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Conserved domains on  [gi|802084235|gb|AKA94332|]
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cytochrome oxidase subunit 1, partial (mitochondrion) [Gracilariopsis silvana]

Protein Classification

heme-copper oxidase family protein( domain architecture ID 14)

heme-copper oxidase family protein may catalyze the transfer of electrons from an electron donor onto molecular oxygen

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Heme_Cu_Oxidase_I super family cl00275
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 2-236 3.52e-154

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 cd01663:

Pssm-ID: 469701  Cd Length: 488  Bit Score: 436.91  E-value: 3.52e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   2 TNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLllGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIMI 81
Cdd:cd01663    1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQL--GNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  82 GSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIST 161
Cdd:cd01663   79 GAPDMAFPRLNNLSFWLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITT 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 802084235 162 ILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:cd01663  159 IFNMRAPGMTLEKMPLFVWSVLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPE 233
 
Name Accession Description Interval E-value
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-236 3.52e-154

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: 436.91  E-value: 3.52e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   2 TNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLllGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIMI 81
Cdd:cd01663    1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQL--GNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  82 GSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIST 161
Cdd:cd01663   79 GAPDMAFPRLNNLSFWLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITT 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 802084235 162 ILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:cd01663  159 IFNMRAPGMTLEKMPLFVWSVLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPE 233
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-236 2.07e-152

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 433.53  E-value: 2.07e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00153   7 STNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLM 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00153  85 LGAPDMAFPRMNNMSFWLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFIT 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00153 165 TIINMRSKGMTLDRMPLFVWSVLITAILLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPE 240
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-236 7.17e-98

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: 294.13  E-value: 7.17e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235    1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIM 80
Cdd:TIGR02891   3 TVDHKRIGILYLVTAFAFFLVGGVLALLMRAQLATPGNTFM--DAETYNQLFTMHGTIMIFLFAIP-ILAGFGNYLLPLM 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:TIGR02891  80 IGARDMAFPRLNAFSYWLYLFGGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIV 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235  161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:TIGR02891 160 TILNMRAPGMTLMRMPLFVWGILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPE 235
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-236 4.75e-93

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 282.79  E-value: 4.75e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLLGNHqiYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIM 80
Cdd:COG0843   12 TVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLLSPET--YNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQ 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:COG0843   89 IGARDMAFPRLNALSFWLYLFGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIV 168

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:COG0843  169 TILKMRAPGMTLMRMPLFTWAALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPE 244
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 6-236 1.71e-57

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: 188.17  E-value: 1.71e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235    6 DIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIMIGSPD 85
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFL--SPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   86 MAFPRLNNISFWLLPPSLCLLIASAiveVGVGTGWTVYPPLssiqshsgGAVDLAIFSLHISGASSILGAINFISTILNM 165
Cdd:pfam00115  78 MAFPRLNALSFWLVVLGAVLLLASF---GGATTGWTEYPPL--------VGVDLWYIGLLLAGVSSLLGAINFIVTILKR 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 802084235  166 RNPGQSMyRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNttffdpAGGGDPVLYQHLFWFFGHPE 236
Cdd:pfam00115 147 RAPGMTL-RMPLFVWAILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPE 210
 
Name Accession Description Interval E-value
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-236 3.52e-154

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: 436.91  E-value: 3.52e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   2 TNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLllGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIMI 81
Cdd:cd01663    1 TNHKDIGTLYLIFGLWSGLVGTSLSLLIRLELSQPGSQL--GNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  82 GSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIST 161
Cdd:cd01663   79 GAPDMAFPRLNNLSFWLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITT 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 802084235 162 ILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:cd01663  159 IFNMRAPGMTLEKMPLFVWSVLITAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPE 233
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-236 2.07e-152

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 433.53  E-value: 2.07e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00153   7 STNHKDIGTLYFIFGAWSGMVGTSLSLLIRAELGQPGS--LIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLM 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00153  85 LGAPDMAFPRMNNMSFWLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFIT 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00153 165 TIINMRSKGMTLDRMPLFVWSVLITAILLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPE 240
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-236 1.08e-137

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 395.97  E-value: 1.08e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00167   9 STNHKDIGTLYFIFGAWAGMVGTALSLLIRAELSQPGS--LLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00167  87 IGAPDMAFPRMNNMSFWLLPPSLLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00167 167 TIINMKPPGITQYQTPLFVWSILVTTILLLLSLPVLAAAITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPE 242
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-236 2.45e-135

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 390.22  E-value: 2.45e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00116   9 STNHKDIGTLYLIFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00116  87 IGAPDMAFPRMNNMSFWLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00116 167 TCINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPE 242
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-236 8.15e-132

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 381.25  E-value: 8.15e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGnqLLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00223   6 STNHKDIGTLYLIFGMWSGLVGTSLSLLIRAELGQPG--ALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLM 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00223  84 LGAPDMAFPRLNNMSFWLLPPSLYLLLSSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFIT 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00223 164 TIINMRSPGMQLERLPLFVWSVKVTAFLLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPE 239
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-236 1.36e-129

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 375.60  E-value: 1.36e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00142   7 STNHKDIGTLYFLFGAWAGMVGTGLSLLIRAELGQPGS--LLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLM 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00142  85 LGAPDMAFPRMNNMSFWLLPPALLLLLSSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFIT 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00142 165 TVINMRAGGMKFERVPLFVWSVKITAILLLLSLPVLAGAITMLLTDRNFNTSFFDPAGGGDPILYQHLFWFFGHPE 240
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-236 9.92e-124

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 361.06  E-value: 9.92e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00182  11 STNHKDIGTLYLVFGAGAGMIGTAFSMLIRLELSAPGA--MLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLY 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00182  89 IGAPDMAFPRLNNISFWLLPPALILLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFIT 168

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00182 169 TIFNMRAPGVTFNRLPLFVWSILITAFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILFQHLFWFFGHPE 244
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-236 2.05e-121

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 354.91  E-value: 2.05e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00037   9 STNHKDIGTLYLIFGAWAGMVGTAMSVIIRTELAQPGS--LLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00037  87 IGAPDMAFPRMNNMSFWLIPPSFLLLLASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00037 167 TIINMRTPGMTFDRLPLFVWSVFITAFLLLLSLPVLAGAITMLLTDRNINTTFFDPAGGGDPILFQHLFWFFGHPE 242
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-236 3.51e-121

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 354.52  E-value: 3.51e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00184  11 STNHKDIGTLYLLFGAFAGMIGTAFSMLIRLELSAPGS--MLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLY 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00184  89 IGAPDMAFPRLNNISFWLLPPALTLLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFIT 168

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00184 169 TIFNMRAPGITMDRMPLFVWSILVTTFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPE 244
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-236 1.04e-119

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 350.34  E-value: 1.04e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00103   9 STNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGT--LLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00103  87 IGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00103 167 TIINMKPPAMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPE 242
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-236 4.93e-119

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 348.85  E-value: 4.93e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00077   9 STNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGT--LLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00077  87 IGAPDMAFPRMNNMSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00077 167 TSINMKPPSMSQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPVLYQHLFWFFGHPE 242
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-236 2.45e-118

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 346.91  E-value: 2.45e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00183   9 STNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGA--LLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00183  87 IGAPDMAFPRMNNMSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFIT 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00183 167 TIINMKPPAISQYQTPLFVWAVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPE 242
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-236 4.44e-116

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 341.11  E-value: 4.44e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00007   6 STNHKDIGTLYFILGVWGGLLGTSMSLLIRIELGQPGA--FLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLM 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00007  84 LGAPDMAFPRLNNMSFWLLPPALILLVSSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFIT 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00007 164 TVINMRWKGLRLERIPLFVWAVVITVVLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPE 239
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-236 9.31e-109

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 323.12  E-value: 9.31e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNqlLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00026  10 SCNHKDIGSLYLVFGALSGAIGTAFSMLIRLELSSPGS--MLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLM 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00026  88 IGAPDMAFPRLNNISFWLLPPALFLLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFIT 167

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00026 168 TVMNMRTPGMTMSRIPLFVWSVFITAILLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWFFGHPE 243
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-236 1.01e-107

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 319.70  E-value: 1.01e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGnqLLLGNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00079  10 SSNHKDIGTLYFLFGLWSGMVGTSLSLIIRLELSKPG--LLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLM 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSiQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00079  88 LGAPDMSFPRLNNLSFWLLPTSLFLILDSCFVDMGPGTSWTVYPPLST-LGHPGSSVDLAIFSLHCAGISSILGGINFMV 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00079 167 TTKNLRSSSISLEHMSLFVWTVFVTVFLLVLSLPVLAGAITMLLTDRNLNTSFFDPSTGGNPLLYQHLFWFFGHPE 242
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 4-236 2.00e-98

Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily.


Pssm-ID: 238461  Cd Length: 463  Bit Score: 294.44  E-value: 2.00e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   4 HKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPiMIGS 83
Cdd:cd00919    1 HKDIGLLYLIFAFVALLLGGLLALLIRLELATPGSLFL--DPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  84 PDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFISTIL 163
Cdd:cd00919   78 RDLAFPRLNNLSFWLFPPGLLLLLSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTIL 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 802084235 164 NMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:cd00919  158 NMRAPGMTLDKMPLFVWSVLVTAILLLLALPVLAAALVMLLLDRNFGTSFFDPAGGGDPVLYQHLFWFFGHPE 230
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-236 7.17e-98

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: 294.13  E-value: 7.17e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235    1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIM 80
Cdd:TIGR02891   3 TVDHKRIGILYLVTAFAFFLVGGVLALLMRAQLATPGNTFM--DAETYNQLFTMHGTIMIFLFAIP-ILAGFGNYLLPLM 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:TIGR02891  80 IGARDMAFPRLNAFSYWLYLFGGLLLLASFFTGGAPDTGWTMYPPLSSTSGSPGVGVDLWLLGLHLLGISSILGAVNFIV 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235  161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:TIGR02891 160 TILNMRAPGMTLMRMPLFVWGILVTSILILLAFPVLIAALILLLLDRLFGTHFFDPARGGDPLLWQHLFWFFGHPE 235
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-236 4.75e-93

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 282.79  E-value: 4.75e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLLGNHqiYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIM 80
Cdd:COG0843   12 TVDHKRIGIMYLVTAFVFLLIGGLLALLMRLQLAGPGLGLLSPET--YNQLFTMHGTIMIFFFATP-FLAGFGNYLVPLQ 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:COG0843   89 IGARDMAFPRLNALSFWLYLFGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIV 168

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:COG0843  169 TILKMRAPGMTLMRMPLFTWAALVTSILILLAFPVLAAALLLLLLDRSLGTHFFDPAGGGDPLLWQHLFWFFGHPE 244
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 1-236 4.67e-77

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: 240.56  E-value: 4.67e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLLGNHqiYNVLITAHAFLMIFFMVMPVMIGgFGNWLVPIM 80
Cdd:cd01662    4 TVDHKRIGIMYIITAFVFFLRGGVDALLMRTQLALPGNDFLSPEH--YNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:cd01662   81 IGARDVAFPRLNALSFWLFLFGGLLLNASLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIV 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:cd01662  161 TILKMRAPGMTLMRMPIFTWTTLVTSILILFAFPVLTAALALLELDRYFGTHFFTNALGGNPMLWQHLFWIFGHPE 236
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 1-236 8.65e-74

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 232.65  E-value: 8.65e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPVMIGGFGNWLVPIM 80
Cdd:MTH00048  10 TLDHKRIGVIYTLLGVWSGFVGLSLSLLIRLNFLDPYYNVI--SLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVevGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:MTH00048  88 LGLSDLNLPRLNALSAWLLVPSIVFLLLSMCL--GAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFIC 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235 161 TILNMRNPGQSmYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:MTH00048 166 TIYSAFMTNVF-SRTSIILWSYLFTSILLLLSLPVLAAAITMLLFDRNFGSAFFDPLGGGDPVLFQHMFWFFGHPE 240
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 6-236 1.71e-57

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: 188.17  E-value: 1.71e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235    6 DIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLlgNHQIYNVLITAHAFLMIFFMVMPvMIGGFGNWLVPIMIGSPD 85
Cdd:pfam00115   1 RIGLLYLVTALVWFLVGGLLGLLIRLQLAFPGLNFL--SPLTYNQLRTLHGNLMIFWFATP-FLFGFGNYLVPLMIGARD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   86 MAFPRLNNISFWLLPPSLCLLIASAiveVGVGTGWTVYPPLssiqshsgGAVDLAIFSLHISGASSILGAINFISTILNM 165
Cdd:pfam00115  78 MAFPRLNALSFWLVVLGAVLLLASF---GGATTGWTEYPPL--------VGVDLWYIGLLLAGVSSLLGAINFIVTILKR 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 802084235  166 RNPGQSMyRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNttffdpAGGGDPVLYQHLFWFFGHPE 236
Cdd:pfam00115 147 RAPGMTL-RMPLFVWAILATAILILLAFPVLAAALLLLLLDRSLG------AGGGDPLLDQHLFWWFGHPE 210
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 1-236 7.82e-48

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: 166.57  E-value: 7.82e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235    1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRMELAQPGNQLLLGNHqiYNVLITAHAFLMIFFMVMPVMIGgFGNWLVPIM 80
Cdd:TIGR02882  47 TVDHKKIGVMYIICAVLMLFRGGIDALLMRAQLTVPDNKFLDAQH--YNEIFTTHGVIMIIFMAMPFIIG-LMNIVVPLQ 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   81 IGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINFIS 160
Cdd:TIGR02882 124 IGARDVAFPVLNALSFWLFFAGAMLFNISFVIGGSPDAGWTNYAPLAGPEFSPGVGVNYYLIALQISGIGTLMTGINFFV 203

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 802084235  161 TILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:TIGR02882 204 TILKMRAPGMKLMQMPMFTWTTLITTLIIIFAFPVLTVALALMTTDRIFDTAFFTVAHGGMPMLWANLFWIWGHPE 279
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 1-236 1.00e-42

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 152.78  E-value: 1.00e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235   1 STNHKDIGTLYLIFGAFSGVLGGCMSMLIRME--LAQPGNQLLLGNHQiYNVLITAHAFLMIFFMVMPVMIGgFGNWLVP 78
Cdd:PRK15017  51 SVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQqaLASAGEAGFLPPHH-YDQIFTAHGVIMIFFVAMPFVIG-LMNLVVP 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 802084235  79 IMIGSPDMAFPRLNNISFWLLPPSLCLLIASAIVEVGVGTGWTVYPPLSSIQSHSGGAVDLAIFSLHISGASSILGAINF 158
Cdd:PRK15017 129 LQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINF 208

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 802084235 159 ISTILNMRNPGQSMYRMPLFVWSIFITAFLLLLAVPVLAGAITMLLTDRNFNTTFFDPAGGGDPVLYQHLFWFFGHPE 236
Cdd:PRK15017 209 FVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPE 286
 
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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