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Conserved domains on  [gi|628818164|gb|AHY80059|]
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cytochrome c oxidase subunit I, partial (mitochondrion) [Circus aeruginosus aeruginosus]

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 ...
 2-216 2.78e-157

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 MTH00116:

Pssm-ID: 469701  Cd Length: 515  Bit Score: 444.92  E-value: 2.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00116  34 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00116 114 ASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00116 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 2-216 2.78e-157

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 444.92  E-value: 2.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00116  34 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00116 114 ASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00116 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-216 3.85e-132

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: 380.29  E-value: 3.85e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:cd01663   25 SLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPPSLLLLL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:cd01663  105 LSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWSVLITAF 184

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:cd01663  185 LLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 239
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-216 4.13e-79

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: 245.21  E-value: 4.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164    2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:TIGR02891  28 ALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLFGGLLLL 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:TIGR02891 107 ASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWGILVTSI 186

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164  162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:TIGR02891 187 LILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFL 241
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-216 8.86e-77

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 240.03  E-value: 8.86e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:COG0843   37 ALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLFGGLLLL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:COG0843  116 ISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWAALVTSI 195

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:COG0843  196 LILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILIL 250
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 2-216 1.89e-48

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: 163.90  E-value: 1.89e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164    2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:pfam00115  21 GLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVLGAVLLL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   82 ASStveAGAGTGWTVYPPLAGnmahagasVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQyQTPLFVWSVLITAV 161
Cdd:pfam00115 100 ASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWAILATAI 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164  162 LLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:pfam00115 168 LILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILIL 216
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 2-216 2.78e-157

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 444.92  E-value: 2.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00116  34 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00116 114 ASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00116 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 2-216 4.78e-143

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 408.89  E-value: 4.78e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00103  34 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00103 114 ASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00103 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 2-216 1.01e-140

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 402.71  E-value: 1.01e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00153  32 SLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPSLTLLL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00153 112 SSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMPLFVWSVLITAI 191

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00153 192 LLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 246
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 2-216 3.34e-132

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 381.33  E-value: 3.34e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00167  34 SLLIRAELSQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00167 114 ASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFITTIINMKPPGITQYQTPLFVWSILVTTI 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00167 194 LLLLSLPVLAAAITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-216 3.85e-132

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: 380.29  E-value: 3.85e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:cd01663   25 SLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPPSLLLLL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:cd01663  105 LSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWSVLITAF 184

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:cd01663  185 LLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 239
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 2-216 9.73e-125

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 362.34  E-value: 9.73e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00077  34 SLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00077 114 ASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTSINMKPPSMSQYQTPLFVWSVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00077 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 248
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 2-216 7.92e-124

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 360.01  E-value: 7.92e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00183  34 SLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00183 114 ASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAISQYQTPLFVWAVLITAV 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00183 194 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 2-216 8.12e-123

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 357.37  E-value: 8.12e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00223  31 SLLIRAELGQPGALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPPSLYLLL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00223 111 SSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTIINMRSPGMQLERLPLFVWSVKVTAF 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00223 191 LLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 245
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 2-216 6.76e-122

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 354.80  E-value: 6.76e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00142  32 SLLIRAELGQPGSLLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALLLLL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00142 112 SSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFITTVINMRAGGMKFERVPLFVWSVKITAI 191

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00142 192 LLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 246
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 2-216 3.37e-108

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 320.24  E-value: 3.37e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00037  34 SVIIRTELAQPGSLLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLIPPSFLLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00037 114 ASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFITTIINMRTPGMTFDRLPLFVWSVFITAF 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00037 194 LLLLSLPVLAGAITMLLTDRNINTTFFDPAGGGDPILFQHLFWFFGHPEVYILIL 248
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 2-216 3.69e-108

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 319.93  E-value: 3.69e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00007  31 SLLIRIELGQPGAFLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPPALILLV 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00007 111 SSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTVINMRWKGLRLERIPLFVWAVVITVV 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00007 191 LLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 245
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-216 2.98e-102

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 305.21  E-value: 2.98e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   1 YSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLL 80
Cdd:MTH00184  35 FSMLIRLELSAPGSMLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLYIGAPDMAFPRLNNISFWLLPPALTLL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  81 LASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITA 160
Cdd:MTH00184 115 LGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFITTIFNMRAPGITMDRMPLFVWSILVTT 194

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 628818164 161 VLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00184 195 FLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 250
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-216 4.85e-102

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 304.82  E-value: 4.85e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   1 YSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLL 80
Cdd:MTH00182  35 FSMLIRLELSAPGAMLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALILL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  81 LASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITA 160
Cdd:MTH00182 115 LGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFITTIFNMRAPGVTFNRLPLFVWSILITA 194

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 628818164 161 VLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00182 195 FLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILFQHLFWFFGHPEVYILIL 250
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 2-216 1.97e-97

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 292.35  E-value: 1.97e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00079  35 SLIIRLELSKPGLLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLMLGAPDMSFPRLNNLSFWLLPTSLFLIL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAgNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:MTH00079 115 DSCFVDMGPGTSWTVYPPLS-TLGHPGSSVDLAIFSLHCAGISSILGGINFMVTTKNLRSSSISLEHMSLFVWTVFVTVF 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00079 194 LLVLSLPVLAGAITMLLTDRNLNTSFFDPSTGGNPLLYQHLFWFFGHPEVYILIL 248
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-216 6.46e-94

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 284.21  E-value: 6.46e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   1 YSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLL 80
Cdd:MTH00026  34 FSMLIRLELSSPGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMIGAPDMAFPRLNNISFWLLPPALFLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  81 LASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITA 160
Cdd:MTH00026 114 LGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFITTVMNMRTPGMTMSRIPLFVWSVFITA 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 628818164 161 VLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00026 194 ILLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 249
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-216 1.17e-84

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: 258.23  E-value: 1.17e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   1 YSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPlMIGAPDMAFPRMNNMSFWLLPPSFLLL 80
Cdd:cd00919   22 LALLIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGARDLAFPRLNNLSFWLFPPGLLLL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  81 LASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITA 160
Cdd:cd00919  101 LSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTILNMRAPGMTLDKMPLFVWSVLVTA 180

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 628818164 161 VLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:cd00919  181 ILLLLALPVLAAALVMLLLDRNFGTSFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 236
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-216 4.13e-79

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: 245.21  E-value: 4.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164    2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:TIGR02891  28 ALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLFGGLLLL 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:TIGR02891 107 ASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWGILVTSI 186

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164  162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:TIGR02891 187 LILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFL 241
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-216 8.86e-77

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 240.03  E-value: 8.86e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:COG0843   37 ALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLFGGLLLL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:COG0843  116 ISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWAALVTSI 195

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:COG0843  196 LILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILIL 250
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 2-216 5.59e-67

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 214.16  E-value: 5.59e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:MTH00048  35 SLLIRLNFLDPYYNVISLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLLLGLSDLNLPRLNALSAWLLVPSIVFLL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  82 ASstVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSqYQTPLFVWSVLITAV 161
Cdd:MTH00048 115 LS--MCLGAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFICTIYSAFMTNVF-SRTSIILWSYLFTSI 191

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164 162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:MTH00048 192 LLLLSLPVLAAAITMLLFDRNFGSAFFDPLGGGDPVLFQHMFWFFGHPEVYVLIL 246
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 3-216 4.00e-66

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: 211.67  E-value: 4.00e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   3 LLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLA 82
Cdd:cd01662   30 LLMRTQLALPGNDFLSPEHYNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQIGARDVAFPRLNALSFWLFLFGGLLLNA 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  83 SSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAVL 162
Cdd:cd01662  109 SLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIVTILKMRAPGMTLMRMPIFTWTTLVTSIL 188

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 628818164 163 LLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:cd01662  189 ILFAFPVLTAALALLELDRYFGTHFFTNALGGNPMLWQHLFWIFGHPEVYILIL 242
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 2-216 1.89e-48

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: 163.90  E-value: 1.89e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164    2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:pfam00115  21 GLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVLGAVLLL 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   82 ASStveAGAGTGWTVYPPLAGnmahagasVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQyQTPLFVWSVLITAV 161
Cdd:pfam00115 100 ASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWAILATAI 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164  162 LLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:pfam00115 168 LILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILIL 216
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 2-216 1.21e-43

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: 154.63  E-value: 1.21e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164    2 SLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 81
Cdd:TIGR02882  72 ALLMRAQLTVPDNKFLDAQHYNEIFTTHGVIMIIFMAMPFIIG-LMNIVVPLQIGARDVAFPVLNALSFWLFFAGAMLFN 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164   82 ASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 161
Cdd:TIGR02882 151 ISFVIGGSPDAGWTNYAPLAGPEFSPGVGVNYYLIALQISGIGTLMTGINFFVTILKMRAPGMKLMQMPMFTWTTLITTL 230

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 628818164  162 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:TIGR02882 231 IIIFAFPVLTVALALMTTDRIFDTAFFTVAHGGMPMLWANLFWIWGHPEVYIVIL 285
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 22-216 5.41e-42

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 150.09  E-value: 5.41e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164  22 YNVIVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLA 101
Cdd:PRK15017  99 YDQIFTAHGVIMIFFVAMPFVIG-LMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLS 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 628818164 102 GNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDR 181
Cdd:PRK15017 178 GIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDR 257

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 628818164 182 NLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 216
Cdd:PRK15017 258 YLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILIL 292
 
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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