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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  76 VLRAGKPTIIEFGANNCVSCREMKPILHALAQDA-RIAVADVDILKEREYIGKYQIRLMPTQVFYNaQGVETGRHMGKIS 154
Cdd:cd02947     6 LIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYpKVKFVKVDVDENPELAEEYGVRSIPTFLFFK-NGKEVDRVVGADP 84

                  ....*...
gi 1278388175 155 AEAILANL 162
Cdd:cd02947    85 KEELEEFL 92

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  76 VLRAGKPTIIEFGANNCVSCREMKPILHALAQDA-RIAVADVDILKEREYIGKYQIRLMPTQVFYNaQGVETGRHMGKIS 154
Cdd:cd02947     6 LIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYpKVKFVKVDVDENPELAEEYGVRSIPTFLFFK-NGKEVDRVVGADP 84

                  ....*...
gi 1278388175 155 AEAILANL 162
Cdd:cd02947    85 KEELEEFL 92

thioredoxin; Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model. Any protein that hits once with a score greater than the second (per domain) trusted cutoff may be taken as thioredoxin. [Energy metabolism, Electron transport]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  74 QVVLRAGKPTIIEFGANNCVSCREMKPILHALAQD--ARIAVADVDILKEREYIGKYQIRLMPTQVFYNaQGVETGRHMG 151
Cdd:TIGR01068   8 ETIASSDKPVLVDFWAPWCGPCKMIAPILEELAKEyeGKVKFVKLNVDENPDIAAKYGIRSIPTLLLFK-NGKEVDRSVG 86

                  ....*...
gi 1278388175 152 KISAEAIL 159
Cdd:TIGR01068  87 ALPKAALK 94

thiol:disulfide interchange protein precursor; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  34 KTSVIVVAIAATLTGF-----WLYAGSSAQGSDPTAAG---IGTADAVQVVL----RAGKPTIIEFGANNCVSCREM-KP 100
Cdd:PRK00293  416 RLLGQILLLAALLASVrplqdWAFGGAAAGAQTQAHLNfqrIKTVAELDQALaeakGKGKPVMLDLYADWCVACKEFeKY 495

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278388175 101 ILHA---LAQDARIAVADVDILK----EREYIGKYQIRLMPTQVFYNAQGVE--TGRHMGKISAEAILANL 162
Cdd:PRK00293  496 TFSDpqvQQALADTVLLQADVTAnnaeDVALLKHYNVLGLPTILFFDAQGQEipDARVTGFMDAAAFAAHL 566

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  76 VLRAGKPTIIEFGANNCVSCREMKPILHALAQDA-RIAVADVDILKEREYIGKYQIRLMPTQVFYNaQGVETGRHMGKIS 154
Cdd:cd02947     6 LIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYpKVKFVKVDVDENPELAEEYGVRSIPTFLFFK-NGKEVDRVVGADP 84

                  ....*...
gi 1278388175 155 AEAILANL 162
Cdd:cd02947    85 KEELEEFL 92

Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, chaperones];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  79 AGKPTIIEFGANNCVSCREMKPILHALAQDAR----IAVA-DVDILKEREYIGK------------------YQIRLMPT 135
Cdd:COG0526    27 KGKPVLVNFWATWCPPCRAEMPVLKELAEEYGgvvfVGVDvDENPEAVKAFLKElglpypvlldpdgelakaYGVRGIPT 106

                          90       100
                  ....*....|....*....|....*..
gi 1278388175 136 QVFYNAQGVETGRHMGKISAEAILANL 162
Cdd:COG0526   107 TVLIDKDGKIVARHVGPLSPEELEEAL 133

DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha). DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing potential from DsbD gamma to target proteins such as the periplasmic protein disulphide isomerases, DsbC and DsbG. This flow of reducing potential from the cytoplasm through DsbD allows DsbC and DsbG to act as isomerases in the oxidizing environment of the bacterial periplasm. DsbD also transfers reducing potential from the cytoplasm to specific reductases in the periplasm which are involved in the maturation of cytochromes.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  77 LRAGKPTIIEFGANNCVSCREMK-------PILHALAQDARIAVADV-----DIlkeREYIGKYQIRLMPTQVFYNAQGV 144
Cdd:cd02953     8 LAQGKPVFVDFTADWCVTCKVNEkvvfsdpEVQAALKKDVVLLRADWtkndpEI---TALLKRFGVFGPPTYLFYGPGGE 84

                          90       100
                  ....*....|....*....|
gi 1278388175 145 ETGRHM-GKISAEAILANLG 163
Cdd:cd02953    85 PEPLRLpGFLTADEFLEALE 104

Thiol:disulfide interchange protein DsbD [Posttranslational modification, protein turnover, chaperones];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  37 VIVVAIAATLTGFWLYAGSSAQGSDPTAAGIG----TADAVQVVLRAGKPTIIEFGANNCVSCREMK-------PILHAL 105
Cdd:COG4232   273 GLALLLGALSGADPLQPLAAGAAAAAAAAGLAwqadLEAALAEARAEGKPVFVDFTADWCVTCKENErtvfsdpEVQAAL 352

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1278388175 106 AQDARIAVADVDILKE--REYIGKYQIRLMPTQVFYNAQGVETGRHMGKISAEAILANL 162
Cdd:COG4232   353 ADDVVLLKADVTDNDPeiTALLKRFGRFGVPTYVFYDPDGEELPRLGFMLTADEFLAAL 411

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 1278388175  79 AGKPTIIEFGANNCVSCREMKPILHALAQDAR--------IAVADVDILKEREYIGK------------------YQIRL 132
Cdd:cd02966    18 KGKVVLVNFWASWCPPCRAEMPELEALAKEYKddgvevvgVNVDDDDPAAVKAFLKKygitfpvlldpdgelakaYGVRG 97

                          90
                  ....*....|....*....
gi 1278388175 133 MPTQVFYNAQGVETGRHMG 151
Cdd:cd02966    98 LPTTFLIDRDGRIRARHVG 116

Thioredoxin-like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  80 GKPTIIEFGANNCVSCREMKP----------ILHALAQDARIAV--------ADVDILKEREYIGKYQIRLMPTQVFYNA 141
Cdd:pfam13098   4 GKPVLVVFTDPDCPYCKKLKKelledpdvtvYLGPNFVFIAVNIwcakevakAFTDILENKELGRKYGVRGTPTIVFFDG 83

                          90
                  ....*....|....*....
gi 1278388175 142 QGVETgRHMGKISAEAILA 160
Cdd:pfam13098  84 KGELL-RLPGYVPAEEFLA 101

TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278388175  79 AGKPTIIEFGANNCVSCREMKPILHALAQDARIAVADVDILKERE-------------------YIGKYQIRL----MPT 135
Cdd:cd03010    24 KGKPYLLNVWASWCAPCREEHPVLMALARQGRVPIYGINYKDNPEnalawlarhgnpyaavgfdPDGRVGIDLgvygVPE 103

                          90       100
                  ....*....|....*....|...
gi 1278388175 136 QVFYNAQGVETGRHMGKISAEAI 158
Cdd:cd03010   104 TFLIDGDGIIRYKHVGPLTPEVW 126

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278388175  84 IIEFGANNCVSCREMKPILHALAQ-DARIAVADVDIL---KEREYIGKYQIRLMPTQVFYNAQGVET 146
Cdd:cd01659     1 LVLFYAPWCPFCQALRPVLAELALlNKGVKFEAVDVDedpALEKELKRYGVGGVPTLVVFGPGIGVK 67

Thioredoxin domain-containing protein; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278388175  82 PTIIEFGANNCVSCREMKPILHALAQDAR--IAVADVDILKEREYIGKYQIRLMPTQVFYN 140
Cdd:PTZ00443   54 PWFVKFYAPWCSHCRKMAPAWERLAKALKgqVNVADLDATRALNLAKRFAIKGYPTLLLFD 114

Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein. It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a large spliceosomal complex involving many protein-protein interactions. U5 snRNP contains seven core proteins (common to all snRNPs) and nine U5-specific proteins, one of which is Dim1. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. It is essential for G2/M phase transition, as a consequence to its role in pre-mRNA splicing.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278388175  84 IIEFGANNCVSCREMKPILHALAQD----ARIAVadVDILKEREYIGKYQIRLMPTQV-FYNaqgvetGRHM 150
Cdd:cd02954    18 VIRFGRDWDPVCMQMDEVLAKIAEDvsnfAVIYL--VDIDEVPDFNKMYELYDPPTVMfFFR------NKHM 81