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Conserved domains on  [gi|1622987525|gb|QCE31209|]
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cytochrome c oxidase subunit I, partial (mitochondrion) [Halcyon coromanda]

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 ...
 1-225 5.13e-163

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: 459.94  E-value: 5.13e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00116   28 MVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00116  108 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00116  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-225 5.13e-163

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 459.94  E-value: 5.13e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00116   28 MVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00116  108 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00116  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-225 4.61e-138

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: 395.70  E-value: 4.61e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:cd01663    19 LVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:cd01663    99 SLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWS 178

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:cd01663   179 VLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 243
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-225 3.16e-82

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: 253.30  E-value: 3.16e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:TIGR02891  22 LVGGVLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:TIGR02891 101 GGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWG 180

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:TIGR02891 181 ILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFLPAFG 245
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-225 2.04e-79

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 247.35  E-value: 2.04e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:COG0843    31 LIGGLLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLF 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:COG0843   110 GGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWA 189

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:COG0843   190 ALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILILPAFG 254
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-225 9.13e-52

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: 172.76  E-value: 9.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:pfam00115  15 LVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASStveAGAGTGWTVYPPLAGnlahggasVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQyQTPLFVWS 160
Cdd:pfam00115  94 GAVLLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWA 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:pfam00115 162 ILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILILPAFG 220
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-225 5.13e-163

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 459.94  E-value: 5.13e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00116   28 MVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00116  108 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00116  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-225 1.70e-148

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 423.14  E-value: 1.70e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00103   28 MVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00103  108 SFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00103  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-225 3.62e-148

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 422.35  E-value: 3.62e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00153   26 MVGTSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPP 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00153  106 SLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMPLFVWS 185

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00153  186 VLITAILLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 250
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-225 1.12e-138

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 398.28  E-value: 1.12e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00167   28 MVGTALSLLIRAELSQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00167  108 SLLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFITTIINMKPPGITQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00167  188 ILVTTILLLLSLPVLAAAITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-225 4.61e-138

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: 395.70  E-value: 4.61e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:cd01663    19 LVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:cd01663    99 SLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWS 178

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:cd01663   179 VLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 243
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-225 4.67e-131

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 378.90  E-value: 4.67e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00077   28 MVGTALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00077  108 SFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTSINMKPPSMSQYQTPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00077  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 252
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-225 1.07e-129

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 375.42  E-value: 1.07e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00183   28 MVGTALSLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLLPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00183  108 SFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAISQYQTPLFVWA 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00183  188 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 252
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-225 1.12e-128

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 372.77  E-value: 1.12e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00223   25 LVGTSLSLLIRAELGQPGALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPP 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00223  105 SLYLLLSSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTIINMRSPGMQLERLPLFVWS 184

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00223  185 VKVTAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 249
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-225 7.76e-128

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 370.59  E-value: 7.76e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00142   26 MVGTGLSLLIRAELGQPGSLLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPP 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00142  106 ALLLLLSSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFITTVINMRAGGMKFERVPLFVWS 185

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00142  186 VKITAILLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 250
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-225 2.98e-114

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 336.03  E-value: 2.98e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00037   28 MVGTAMSVIIRTELAQPGSLLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLIPP 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00037  108 SFLLLLASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFITTIINMRTPGMTFDRLPLFVWS 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00037  188 VFITAFLLLLSLPVLAGAITMLLTDRNINTTFFDPAGGGDPILFQHLFWFFGHPEVYILILPGFG 252
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-225 5.96e-112

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 329.94  E-value: 5.96e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00007   25 LLGTSMSLLIRIELGQPGAFLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPP 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00007  105 ALILLVSSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTVINMRWKGLRLERIPLFVWA 184

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00007  185 VVITVVLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 249
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-225 1.03e-107

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 319.84  E-value: 1.03e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00182   30 MIGTAFSMLIRLELSAPGAMLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00182  110 ALILLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFITTIFNMRAPGVTFNRLPLFVWS 189

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00182  190 ILITAFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILFQHLFWFFGHPEVYILILPGFG 254
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-225 1.35e-106

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 316.77  E-value: 1.35e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00184   30 MIGTAFSMLIRLELSAPGSMLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLYIGAPDMAFPRLNNISFWLLPP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00184  110 ALTLLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFITTIFNMRAPGITMDRMPLFVWS 189

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00184  190 ILVTTFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 254
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-225 1.85e-102

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 305.84  E-value: 1.85e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:MTH00079   29 MVGTSLSLIIRLELSKPGLLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLMLGAPDMSFPRLNNLSFWLLPT 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAgNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:MTH00079  109 SLFLILDSCFVDMGPGTSWTVYPPLS-TLGHPGSSVDLAIFSLHCAGISSILGGINFMVTTKNLRSSSISLEHMSLFVWT 187

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00079  188 VFVTVFLLVLSLPVLAGAITMLLTDRNLNTSFFDPSTGGNPLLYQHLFWFFGHPEVYILILPAFG 252
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 2-225 7.68e-98

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 294.61  E-value: 7.68e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   2 VGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPS 81
Cdd:MTH00026   30 IGTAFSMLIRLELSSPGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMIGAPDMAFPRLNNISFWLLPPA 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  82 FLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWSV 161
Cdd:MTH00026  110 LFLLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFITTVMNMRTPGMTMSRIPLFVWSV 189

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622987525 162 LITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00026  190 FITAILLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFG 253
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-225 2.17e-89

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: 270.56  E-value: 2.17e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPlMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:cd00919    17 LLGGLLALLIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGARDLAFPRLNNLSFWLFPP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:cd00919    96 GLLLLLSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTILNMRAPGMTLDKMPLFVWS 175

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:cd00919   176 VLVTAILLLLALPVLAAALVMLLLDRNFGTSFFDPAGGGDPVLYQHLFWFFGHPEVYILILPAFG 240
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-225 3.16e-82

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: 253.30  E-value: 3.16e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:TIGR02891  22 LVGGVLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:TIGR02891 101 GGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWG 180

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:TIGR02891 181 ILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFLPAFG 245
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-225 2.04e-79

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 247.35  E-value: 2.04e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:COG0843    31 LIGGLLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLF 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWS 160
Cdd:COG0843   110 GGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWA 189

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:COG0843   190 ALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILILPAFG 254
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 2-225 1.32e-72

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 229.18  E-value: 1.32e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   2 VGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPS 81
Cdd:MTH00048   30 VGLSLSLLIRLNFLDPYYNVISLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLLLGLSDLNLPRLNALSAWLLVPS 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  82 FLLLLASstVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSqYQTPLFVWSV 161
Cdd:MTH00048  110 IVFLLLS--MCLGAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFICTIYSAFMTNVF-SRTSIILWSY 186

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622987525 162 LITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:MTH00048  187 LFTSILLLLSLPVLAAAITMLLFDRNFGSAFFDPLGGGDPVLFQHMFWFFGHPEVYVLILPGFG 250
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 3-225 3.46e-67

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: 214.75  E-value: 3.46e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   3 GTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSF 82
Cdd:cd01662    25 GGVDALLMRTQLALPGNDFLSPEHYNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQIGARDVAFPRLNALSFWLFLFGG 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  83 LLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWSVL 162
Cdd:cd01662   104 LLLNASLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIVTILKMRAPGMTLMRMPIFTWTTL 183

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622987525 163 ITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:cd01662   184 VTSILILFAFPVLTAALALLELDRYFGTHFFTNALGGNPMLWQHLFWIFGHPEVYILILPAFG 246
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-225 9.13e-52

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: 172.76  E-value: 9.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   1 MVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPP 80
Cdd:pfam00115  15 LVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  81 SFLLLLASStveAGAGTGWTVYPPLAGnlahggasVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQyQTPLFVWS 160
Cdd:pfam00115  94 GAVLLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWA 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622987525 161 VLITAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:pfam00115 162 ILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILILPAFG 220
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 3-225 1.46e-45

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: 160.02  E-value: 1.46e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525   3 GTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSF 82
Cdd:TIGR02882  68 GGIDALLMRAQLTVPDNKFLDAQHYNEIFTTHGVIMIIFMAMPFIIG-LMNIVVPLQIGARDVAFPVLNALSFWLFFAGA 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  83 LLLLASSTVEAGAGTGWTVYPPLAGNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWSVL 162
Cdd:TIGR02882 147 MLFNISFVIGGSPDAGWTNYAPLAGPEFSPGVGVNYYLIALQISGIGTLMTGINFFVTILKMRAPGMKLMQMPMFTWTTL 226

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622987525 163 ITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:TIGR02882 227 ITTLIIIFAFPVLTVALALMTTDRIFDTAFFTVAHGGMPMLWANLFWIWGHPEVYIVILPAFG 289
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 27-225 1.01e-42

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 152.40  E-value: 1.01e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525  27 YNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLA 106
Cdd:PRK15017   99 YDQIFTAHGVIMIFFVAMPFVIG-LMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLS 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622987525 107 GNLAHGGASVDLAIFSLHLAGVSSILGAINFITTATNMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDR 186
Cdd:PRK15017  178 GIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDR 257

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1622987525 187 NLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILILPGFG 225
Cdd:PRK15017  258 YLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFG 296
 
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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