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Conserved domains on  [gi|1530778832|gb|AZJ25383|]
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cytochrome c oxidase subunit 1, partial (mitochondrion) [Retrotheristus sp. 2 LM-2017]

Protein Classification

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Heme_Cu_Oxidase_I super family cl00275
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 2-131 3.51e-79

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: 241.70  E-value: 3.51e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00153  244 LILPGFGMISHIISQESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLA 323

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00153  324 TLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVA 373
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 2-131 3.51e-79

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 241.70  E-value: 3.51e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00153  244 LILPGFGMISHIISQESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLA 323

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00153  324 TLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVA 373
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-131 9.49e-78

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: 237.38  E-value: 9.49e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:cd01663   237 LILPGFGIISHIISTFSGKKPVFGYLGMVYAMLSIGILGFIVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGIKVFSWLA 316

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:cd01663   317 TMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVA 366
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-131 1.61e-44

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: 151.22  E-value: 1.61e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:TIGR02891 239 IFLPAFGIISEILPTFARKP-IFGYRAMVYATVAIGFLSFGVWAHHMFTTGMPPLALAFFSAATMLIAVPTGVKVFNWIA 317

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:TIGR02891 318 TLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVA 367
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-131 4.47e-43

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 147.97  E-value: 4.47e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:COG0843   248 LILPAFGIVSEIIPTFSRKP-LFGYKAMVLATVAIAFLSFLVWAHHMFTPGISPLVKAFFSIATMLIAVPTGVKVFNWIA 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:COG0843   327 TMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVA 376
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 2-131 9.88e-29

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: 108.04  E-value: 9.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:pfam00115 214 LILPAFGIIYYILPKFAGRP-LFGYKLSVLAFWLIAFLGFLVWAHHLFTTGLPPWLQALFSVFSMLIAVPSGVKVFNWLA 292

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1530778832  82 SILGSKMK-YTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:pfam00115 293 TLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVA 343
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 2-131 3.51e-79

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 241.70  E-value: 3.51e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00153  244 LILPGFGMISHIISQESGKKETFGTLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLA 323

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00153  324 TLHGSQINYSPSLLWALGFVFLFTIGGLTGVVLANSSIDIILHDTYYVVA 373
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 2-131 9.49e-78

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: 237.38  E-value: 9.49e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:cd01663   237 LILPGFGIISHIISTFSGKKPVFGYLGMVYAMLSIGILGFIVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGIKVFSWLA 316

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:cd01663   317 TMWGGSIKFETPMLWALGFIFLFTIGGLTGVVLANSSLDIALHDTYYVVA 366
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 2-131 3.68e-71

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 221.00  E-value: 3.68e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00223  243 LILPGFGMISHIVSHYSSKKEVFGTLGMIYAMLSIGVLGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLA 322

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00223  323 TIYGSKIKYEAPMLWALGFIFLFTVGGLTGIILSNSSLDIMLHDTYYVVA 372
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 2-131 3.13e-68

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 213.39  E-value: 3.13e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00079  246 LILPAFGIISQSTLYLTGKKEVFGSLGMVYAILSIGLIGCVVWAHHMYTVGMDLDSRAYFTAATMVIAVPTGVKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00079  326 TLFGMKMKFQPLLLWVLGFIFLFTIGGLTGVILSNSSLDIILHDTYYVVS 375
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 2-131 4.84e-68

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 213.00  E-value: 4.84e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00167  246 LILPGFGMISHIVVYYSGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00167  326 TLHGGKIKWETPMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVA 375
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 2-131 4.00e-66

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 208.04  E-value: 4.00e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00142  244 LILPGFGMISHIINHYSGKKEVFGTLGMIYAMLSIGLLGFIVWAHHMFTVGMDVDTRAYFTAATMVIAVPTGIKVFSWLA 323

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00142  324 TLHGSKVKYEPPMLWALGFIFLFTVGGLTGIVLANSSLDVVLHDTYYVVA 373
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 2-131 5.01e-66

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 208.02  E-value: 5.01e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00116  246 LILPGFGIISHIVTYYAGKKEPFGYMGMVWAMLSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGIKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00116  326 TLHGGTIKWDPPMLWALGFIFLFTIGGLTGIVLANSSLDIVLHDTYYVVA 375
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 2-131 1.34e-57

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 185.86  E-value: 1.34e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00103  246 LILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00103  326 TLHGGNIKWSPAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVA 375
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 2-131 2.11e-57

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 185.49  E-value: 2.11e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00007  243 LILPGFGAISHIVTHYAGKLEPFGTLGMIYAMLGIGVLGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLA 322

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00007  323 TIHGSPIKYETPMLWALGFIFLFTTGGLTGIVLSNSSLDIILHDTYYVVA 372
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 2-131 6.19e-57

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 184.26  E-value: 6.19e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00037  246 LILPGFGMISHVIAHYSGKQEPFGYLGMVYAMIAIGILGFLVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWMA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00037  326 TLQGSNLRWETPLLWALGFVFLFTIGGLTGIVLANSSIDVVLHDTYYVVA 375
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 2-131 1.77e-56

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 183.20  E-value: 1.77e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00183  246 LILPGFGMISHIVAYYSGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00183  326 TLHGGSIKWETPLLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVA 375
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 2-131 6.77e-54

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 176.28  E-value: 6.77e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00077  246 LILPGFGMISHIVTYYSAKKEPFGYMGMVWAMMSIGLLGFIVWAHHMFTVDLNVDTRAYFTSATMIIAIPTGVKVFSWLA 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00077  326 TMHGGAIKWDAAMLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVA 375
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 2-131 7.03e-53

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 173.86  E-value: 7.03e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00184  248 LILPGFGIISQIIPTFAAKKQIFGYLGMVYAMVSIGILGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKIFSWIA 327

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00184  328 TIFGGSLRLDTPMLWAIGFVFLFTMGGLTGIVLANSSLDVVLHDTYYVVA 377
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 2-131 8.15e-53

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 173.85  E-value: 8.15e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00182  248 LILPGFGMISQIIPTFVAKKQIFGYLGMVYAMLSIGILGFIVWAHHMFTVGMDVDTRAYFTAATMIIAVPTGIKVFSWLA 327

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00182  328 TIYGGTLRLDTPMLWAMGFVFLFTLGGLTGVVLANSSLDIVLHDTYYVVA 377
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 2-131 1.63e-47

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: 158.46  E-value: 1.63e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:cd00919   234 LILPAFGAISEIIPTFSGKP-LFGYKLMVYAFLAIGFLSFLVWAHHMFTVGLPVDTRAYFTAATMIIAVPTGIKVFNWLA 312

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:cd00919   313 TLWGGRIRFDPPMLFALGFLFLFTIGGLTGVVLANVPLDIVLHDTYYVVA 362
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 2-131 2.01e-46

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 156.38  E-value: 2.01e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00048  244 LILPGFGIISHICLSLSNNDDPFGYYGLVFAMFSIVCLGSVVWAHHMFTVGLDVKTAVFFSSVTMIIGVPTGIKVFSWLY 323

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1530778832  82 SILGSKM-KYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00048  324 MLLNSRVrKSDPVVWWVVSFIVLFTIGGVTGIVLSASVLDNVLHDTWFVVA 374
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 2-131 1.62e-45

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 154.40  E-value: 1.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:MTH00026  247 LILPGFGIISQILSLFSYKKQIFGYLGMVYAMLAIGVLGFIVWAHHMYVVGMDVDTRAYFTAATMIIAVPTGIKIFSWLA 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1530778832  82 SILGS--KMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:MTH00026  327 TVSGSgrNLIFTTPMAWALGFIFLFTIGGLTGIVLSNSSLDILLHDTYYVVA 378
CtaD_CoxA TIGR02891
cytochrome c oxidase, subunit I; This large family represents subunit I's (CtaD, CoxA, CaaA) ...
 2-131 1.61e-44

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: 151.22  E-value: 1.61e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:TIGR02891 239 IFLPAFGIISEILPTFARKP-IFGYRAMVYATVAIGFLSFGVWAHHMFTTGMPPLALAFFSAATMLIAVPTGVKVFNWIA 317

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:TIGR02891 318 TLWGGSIRFTTPMLFALGFIFLFVIGGLTGVMLASVPLDWQLHDTYFVVA 367
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
2-131 4.47e-43

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 147.97  E-value: 4.47e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:COG0843   248 LILPAFGIVSEIIPTFSRKP-LFGYKAMVLATVAIAFLSFLVWAHHMFTPGISPLVKAFFSIATMLIAVPTGVKVFNWIA 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:COG0843   327 TMWRGRIRFTTPMLFALGFIILFVIGGLTGVMLASVPLDYQVHDTYFVVA 376
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 2-131 8.98e-40

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: 138.48  E-value: 8.98e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAI-MFSagKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWL 80
Cdd:cd01662   240 LILPAFGIFSEIVpTFS--RKPLFGYRSMVYATVAIGFLSFGVWVHHMFTTGAGALVNAFFSIATMIIAVPTGVKIFNWL 317

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1530778832  81 ASILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:cd01662   318 FTMWRGRIRFETPMLWAIGFLVTFVIGGLTGVMLASPPADFQVHDTYFVVA 368
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 2-131 9.88e-29

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: 108.04  E-value: 9.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHAIMFSAGKKeVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:pfam00115 214 LILPAFGIIYYILPKFAGRP-LFGYKLSVLAFWLIAFLGFLVWAHHLFTTGLPPWLQALFSVFSMLIAVPSGVKVFNWLA 292

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1530778832  82 SILGSKMK-YTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:pfam00115 293 TLWGGWIRfRTTPMLFFLGFAFLFIIGGLTGVMLALPPVNYYVHDTYFVVA 343
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 2-131 7.73e-26

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 101.17  E-value: 7.73e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1530778832   2 LILPAFGVISHaIMFSAGKKEVFGLLGMIYAMMSIGLLGCVVWAHHMFTVGMDLDSRAYFTGATMVIAVPTGIKIFSWLA 81
Cdd:PRK15017  290 LILPVFGVFSE-IAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLF 368

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1530778832  82 SILGSKMKYTPVFLWILGFLFLFTLGGVTGIVLSNSCLDVSLHDTYYVVA 131
Cdd:PRK15017  369 TMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIA 418
 
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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