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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633  40 FNLFDQHG-PVTHESYPGKYLLLSIGYSSCPDICPTTLYEYGYAMKRL--QHADMLQPLFLTIDPVNDEINRLNAYTQYF 116
Cdd:cd02968    5 FTLTDQDGrPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLgaDGGDDVQVVFISVDPERDTPEVLKAYAKAF 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881049633 117 DERIVGLSGEMKDIEDVAKQLGATFgyrlngqrIDNPEPGMGYTVYHSAMIYLITPEREILDVFDY 182
Cdd:cd02968   85 GPGWIGLTGTPEEIEALAKAFGVYY--------EKVPEDDGDYLVDHSAAIYLVDPDGKLVRYYGG 142

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633  40 FNLFDQHG-PVTHESYPGKYLLLSIGYSSCPDICPTTLYEYGYAMKRL--QHADMLQPLFLTIDPVNDEINRLNAYTQYF 116
Cdd:cd02968    5 FTLTDQDGrPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLgaDGGDDVQVVFISVDPERDTPEVLKAYAKAF 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881049633 117 DERIVGLSGEMKDIEDVAKQLGATFgyrlngqrIDNPEPGMGYTVYHSAMIYLITPEREILDVFDY 182
Cdd:cd02968   85 GPGWIGLTGTPEEIEALAKAFGVYY--------EKVPEDDGDYLVDHSAAIYLVDPDGKLVRYYGG 142

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633   40 FNLFDQHG-PVTHESYPGKYLLLSIGYSSCPDICPTTLYEYGYAMKRL-QHADMLQPLFLTIDPVNDEINRLNAYTQYFD 117
Cdd:pfam02630   4 FELVDQDGkAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALgEEGIDVQPVFITVDPERDTPEVLAEYLEAFG 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 881049633  118 ERIVGLSGEMKDIEDVAKQlgatfgYRLNGQRidNPEPGMGYTVYHSAMIYLITPEREI 176
Cdd:pfam02630  84 PRIIGLTGSPEQIAAAARA------FRVYYEK--VPDDGGDYTVDHTASVYLVDPDGRF 134

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633 253 LLNLWALWCAPCRQELPLLEKWAAL--QNELDIITINVGDS-IEKINSFFEEQGFsHLPKYQIENFNLLRQLGGMGLPFN 329
Cdd:cd02966   23 LVNFWASWCPPCRAEMPELEALAKEykDDGVEVVGVNVDDDdPAAVKAFLKKYGI-TFPVLLDPDGELAKAYGVRGLPTT 101

                 ...
gi 881049633 330 ALF 332
Cdd:cd02966  102 FLI 104

Thioredoxin-like; Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633  253 LLNLWALWCAPCRQELPLL----EKWAALQNeLDIITINVGDSIEKINSFFEEQGFS--HLPKYQIENFNLLRQLGGMGL 326
Cdd:pfam13905   5 LLYFGASWCKPCRRFTPLLkelyEKLKKKKN-VEIVFVSLDRDLEEFKDYLKKMPKDwlSVPFDDDERNELKRKYGVNAI 83

                  ....*.
gi 881049633  327 PFNALF 332
Cdd:pfam13905  84 PTLVLL 89

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633  40 FNLFDQHG-PVTHESYPGKYLLLSIGYSSCPDICPTTLYEYGYAMKRL--QHADMLQPLFLTIDPVNDEINRLNAYTQYF 116
Cdd:cd02968    5 FTLTDQDGrPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLgaDGGDDVQVVFISVDPERDTPEVLKAYAKAF 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881049633 117 DERIVGLSGEMKDIEDVAKQLGATFgyrlngqrIDNPEPGMGYTVYHSAMIYLITPEREILDVFDY 182
Cdd:cd02968   85 GPGWIGLTGTPEEIEALAKAFGVYY--------EKVPEDDGDYLVDHSAAIYLVDPDGKLVRYYGG 142

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633   40 FNLFDQHG-PVTHESYPGKYLLLSIGYSSCPDICPTTLYEYGYAMKRL-QHADMLQPLFLTIDPVNDEINRLNAYTQYFD 117
Cdd:pfam02630   4 FELVDQDGkAVTEADFEGRPSLVFFGFTHCPDVCPTTLPNMAQVLDALgEEGIDVQPVFITVDPERDTPEVLAEYLEAFG 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 881049633  118 ERIVGLSGEMKDIEDVAKQlgatfgYRLNGQRidNPEPGMGYTVYHSAMIYLITPEREI 176
Cdd:pfam02630  84 PRIIGLTGSPEQIAAAARA------FRVYYEK--VPDDGGDYTVDHTASVYLVDPDGRF 134

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633 253 LLNLWALWCAPCRQELPLLEKWAAL--QNELDIITINVGDS-IEKINSFFEEQGFsHLPKYQIENFNLLRQLGGMGLPFN 329
Cdd:cd02966   23 LVNFWASWCPPCRAEMPELEALAKEykDDGVEVVGVNVDDDdPAAVKAFLKKYGI-TFPVLLDPDGELAKAYGVRGLPTT 101

                 ...
gi 881049633 330 ALF 332
Cdd:cd02966  102 FLI 104

periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins. [Protein fate, Protein folding and stabilization]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 881049633  245 VEPEANTQ----LLNLWALWCAPCRQELPLLEKWAAlqNELDIITINVGDSIEKINSFFEEQG 303
Cdd:TIGR00385  55 YTADVLTQgkpvLLNVWASWCPPCRAEHPYLNELAK--QGLPIVGVDYKDDRQNAIKFLKELG 115

TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 881049633 253 LLNLWALWCAPCRQELPLLEKWAALQNELDIITINVGDSIE 293
Cdd:cd02947   14 VVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPE 54

Thioredoxin-like; Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633  253 LLNLWALWCAPCRQELPLL----EKWAALQNeLDIITINVGDSIEKINSFFEEQGFS--HLPKYQIENFNLLRQLGGMGL 326
Cdd:pfam13905   5 LLYFGASWCKPCRRFTPLLkelyEKLKKKKN-VEIVFVSLDRDLEEFKDYLKKMPKDwlSVPFDDDERNELKRKYGVNAI 83

                  ....*.
gi 881049633  327 PFNALF 332
Cdd:pfam13905  84 PTLVLL 89

thioredoxin TrxA;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881049633 253 LLNLWALWCAPCRQELPLLEKWA-ALQNELDIITINVgdsiekinsffeEQGFSHLPKYQIEnfnllrqlggmGLPFNAL 331
Cdd:PRK09381  25 LVDFWAEWCGPCKMIAPILDEIAdEYQGKLTVAKLNI------------DQNPGTAPKYGIR-----------GIPTLLL 81

                         90
                 ....*....|....*
gi 881049633 332 FVNDSIVGIKSGIIT 346
Cdd:PRK09381  82 FKNGEVAATKVGALS 96

Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include TRX, protein disulfide isomerase (PDI), tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein families. Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins and glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 881049633 253 LLNLWALWCAPCRQELPLLEKWAALQNELDIITINVgDSIEKINSFFEEQGFSHLP 308
Cdd:cd01659    1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDV-DEDPALEKELKRYGVGGVP 55