385

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLF 158
Cdd:cd01662  386 FYYWFPKMFGRMLNERLGKWSFWLWFIGFNLTFFPMHILGLMGMPRRVYTYLpgPGWDPLNLISTIGAFLIAAGVLLFLI 465

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 313877314 159 IIWESLVTQRQVIY--PMQlSSSIEWLQNTPPAEHSY 193
Cdd:cd01662  466 NVIVSIRKGKRDATgdPWG-ARTLEWATSSPPPAYNF 501
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-199 4.03e-58

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 190.99  E-value: 4.03e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLN--YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIM 78
Cdd:MTH00026 314 AVPTGIKIFSWLATVSGSGRNliFTTPMAWALGFIFLFTIGGLTGIVLSNSSLDILLHDTYYVVAHFHFVLSMGAVFAIF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  79 AGFVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLF 158
Cdd:MTH00026 394 GGFYLWFGKITGYAYKDIYGLIHFWLMFIGVNITFFPQHFLGLAGLPRRYADYPDNFEDFNQISSFGSIISIIAVIWFIV 473

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 313877314 159 IIWESL---------VTQRQVIYPMQLS----SSIEWLQNTPPAEHSYSELPLL 199
Cdd:MTH00026 474 VIFDAYyreepfdinIMAKGPLIPFSCQpahfDTLEWSLTSPPEHHTYNELPYI 527
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 1-192 5.31e-56

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 184.88  E-value: 5.31e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYS-PAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMA 79
Cdd:MTH00048 311 GVPTGIKVFSWLYMLLNSRVRKSdPVVWWVVSFIVLFTIGGVTGIVLSASVLDNVLHDTWFVVAHFHYVLSLGSYSSVVI 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  80 GFVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFI 159
Cdd:MTH00048 391 MFIWWWPLITGLSLNKYLLQCHCIISMIGFNLCFFPMHYFGLCGLPRRVCVYEPSYYWINVVCTVGSFISAFSGCFFVFI 470

                        170       180       190
                 ....*....|....*....|....*....|...
gi 313877314 160 IWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHS 192
Cdd:MTH00048 471 LWESLVVKNEVLGLWGSSSCVVNVLMSPVPYHN 503
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-148 3.92e-46

Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members.


Pssm-ID: 459678  Cd Length: 432  Bit Score: 157.35  E-value: 3.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314    1 AVPTGIKIFSWLATLHGTQLN-YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMA 79
Cdd:pfam00115 280 AVPSGVKVFNWLATLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFG 359

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 313877314   80 GFVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYS----DYPDAYTTWNVVSTIGSSI 148
Cdd:pfam00115 360 GIYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFFPMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 1-197 9.73e-41

cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. [Energy metabolism, Electron transport]


Pssm-ID: 131928  Cd Length: 643  Bit Score: 145.77  E-value: 9.73e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314    1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:TIGR02882 349 AIPTGVKIFNWLLTLYKGKIRFTTPMLFSLAFIPNFLIGGVTGVMLAMASADYQYHNTYFLVAHFHYVLITGVVFACLAG 428

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDY--PDAYTTWNVVSTIGSSISLLGILFFLF 158
Cdd:TIGR02882 429 LIYWYPKMFGYKLNERLGKWCFWFFMIGFNVCFFPMYILGLDGMPRRMYTYspSDGWFPLNLISTIGALLMAIGFIFLVY 508

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 313877314  159 -IIWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELP 197
Cdd:TIGR02882 509 nIYYSHRKSPREATGDPWNGRTLEWATASPPPKYNFAVTP 548
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 1-197 2.01e-34

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 128.51  E-value: 2.01e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   1 AVPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 80
Cdd:PRK15017 356 AIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAG 435

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  81 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPD-AYTTWNVVSTIGSSISLLGILFFLFI 159
Cdd:PRK15017 436 MTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDpQFHTMLMIAASGAALIALGILCQVIQ 515

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877314 160 IWESLVTQ---RQVIYPMQLSSSIEWLQNTPPAEHSYSELP 197
Cdd:PRK15017 516 MYVSIRDRdqnRDLTGDPWGGRTLEWATSSPPPFYNFAVVP 556
ba3-like_Oxidase_I cd01660
ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are ...
 5-165 3.94e-14

ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea which catalyze the reduction of O2 and simultaneously pump protons across the membrane. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. The ba3 family contains oxidases that lack the conserved residues that form the D- and K-pathways in CcO and ubiquinol oxidase. Instead they contain a potential alternative K-pathway. Additional proton channels have been proposed for this family of oxidases but none have been identified definitively. For general information on the heme-copper oxidase superfamily, please see cd00919.


Pssm-ID: 238830  Cd Length: 473  Bit Score: 70.01  E-value: 3.94e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314   5 GIKIFSWLATLHGTQLNYSPAMLWALGFVFlftvGGLTGVVLANSSVDIILHDTYYVVAHFHyvLSMGAVFAIMA-GFVH 83
Cdd:cd01660  309 GKGLFGWIRALPWGDPMFLALFLAMLMFIP----GGAGGIINASYQLNYVVHNTAWVPGHFH--LTVGGAVALTFmAVAY 382

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877314  84 WY-PLFTGLVLNPKWLKS-QFIIMFIGVNLTFFPQHFLGLAGMPRR--YSDYPDAY-----TTWNVVSTIGSSISLLGIL 154
Cdd:cd01660  383 WLvPHLTGRELAAKRLALaQPWLWFVGMTIMSTAMHVAGLLGAPRRtaEAQYGGLPaagewAPYQQLMAIGGTILFVSGA 462

                        170
                 ....*....|.
gi 313877314 155 FFLFIIWESLV 165
Cdd:cd01660  463 LFLYILFRTLL 473
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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