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Conserved domains on  [gi|2118838443|gb|UDE31258|]
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cytochrome c oxidase subunit I, partial (mitochondrion) [Alloxysta brachyptera]

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 ...
 1-167 2.99e-104

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: 308.34  E-value: 2.99e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00153   21 GAWSGMVGTSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00153  101 WLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMP 180


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00153  181 LFVWSVL 187
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-167 2.99e-104

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 308.34  E-value: 2.99e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00153   21 GAWSGMVGTSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00153  101 WLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMP 180


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00153  181 LFVWSVL 187
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-167 9.60e-101

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: 298.63  E-value: 9.60e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:cd01663    14 GLWSGLVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:cd01663    94 WLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMP 173


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:cd01663   174 LFVWSVL 180
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
6-167 2.40e-59

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 193.42  E-value: 2.40e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   6 MIGSALSMIIRMELGTPS-QLIGNDQiYNSIVTAHAFIMIFFMVMPIMVGgFGNYMVPLMLSAPDMAFPRLNNMSYWLLI 84
Cdd:COG0843    31 LIGGLLALLMRLQLAGPGlGLLSPET-YNQLFTMHGTIMIFFFATPFLAG-FGNYLVPLQIGARDMAFPRLNALSFWLYL 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  85 PALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKISLFVW 164
Cdd:COG0843   109 FGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTW 188


                  ...
gi 2118838443 165 SIF 167
Cdd:COG0843   189 AAL 191
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-167 7.64e-37

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: 131.93  E-value: 7.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMvGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:pfam00115  10 ALVWFLVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATPFL-FGFGNYLVPLMIGARDMAFPRLNALSF 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMfidQGAGTGWTVYPPLssnlghpgISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMdKIS 160
Cdd:pfam00115  89 WLVVLGAVLLLASF---GGATTGWTEYPPL--------VGVDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMP 156


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:pfam00115 157 LFVWAIL 163
 
Name Accession Description Interval E-value
COX1 MTH00153
cytochrome c oxidase subunit I; Provisional
 1-167 2.99e-104

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177210  Cd Length: 511  Bit Score: 308.34  E-value: 2.99e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00153   21 GAWSGMVGTSLSLLIRAELGQPGSLIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00153  101 WLLPPSLTLLLSSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSILGAINFITTIINMRSKGMTLDRMP 180


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00153  181 LFVWSVL 187
Cyt_c_Oxidase_I cd01663
Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-167 9.60e-101

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: 298.63  E-value: 9.60e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:cd01663    14 GLWSGLVGTSLSLLIRLELSQPGSQLGNDQLYNVIVTAHALIMIFFMVMPALIGGFGNWLVPLMIGAPDMAFPRLNNLSF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:cd01663    94 WLLPPSLLLLLLSALVEGGAGTGWTVYPPLSSILAHSGPSVDLAIFSLHLAGISSILGAINFITTIFNMRAPGMTLEKMP 173


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:cd01663   174 LFVWSVL 180
COX1 MTH00167
cytochrome c oxidase subunit I; Provisional
 1-167 1.35e-93

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177222  Cd Length: 512  Bit Score: 281.18  E-value: 1.35e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00167   23 GAWAGMVGTALSLLIRAELSQPGSLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00167  103 WLLPPSLLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGSINFITTIINMKPPGITQYQTP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00167  183 LFVWSIL 189
COX1 MTH00223
cytochrome c oxidase subunit I; Provisional
 1-167 1.68e-89

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177260  Cd Length: 512  Bit Score: 270.70  E-value: 1.68e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00223   20 GMWSGLVGTSLSLLIRAELGQPGALLGDDQLYNVIVTAHAFVMIFFLVMPMMIGGFGNWLVPLMLGAPDMAFPRLNNMSF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00223  100 WLLPPSLYLLLSSSAVESGVGTGWTVYPPLSSNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTIINMRSPGMQLERLP 179


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00223  180 LFVWSVK 186
COX1 MTH00116
cytochrome c oxidase subunit I; Provisional
 1-167 8.11e-89

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177177  Cd Length: 515  Bit Score: 269.27  E-value: 8.11e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00116   23 GAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00116  103 WLLPPSFLLLLASSTVEAGAGTGWTVYPPLAGNLAHAGASVDLAIFSLHLAGVSSILGAINFITTCINMKPPAMSQYQTP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00116  183 LFVWSVL 189
COX1 MTH00142
cytochrome c oxidase subunit I; Provisional
 1-167 1.04e-85

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214431  Cd Length: 511  Bit Score: 260.81  E-value: 1.04e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00142   21 GAWAGMVGTGLSLLIRAELGQPGSLLGDDQLYNVIVTAHAFVMIFFMVMPVMIGGFGNWLVPLMLGAPDMAFPRMNNMSF 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00142  101 WLLPPALLLLLSSAAVESGAGTGWTVYPPLSSNLAHSGGSVDLAIFSLHLAGVSSILGAINFITTVINMRAGGMKFERVP 180


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00142  181 LFVWSVK 187
COX1 MTH00103
cytochrome c oxidase subunit I; Validated
 1-167 5.87e-78

cytochrome c oxidase subunit I; Validated


Pssm-ID: 177165  Cd Length: 513  Bit Score: 240.94  E-value: 5.87e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00103   23 GAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00103  103 WLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00103  183 LFVWSVL 189
COX1 MTH00183
cytochrome c oxidase subunit I; Provisional
 1-167 5.74e-77

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177234  Cd Length: 516  Bit Score: 238.67  E-value: 5.74e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00183   23 GAWAGMVGTALSLLIRAELSQPGALLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00183  103 WLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAISQYQTP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00183  183 LFVWAVL 189
COX1 MTH00077
cytochrome c oxidase subunit I; Provisional
 1-167 9.86e-77

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214419  Cd Length: 514  Bit Score: 237.92  E-value: 9.86e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00077   23 GAWAGMVGTALSLLIRAELSQPGTLLGDDQIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00077  103 WLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTSINMKPPSMSQYQTP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00077  183 LFVWSVL 189
COX1 MTH00007
cytochrome c oxidase subunit I; Validated
 1-166 5.03e-76

cytochrome c oxidase subunit I; Validated


Pssm-ID: 133649  Cd Length: 511  Bit Score: 235.95  E-value: 5.03e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00007   20 GVWGGLLGTSMSLLIRIELGQPGAFLGSDQLYNTIVTAHAFLMIFFLVMPVFIGGFGNWLVPLMLGAPDMAFPRLNNMSF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00007  100 WLLPPALILLVSSAAVEKGVGTGWTVYPPLASNLAHAGPSVDLAIFSLHLAGVSSILGAINFITTVINMRWKGLRLERIP 179


                  ....*.
gi 2118838443 161 LFVWSI 166
Cdd:MTH00007  180 LFVWAV 185
COX1 MTH00037
cytochrome c oxidase subunit I; Provisional
 1-167 9.90e-76

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177112  Cd Length: 517  Bit Score: 235.49  E-value: 9.90e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00037   23 GAWAGMVGTAMSVIIRTELAQPGSLLQDDQIYNVIVTAHALVMIFFMVMPIMIGGFGNWLIPLMIGAPDMAFPRMNNMSF 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00037  103 WLIPPSFLLLLASAGVESGAGTGWTIYPPLSSNIAHAGGSVDLAIFSLHLAGASSILASINFITTIINMRTPGMTFDRLP 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00037  183 LFVWSVF 189
COX1 MTH00182
cytochrome c oxidase subunit I; Provisional
 1-183 1.03e-74

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 214451  Cd Length: 525  Bit Score: 233.17  E-value: 1.03e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00182   25 GAGAGMIGTAFSMLIRLELSAPGAMLGDDHLYNVIVTAHAFIMIFFLVMPVMIGGFGNWLVPLYIGAPDMAFPRLNNISF 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00182  105 WLLPPALILLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGAVDMAIFSLHLAGVSSILGAINFITTIFNMRAPGVTFNRLP 184

                         170       180
                  ....*....|....*....|...
gi 2118838443 161 LFVWSIFLTTILLLLSLPVLAGG 183
Cdd:MTH00182  185 LFVWSILITAFLLLLSLPVLAGA 207
COX1 MTH00184
cytochrome c oxidase subunit I; Provisional
 1-183 1.41e-74

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177235  Cd Length: 519  Bit Score: 232.41  E-value: 1.41e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00184   25 GAFAGMIGTAFSMLIRLELSAPGSMLGDDHLYNVIVTAHAFVMIFFLVMPVMIGGFGNWFVPLYIGAPDMAFPRLNNISF 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00184  105 WLLPPALTLLLGSAFVEQGAGTGWTVYPPLSSIQAHSGGSVDMAIFSLHLAGISSILGAMNFITTIFNMRAPGITMDRMP 184

                         170       180
                  ....*....|....*....|...
gi 2118838443 161 LFVWSIFLTTILLLLSLPVLAGG 183
Cdd:MTH00184  185 LFVWSILVTTFLLLLSLPVLAGA 207
COX1 MTH00079
cytochrome c oxidase subunit I; Provisional
 1-167 3.06e-74

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177148  Cd Length: 508  Bit Score: 231.49  E-value: 3.06e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00079   24 GLWSGMVGTSLSLIIRLELSKPGLLLGNGQLYNSVITAHAILMIFFMVMPSMIGGFGNWMLPLMLGAPDMSFPRLNNLSF 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSnLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00079  104 WLLPTSLFLILDSCFVDMGPGTSWTVYPPLST-LGHPGSSVDLAIFSLHCAGISSILGGINFMVTTKNLRSSSISLEHMS 182


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:MTH00079  183 LFVWTVF 189
Heme_Cu_Oxidase_I cd00919
Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in ...
 1-167 3.70e-65

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: 206.61  E-value: 3.70e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPlMLSAPDMAFPRLNNMSY 80
Cdd:cd00919    12 AFVALLLGGLLALLIRLELATPGSLFLDPQLYNQLVTAHGVIMIFFFVMPAIFGGFGNLLPP-LIGARDLAFPRLNNLSF 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:cd00919    91 WLFPPGLLLLLSSVLVGGGAGTGWTFYPPLSTLSYSSGVGVDLAILGLHLAGVSSILGAINFITTILNMRAPGMTLDKMP 170


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:cd00919   171 LFVWSVL 177
COX1 MTH00026
cytochrome c oxidase subunit I; Provisional
 1-183 2.22e-64

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 164599  Cd Length: 534  Bit Score: 206.40  E-value: 2.22e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00026   24 GALSGAIGTAFSMLIRLELSSPGSMLGDDHLYNVIVTAHAFVMIFFLVMPTMIGGFGNWFVPLMIGAPDMAFPRLNNISF 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKIS 160
Cdd:MTH00026  104 WLLPPALFLLLGSSLVEQGAGTGWTVYPPLASIQAHSGGSVDMAIFSLHLAGLSSILGAMNFITTVMNMRTPGMTMSRIP 183

                         170       180
                  ....*....|....*....|...
gi 2118838443 161 LFVWSIFLTTILLLLSLPVLAGG 183
Cdd:MTH00026  184 LFVWSVFITAILLLLSLPVLAGA 206
CyoB COG0843
Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion];
6-167 2.40e-59

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


Pssm-ID: 440605  Cd Length: 535  Bit Score: 193.42  E-value: 2.40e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   6 MIGSALSMIIRMELGTPS-QLIGNDQiYNSIVTAHAFIMIFFMVMPIMVGgFGNYMVPLMLSAPDMAFPRLNNMSYWLLI 84
Cdd:COG0843    31 LIGGLLALLMRLQLAGPGlGLLSPET-YNQLFTMHGTIMIFFFATPFLAG-FGNYLVPLQIGARDMAFPRLNALSFWLYL 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  85 PALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKISLFVW 164
Cdd:COG0843   109 FGGLLLLISLFVGGAADVGWTFYPPLSGLEASPGVGVDLWLLGLALFGVGSILGGVNFIVTILKMRAPGMTLMRMPLFTW 188


                  ...
gi 2118838443 165 SIF 167
Cdd:COG0843   189 AAL 191
COX1 MTH00048
cytochrome c oxidase subunit I; Provisional
 1-165 1.54e-49

cytochrome c oxidase subunit I; Provisional


Pssm-ID: 177123  Cd Length: 511  Bit Score: 167.16  E-value: 1.54e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMVGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:MTH00048   24 GVWSGFVGLSLSLLIRLNFLDPYYNVISLDVYNFLITNHGIIMIFFFLMPVLIGGFGNYLLPLLLGLSDLNLPRLNALSA 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMFIdqGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMdKIS 160
Cdd:MTH00048  104 WLLVPSIVFLLLSMCL--GAGVGWTFYPPLSSSLFSSSWGVDFLMFSLHLAGVSSLFGSINFICTIYSAFMTNVFS-RTS 180


                  ....*
gi 2118838443 161 LFVWS 165
Cdd:MTH00048  181 IILWS 185
Ubiquinol_Oxidase_I cd01662
Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory ...
 7-167 2.31e-49

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: 166.22  E-value: 2.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   7 IGSALSMIIRMELGTP-SQLIGNDQiYNSIVTAHAFIMIFFMVMPIMVGgFGNYMVPLMLSAPDMAFPRLNNMSYWLLIP 85
Cdd:cd01662    24 RGGVDALLMRTQLALPgNDFLSPEH-YNQIFTMHGTIMIFLFAMPLVFG-LMNYLVPLQIGARDVAFPRLNALSFWLFLF 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  86 ALILLTSSMFIDQGAGTGWTVYPPLSSNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKISLFVWS 165
Cdd:cd01662   102 GGLLLNASLLIGGFPDAGWFAYPPLSGLEYSPGVGVDYWILGLQFSGIGTLLGAINFIVTILKMRAPGMTLMRMPIFTWT 181


                  ..
gi 2118838443 166 IF 167
Cdd:cd01662   182 TL 183
COX1 pfam00115
Cytochrome C and Quinol oxidase polypeptide I; Cytochrome c oxidase (E.C:7.1.1.9) is a key ...
 1-167 7.64e-37

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: 131.93  E-value: 7.64e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443   1 GIWSGMIGSALSMIIRMELGTPSQLIGNDQIYNSIVTAHAFIMIFFMVMPIMvGGFGNYMVPLMLSAPDMAFPRLNNMSY 80
Cdd:pfam00115  10 ALVWFLVGGLLGLLIRLQLAFPGLNFLSPLTYNQLRTLHGNLMIFWFATPFL-FGFGNYLVPLMIGARDMAFPRLNALSF 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  81 WLLIPALILLTSSMfidQGAGTGWTVYPPLssnlghpgISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMdKIS 160
Cdd:pfam00115  89 WLVVLGAVLLLASF---GGATTGWTEYPPL--------VGVDLWYIGLLLAGVSSLLGAINFIVTILKRRAPGMTL-RMP 156


                  ....*..
gi 2118838443 161 LFVWSIF 167
Cdd:pfam00115 157 LFVWAIL 163
PRK15017 PRK15017
cytochrome o ubiquinol oxidase subunit I; Provisional
 32-165 4.92e-33

cytochrome o ubiquinol oxidase subunit I; Provisional


Pssm-ID: 184978  Cd Length: 663  Bit Score: 123.89  E-value: 4.92e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118838443  32 YNSIVTAHAFIMIFFMVMPIMVGgFGNYMVPLMLSAPDMAFPRLNNMSYWLLIPALILLTSSMFIDQGAGTGWTVYPPLS 111
Cdd:PRK15017   99 YDQIFTAHGVIMIFFVAMPFVIG-LMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLS 177

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2118838443 112 SNLGHPGISVDLTIFSLHLSGISSILGSINFITTILNMRPKNMTMDKISLFVWS 165
Cdd:PRK15017  178 GIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWA 231
 
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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