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Conserved domains on  [gi|117372714|gb|ABK34271|]
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cytochrome oxidase subunit 1, partial (mitochondrion) [Zonotrichia leucophrys]

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 ...
 1-218 1.02e-158

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: 448.77  E-value: 1.02e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00116  31 TALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00116 111 LLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00116 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-218 1.02e-158

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 448.77  E-value: 1.02e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00116  31 TALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00116 111 LLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00116 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-218 1.50e-133

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: 383.76  E-value: 1.50e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:cd01663   22 TSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPPSLL 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:cd01663  102 LLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWSVLI 181

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:cd01663  182 TAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 239
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-218 1.13e-79

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


Pssm-ID: 213748  Cd Length: 499  Bit Score: 246.75  E-value: 1.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714    2 ALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLL 81
Cdd:TIGR02891  26 VLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLFGGLL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   82 LLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLIT 161
Cdd:TIGR02891 105 LLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWGILVT 184

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 117372714  162 AVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:TIGR02891 185 SILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFL 241
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-218 6.64e-77

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 240.41  E-value: 6.64e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   2 ALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLL 81
Cdd:COG0843   35 LLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLFGGLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  82 LLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLIT 161
Cdd:COG0843  114 LLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWAALVT 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 117372714 162 AVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:COG0843  194 SILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILIL 250
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-218 6.52e-49

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: 165.05  E-value: 6.52e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714    1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:pfam00115  18 GLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVLGAV 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   81 LLLASStveAGVGTGWTVYPPLAGnlahagasVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQyQTPLFVWSVLI 160
Cdd:pfam00115  97 LLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWAILA 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714  161 TAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:pfam00115 165 TAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILIL 216
 
Name Accession Description Interval E-value
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-218 1.02e-158

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 448.77  E-value: 1.02e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00116  31 TALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00116 111 LLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTPLFVWSVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00116 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-218 3.22e-142

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 406.56  E-value: 3.22e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00153  29 TSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPSLT 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00153 109 LLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMPLFVWSVLI 188

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00153 189 TAILLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 246
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-218 2.87e-134

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 386.72  E-value: 2.87e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00167  31 TALSLLIRAELSQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00167 111 LLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFITTIINMKPPGITQYQTPLFVWSILV 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00167 191 TTILLLLSLPVLAAAITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-218 1.50e-133

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: 383.76  E-value: 1.50e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:cd01663   22 TSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSFWLLPPSLL 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:cd01663  102 LLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMPLFVWSVLI 181

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:cd01663  182 TAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 239
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-218 1.75e-127

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 369.60  E-value: 1.75e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00103  31 TALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00103 111 LLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00103 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-218 1.07e-125

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 365.03  E-value: 1.07e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00077  31 TALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00077 111 LLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTSINMKPPSMSQYQTPLFVWSVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00077 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 248
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-218 3.86e-125

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 363.47  E-value: 3.86e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00183  31 TALSLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLLPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00183 111 LLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAISQYQTPLFVWAVLI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00183 191 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 248
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-218 6.87e-125

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 362.76  E-value: 6.87e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00223  28 TSLSLLIRAELGQPGALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPPSLY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00223 108 LLLSSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTIINMRSPGMQLERLPLFVWSVKV 187

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00223 188 TAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 245
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-218 7.14e-123

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 357.50  E-value: 7.14e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00142  29 TGLSLLIRAELGQPGSLLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALL 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00142 109 LLLSSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFITTVINMRAGGMKFERVPLFVWSVKI 188

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00142 189 TAILLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 246
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-218 4.96e-110

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 324.86  E-value: 4.96e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00037  31 TAMSVIIRTELAQPGSLLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSFWLIPPSFL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00037 111 LLLASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFITTIINMRTPGMTFDRLPLFVWSVFI 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00037 191 TAFLLLLSLPVLAGAITMLLTDRNINTTFFDPAGGGDPILFQHLFWFFGHPEVYILIL 248
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-218 2.43e-109

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 323.01  E-value: 2.43e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00007  28 TSMSLLIRIELGQPGAFLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPPALI 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00007 108 LLVSSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTVINMRWKGLRLERIPLFVWAVVI 187

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00007 188 TVVLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILIL 245
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-218 1.66e-103

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 308.67  E-value: 1.66e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00182  33 TAFSMLIRLELSAPGAMLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISFWLLPPALI 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00182 113 LLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFITTIFNMRAPGVTFNRLPLFVWSILI 192

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00182 193 TAFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILFQHLFWFFGHPEVYILIL 250
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-218 3.79e-102

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 304.83  E-value: 3.79e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00184  33 TAFSMLIRLELSAPGSMLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLYIGAPDMAFPRLNNISFWLLPPALT 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00184 113 LLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFITTIFNMRAPGITMDRMPLFVWSILV 192

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00184 193 TTFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 250
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-218 8.54e-99

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 295.82  E-value: 8.54e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00079  32 TSLSLIIRLELSKPGLLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLMLGAPDMSFPRLNNLSFWLLPTSLF 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAgNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00079 112 LILDSCFVDMGPGTSWTVYPPLS-TLGHPGSSVDLAIFSLHCAGISSILGGINFMVTTKNLRSSSISLEHMSLFVWTVFV 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00079 191 TVFLLVLSLPVLAGAITMLLTDRNLNTSFFDPSTGGNPLLYQHLFWFFGHPEVYILIL 248
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-218 9.55e-94

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 283.83  E-value: 9.55e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:MTH00026  32 TAFSMLIRLELSSPGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMIGAPDMAFPRLNNISFWLLPPALF 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:MTH00026 112 LLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFITTVMNMRTPGMTMSRIPLFVWSVFI 191

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00026 192 TAILLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPEVYILIL 249
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-218 4.01e-85

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: 259.39  E-value: 4.01e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPlMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:cd00919   20 GLLALLIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGARDLAFPRLNNLSFWLFPPGLL 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  81 LLLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLI 160
Cdd:cd00919   99 LLLSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTILNMRAPGMTLDKMPLFVWSVLV 178

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714 161 TAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:cd00919  179 TAILLLLALPVLAAALVMLLLDRNFGTSFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 236
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-218 1.13e-79

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


Pssm-ID: 213748  Cd Length: 499  Bit Score: 246.75  E-value: 1.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714    2 ALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMiGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLL 81
Cdd:TIGR02891  26 VLALLMRAQLATPGNTFMDAETYNQLFTMHGTIMIFLFAIPIL-AGFGNYLLPLMIGARDMAFPRLNAFSYWLYLFGGLL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   82 LLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLIT 161
Cdd:TIGR02891 105 LLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIVTILNMRAPGMTLMRMPLFVWGILVT 184

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 117372714  162 AVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:TIGR02891 185 SILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPEVYIIFL 241
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-218 6.64e-77

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 240.41  E-value: 6.64e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   2 ALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLL 81
Cdd:COG0843   35 LLALLMRLQLAGPGLGLLSPETYNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQIGARDMAFPRLNALSFWLYLFGGLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  82 LLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLIT 161
Cdd:COG0843  114 LLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTWAALVT 193

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 117372714 162 AVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:COG0843  194 SILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPEVYILIL 250
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 3-218 5.33e-68

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 216.85  E-value: 5.33e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   3 LSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLL 82
Cdd:MTH00048  34 LSLLIRLNFLDPYYNVISLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLLLGLSDLNLPRLNALSAWLLVPSIVFL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  83 LASstVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSqYQTPLFVWSVLITA 162
Cdd:MTH00048 114 LLS--MCLGAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFICTIYSAFMTNVF-SRTSIILWSYLFTS 190

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 117372714 163 VLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:MTH00048 191 ILLLLSLPVLAAAITMLLFDRNFGSAFFDPLGGGDPVLFQHMFWFFGHPEVYVLIL 246
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 2-218 5.16e-66

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


Pssm-ID: 238832  Cd Length: 501  Bit Score: 211.29  E-value: 5.16e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   2 ALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLL 81
Cdd:cd01662   27 VDALLMRTQLALPGNDFLSPEHYNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQIGARDVAFPRLNALSFWLFLFGGLL 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  82 LLASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLIT 161
Cdd:cd01662  106 LNASLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIVTILKMRAPGMTLMRMPIFTWTTLVT 185

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 117372714 162 AVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:cd01662  186 SILILFAFPVLTAALALLELDRYFGTHFFTNALGGNPMLWQHLFWIFGHPEVYILIL 242
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-218 6.52e-49

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: 165.05  E-value: 6.52e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714    1 TALSLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPiMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFL 80
Cdd:pfam00115  18 GLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARDMAFPRLNALSFWLVVLGAV 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   81 LLLASStveAGVGTGWTVYPPLAGnlahagasVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQyQTPLFVWSVLI 160
Cdd:pfam00115  97 LLLASF---GGATTGWTEYPPLVG--------VDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMPLFVWAILA 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 117372714  161 TAVLLLLSLPVLAAGITMLLTDRNLNttffdpAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:pfam00115 165 TAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPEVYILIL 216
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 4-218 2.30e-43

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


Pssm-ID: 131928  Cd Length: 643  Bit Score: 153.86  E-value: 2.30e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714    4 SLLIRAELGQPGALLGDDQVYNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLL 83
Cdd:TIGR02882  72 ALLMRAQLTVPDNKFLDAQHYNEIFTTHGVIMIIFMAMPFIIG-LMNIVVPLQIGARDVAFPVLNALSFWLFFAGAMLFN 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714   84 ASSTVEAGVGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAV 163
Cdd:TIGR02882 151 ISFVIGGSPDAGWTNYAPLAGPEFSPGVGVNYYLIALQISGIGTLMTGINFFVTILKMRAPGMKLMQMPMFTWTTLITTL 230

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 117372714  164 LLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:TIGR02882 231 IIIFAFPVLTVALALMTTDRIFDTAFFTVAHGGMPMLWANLFWIWGHPEVYIVIL 285
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 24-218 5.08e-41

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 147.39  E-value: 5.08e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714  24 YNVVVTAHAFVMIFFMVMPIMIGgFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGVGTGWTVYPPLA 103
Cdd:PRK15017  99 YDQIFTAHGVIMIFFVAMPFVIG-LMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLS 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117372714 104 GNLAHAGASVDLAIFSLHLAGISSILGAINFITTAINMKPPALSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDR 183
Cdd:PRK15017 178 GIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDR 257

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 117372714 184 NLNTTFFDPAGGGDPVLYQHLFWFFGHPEVYILIL 218
Cdd:PRK15017 258 YLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILIL 292
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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