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Conserved domains on  [gi|388612305|gb|AFK76790|]
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cytochrome oxidase subunit I, partial (mitochondrion) [Phaulacridium marginale]

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 ...
 1-217 6.10e-164

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 MTH00153:

Pssm-ID: 469701  Cd Length: 511  Bit Score: 462.03  E-value: 6.10e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   1 QESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLL 80
Cdd:MTH00153 258 QESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGSQINYSPSLL 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  81 WALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFI 160
Cdd:MTH00153 338 WALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFTGLTMNPKWLKIQFFIMFI 417

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 388612305 161 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00153 418 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESM 474
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-217 6.10e-164

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 462.03  E-value: 6.10e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   1 QESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLL 80
Cdd:MTH00153 258 QESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGSQINYSPSLL 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  81 WALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFI 160
Cdd:MTH00153 338 WALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFTGLTMNPKWLKIQFFIMFI 417

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 388612305 161 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00153 418 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESM 474
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-217 2.16e-141

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: 403.79  E-value: 2.16e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   2 ESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLW 81
Cdd:cd01663  252 FSGKKPVFGYLGMVYAMLSIGILGFIVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGIKVFSWLATMWGGSIKFETPMLW 331

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  82 ALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIG 161
Cdd:cd01663  332 ALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAGFYYWFPKITGLSYNETLGKIHFWLMFIG 411

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 388612305 162 VNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:cd01663  412 VNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVWESF 467
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
9-217 1.72e-87

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 267.76  E-value: 1.72e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:COG0843  269 FGYKAMVLATVAIAFLSFLVWAHHMFTPGISPLVKAFFSIATMLIAVPTGVKVFNWIATMWRGRIRFTTPMLFALGFIIL 348

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:COG0843  349 FVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAGLYYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFP 428

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 388612305 169 QHFLGLAGMPRRYSDYP--DAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:COG0843  429 MHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLINLVVSL 479
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 9-217 2.86e-85

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: 261.00  E-value: 2.86e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305    9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:TIGR02891 260 FGYRAMVYATVAIGFLSFGVWAHHMFTTGMPPLALAFFSAATMLIAVPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFL 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:TIGR02891 340 FVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAAIYYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFP 419

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 388612305  169 QHFLGLAGMPRRYSDYPDA--YTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:TIGR02891 420 MHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLWNLIWSL 470
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 9-201 4.12e-59

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: 191.63  E-value: 4.12e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305    9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFN-PPLLWALGFIF 87
Cdd:pfam00115 235 FGYKLSVLAFWLIAFLGFLVWAHHLFTTGLPPWLQALFSVFSMLIAVPSGVKVFNWLATLWGGWIRFRtTPMLFFLGFAF 314

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   88 LFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFF 167
Cdd:pfam00115 315 LFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFGGIYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFF 394

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 388612305  168 PQHFLGLAGMPRRYS----DYPDAYTSWNVVSSIGSTI 201
Cdd:pfam00115 395 PMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-217 6.10e-164

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 462.03  E-value: 6.10e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   1 QESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLL 80
Cdd:MTH00153 258 QESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGSQINYSPSLL 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  81 WALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFI 160
Cdd:MTH00153 338 WALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFTGLTMNPKWLKIQFFIMFI 417

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 388612305 161 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00153 418 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIWESM 474
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-217 2.16e-141

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: 403.79  E-value: 2.16e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   2 ESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLW 81
Cdd:cd01663  252 FSGKKPVFGYLGMVYAMLSIGILGFIVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGIKVFSWLATMWGGSIKFETPMLW 331

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  82 ALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIG 161
Cdd:cd01663  332 ALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAGFYYWFPKITGLSYNETLGKIHFWLMFIG 411

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 388612305 162 VNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:cd01663  412 VNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVWESF 467
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 3-217 2.60e-135

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 389.04  E-value: 2.60e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00167 262 SGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLHGGKIKWETPMLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00167 342 LGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGFTHWFPLFTGLTLNETWTKIHFFVMFIGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00167 422 NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNVVSSIGSLISLVAVILFLFIIWEAF 476
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 3-217 1.15e-133

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 385.21  E-value: 1.15e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00116 262 AGKKEPFGYMGMVWAMLSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGIKVFSWLATLHGGTIKWDPPMLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00116 342 LGFIFLFTIGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGFTHWFPLFTGYTLHQTWTKAQFGVMFTGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00116 422 NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTISSIGSLISMTAVIMLMFIIWEAF 476
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 3-217 8.17e-132

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 380.48  E-value: 8.17e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00223 259 SSKKEVFGTLGMIYAMLSIGVLGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLATIYGSKIKYEAPMLWA 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00223 339 LGFIFLFTVGGLTGIILSNSSLDIMLHDTYYVVAHFHYVLSMGAVFALFAGFNHWFPLFTGVTLHRRWAKAHFFLMFLGV 418

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00223 419 NLTFFPQHFLGLAGMPRRYSDYPDCYTKWNQVSSFGSMISFVSVLFFMFIVWEAF 473
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 3-217 1.16e-130

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 377.53  E-value: 1.16e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00142 260 SGKKEVFGTLGMIYAMLSIGLLGFIVWAHHMFTVGMDVDTRAYFTAATMVIAVPTGIKVFSWLATLHGSKVKYEPPMLWA 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00142 340 LGFIFLFTVGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFALFAGFIHWFPLFTGLTLNPRWLKAHFYTMFIGV 419

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00142 420 NLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSSLGSMISFIAVLMFVFIVWESF 474
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 3-216 1.91e-116

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 341.52  E-value: 1.91e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00183 262 SGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGSIKWETPLLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00183 342 LGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAAFVHWFPLFSGYTLHSTWTKIHFGVMFVGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00183 422 NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMFLFILWEA 475
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 3-216 2.33e-116

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 341.09  E-value: 2.33e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00103 262 SGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00103 342 LGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFTIMFVGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00103 422 NMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSSMGSFISLTAVMLMIFMIWEA 475
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-217 6.03e-115

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 337.26  E-value: 6.03e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   1 QESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLL 80
Cdd:MTH00007 257 HYAGKLEPFGTLGMIYAMLGIGVLGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLATIHGSPIKYETPML 336

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  81 WALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFI 160
Cdd:MTH00007 337 WALGFIFLFTTGGLTGIVLSNSSLDIILHDTYYVVAHFHYVLSMGAVFAIFAAFNHWFPLFTGLTLHDRWAKAHFFLMFL 416

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 388612305 161 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00007 417 GVNLTFFPQHFLGLSGMPRRYSDYPDAYTKWNVVSSFGSMLSFVALLLFIFILWEAF 473
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 3-217 2.37e-114

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 336.03  E-value: 2.37e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00037 262 SGKQEPFGYLGMVYAMIAIGILGFLVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWMATLQGSNLRWETPLLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00037 342 LGFVFLFTIGGLTGIVLANSSIDVVLHDTYYVVAHFHYVLSMGAVFAIFAGFTHWFPLFSGVSLHPLWSKVHFFLMFIGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00037 422 NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSTISLVATLFFLFLIWEAF 476
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 3-216 4.15e-114

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 335.37  E-value: 4.15e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00077 262 SAKKEPFGYMGMVWAMMSIGLLGFIVWAHHMFTVDLNVDTRAYFTSATMIIAIPTGVKVFSWLATMHGGAIKWDAAMLWA 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00077 342 LGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLHSTWSKIHFGVMFIGV 421

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00077 422 NLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMMMFIIWEA 475
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 2-216 6.31e-104

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 308.92  E-value: 6.31e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   2 ESGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLW 81
Cdd:MTH00079 261 LTGKKEVFGSLGMVYAILSIGLIGCVVWAHHMYTVGMDLDSRAYFTAATMVIAVPTGVKVFSWLATLFGMKMKFQPLLLW 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  82 ALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIG 161
Cdd:MTH00079 341 VLGFIFLFTIGGLTGVILSNSSLDIILHDTYYVVSHFHYVLSLGAVFGIFTGISLWWPFMTGIVYDKLMMSAVFFLMFVG 420

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 388612305 162 VNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00079 421 VNLTFFPLHFAGLHGMPRKYLDYPDVYSVWNVISSYGSMISVFALFLFIYVLLES 475
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 3-215 1.69e-102

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 305.98  E-value: 1.69e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00182 264 VAKKQIFGYLGMVYAMLSIGILGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLATIYGGTLRLDTPMLWA 343

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00182 344 MGFVFLFTLGGLTGVVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIFGGFYYWFGKITGYCYNELYGKIHFWLMFIGV 423

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWE 215
Cdd:MTH00182 424 NLTFFPQHFLGLAGFPRRYSDFADAFAGWNLVSSLGSIISIVGVVWFIYIIYD 476
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 3-216 1.71e-98

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 295.58  E-value: 1.71e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWA 82
Cdd:MTH00184 264 AAKKQIFGYLGMVYAMVSIGILGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKIFSWIATIFGGSLRLDTPMLWA 343

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  83 LGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGV 162
Cdd:MTH00184 344 IGFVFLFTMGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFAIFGGFYYWFGKITGYCYNEVYGKIHFWLMFIGV 423

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 388612305 163 NLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00184 424 NLTFFPQHFLGLAGLPRRYSDFHDSFAGWNQISSLGSVISIVGVVWFIYIVYDA 477
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 9-217 3.79e-94

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: 282.50  E-value: 3.79e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:cd00919  255 FGYKLMVYAFLAIGFLSFLVWAHHMFTVGLPVDTRAYFTAATMIIAVPTGIKVFNWLATLWGGRIRFDPPMLFALGFLFL 334

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:cd00919  335 FTIGGLTGVVLANVPLDIVLHDTYYVVAHFHYVLSGGVVFAIFAGLYYWFPKMTGRMLSEKLGKIHFWLWFIGFNLTFFP 414

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 388612305 169 QHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:cd00919  415 MHFLGLLGMPRRYADYPDGFAPWNFISSVGAFILGLGLLLFLGNLFLSL 463
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
9-217 1.72e-87

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 267.76  E-value: 1.72e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:COG0843  269 FGYKAMVLATVAIAFLSFLVWAHHMFTPGISPLVKAFFSIATMLIAVPTGVKVFNWIATMWRGRIRFTTPMLFALGFIIL 348

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:COG0843  349 FVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAGLYYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFP 428

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 388612305 169 QHFLGLAGMPRRYSDYP--DAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:COG0843  429 MHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLINLVVSL 479
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 9-217 2.86e-85

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: 261.00  E-value: 2.86e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305    9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:TIGR02891 260 FGYRAMVYATVAIGFLSFGVWAHHMFTTGMPPLALAFFSAATMLIAVPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFL 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:TIGR02891 340 FVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAAIYYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFP 419

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 388612305  169 QHFLGLAGMPRRYSDYPDA--YTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:TIGR02891 420 MHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLWNLIWSL 470
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 3-216 5.47e-83

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 256.09  E-value: 5.47e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGT--KFKFNPPLL 80
Cdd:MTH00026 263 SYKKQIFGYLGMVYAMLAIGVLGFIVWAHHMYVVGMDVDTRAYFTAATMIIAVPTGIKIFSWLATVSGSgrNLIFTTPMA 342

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  81 WALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFI 160
Cdd:MTH00026 343 WALGFIFLFTIGGLTGIVLSNSSLDILLHDTYYVVAHFHFVLSMGAVFAIFGGFYLWFGKITGYAYKDIYGLIHFWLMFI 422

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 388612305 161 GVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:MTH00026 423 GVNITFFPQHFLGLAGLPRRYADYPDNFEDFNQISSFGSIISIIAVIWFIVVIFDA 478
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 9-217 4.26e-78

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: 242.49  E-value: 4.26e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:cd01662  261 FGYRSMVYATVAIGFLSFGVWVHHMFTTGAGALVNAFFSIATMIIAVPTGVKIFNWLFTMWRGRIRFETPMLWAIGFLVT 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:cd01662  341 FVIGGLTGVMLASPPADFQVHDTYFVVAHFHYVLIGGVVFPLFAGFYYWFPKMFGRMLNERLGKWSFWLWFIGFNLTFFP 420

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 388612305 169 QHFLGLAGMPRRYSDYP--DAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:cd01662  421 MHILGLMGMPRRVYTYLpgPGWDPLNLISTIGAFLIAAGVLLFLINVIVSI 471
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 3-217 3.16e-75

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 235.34  E-value: 3.16e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   3 SGKIESFGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLL-W 81
Cdd:MTH00048 260 SNNDDPFGYYGLVFAMFSIVCLGSVVWAHHMFTVGLDVKTAVFFSSVTMIIGVPTGIKVFSWLYMLLNSRVRKSDPVVwW 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  82 ALGFIFLFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIG 161
Cdd:MTH00048 340 VVSFIVLFTIGGVTGIVLSASVLDNVLHDTWFVVAHFHYVLSLGSYSSVVIMFIWWWPLITGLSLNKYLLQCHCIISMIG 419

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 388612305 162 VNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:MTH00048 420 FNLCFFPMHYFGLCGLPRRVCVYEPSYYWINVVCTVGSFISAFSGCFFVFILWESL 475
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 9-201 4.12e-59

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: 191.63  E-value: 4.12e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305    9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFN-PPLLWALGFIF 87
Cdd:pfam00115 235 FGYKLSVLAFWLIAFLGFLVWAHHLFTTGLPPWLQALFSVFSMLIAVPSGVKVFNWLATLWGGWIRFRtTPMLFFLGFAF 314

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   88 LFTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFF 167
Cdd:pfam00115 315 LFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFGGIYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFF 394

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 388612305  168 PQHFLGLAGMPRRYS----DYPDAYTSWNVVSSIGSTI 201
Cdd:pfam00115 395 PMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 9-216 4.32e-49

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


Pssm-ID: 131928  Cd Length: 643  Bit Score: 169.26  E-value: 4.32e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305    9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:TIGR02882 304 FGYKSMVWSTVGIAFLSFLVWVHHFFTMGNGALINSFFSITTMAIAIPTGVKIFNWLLTLYKGKIRFTTPMLFSLAFIPN 383

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:TIGR02882 384 FLIGGVTGVMLAMASADYQYHNTYFLVAHFHYVLITGVVFACLAGLIYWYPKMFGYKLNERLGKWCFWFFMIGFNVCFFP 463

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 388612305  169 QHFLGLAGMPRRYSDY--PDAYTSWNVVSSIGSTISIVGIIMFIVIMWES 216
Cdd:TIGR02882 464 MYILGLDGMPRRMYTYspSDGWFPLNLISTIGALLMAIGFIFLVYNIYYS 513
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 9-217 2.02e-45

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 159.72  E-value: 2.02e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305   9 FGTLGMIYAMLSIGLMGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLATLYGTKFKFNPPLLWALGFIFL 88
Cdd:PRK15017 311 FGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVT 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  89 FTIGGLTGLVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGIIQWYPLFTGLTMNNTWLKIQFTIMFIGVNLTFFP 168
Cdd:PRK15017 391 FSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMP 470

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 388612305 169 QHFLGLAGMPRRYSDYPDA-YTSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:PRK15017 471 LYALGFMGMTRRLSQQIDPqFHTMLMIAASGAALIALGILCQVIQMYVSI 520
ba3-like_Oxidase_I cd01660
ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are ...
 50-217 7.82e-15

ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea which catalyze the reduction of O2 and simultaneously pump protons across the membrane. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. The ba3 family contains oxidases that lack the conserved residues that form the D- and K-pathways in CcO and ubiquinol oxidase. Instead they contain a potential alternative K-pathway. Additional proton channels have been proposed for this family of oxidases but none have been identified definitively. For general information on the heme-copper oxidase superfamily, please see cd00919.


Pssm-ID: 238830  Cd Length: 473  Bit Score: 72.32  E-value: 7.82e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305  50 TMIIAVPTGIKVFSWLATL-YGTKFKFNPPLLW---------------ALGFIFlFTIGGLTGLVLANSSLDIVLHDTYY 113
Cdd:cd01660  282 TFMVALPSLLTAFTVFASLeIAGRLRGGKGLFGwiralpwgdpmflalFLAMLM-FIPGGAGGIINASYQLNYVVHNTAW 360

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 388612305 114 VVAHFHyvLSMGAVFAIMG-GIIQWY-PLFTGLTMNNTWL-KIQFTIMFIGVNLTFFPQHFLGLAGMPRR--YSDYPDAY 188
Cdd:cd01660  361 VPGHFH--LTVGGAVALTFmAVAYWLvPHLTGRELAAKRLaLAQPWLWFVGMTIMSTAMHVAGLLGAPRRtaEAQYGGLP 438

                        170       180       190
                 ....*....|....*....|....*....|....
gi 388612305 189 -----TSWNVVSSIGSTISIVGIIMFIVIMWESM 217
Cdd:cd01660  439 aagewAPYQQLMAIGGTILFVSGALFLYILFRTL 472
 
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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