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Conserved domains on  [gi|962172204|gb|KTC60029|]
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photosynthetic protein synthase I [Pseudomonas savastanoi]

Protein Classification

SCO family protein( domain architecture ID 10005092)

SCO (Synthesis of Cytochrome c Oxidase) family protein is required for the proper assembly of cytochrome c oxidase

CATH:  3.40.30.10
Gene Ontology:  GO:0046872
PubMed:  10049365|15558583|10954195
SCOP:  3000031

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-199 2.09e-51

Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 441602  Cd Length: 156  Bit Score: 162.76  E-value: 2.09e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  49 RLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKT-LQVVFITLDPERDTPEVIDAYVKAFD 127
Cdd:COG1999    4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGGDdVQVLFISVDPERDTPEVLKAYAEAFG 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 962172204 128 -PTFVALSGTLEETAATAKEFGVFFEKVPLGDtYTISHTATSYVYDTRGVLRLGLSHRLSAQQCTEDLLTLME 199
Cdd:COG1999   84 aPRWIGLTGDPEEIAALAKAFGVYYEKVPDGD-YTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
 
Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-199 2.09e-51

Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441602  Cd Length: 156  Bit Score: 162.76  E-value: 2.09e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  49 RLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKT-LQVVFITLDPERDTPEVIDAYVKAFD 127
Cdd:COG1999    4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGGDdVQVLFISVDPERDTPEVLKAYAEAFG 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 962172204 128 -PTFVALSGTLEETAATAKEFGVFFEKVPLGDtYTISHTATSYVYDTRGVLRLGLSHRLSAQQCTEDLLTLME 199
Cdd:COG1999   84 aPRWIGLTGDPEEIAALAKAFGVYYEKVPDGD-YTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 44-178 3.10e-51

SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.


Pssm-ID: 239266  Cd Length: 142  Bit Score: 162.00  E-value: 3.10e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  44 VGRNFRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKT-LQVVFITLDPERDTPEVIDAY 122
Cdd:cd02968    1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDdVQVVFISVDPERDTPEVLKAY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 962172204 123 VKAFDPTFVALSGTLEETAATAKEFGVFFEKVPLGD-TYTISHTATSYVYDTRGVLR 178
Cdd:cd02968   81 AKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPEDDgDYLVDHSAAIYLVDPDGKLV 137
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 48-175 6.81e-49

SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.


Pssm-ID: 460630  Cd Length: 134  Bit Score: 155.42  E-value: 6.81e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204   48 FRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKTLQVVFITLDPERDTPEVIDAYVKAFD 127
Cdd:pfam02630   4 FELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALGEEGIDVQPVFITVDPERDTPEVLAEYLEAFG 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 962172204  128 PTFVALSGTLEETAATAKEFGVFFEKVPL-GDTYTISHTATSYVYDTRG 175
Cdd:pfam02630  84 PRIIGLTGSPEQIAAAARAFRVYYEKVPDdGGDYTVDHTASVYLVDPDG 132
 
Name Accession Description Interval E-value
Sco1 COG1999
Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, ...
 49-199 2.09e-51

Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441602  Cd Length: 156  Bit Score: 162.76  E-value: 2.09e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  49 RLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKT-LQVVFITLDPERDTPEVIDAYVKAFD 127
Cdd:COG1999    4 TLTDQDGKPVTLADLRGKPVLVFFGYTSCPDVCPTTLANLAQVQEALGEDGGDdVQVLFISVDPERDTPEVLKAYAEAFG 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 962172204 128 -PTFVALSGTLEETAATAKEFGVFFEKVPLGDtYTISHTATSYVYDTRGVLRLGLSHRLSAQQCTEDLLTLME 199
Cdd:COG1999   84 aPRWIGLTGDPEEIAALAKAFGVYYEKVPDGD-YTFDHSAAVYLVDPDGRLRGYYPAGEDPEELAADLKALLE 155
SCO cd02968
SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to ...
 44-178 3.10e-51

SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II.


Pssm-ID: 239266  Cd Length: 142  Bit Score: 162.00  E-value: 3.10e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  44 VGRNFRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKT-LQVVFITLDPERDTPEVIDAY 122
Cdd:cd02968    1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDdVQVVFISVDPERDTPEVLKAY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 962172204 123 VKAFDPTFVALSGTLEETAATAKEFGVFFEKVPLGD-TYTISHTATSYVYDTRGVLR 178
Cdd:cd02968   81 AKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPEDDgDYLVDHSAAIYLVDPDGKLV 137
SCO1-SenC pfam02630
SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. ...
 48-175 6.81e-49

SCO1/SenC; This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus.


Pssm-ID: 460630  Cd Length: 134  Bit Score: 155.42  E-value: 6.81e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204   48 FRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPAICPTALARAAQIRKLMGEEGKTLQVVFITLDPERDTPEVIDAYVKAFD 127
Cdd:pfam02630   4 FELVDQDGKAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALGEEGIDVQPVFITVDPERDTPEVLAEYLEAFG 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 962172204  128 PTFVALSGTLEETAATAKEFGVFFEKVPL-GDTYTISHTATSYVYDTRG 175
Cdd:pfam02630  84 PRIIGLTGSPEQIAAAARAFRVYYEKVPDdGGDYTVDHTASVYLVDPDG 132
AhpC-TSA pfam00578
AhpC/TSA family; This family contains proteins related to alkyl hydroperoxide reductase (AhpC) ...
 47-178 6.79e-08

AhpC/TSA family; This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).


Pssm-ID: 425763 [Multi-domain]  Cd Length: 124  Bit Score: 49.14  E-value: 6.79e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204   47 NFRLKDAQGNVKTLSSFRGLMPMIFF-GFTQCPaICPTALARaaqIRKLMGE-EGKTLQVVFITLdperDTPEVIDAYVK 124
Cdd:pfam00578   7 DFELPDGDGGTVSLSDYRGKWVVLFFyPADWTP-VCTTELPA---LADLYEEfKKLGVEVLGVSV----DSPESHKAFAE 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 962172204  125 AFDPTFVALSgtlEETAATAKEFGVFFEKVPLGdtytishTATSYVYDTRGVLR 178
Cdd:pfam00578  79 KYGLPFPLLS---DPDGEVARAYGVLNEEEGGA-------LRATFVIDPDGKVR 122
Bcp COG1225
Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];
47-178 6.84e-07

Peroxiredoxin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440838 [Multi-domain]  Cd Length: 136  Bit Score: 46.78  E-value: 6.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  47 NFRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPaICptaLARAAQIRKLMGE-EGKTLQVVFITldpeRDTPEVIDAYVKA 125
Cdd:COG1225    3 DFTLPDLDGKTVSLSDLRGKPVVLYFYATWCP-GC---TAELPELRDLYEEfKDKGVEVLGVS----SDSDEAHKKFAEK 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 962172204 126 FDPTFVALSGtleETAATAKEFGVFFekvplgdtytishTATSYVYDTRGVLR 178
Cdd:COG1225   75 YGLPFPLLSD---PDGEVAKAYGVRG-------------TPTTFLIDPDGKIR 111
TlpA_like_family cd02966
TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are ...
 47-178 1.03e-06

TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.


Pssm-ID: 239264 [Multi-domain]  Cd Length: 116  Bit Score: 45.69  E-value: 1.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  47 NFRLKDAQGNVKTLSSFRGLMPMIFFGFTQCPaICPTALARAAQIRKLMGEEGktLQVVFITLDpeRDTPEVIDAYVKAF 126
Cdd:cd02966    1 DFSLPDLDGKPVSLSDLKGKVVLVNFWASWCP-PCRAEMPELEALAKEYKDDG--VEVVGVNVD--DDDPAAVKAFLKKY 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 962172204 127 DPTFVALsgtLEETAATAKEFGVFFekVPlgdtytishtaTSYVYDTRGVLR 178
Cdd:cd02966   76 GITFPVL---LDPDGELAKAYGVRG--LP-----------TTFLIDRDGRIR 111
PRX_like1 cd02969
Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. ...
 47-148 2.53e-04

Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.


Pssm-ID: 239267 [Multi-domain]  Cd Length: 171  Bit Score: 39.91  E-value: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 962172204  47 NFRLKDAQGNVKTLSSFRG-----LMpmiffgFTqCpAICPTALARAAQIRKLMGE-EGKTLQVVFI-----TLDPErDT 115
Cdd:cd02969    6 DFSLPDTDGKTYSLADFADgkalvVM------FI-C-NHCPYVKAIEDRLNRLAKEyGAKGVAVVAInsndiEAYPE-DS 76

                         90       100       110
                 ....*....|....*....|....*....|...
gi 962172204 116 PEVIDAYVKAFDPTFVALsgtLEETAATAKEFG 148
Cdd:cd02969   77 PENMKAKAKEHGYPFPYL---LDETQEVAKAYG 106
 
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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