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Conserved domains on  [gi|1318866609|gb|AUJ87880|]
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cytochrome oxidase subunit I, partial (mitochondrion) [Ornithomya avicularia]

Protein Classification

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 ...
 1-70 3.35e-29

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: 107.26  E-value: 3.35e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00153  437 RYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSEL 506
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-70 3.35e-29

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 107.26  E-value: 3.35e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00153  437 RYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSEL 506
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-56 3.94e-12

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: 59.03  E-value: 3.94e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMF-PTQLNSSIEW 56
Cdd:cd01663   430 RYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVWESFVSGRKVIFnVGEGSTSLEW 486
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-70 3.35e-29

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 107.26  E-value: 3.35e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00153  437 RYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSEL 506
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-70 2.73e-20

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 82.08  E-value: 2.73e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00142  437 RYSDYPDAYTTWNVVSSLGSMISFIAVLMFVFIVWESFVSQRLVMWSSHLSTSLEWSHRLPPDFHTYDEL 506
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-70 1.31e-16

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 71.93  E-value: 1.31e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00223  436 RYSDYPDCYTKWNQVSSFGSMISFVSVLFFMFIVWEAFVSQRSVVWSGHLSTSLEWDNLLPADFHNNSET 505
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-69 7.09e-16

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 69.74  E-value: 7.09e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00116  439 RYSDYPDAYTLWNTISSIGSLISMTAVIMLMFIIWEAFSSKRKVLQPELTTTNIEWIHGCPPPYHTFEE 507
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-69 1.98e-15

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 68.55  E-value: 1.98e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00167  439 RYSDYPDAYTLWNVVSSIGSLISLVAVILFLFIIWEAFSSKRKLLPVELTSTNVEWLHGCPPPHHTWEE 507
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-69 3.23e-15

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 67.93  E-value: 3.23e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEW-FQNTPPAEHSYSE 69
Cdd:MTH00037  439 RYSDYPDAYTLWNTVSSIGSTISLVATLFFLFLIWEAFASQREVISPEFSSSSLEWqYSSFPPSHHTFDE 508
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-69 1.27e-13

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 63.38  E-value: 1.27e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00007  436 RYSDYPDAYTKWNVVSSFGSMLSFVALLLFIFILWEAFSAQRGVIASPHMSSSLEWQDTLPLDFHNLPE 504
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-69 3.51e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 62.25  E-value: 3.51e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00183  439 RYSDYPDAYTLWNTVSSIGSLISLVAVIMFLFILWEAFAAKREVLSVELTSTNVEWLHGCPPPYHTFEE 507
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-69 3.71e-13

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 61.88  E-value: 3.71e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00077  439 RYSDYPDAYTLWNTVSSIGSLISLVAVIMMMFIIWEAFSSKREVLTTELTSTNIEWLHGCPPPYHTFEE 507
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-69 6.43e-13

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 61.44  E-value: 6.43e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMFPTQLNSSIEWFQNTPPAEHSYSE 69
Cdd:MTH00103  439 RYSDYPDAYTTWNTVSSMGSFISLTAVMLMIFMIWEAFASKREVLTVELTTTNLEWLHGCPPPYHTFEE 507
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-56 3.94e-12

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: 59.03  E-value: 3.94e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLVMF-PTQLNSSIEW 56
Cdd:cd01663   430 RYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVWESFVSGRKVIFnVGEGSTSLEW 486
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-70 3.30e-09

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 50.98  E-value: 3.30e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQRLV---MFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00184  441 RYSDFHDSFAGWNQISSLGSVISIVGVVWFIYIVYDAYVREIKFvgwVEDSGHYPSLEWAQTSPPAHHTYNEL 513
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-70 3.41e-08

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 47.89  E-value: 3.41e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQR----LVMFPTQLNSSIEWFQNTPPAEHSYSEL 70
Cdd:MTH00182  441 RYSDFADAFAGWNLVSSLGSIISIVGVVWFIYIIYDAYVREEkfigWKEGTGESWASLEWVHSSPPLFHTYNEL 514
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-38 1.33e-03

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: 34.81  E-value: 1.33e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESI 38
Cdd:cd00919   426 RYADYPDGFAPWNFISSVGAFILGLGLLLFLGNLFLSL 463
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-70 4.28e-03

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 33.45  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1318866609   1 RYSDYPDAYTSWNIISSIGSTISFLGILYFFFIIWESIMSQR-----------LVMFPTQLN--SSIEWFQNTPPAEHSY 67
Cdd:MTH00026  442 RYADYPDNFEDFNQISSFGSIISIIAVIWFIVVIFDAYYREEpfdinimakgpLIPFSCQPAhfDTLEWSLTSPPEHHTY 521


                  ...
gi 1318866609  68 SEL 70
Cdd:MTH00026  522 NEL 524
 
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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