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 1032303881  11 ESWNFYVSQAKnqncPIVAHFTALWCIPSVFMNSFFEELAFNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAM 90
Cdd:cd02947     1 EEFEELIKSAK----PVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEV 76

                          90
                  ....*....|....*..
gi 1032303881  91 DKLVGANP-DEIKKRVD 106
Cdd:cd02947    77 DRVVGADPkEELEEFLE 93

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 1032303881  11 ESWNFYVSQAKnqncPIVAHFTALWCIPSVFMNSFFEELAFNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAM 90
Cdd:cd02947     1 EEFEELIKSAK----PVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEV 76

                          90
                  ....*....|....*..
gi 1032303881  91 DKLVGANP-DEIKKRVD 106
Cdd:cd02947    77 DRVVGADPkEELEEFLE 93

thioredoxin; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032303881  23 QNCPIVAHFTALWCIPSVFMNSFFEELAFNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVGANPDEIK 102
Cdd:PTZ00051   17 QNELVIVDFYAEWCGPCKRIAPFYEECSKEYTKMVFVKVDVDELSEVAEKENITSMPTFKVFKNGSVVDTLLGANDEALK 96

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1032303881  21 KNQNCPIVAHFTALWCIPSVFMNSFFEELAFNYK-DALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVGANP 98
Cdd:TIGR01068  11 ASSDKPVLVDFWAPWCGPCKMIAPILEELAKEYEgKVKFVKLNVDENPDIAAKYGIRSIPTLLLFKNGKEVDRSVGALP 89

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 1032303881  11 ESWNFYVSQAKnqncPIVAHFTALWCIPSVFMNSFFEELAFNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAM 90
Cdd:cd02947     1 EEFEELIKSAK----PVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEV 76

                          90
                  ....*....|....*..
gi 1032303881  91 DKLVGANP-DEIKKRVD 106
Cdd:cd02947    77 DRVVGADPkEELEEFLE 93

Thioredoxin; Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032303881   4 VVKIDSAESWNFYVSQAKNqncPIVAHFTALWCIPSVFMNSFFEELAFNYK-DALFLIVDVDEVKEVASQLEVKAMPTFL 82
Cdd:pfam00085   1 VVVVLTDANFDEVVQKSSK---PVLVDFYAPWCGPCKMLAPEYEELAQEYKgNVVFAKVDVDENPDLASKYGVRGYPTLI 77

                          90
                  ....*....|....*....
gi 1032303881  83 FLKDGNAMDKLVGANPDEI 101
Cdd:pfam00085  78 FFKNGQPVDDYVGARPKDA 96

Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family [Posttranslational modification, protein turnover, chaperones];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032303881  26 PIVAHFTALWCIPSVFMNSFFEELAFNYKDAL-FLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVGANP-DEIKK 103
Cdd:COG3118    20 PVLVDFWAPWCGPCKMLAPVLEELAAEYGGKVkFVKVDVDENPELAAQFGVRSIPTLLLFKDGQPVDRFVGALPkEQLRE 99

                  ....*.
gi 1032303881 104 RVDGFV 109
Cdd:COG3118   100 FLDKVL 105

ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032303881  26 PIVAHFTALWCIPSVFMNSFFEELAFNYKDALFLI-VDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVGANPDE-IKK 103
Cdd:cd02956    14 PVVVDFWAPRSPPSKELLPLLERLAEEYQGQFVLAkVNCDAQPQIAQQFGVQALPTVYLFAAGQPVDGFQGAQPEEqLRQ 93

                  ...
gi 1032303881 104 RVD 106
Cdd:cd02956    94 MLD 96

thioredoxin 2; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032303881  26 PIVAHFTALWCIPSVFMNSFFEELAFNYKDAL-FLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVGANP 98
Cdd:PRK10996   54 PVVIDFWAPWCGPCRNFAPIFEDVAAERSGKVrFVKVNTEAERELSARFRIRSIPTIMIFKNGQVVDMLNGAVP 127

Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif. The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that both PLP1 and PhLP3 are non-essential proteins. Unlike Phd and most Phd-like proteins, members of this group do not contain the Phd N-terminal helical domain which is implicated in binding to the G protein betagamma subunit.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1032303881  42 MNSFFEELAFNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGNAMDKLVG 95
Cdd:cd02989    40 MDKHLEILAKKHLETKFIKVNAEKAPFLVEKLNIKVLPTVILFKNGKTVDRIVG 93

Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1032303881  31 FTALWCIPSVFMNSFFEELA---FNYKDALFLIVDVDEVKEVASQLEVKAMPTFLFLKDGN 88
Cdd:cd02961    22 FYAPWCGHCKALAPEYEKLAkelKGDGKVVVAKVDCTANNDLCSEYGVRGYPTIKLFPNGS 82

Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Also included in this family is a PhLP characterized as a viral inhibitor of apoptosis (IAP)-associated factor, named VIAF, that functions in caspase activation during apoptosis.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1032303881  42 MNSFFEELAFNYKDALFLIVDVDEVkEVASQLEVKAMPTFLFLKDGNAMDKLVG 95
Cdd:cd02957    42 LDSHLEELAAKYPETKFVKINAEKA-FLVNYLDIKVLPTLLVYKNGELIDNIVG 94