Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684211  194 QAANSPEIQQLQADYAKAKS-PEIAVKLANQLHQVSRNEEALELLYDWLKHDLSAGNGEIKKQFLATLSAMGNSDPLVPK 272
Cdd:pfam14561   1 QAADAPELAALEARLAADPDdLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAK 80

                          90
                  ....*....|
gi 544684211  273 YRRQLYSLLY 282
Cdd:pfam14561  81 YRRKLSSLLF 90

Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684211  194 QAANSPEIQQLQADYAKAKS-PEIAVKLANQLHQVSRNEEALELLYDWLKHDLSAGNGEIKKQFLATLSAMGNSDPLVPK 272
Cdd:pfam14561   1 QAADAPELAALEARLAADPDdLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAK 80

                          90
                  ....*....|
gi 544684211  273 YRRQLYSLLY 282
Cdd:pfam14561  81 YRRKLSSLLF 90

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 544684211    7 VNNTNFSEVIKAAAEVPVVFHFISSREP-RSLEMEayFRRLNDEYPKQFLLAIVNCDEYPMIAAQFRIQAVPTSYFFANG 85
Cdd:pfam00085   5 LTDANFDEVVQKSSKPVLVDFYAPWCGPcKMLAPE--YEELAQEYKGNVVFAKVDVDENPDLASKYGVRGYPTLIFFKNG 82

                          90
                  ....*....|....*.
gi 544684211   86 QPVDVIEGEINEQELR 101
Cdd:pfam00085  83 QPVDDYVGARPKDALA 98

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 544684211   43 FRRLNDEYPKQFLLAIVNCDEYPMIAAQFRIQAVPTSYFFANGQPVDVIEG 93
Cdd:TIGR01068  36 LEELAKEYEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLFKNGKEVDRSVG 86

Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 544684211 117 AQALEFLEAEQYELALPLLKNAWELtDKKNSDFALLYAETYIAMKQVEPAKAILIQ 172
Cdd:cd24142    5 EKAEELLDQGNFELALKFLQRALEL-EPNNVEALELLGEILLELGDVEEAREVLLR 59

Tetratricopeptide repeat;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684211  194 QAANSPEIQQLQADYAKAKS-PEIAVKLANQLHQVSRNEEALELLYDWLKHDLSAGNGEIKKQFLATLSAMGNSDPLVPK 272
Cdd:pfam14561   1 QAADAPELAALEARLAADPDdLDARLDLALALHAAGRNEEALELLLEILRRDRNWNDGAARKQLLDIFEALGPGDPLVAK 80

                          90
                  ....*....|
gi 544684211  273 YRRQLYSLLY 282
Cdd:pfam14561  81 YRRKLSSLLF 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 544684211  11 NFSEVIKAAaeVPVVFHFISSREPRSLEMEAYFRRLNDEYPKqFLLAIVNCDEYPMIAAQFRIQAVPTSYFFANGQPVDV 90
Cdd:cd02947    2 EFEELIKSA--KPVVVDFWAPWCGPCKAIAPVLEELAEEYPK-VKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEVDR 78

                         90
                 ....*....|.
gi 544684211  91 IEGEINEQELR 101
Cdd:cd02947   79 VVGADPKEELE 89

TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684211  12 FSEVIKAAAEVPVVFHFISSREPRSLEMEAYFRRLNDEYPKQFLLAIVNCDEYPMIAAQFRIQAVPTSYFFANGQPVDVI 91
Cdd:cd02984    5 FEELLKSDASKLLVLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTFVFFRNGTIVDRV 84

                 ..
gi 544684211  92 EG 93
Cdd:cd02984   85 SG 86

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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 544684211   43 FRRLNDEYPKQFLLAIVNCDEYPMIAAQFRIQAVPTSYFFANGQPVDVIEG 93
Cdd:TIGR01068  36 LEELAKEYEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLFKNGKEVDRSVG 86

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 544684211   5 INVNNTNFSEVIKAAAEVPVVFHfiSSREPRSLEMEAYFRRLNDEYPK--QFLLAIVNCDEYPMIAAQFRIQAVPTSYFF 82
Cdd:cd02961    1 VELTDDNFDELVKDSKDVLVEFY--APWCGHCKALAPEYEKLAKELKGdgKVVVAKVDCTANNDLCSEYGVRGYPTIKLF 78

                         90       100
                 ....*....|....*....|.
gi 544684211  83 ANG--QPVDViEGEINEQELR 101
Cdd:cd02961   79 PNGskEPVKY-EGPRTLESLV 98

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 544684211   4 LINVNNTNFSEVIkAAAEVpVVFHFISSREPRSLEMEAYF----RRLNDEYPK--QFLLAIVNCDEYPMIAAQFRIQAVP 77
Cdd:cd02996    3 IVSLTSGNIDDIL-QSAEL-VLVNFYADWCRFSQMLHPIFeeaaAKIKEEFPDagKVVWGKVDCDKESDIADRYRINKYP 80

                 ....*....
gi 544684211  78 TSYFFANGQ 86
Cdd:cd02996   81 TLKLFRNGM 89

Assembly chaperone of ribosomal protein L4 and similar proteins; Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 544684211 117 AQALEFLEAEQYELALPLLKNAWELtDKKNSDFALLYAETYIAMKQVEPAKAILIQ 172
Cdd:cd24142    5 EKAEELLDQGNFELALKFLQRALEL-EPNNVEALELLGEILLELGDVEEAREVLLR 59