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Conserved domains on  [gi|313877301|gb|ADR82389|]
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cytochrome oxidase subunit I, partial (mitochondrion) [Zeugodacus cucurbitae]

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 ...
 1-200 2.08e-144

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: 411.57  E-value: 2.08e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00153 312 VPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGF 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00153 392 IHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIW 471

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00153 472 ESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-200 2.08e-144

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 411.57  E-value: 2.08e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00153 312 VPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGF 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00153 392 IHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIW 471

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00153 472 ESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-183 4.99e-111

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: 325.59  E-value: 4.99e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:cd01663  305 VPTGIKVFSWLATMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAGF 384

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:cd01663  385 YYWFPKITGLSYNETLGKIHFWLMFIGVNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVW 464

                        170       180
                 ....*....|....*....|....
gi 313877301 161 ESLVTQRQVIY-PMQLSSSIEWLQ 183
Cdd:cd01663  465 ESFVSGRKVIFnVGEGSTSLEWTL 488
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-199 3.22e-70

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 222.31  E-value: 3.22e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:COG0843  315 VPTGVKVFNWIATMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAGL 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:COG0843  395 YYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFPMHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLIN 474

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 313877301 159 IWESLVTQRQV-IYPMQlSSSIEWLQNTPPAEHSYSELPLLT 199
Cdd:COG0843  475 LVVSLRKGPKAgGNPWG-ARTLEWATPSPPPLYNFASIPVVR 515
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-192 4.67e-67

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: 213.24  E-value: 4.67e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301    1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:TIGR02891 306 VPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAAI 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDA--YTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:TIGR02891 386 YYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFPMHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLWN 465

                         170       180       190
                  ....*....|....*....|....*....|....
gi 313877301  159 IWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSY 192
Cdd:TIGR02891 466 LIWSLRKGPKAGANPWGATTLEWTTSSPPPAHNF 499
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-147 1.03e-45

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: 156.19  E-value: 1.03e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301    1 VPTGIKIFSWLATLHGTQLN-YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 79
Cdd:pfam00115 281 VPSGVKVFNWLATLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFGG 360

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 313877301   80 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYS----DYPDAYTTWNVVSTIGSSI 147
Cdd:pfam00115 361 IYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFFPMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-200 2.08e-144

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 411.57  E-value: 2.08e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00153 312 VPTGIKIFSWLATLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVAHFHYVLSMGAVFAIMGGF 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00153 392 IHWFPLFTGLTMNPKWLKIQFFIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTSWNVISSIGSTISLISILFFIFIIW 471

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00153 472 ESMISKRPVLFSLNLSSSIEWLQNLPPAEHSYSELPLLTN 511
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-183 4.99e-111

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: 325.59  E-value: 4.99e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:cd01663  305 VPTGIKVFSWLATMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVAHFHYVLSMGAVFAIFAGF 384

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:cd01663  385 YYWFPKITGLSYNETLGKIHFWLMFIGVNLTFFPQHFLGLAGMPRRYPDYPDAYAGWNMISSIGSLISFVSVLLFLFIVW 464

                        170       180
                 ....*....|....*....|....
gi 313877301 161 ESLVTQRQVIY-PMQLSSSIEWLQ 183
Cdd:cd01663  465 ESFVSGRKVIFnVGEGSTSLEWTL 488
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-200 5.39e-110

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 323.98  E-value: 5.39e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00142 312 VPTGIKVFSWLATLHGSKVKYEPPMLWALGFIFLFTVGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFALFAGF 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00142 392 IHWFPLFTGLTLNPRWLKAHFYTMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSSLGSMISFIAVLMFVFIVW 471

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00142 472 ESFVSQRLVMWSSHLSTSLEWSHRLPPDFHTYDELPILVV 511
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-198 2.11e-109

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 322.40  E-value: 2.11e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00167 314 VPTGIKVFSWLATLHGGKIKWETPMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00167 394 THWFPLFTGLTLNETWTKIHFFVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNVVSSIGSLISLVAVILFLFIIW 473

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLL 198
Cdd:MTH00167 474 EAFSSKRKLLPVELTSTNVEWLHGCPPPHHTWEEPPFV 511
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-200 4.09e-109

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 321.66  E-value: 4.09e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00116 314 IPTGIKVFSWLATLHGGTIKWDPPMLWALGFIFLFTIGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAGF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00116 394 THWFPLFTGYTLHQTWTKAQFGVMFTGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTISSIGSLISMTAVIMLMFIIW 473

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00116 474 EAFSSKRKVLQPELTTTNIEWIHGCPPPYHTFEEPAFVQV 513
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-196 4.38e-109

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 321.54  E-value: 4.38e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00223 311 VPTGIKVFSWLATIYGSKIKYEAPMLWALGFIFLFTVGGLTGIILSNSSLDIMLHDTYYVVAHFHYVLSMGAVFALFAGF 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00223 391 NHWFPLFTGVTLHRRWAKAHFFLMFLGVNLTFFPQHFLGLAGMPRRYSDYPDCYTKWNQVSSFGSMISFVSVLFFMFIVW 470

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELP 196
Cdd:MTH00223 471 EAFVSQRSVVWSGHLSTSLEWDNLLPADFHNNSETG 506
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-197 4.03e-96

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 288.65  E-value: 4.03e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00037 314 VPTGIKVFSWMATLQGSNLRWETPLLWALGFVFLFTIGGLTGIVLANSSIDVVLHDTYYVVAHFHYVLSMGAVFAIFAGF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00037 394 THWFPLFSGVSLHPLWSKVHFFLMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSTISLVATLFFLFLIW 473

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNT-PPAEHSYSELPL 197
Cdd:MTH00037 474 EAFASQREVISPEFSSSSLEWQYSSfPPSHHTFDETPS 511
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-194 1.03e-95

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 287.55  E-value: 1.03e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00103 314 IPTGVKVFSWLATLHGGNIKWSPAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00103 394 VHWFPLFSGYTLNDTWAKIHFTIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTTWNTVSSMGSFISLTAVMLMIFMIW 473

                        170       180       190
                 ....*....|....*....|....*....|....
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 194
Cdd:MTH00103 474 EAFASKREVLTVELTTTNLEWLHGCPPPYHTFEE 507
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-200 1.42e-93

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 282.21  E-value: 1.42e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00077 314 IPTGVKVFSWLATMHGGAIKWDAAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00077 394 VHWFPLFSGYTLHSTWSKIHFGVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMMMFIIW 473

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLTN 200
Cdd:MTH00077 474 EAFSSKREVLTTELTSTNIEWLHGCPPPYHTFEEPSFVQT 513
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-194 5.98e-92

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 277.96  E-value: 5.98e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00183 314 IPTGVKVFSWLATLHGGSIKWETPLLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAAF 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00183 394 VHWFPLFSGYTLHSTWTKIHFGVMFVGVNLTFFPQHFLGLAGMPRRYSDYPDAYTLWNTVSSIGSLISLVAVIMFLFILW 473

                        170       180       190
                 ....*....|....*....|....*....|....
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 194
Cdd:MTH00183 474 EAFAAKREVLSVELTSTNVEWLHGCPPPYHTFEE 507
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-199 7.50e-92

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 277.55  E-value: 7.50e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00007 311 VPTGIKVFSWLATIHGSPIKYETPMLWALGFIFLFTTGGLTGIVLSNSSLDIILHDTYYVVAHFHYVLSMGAVFAIFAAF 390

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00007 391 NHWFPLFTGLTLHDRWAKAHFFLMFLGVNLTFFPQHFLGLSGMPRRYSDYPDAYTKWNVVSSFGSMLSFVALLLFIFILW 470

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELPLLT 199
Cdd:MTH00007 471 EAFSAQRGVIASPHMSSSLEWQDTLPLDFHNLPETGIIT 509
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-198 4.74e-79

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 245.12  E-value: 4.74e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00182 316 VPTGIKVFSWLATIYGGTLRLDTPMLWAMGFVFLFTLGGLTGVVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIFGGF 395

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00182 396 YYWFGKITGYCYNELYGKIHFWLMFIGVNLTFFPQHFLGLAGFPRRYSDFADAFAGWNLVSSLGSIISIVGVVWFIYIIY 475

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 313877301 161 ESLVTQRQVI----YPMQLSSSIEWLQNTPPAEHSYSELPLL 198
Cdd:MTH00182 476 DAYVREEKFIgwkeGTGESWASLEWVHSSPPLFHTYNELPFV 517
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-194 1.15e-77

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 241.12  E-value: 1.15e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00079 314 VPTGVKVFSWLATLFGMKMKFQPLLLWVLGFIFLFTIGGLTGVILSNSSLDIILHDTYYVVSHFHYVLSLGAVFGIFTGI 393

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00079 394 SLWWPFMTGIVYDKLMMSAVFFLMFVGVNLTFFPLHFAGLHGMPRKYLDYPDVYSVWNVISSYGSMISVFALFLFIYVLL 473

                        170       180       190
                 ....*....|....*....|....*....|....
gi 313877301 161 ESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSE 194
Cdd:MTH00079 474 ESFFSYRLVLHDNYINSSPEYSLSSYVFGHSYQS 507
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-198 9.81e-76

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 236.26  E-value: 9.81e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:MTH00184 316 VPTGIKIFSWIATIFGGSLRLDTPMLWAIGFVFLFTMGGLTGIVLANSSLDVVLHDTYYVVAHFHYVLSMGAVFAIFGGF 395

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:MTH00184 396 YYWFGKITGYCYNEVYGKIHFWLMFIGVNLTFFPQHFLGLAGLPRRYSDFHDSFAGWNQISSLGSVISIVGVVWFIYIVY 475

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 313877301 161 ESLVTQRQVIYPMQLS---SSIEWLQNTPPAEHSYSELPLL 198
Cdd:MTH00184 476 DAYVREIKFVGWVEDSghyPSLEWAQTSPPAHHTYNELPYV 516
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-163 4.00e-74

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: 230.50  E-value: 4.00e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:cd00919  301 VPTGIKVFNWLATLWGGRIRFDPPMLFALGFLFLFTIGGLTGVVLANVPLDIVLHDTYYVVAHFHYVLSGGVVFAIFAGL 380

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFIIW 160
Cdd:cd00919  381 YYWFPKMTGRMLSEKLGKIHFWLWFIGFNLTFFPMHFLGLLGMPRRYADYPDGFAPWNFISSVGAFILGLGLLLFLGNLF 460


                 ...
gi 313877301 161 ESL 163
Cdd:cd00919  461 LSL 463
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
1-199 3.22e-70

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 222.31  E-value: 3.22e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:COG0843  315 VPTGVKVFNWIATMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVAHFHYVLIGGVVFAFFAGL 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:COG0843  395 YYWFPKMTGRMLNERLGKIHFWLWFIGFNLTFFPMHILGLLGMPRRYATYPpePGWQPLNLISTIGAFILAVGFLLFLIN 474

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 313877301 159 IWESLVTQRQV-IYPMQlSSSIEWLQNTPPAEHSYSELPLLT 199
Cdd:COG0843  475 LVVSLRKGPKAgGNPWG-ARTLEWATPSPPPLYNFASIPVVR 515
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 1-192 4.67e-67

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: 213.24  E-value: 4.67e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301    1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:TIGR02891 306 VPTGVKVFNWIATLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVAHFHYVLVGGSVFAIFAAI 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDA--YTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:TIGR02891 386 YYWFPKVTGRMYNERLGRWHFWLTFVGFNLTFFPMHLLGLLGMPRRYYTYPPQmgFATLNLISTIGAFILAAGFLVFLWN 465

                         170       180       190
                  ....*....|....*....|....*....|....
gi 313877301  159 IWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSY 192
Cdd:TIGR02891 466 LIWSLRKGPKAGANPWGATTLEWTTSSPPPAHNF 499
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 1-192 1.29e-60

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: 196.65  E-value: 1.29e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:cd01662  307 VPTGVKIFNWLFTMWRGRIRFETPMLWAIGFLVTFVIGGLTGVMLASPPADFQVHDTYFVVAHFHYVLIGGVVFPLFAGF 386

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYP--DAYTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:cd01662  387 YYWFPKMFGRMLNERLGKWSFWLWFIGFNLTFFPMHILGLMGMPRRVYTYLpgPGWDPLNLISTIGAFLIAAGVLLFLIN 466

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 313877301 159 IWESLVTQRQVIY--PMQlSSSIEWLQNTPPAEHSY 192
Cdd:cd01662  467 VIVSIRKGKRDATgdPWG-ARTLEWATSSPPPAYNF 501
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-198 1.32e-57

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 189.45  E-value: 1.32e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLN--YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMA 78
Cdd:MTH00026 315 VPTGIKIFSWLATVSGSGRNliFTTPMAWALGFIFLFTIGGLTGIVLSNSSLDILLHDTYYVVAHFHFVLSMGAVFAIFG 394

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  79 GFVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFI 158
Cdd:MTH00026 395 GFYLWFGKITGYAYKDIYGLIHFWLMFIGVNITFFPQHFLGLAGLPRRYADYPDNFEDFNQISSFGSIISIIAVIWFIVV 474

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 313877301 159 IWESL---------VTQRQVIYPMQLS----SSIEWLQNTPPAEHSYSELPLL 198
Cdd:MTH00026 475 IFDAYyreepfdinIMAKGPLIPFSCQpahfDTLEWSLTSPPEHHTYNELPYI 527
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 1-191 8.79e-56

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 184.11  E-value: 8.79e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYS-PAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 79
Cdd:MTH00048 312 VPTGIKVFSWLYMLLNSRVRKSdPVVWWVVSFIVLFTIGGVTGIVLSASVLDNVLHDTWFVVAHFHYVLSLGSYSSVVIM 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  80 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNVVSTIGSSISLLGILFFLFII 159
Cdd:MTH00048 392 FIWWWPLITGLSLNKYLLQCHCIISMIGFNLCFFPMHYFGLCGLPRRVCVYEPSYYWINVVCTVGSFISAFSGCFFVFIL 471

                        170       180       190
                 ....*....|....*....|....*....|..
gi 313877301 160 WESLVTQRQVIYPMQLSSSIEWLQNTPPAEHS 191
Cdd:MTH00048 472 WESLVVKNEVLGLWGSSSCVVNVLMSPVPYHN 503
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-147 1.03e-45

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: 156.19  E-value: 1.03e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301    1 VPTGIKIFSWLATLHGTQLN-YSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAG 79
Cdd:pfam00115 281 VPSGVKVFNWLATLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVAHFHYVLFGGVVFALFGG 360

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 313877301   80 FVHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYS----DYPDAYTTWNVVSTIGSSI 147
Cdd:pfam00115 361 IYYWLPKLTGRMYSEKLGKLHFWLLFIGFNLTFFPMHILGLLGMPRRYAppfiETVPAFQPLNWIRTIGGVL 432
QoxB TIGR02882
cytochrome aa3 quinol oxidase, subunit I; This family (QoxB) encodes subunit I of the aa3-type ...
 1-196 3.47e-40

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: 144.23  E-value: 3.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301    1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:TIGR02882 350 IPTGVKIFNWLLTLYKGKIRFTTPMLFSLAFIPNFLIGGVTGVMLAMASADYQYHNTYFLVAHFHYVLITGVVFACLAGL 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDY--PDAYTTWNVVSTIGSSISLLGILFFLF- 157
Cdd:TIGR02882 430 IYWYPKMFGYKLNERLGKWCFWFFMIGFNVCFFPMYILGLDGMPRRMYTYspSDGWFPLNLISTIGALLMAIGFIFLVYn 509

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 313877301  158 IIWESLVTQRQVIYPMQLSSSIEWLQNTPPAEHSYSELP 196
Cdd:TIGR02882 510 IYYSHRKSPREATGDPWNGRTLEWATASPPPKYNFAVTP 548
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 1-196 6.98e-34

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 126.97  E-value: 6.98e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   1 VPTGIKIFSWLATLHGTQLNYSPAMLWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGF 80
Cdd:PRK15017 357 IPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGM 436

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  81 VHWYPLFTGLVLNPKWLKSQFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPD-AYTTWNVVSTIGSSISLLGILFFLFII 159
Cdd:PRK15017 437 TYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDpQFHTMLMIAASGAALIALGILCQVIQM 516

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 313877301 160 WESLVTQ---RQVIYPMQLSSSIEWLQNTPPAEHSYSELP 196
Cdd:PRK15017 517 YVSIRDRdqnRDLTGDPWGGRTLEWATSSPPPFYNFAVVP 556
ba3-like_Oxidase_I cd01660
ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are ...
 4-164 3.60e-14

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: 70.01  E-value: 3.60e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301   4 GIKIFSWLATLHGTQLNYSPAMLWALGFVFlftvGGLTGVVLANSSVDIILHDTYYVVAHFHyvLSMGAVFAIMA-GFVH 82
Cdd:cd01660  309 GKGLFGWIRALPWGDPMFLALFLAMLMFIP----GGAGGIINASYQLNYVVHNTAWVPGHFH--LTVGGAVALTFmAVAY 382

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 313877301  83 WY-PLFTGLVLNPKWLKS-QFIIMFIGVNLTFFPQHFLGLAGMPRR--YSDYPDAY-----TTWNVVSTIGSSISLLGIL 153
Cdd:cd01660  383 WLvPHLTGRELAAKRLALaQPWLWFVGMTIMSTAMHVAGLLGAPRRtaEAQYGGLPaagewAPYQQLMAIGGTILFVSGA 462

                        170
                 ....*....|.
gi 313877301 154 FFLFIIWESLV 164
Cdd:cd01660  463 LFLYILFRTLL 473
 
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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