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Conserved domains on  [gi|292388993|gb|ADE23498|]
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cytochrome oxidase subunit 1, partial (mitochondrion) [Circus 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 ...
 1-247 2.02e-179

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: 502.70  E-value: 2.02e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00116   8 FSTNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00116  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00116 168 CINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00116 248 LPGFGII 254
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-247 2.02e-179

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 502.70  E-value: 2.02e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00116   8 FSTNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00116  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00116 168 CINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00116 248 LPGFGII 254
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 5-247 2.98e-153

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: 435.37  E-value: 2.98e-153
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPD 84
Cdd:cd01663    3 HKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:cd01663   83 MAFPRLNNLSFWLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNM 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:cd01663  163 RAPGMTLEKMPLFVWSVLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 242


                 ...
gi 292388993 245 GII 247
Cdd:cd01663  243 GII 245
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 5-247 1.96e-90

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: 275.64  E-value: 1.96e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993    5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPD 84
Cdd:TIGR02891   6 HKRIGILYLVTAFAFFLVGGVLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:TIGR02891  85 MAFPRLNAFSYWLYLFGGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNM 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:TIGR02891 165 RAPGMTLMRMPLFVWGILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFLPAF 244


                  ...
gi 292388993  245 GII 247
Cdd:TIGR02891 245 GII 247
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-247 8.51e-88

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 269.69  E-value: 8.51e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMI 80
Cdd:COG0843   11 TTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:COG0843   90 GARDMAFPRLNALSFWLYLFGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVT 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:COG0843  170 ILKMRAPGMTLMRMPLFTWAALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILI 249


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:COG0843  250 LPAFGIV 256
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 7-247 3.91e-56

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: 185.08  E-value: 3.91e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993    7 DIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMA 86
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   87 FPRMNNMSFWLLPPSFLLLLASStveAGAGTGWTVYPPLAGnmahagasVDLAIFSLHLAGISSILGAINFITTAINMKP 166
Cdd:pfam00115  80 FPRLNALSFWLVVLGAVLLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRA 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  167 PALSQyQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPILYQHLFWFFGHPEVYILILPGFGI 246
Cdd:pfam00115 149 PGMTL-RMPLFVWAILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILILPAFGI 221


                  .
gi 292388993  247 I 247
Cdd:pfam00115 222 I 222
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-247 2.02e-179

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 502.70  E-value: 2.02e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00116   8 FSTNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00116  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00116 168 CINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00116 248 LPGFGII 254
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-247 6.56e-165

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 465.50  E-value: 6.56e-165
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00153   6 FSTNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLML 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00153  86 GAPDMAFPRMNNMSFWLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00153 166 IINMRSKGMTLDRMPLFVWSVLITAILLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILI 245


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00153 246 LPGFGMI 252
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-247 1.55e-154

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 439.50  E-value: 1.55e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00167   8 FSTNHKDIGTLYFIFGAWAGMVGTALSLLIRAELSQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00167  88 GAPDMAFPRMNNMSFWLLPPSLLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00167 168 IINMKPPGITQYQTPLFVWSILVTTILLLLSLPVLAAAITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00167 248 LPGFGMI 254
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 5-247 2.98e-153

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: 435.37  E-value: 2.98e-153
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPD 84
Cdd:cd01663    3 HKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:cd01663   83 MAFPRLNNLSFWLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNM 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:cd01663  163 RAPGMTLEKMPLFVWSVLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 242


                 ...
gi 292388993 245 GII 247
Cdd:cd01663  243 GII 245
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-247 1.66e-146

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 418.90  E-value: 1.66e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00103   8 FSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00103  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00103 168 IINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00103 248 LPGFGMI 254
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-247 3.00e-146

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 418.58  E-value: 3.00e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00077   8 FSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00077  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00077 168 SINMKPPSMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00077 248 LPGFGMI 254
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-247 1.77e-144

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 413.94  E-value: 1.77e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00183   8 FSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00183  88 GAPDMAFPRMNNMSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00183 168 IINMKPPAISQYQTPLFVWAVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00183 248 LPGFGMI 254
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-247 3.67e-143

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 410.52  E-value: 3.67e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00223   5 FSTNHKDIGTLYLIFGMWSGLVGTSLSLLIRAELGQPGALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLML 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00223  85 GAPDMAFPRLNNMSFWLLPPSLYLLLSSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFITT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00223 165 IINMRSPGMQLERLPLFVWSVKVTAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILI 244


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00223 245 LPGFGMI 251
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-247 6.90e-143

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 409.88  E-value: 6.90e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00142   6 FSTNHKDIGTLYFLFGAWAGMVGTGLSLLIRAELGQPGSLLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLML 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00142  86 GAPDMAFPRMNNMSFWLLPPALLLLLSSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFITT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00142 166 VINMRAGGMKFERVPLFVWSVKITAILLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILI 245


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00142 246 LPGFGMI 252
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-247 3.79e-129

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 374.94  E-value: 3.79e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00037   8 FSTNHKDIGTLYLIFGAWAGMVGTAMSVIIRTELAQPGSLLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLMI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00037  88 GAPDMAFPRMNNMSFWLIPPSFLLLLASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFITT 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00037 168 IINMRTPGMTFDRLPLFVWSVFITAFLLLLSLPVLAGAITMLLTDRNINTTFFDPAGGGDPILFQHLFWFFGHPEVYILI 247


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00037 248 LPGFGMI 254
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-247 5.65e-125

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 364.22  E-value: 5.65e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00007   5 YSTNHKDIGTLYFILGVWGGLLGTSMSLLIRIELGQPGAFLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLML 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00007  85 GAPDMAFPRLNNMSFWLLPPALILLVSSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFITT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00007 165 VINMRWKGLRLERIPLFVWAVVITVVLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILI 244


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00007 245 LPGFGAI 251
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-247 5.84e-120

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 351.82  E-value: 5.84e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00182  10 FSTNHKDIGTLYLVFGAGAGMIGTAFSMLIRLELSAPGAMLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLYI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00182  90 GAPDMAFPRLNNISFWLLPPALILLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFITT 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00182 170 IFNMRAPGVTFNRLPLFVWSILITAFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILFQHLFWFFGHPEVYILI 249


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00182 250 LPGFGMI 256
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-247 7.75e-120

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 351.44  E-value: 7.75e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00184  10 FSTNHKDIGTLYLLFGAFAGMIGTAFSMLIRLELSAPGSMLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLYI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00184  90 GAPDMAFPRLNNISFWLLPPALTLLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFITT 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00184 170 IFNMRAPGITMDRMPLFVWSILVTTFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 249


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00184 250 LPGFGII 256
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 2-247 7.77e-115

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 338.19  E-value: 7.77e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   2 SPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIG 81
Cdd:MTH00079  10 SSNHKDIGTLYFLFGLWSGMVGTSLSLIIRLELSKPGLLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLMLG 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  82 APDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAgNMAHAGASVDLAIFSLHLAGISSILGAINFITTA 161
Cdd:MTH00079  90 APDMSFPRLNNLSFWLLPTSLFLILDSCFVDMGPGTSWTVYPPLS-TLGHPGSSVDLAIFSLHCAGISSILGGINFMVTT 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 162 INMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 241
Cdd:MTH00079 169 KNLRSSSISLEHMSLFVWTVFVTVFLLVLSLPVLAGAITMLLTDRNLNTSFFDPSTGGNPLLYQHLFWFFGHPEVYILIL 248


                 ....*.
gi 292388993 242 PGFGII 247
Cdd:MTH00079 249 PAFGII 254
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-247 1.62e-108

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 323.12  E-value: 1.62e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00026   9 FSCNHKDIGSLYLVFGALSGAIGTAFSMLIRLELSSPGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMI 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00026  89 GAPDMAFPRLNNISFWLLPPALFLLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFITT 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00026 169 VMNMRTPGMTMSRIPLFVWSVFITAILLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 248


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00026 249 LPGFGII 255
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 5-247 8.88e-98

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: 293.28  E-value: 8.88e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPlMIGAPD 84
Cdd:cd00919    1 HKDIGLLYLIFAFVALLLGGLLALLIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGARD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:cd00919   80 LAFPRLNNLSFWLFPPGLLLLLSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTILNM 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:cd00919  160 RAPGMTLDKMPLFVWSVLVTAILLLLALPVLAAALVMLLLDRNFGTSFFDPAGGGDPVLYQHLFWFFGHPEVYILILPAF 239


                 ...
gi 292388993 245 GII 247
Cdd:cd00919  240 GAI 242
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 5-247 1.96e-90

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: 275.64  E-value: 1.96e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993    5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPD 84
Cdd:TIGR02891   6 HKRIGILYLVTAFAFFLVGGVLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:TIGR02891  85 MAFPRLNAFSYWLYLFGGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNM 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:TIGR02891 165 RAPGMTLMRMPLFVWGILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFLPAF 244


                  ...
gi 292388993  245 GII 247
Cdd:TIGR02891 245 GII 247
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-247 8.51e-88

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 269.69  E-value: 8.51e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMI 80
Cdd:COG0843   11 TTVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:COG0843   90 GARDMAFPRLNALSFWLYLFGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVT 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:COG0843  170 ILKMRAPGMTLMRMPLFTWAALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILI 249


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:COG0843  250 LPAFGIV 256
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 1-247 4.19e-81

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 251.91  E-value: 4.19e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   1 FSPTHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMI 80
Cdd:MTH00048   9 FTLDHKRIGVIYTLLGVWSGFVGLSLSLLIRLNFLDPYYNVISLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLLL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  81 GAPDMAFPRMNNMSFWLLPPSFLLLLASstVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITT 160
Cdd:MTH00048  89 GLSDLNLPRLNALSAWLLVPSIVFLLLS--MCLGAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFICT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 161 AINMKPPALSqYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILI 240
Cdd:MTH00048 167 IYSAFMTNVF-SRTSIILWSYLFTSILLLLSLPVLAAAITMLLFDRNFGSAFFDPLGGGDPVLFQHMFWFFGHPEVYVLI 245


                 ....*..
gi 292388993 241 LPGFGII 247
Cdd:MTH00048 246 LPGFGII 252
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 5-247 2.30e-73

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: 231.70  E-value: 2.30e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPD 84
Cdd:cd01662    7 HKRIGIMYIITAFVFFLRGGVDALLMRTQLALPGNDFLSPEHYNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQIGARD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:cd01662   86 VAFPRLNALSFWLFLFGGLLLNASLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIVTILKM 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:cd01662  166 RAPGMTLMRMPIFTWTTLVTSILILFAFPVLTAALALLELDRYFGTHFFTNALGGNPMLWQHLFWIFGHPEVYILILPAF 245


                 ...
gi 292388993 245 GII 247
Cdd:cd01662  246 GIF 248
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 7-247 3.91e-56

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: 185.08  E-value: 3.91e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993    7 DIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMA 86
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   87 FPRMNNMSFWLLPPSFLLLLASStveAGAGTGWTVYPPLAGnmahagasVDLAIFSLHLAGISSILGAINFITTAINMKP 166
Cdd:pfam00115  80 FPRLNALSFWLVVLGAVLLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRA 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  167 PALSQyQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPILYQHLFWFFGHPEVYILILPGFGI 246
Cdd:pfam00115 149 PGMTL-RMPLFVWAILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILILPAFGI 221


                  .
gi 292388993  247 I 247
Cdd:pfam00115 222 I 222
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 5-246 1.82e-49

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: 171.58  E-value: 1.82e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993    5 HKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPD 84
Cdd:TIGR02882  50 HKKIGVMYIICAVLMLFRGGIDALLMRAQLTVPDNKFLDAQHYNEIFTTHGVIMIIFMAMPFIIG-LMNIVVPLQIGARD 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   85 MAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAINFITTAINM 164
Cdd:TIGR02882 129 VAFPVLNALSFWLFFAGAMLFNISFVIGGSPDAGWTNYAPLAGPEFSPGVGVNYYLIALQISGIGTLMTGINFFVTILKM 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  165 KPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGF 244
Cdd:TIGR02882 209 RAPGMKLMQMPMFTWTTLITTLIIIFAFPVLTVALALMTTDRIFDTAFFTVAHGGMPMLWANLFWIWGHPEVYIVILPAF 288


                  ..
gi 292388993  245 GI 246
Cdd:TIGR02882 289 GI 290
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 2-246 9.44e-46

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 161.64  E-value: 9.44e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993   2 SPTHKDIGTLYLIFGAWAGMVGTALSLLIR-----AELGQPGTLlgDDQIYNVIVTAHAFVMIFFMVMPIMIGgFGNWLV 76
Cdd:PRK15017  51 SVDHKRLGIMYIIVAIVMLLRGFADAIMMRsqqalASAGEAGFL--PPHHYDQIFTAHGVIMIFFVAMPFVIG-LMNLVV 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993  77 PLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNMAHAGASVDLAIFSLHLAGISSILGAIN 156
Cdd:PRK15017 128 PLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGIN 207

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292388993 157 FITTAINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEV 236
Cdd:PRK15017 208 FFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEV 287

                        250
                 ....*....|
gi 292388993 237 YILILPGFGI 246
Cdd:PRK15017 288 YILILPVFGV 297
 
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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