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 1554477403   6 SEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEIM 85
Cdd:COG3118     6 TDENFEEEVLESDKPVLVDFWAPWCGPCKMLAPVLEELAAEYGGKVKFVKVDVDENPELAAQFGVRSIPTLLLFKDGQPV 85

                          90
                  ....*....|....*..
gi 1554477403  86 DTMVGASSKDAIMQRLR 102
Cdd:COG3118    86 DRFVGALPKEQLREFLD 102

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 1554477403   6 SEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEIM 85
Cdd:COG3118     6 TDENFEEEVLESDKPVLVDFWAPWCGPCKMLAPVLEELAAEYGGKVKFVKVDVDENPELAAQFGVRSIPTLLLFKDGQPV 85

                          90
                  ....*....|....*..
gi 1554477403  86 DTMVGASSKDAIMQRLR 102
Cdd:COG3118    86 DRFVGALPKEQLREFLD 102

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 1554477403   4 VFSEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGE 83
Cdd:pfam00085   4 VLTDANFDEVVQKSSKPVLVDFYAPWCGPCKMLAPEYEELAQEYKGNVVFAKVDVDENPDLASKYGVRGYPTLIFFKNGQ 83

                          90
                  ....*....|....
gi 1554477403  84 IMDTMVGASSKDAI 97
Cdd:pfam00085  84 PVDDYVGARPKDAL 97

thioredoxin TrxA;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   5 FSEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEI 84
Cdd:PRK09381    8 LTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEV 87

                          90
                  ....*....|....*..
gi 1554477403  85 MDTMVGASSKDAIMQRL 101
Cdd:PRK09381   88 AATKVGALSKGQLKEFL 104

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 1554477403   6 SEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEIM 85
Cdd:COG3118     6 TDENFEEEVLESDKPVLVDFWAPWCGPCKMLAPVLEELAAEYGGKVKFVKVDVDENPELAAQFGVRSIPTLLLFKDGQPV 85

                          90
                  ....*....|....*..
gi 1554477403  86 DTMVGASSKDAIMQRLR 102
Cdd:COG3118    86 DRFVGALPKEQLREFLD 102

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 1554477403   4 VFSEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGE 83
Cdd:pfam00085   4 VLTDANFDEVVQKSSKPVLVDFYAPWCGPCKMLAPEYEELAQEYKGNVVFAKVDVDENPDLASKYGVRGYPTLIFFKNGQ 83

                          90
                  ....*....|....
gi 1554477403  84 IMDTMVGASSKDAI 97
Cdd:pfam00085  84 PVDDYVGARPKDAL 97

thioredoxin TrxA;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   5 FSEANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEI 84
Cdd:PRK09381    8 LTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEV 87

                          90
                  ....*....|....*..
gi 1554477403  85 MDTMVGASSKDAIMQRL 101
Cdd:PRK09381   88 AATKVGALSKGQLKEFL 104

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   4 VFSEANFEDEVLKSDiPVLVDFWATWCGPCRMIAPIIDQLSTELA--GKIKVGKVDVDANNGLAATYGVRTIPTLLIIKD 81
Cdd:cd02961     2 ELTDDNFDELVKDSK-DVLVEFYAPWCGHCKALAPEYEKLAKELKgdGKVVVAKVDCTANNDLCSEYGVRGYPTIKLFPN 80

                          90
                  ....*....|....*....
gi 1554477403  82 G-EIMDTMVGASSKDAIMQ 99
Cdd:cd02961    81 GsKEPVKYEGPRTLESLVE 99

PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1554477403   7 EANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDG 82
Cdd:cd03001     7 DSNFDKKVLNSDDVWLVEFYAPWCGHCKNLAPEWKKAAKALKGIVKVGAVDADVHQSLAQQYGVRGFPTIKVFGAG 82

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  20 PVLVDFWATWCGPCRMIAPIIDQLSTELAGkIKVGKVDV----------------------DANNGLAATYGVRTIPTLL 77
Cdd:COG0526    30 PVLVNFWATWCPPCRAEMPVLKELAEEYGG-VVFVGVDVdenpeavkaflkelglpypvllDPDGELAKAYGVRGIPTTV 108

                          90       100
                  ....*....|....*....|....*....
gi 1554477403  78 II-KDGEIMDTMVGASSKDAIMQRLRPFM 105
Cdd:COG0526   109 LIdKDGKIVARHVGPLSPEELEEALEKLL 137

protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   4 VFSEANFeDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGK---IKVGKVDVDANNGLAATYGVRTIPTLLIIK 80
Cdd:TIGR01130   5 VLTKDNF-DDFIKSHEFVLVEFYAPWCGHCKSLAPEYEKAADELKKKgppIKLAKVDATEEKDLAQKYGVSGYPTLKIFR 83

                          90       100
                  ....*....|....*....|...
gi 1554477403  81 DGEIMDT-MVGASSKDAIMQRLR 102
Cdd:TIGR01130  84 NGEDSVSdYNGPRDADGIVKYMK 106

PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   6 SEANFEDEVLKSdiPVLVDFWATWCGPCRMIAPIIDQLSTEL---AGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDG 82
Cdd:cd03005     6 TEDNFDHHIAEG--NHFVKFFAPWCGHCKRLAPTWEQLAKKFnneNPSVKIAKVDCTQHRELCSEFQVRGYPTLLLFKDG 83

                  .
gi 1554477403  83 E 83
Cdd:cd03005    84 E 84

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 1554477403  20 PVLVDFWATWCGPCRMIAPIIDQLSTELAGK--------------------IKVGKVD----VDANNGLAATYGVRTIPT 75
Cdd:cd02966    21 VVLVNFWASWCPPCRAEMPELEALAKEYKDDgvevvgvnvddddpaavkafLKKYGITfpvlLDPDGELAKAYGVRGLPT 100

                          90
                  ....*....|....*.
gi 1554477403  76 LLII-KDGEIMDTMVG 90
Cdd:cd02966   101 TFLIdRDGRIRARHVG 116

PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1554477403   9 NFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKV--DVDANNGLAATYGVRTIPTLLIIK 80
Cdd:cd03002     9 NFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEYAKAAKELDGLVQVAAVdcDEDKNKPLCGKYGVQGFPTLKVFR 82

disulphide isomerase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   4 VFSEANFEDEVLKSDIpVLVDFWATWCGPCRMIAPIIDQLSTELA---GKIKVGKVDVDANNGLAATYGVRTIPTLLIIK 80
Cdd:PTZ00102   36 VLTDSTFDKFITENEI-VLVKFYAPWCGHCKRLAPEYKKAAKMLKekkSEIVLASVDATEEMELAQEFGVRGYPTIKFFN 114

                          90
                  ....*....|....*..
gi 1554477403  81 DGEIMDtMVGASSKDAI 97
Cdd:PTZ00102  115 KGNPVN-YSGGRTADGI 130

Thioredoxin domain-containing protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   5 FSEANFEDEVLKSDI----PVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAATYGVRTIPTLLIIK 80
Cdd:PTZ00443   35 LNDKNFEKLTQASTGattgPWFVKFYAPWCSHCRKMAPAWERLAKALKGQVNVADLDATRALNLAKRFAIKGYPTLLLFD 114

                  ....
gi 1554477403  81 DGEI 84
Cdd:PTZ00443  115 KGKM 118

PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403   5 FSEANFeDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTEL--AGKIKVGKVDV--DANNGLAATYGVRTIPTLLIIK 80
Cdd:cd02997     5 LTDEDF-RKFLKKEKHVLVMFYAPWCGHCKKMKPEFTKAATELkeDGKGVLAAVDCtkPEHDALKEEYNVKGFPTFKYFE 83

                          90
                  ....*....|....*..
gi 1554477403  81 DGEIMDTMVGASSKDAI 97
Cdd:cd02997    84 NGKFVEKYEGERTAEDI 100

PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  12 DEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTEL------AGKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEIM 85
Cdd:cd02996    12 DDILQSAELVLVNFYADWCRFSQMLHPIFEEAAAKIkeefpdAGKVVWGKVDCDKESDIADRYRINKYPTLKLFRNGMMM 91

protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1554477403   9 NFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAG---KIKVGKVDVDANNglAATYGVRTIPTLLIIKDGE 83
Cdd:TIGR01130 355 NFDEIVLDETKDVLVEFYAPWCGHCKNLAPIYEELAEKYKDaesDVVIAKMDATAND--VPPFEVEGFPTIKFVPAGK 430

PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  22 LVDFWATWCGPCRMIAPIIDQLST---ELagKIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGeIMDTMVGASSKDAIM 98
Cdd:cd02994    20 MIEFYAPWCPACQQLQPEWEEFADwsdDL--GINVAKVDVTQEPGLSGRFFVTALPTIYHAKDG-VFRRYQGPRDKEDLI 96

PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein containing an N-terminal redox active TRX domain, similar to that of PDI, and a small C-terminal flavin adenine dinucleotide (FAD)-binding domain homologous to the yeast ERV1p protein. QSOX oxidizes thiol groups to disulfides like PDI, however, unlike PDI, this oxidation is accompanied by the reduction of oxygen to hydrogen peroxide. QSOX is localized in high concentrations in cells with heavy secretory load and prefers peptides and proteins as substrates, not monothiols like glutathione. Inside the cell, QSOX is found in the endoplasmic reticulum and Golgi. The flow of reducing equivalents in a QSOX-catalyzed reaction goes from the dithiol substrate -> dithiol of the QSOX TRX domain -> dithiols of the QSOX ERV1p domain -> FAD -> oxygen.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1554477403   8 ANFEDEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELA---GKIKVGKVDV--DANNGLAATYGVRTIPTL 76
Cdd:cd02992     9 ASFNSALLGSPSAWLVEFYASWCGHCRAFAPTWKKLARDLRkwrPVVRVAAVDCadEENVALCRDFGVTGYPTL 82

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 1554477403   5 FSEANFEDEvlksdiPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIkVG----------------------KVDVDANN 62
Cdd:cd03010    18 LTSADLKGK------PYLLNVWASWCAPCREEHPVLMALARQGRVPI-YGinykdnpenalawlarhgnpyaAVGFDPDG 90

                          90       100       110
                  ....*....|....*....|....*....|
gi 1554477403  63 GLAATYGVRTIP-TLLIIKDGEIMDTMVGA 91
Cdd:cd03010    91 RVGIDLGVYGVPeTFLIDGDGIIRYKHVGP 120

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 1554477403  20 PVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKV---------------------------GKVDVDANNGLAATYGVRT 72
Cdd:pfam13905   3 VVLLYFGASWCKPCRRFTPLLKELYEKLKKKKNVeivfvsldrdleefkdylkkmpkdwlsVPFDDDERNELKRKYGVNA 82

                          90
                  ....*....|...
gi 1554477403  73 IPTLLII-KDGEI 84
Cdd:pfam13905  83 IPTLVLLdPNGEV 95

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  20 PVLVDFWATWCGPCRMIAPII---DQLSTELAGKIKVGKVDVDANN----GLAATYGVRTIPTLLII-KDGEIMDTMVGA 91
Cdd:COG4232   322 PVFVDFTADWCVTCKENERTVfsdPEVQAALADDVVLLKADVTDNDpeitALLKRFGRFGVPTYVFYdPDGEELPRLGFM 401

                          90
                  ....*....|.
gi 1554477403  92 SSKDAIMQRLR 102
Cdd:COG4232   402 LTADEFLAALE 412

TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  12 DEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGKIKVGKVDVDANNGLAAT--YGVRTIPTLLII-KDGEIMDTM 88
Cdd:cd02950    14 EVALSNGKPTLVEFYADWCTVCQEMAPDVAKLKQKYGDQVNFVMLNVDNPKWLPEIdrYRVDGIPHFVFLdREGNEEGQS 93

                          90
                  ....*....|...
gi 1554477403  89 VGASSKDAIMQRL 101
Cdd:cd02950    94 IGLQPKQVLAQNL 106

TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  10 FEDEVL-KS-DIPVLVDFWATWCGPCRMIAPIIDQLSTELAG-KIKVGKVDVDANNGLAATYGVRTIPTLLIIKDGEIMD 86
Cdd:cd02963    14 YENEIVpKSfKKPYLIKITSDWCFSCIHIEPVWKEVIQELEPlGVGIATVNAGHERRLARKLGAHSVPAIVGIINGQVTF 93

                          90
                  ....*....|....*.
gi 1554477403  87 TMVGASSKDAIMQRLR 102
Cdd:cd02963    94 YHDSSFTKQHVVDFVR 109

F plasmid transfer operon protein; TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character. F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localized to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  30 CGPCRMIAPIIDQLSTELAgkIKVGKVDVD-----------ANNGLAATYGVRTIPTLLII--KDGEIMDTMVGASSKDA 96
Cdd:pfam13728 141 CPYCEAQAPILQAFADKYG--WTVRPVSVDgrplpgfpnyrVDNGQAARLGVKRTPALFLVnpPSGDVVPVAAGVLSLDE 218

                  ....*
gi 1554477403  97 IMQRL 101
Cdd:pfam13728 219 LEERI 223

Thioredoxin-related protein SoxW [Posttranslational modification, protein turnover, chaperones];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  16 KSDIPVLVDFWATWCGPCRMI-------APIIDQLST-------ELAGKIKVgkVDVD----ANNGLAATYGVRTIPTLL 77
Cdd:COG2143    38 AEGKPILLFFESDWCPYCKKLhkevfsdPEVAAYLKEnfvvvqlDAEGDKEV--TDFDgetlTEKELARKYGVRGTPTLV 115

                          90       100
                  ....*....|....*....|....*.
gi 1554477403  78 II-KDGEIMDTMVGASSKDAIMQRLR 102
Cdd:COG2143   116 FFdAEGKEIARIPGYLKPETFLALLK 141

TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which is also associated with microtubular structures. The other members of this group are hypothetical insect proteins containing a TRX domain and outer arm dynein light chains (14 and 16kDa) of Chlamydomonas reinhardtii. Using standard assays, the fusion proteins have shown no TRX enzymatic activity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  12 DEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAG---KIKVGKVD-VDAnnglAATYGVRTIPTLLIIKDGEIMDT 87
Cdd:cd02948    11 EELLSNKGLTVVDVYQEWCGPCKAVVSLFKKIKNELGDdllHFATAEADtIDT----LKRYRGKCEPTFLFYKNGELVAV 86

                  ....
gi 1554477403  88 MVGA 91
Cdd:cd02948    87 IRGA 90

PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH -> C-terminal TRX domain -> N-terminal reductase domain -> APS. Plant-type APS reductase shows no homology to that of dissimilatory sulfate-reducing bacteria, which is an iron-sulfur flavoenzyme. Also included in the alignment is EYE2 from Chlamydomonas reinhardtii, a protein required for eyespot assembly.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1554477403  16 KSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAG-KIKVGKVDVDANNGLAA--TYGVRTIPTLL 77
Cdd:cd02993    19 RRNQSTLVVLYAPWCPFCQAMEASYEELAEKLAGsNVKVAKFNADGEQREFAkeELQLKSFPTIL 83

bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  12 DEVLKSDIPVLVDFWATWCGPCRMIAPIIDQLSTELAGK----IKVG-------------------------KVDVDANN 62
Cdd:PRK14018   50 SVYLKKDKPTLIKFWASWCPLCLSELGETEKWAQDAKFSsanlITVAspgflhekkdgdfqkwyagldypklPVLTDNGG 129

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1554477403  63 GLAATYGVRTIPTLLII-KDGEIMDTMVGASSKDAI 97
Cdd:PRK14018  130 TLAQSLNISVYPSWAIIgKDGDVQRIVKGSISEAQA 165

TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1554477403  21 VLVDFWATWCGPCRMIAPIIDQLSTELaGKIKVGKVDVDANNG---LAATYGVRTIPTLLIIKDGEIMDTMVGaSSKDAI 97
Cdd:cd02985    18 VVLEFALKHSGPSVKIYPTMVKLSRTC-NDVVFLLVNGDENDStmeLCRREKIIEVPHFLFYKDGEKIHEEEG-IGPDEL 95

                  .
gi 1554477403  98 M 98
Cdd:cd02985    96 I 96