Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125  202 TPEIRDLQQKFEQNPTDLVLLLELSKALHAAHRDDEALDLLFGVLSKDLGAENGTVKQVFMEVLTALGQGNPIANQYRRK 281
Cdd:pfam14561   5 APELAALEARLAADPDDLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAKYRRK 84

                  ....*.
gi 501583125  282 LYTLLY 287
Cdd:pfam14561  85 LSSLLF 90

Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125  202 TPEIRDLQQKFEQNPTDLVLLLELSKALHAAHRDDEALDLLFGVLSKDLGAENGTVKQVFMEVLTALGQGNPIANQYRRK 281
Cdd:pfam14561   5 APELAALEARLAADPDDLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAKYRRK 84

                  ....*.
gi 501583125  282 LYTLLY 287
Cdd:pfam14561  85 LSSLLF 90

thioredoxin 2; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125   1 MDNILSLTKDNIQQVVDasmqqivvlaFWAQPQEQSVAMLHTLEQIAAQNAG--RFVlaKVDCEAELEIANYFRIQSLPT 78
Cdd:PRK10996  42 GETLDKLLQDDLPVVID----------FWAPWCGPCRNFAPIFEDVAAERSGkvRFV--KVNTEAERELSARFRIRSIPT 109

                         90       100       110
                 ....*....|....*....|....*....|
gi 501583125  79 TLVLDKGQPVDGFAGLQDAAQVTAMLDKHL 108
Cdd:PRK10996 110 IMIFKNGQVVDMLNGAVPKAPFDSWLNEAL 139

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 501583125    3 NILSLTKDNIQQVVdASMQQIVVLAFWAQ---PQEqsvAMLHTLEQIAAQNAGRFVLAKVDCEAELEIANYFRIQSLPTT 79
Cdd:pfam00085   1 VVVVLTDANFDEVV-QKSSKPVLVDFYAPwcgPCK---MLAPEYEELAQEYKGNVVFAKVDVDENPDLASKYGVRGYPTL 76

                          90       100
                  ....*....|....*....|....*..
gi 501583125   80 LVLDKGQPVDGFAGLQDAAQVTAMLDK 106
Cdd:pfam00085  77 IFFKNGQPVDDYVGARPKDALAAFLKA 103

Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125  202 TPEIRDLQQKFEQNPTDLVLLLELSKALHAAHRDDEALDLLFGVLSKDLGAENGTVKQVFMEVLTALGQGNPIANQYRRK 281
Cdd:pfam14561   5 APELAALEARLAADPDDLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAKYRRK 84

                  ....*.
gi 501583125  282 LYTLLY 287
Cdd:pfam14561  85 LSSLLF 90

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 501583125  10 DNIQQVVDASmqQIVVLAFWAQPQEQSVAMLHTLEQIAAQNaGRFVLAKVDCEAELEIANYFRIQSLPTTLVLDKGQPVD 89
Cdd:cd02947    1 EEFEELIKSA--KPVVVDFWAPWCGPCKAIAPVLEELAEEY-PKVKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEVD 77

                         90
                 ....*....|....*.
gi 501583125  90 GFAGLQDAAQVTAMLD 105
Cdd:cd02947   78 RVVGADPKEELEEFLE 93

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 501583125   24 VVLAFWAqPQEQSVAMLH-TLEQIAAQNAGRFVLAKVDCEAELEIANYFRIQSLPTTLVLDKGQPVDGFAGLQDAAQVTA 102
Cdd:TIGR01068  17 VLVDFWA-PWCGPCKMIApILEELAKEYEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLFKNGKEVDRSVGALPKAALKQ 95

                  ....*.
gi 501583125  103 MLDKHL 108
Cdd:TIGR01068  96 LINKNL 101

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 501583125   3 NILSLTKDNIQQVVDASmqQIVVLAFWAQ--PQEQsvaMLH-TLEQIAAQ------NAGRFVLAKVDCEAELEIANYFRI 73
Cdd:cd02996    2 EIVSLTSGNIDDILQSA--ELVLVNFYADwcRFSQ---MLHpIFEEAAAKikeefpDAGKVVWGKVDCDKESDIADRYRI 76

                         90
                 ....*....|...
gi 501583125  74 QSLPTTLVLDKGQ 86
Cdd:cd02996   77 NKYPTLKLFRNGM 89

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 501583125   5 LSLTKDNIQQVVDASmqQIVVLAFWAQPQEQSVAMLHTLEQIAA--QNAGRFVLAKVDCEAELEIANYFRIQSLPTTLVL 82
Cdd:cd02961    1 VELTDDNFDELVKDS--KDVLVEFYAPWCGHCKALAPEYEKLAKelKGDGKVVVAKVDCTANNDLCSEYGVRGYPTIKLF 78

                 ...
gi 501583125  83 DKG 85
Cdd:cd02961   79 PNG 81

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125  22 QIVVLAFWAQ---PqeqSVAMLHTLEQIAAQNAG-RFVLAKVD--------------------CEAELEIANYFRIQSLP 77
Cdd:COG0526   29 KPVLVNFWATwcpP---CRAEMPVLKELAEEYGGvVFVGVDVDenpeavkaflkelglpypvlLDPDGELAKAYGVRGIP 105

                         90       100       110
                 ....*....|....*....|....*....|..
gi 501583125  78 TTLVLDK-GQPVDGFAGLQDAAQVTAMLDKHL 108
Cdd:COG0526  106 TTVLIDKdGKIVARHVGPLSPEELEEALEKLL 137

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125   9 KDNIQQVVDASMQQIVVLAFWAQPQEQSVAMLHTLEQIAAQNAG-RFVlaKVDCEAeLEIANYFRIQSLPTTLVLDKGQP 87
Cdd:cd02957   12 KEFLEEVTKASKGTRVVVHFYEPGFPRCKILDSHLEELAAKYPEtKFV--KINAEK-AFLVNYLDIKVLPTLLVYKNGEL 88

                 ....*....
gi 501583125  88 VDGFAGLQD 96
Cdd:cd02957   89 IDNIVGFEE 97

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501583125 132 DLATAAVLLKDAHAGSNQAGEVSLVLADVYLMQGELVLAQAMLEKVgLADQDGYYQSLKAKLALALDAADTPEIRDLQQK 211
Cdd:COG2956  159 DYDEAIEALEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERA-LEQDPDYLPALPRLAELYEKLGDPEEALELLRK 237

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501583125 212 FEQNPTDLVLLLELSKALHAAHRDDEALDLLFGVLSKD 249
Cdd:COG2956  238 ALELDPSDDLLLALADLLERKEGLEAALALLERQLRRH 275