RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780822|ref|YP_003065235.1| thioredoxin [Candidatus Liberibacter asiaticus str. psy62] (107 letters) >gnl|CDD|143866 pfam00085, Thioredoxin, 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. Length = 104 Score = 108 bits (272), Expect = 3e-25 Identities = 35/103 (33%), Positives = 61/103 (59%), Gaps = 1/103 (0%) Query: 4 LKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESS 63 + ++FD EV + PV+VDF+A WC PC L+P + +A E D VK K+D +E+ Sbjct: 3 KVLTDENFDEEVAKSDKPVLVDFYAPWCGPCKALAPEYEKLAQEYKDDVKFAKVDADENP 62 Query: 64 EISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWILSR 106 ++++ Y + PT+ FK+GK + + GA ++ D++ +I Sbjct: 63 DLASEYGVRGFPTIKFFKNGKKVSDYV-GARTKDDLVAFIKKH 104 >gnl|CDD|48496 cd02947, TRX_family, 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.. Length = 93 Score = 100 bits (251), Expect = 8e-23 Identities = 37/95 (38%), Positives = 66/95 (69%), Gaps = 3/95 (3%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR 68 + F+ + + PVVVDFWA WC PC ++P+++++A+E KVK K+D++E+ E++ Sbjct: 1 EEFEELIKS-AKPVVVDFWAPWCGPCKAIAPVLEELAEE-YPKVKFVKVDVDENPELAEE 58 Query: 69 YQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 Y + SIPT + FK+GK +DR++ GA + ++ E++ Sbjct: 59 YGVRSIPTFLFFKNGKEVDRVV-GADPKEELEEFL 92 >gnl|CDD|36128 KOG0910, KOG0910, KOG0910, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]. Length = 150 Score = 98.5 bits (245), Expect = 4e-22 Identities = 37/99 (37%), Positives = 61/99 (61%), Gaps = 1/99 (1%) Query: 5 KVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSE 64 FD +V+ PV+VDF A WC PC L PI++++ E A K K+ K+D +E E Sbjct: 47 VQSDSEFDDKVINSDVPVLVDFHAEWCGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPE 106 Query: 65 ISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 ++ Y+IS++PT+++FK+G+ +DR + GA + + I Sbjct: 107 LAEDYEISAVPTVLVFKNGEKVDRFV-GAVPKEQLRSLI 144 >gnl|CDD|32932 COG3118, COG3118, Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]. Length = 304 Score = 94.6 bits (235), Expect = 6e-21 Identities = 35/102 (34%), Positives = 62/102 (60%), Gaps = 3/102 (2%) Query: 4 LKVDTKSFDSEVLECS--NPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEE 61 V +F+ EV++ S PV+VDFWA WC PC +L+P ++ +A E K K+ K++ + Sbjct: 26 KDVTEANFEQEVIQSSREVPVLVDFWAPWCGPCKQLTPTLEKLAAEYKGKFKLAKVNCDA 85 Query: 62 SSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 ++ ++ + SIPT+ FKDG+ +D GA +S + +++ Sbjct: 86 EPMVAAQFGVQSIPTVYAFKDGQPVDGFQ-GAQPESQLRQFL 126 >gnl|CDD|48510 cd02961, PDI_a_family, 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.. Length = 101 Score = 80.7 bits (199), Expect = 8e-17 Identities = 29/102 (28%), Positives = 54/102 (52%), Gaps = 3/102 (2%) Query: 4 LKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELA--DKVKITKLDIEE 61 +++ +FD V + S V+V+F+A WC C L+P + +A EL KV + K+D Sbjct: 1 VELTDDNFDELVKD-SKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTA 59 Query: 62 SSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 ++++ + Y + PT+ LF +G G + ++E+I Sbjct: 60 NNDLCSEYGVRGYPTIKLFPNGSKEPVKYEGPRTLESLVEFI 101 >gnl|CDD|48505 cd02956, ybbN, 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.. Length = 96 Score = 73.3 bits (180), Expect = 1e-14 Identities = 25/95 (26%), Positives = 53/95 (55%), Gaps = 2/95 (2%) Query: 10 SFDSEVLECSN-PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR 68 +F + E + PVVVDFWA P +L P+++ +A+E + + K++ + +I+ + Sbjct: 2 NFQQVLQESTQVPVVVDFWAPRSPPSKELLPLLERLAEEYQGQFVLAKVNCDAQPQIAQQ 61 Query: 69 YQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 + + ++PT+ LF G+ +D GA + + + + Sbjct: 62 FGVQALPTVYLFAAGQPVD-GFQGAQPEEQLRQML 95 >gnl|CDD|48533 cd02984, TRX_PICOT, 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.. Length = 97 Score = 72.6 bits (178), Expect = 2e-14 Identities = 23/71 (32%), Positives = 46/71 (64%) Query: 19 SNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLI 78 S +V+ FWA W PC +++ + +++A E V ++ EE EIS +++I+++PT + Sbjct: 14 SKLLVLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTFV 73 Query: 79 LFKDGKVIDRM 89 F++G ++DR+ Sbjct: 74 FFRNGTIVDRV 84 >gnl|CDD|36125 KOG0907, KOG0907, KOG0907, Thioredoxin [Posttranslational modification, protein turnover, chaperones]. Length = 106 Score = 70.3 bits (172), Expect = 9e-14 Identities = 28/93 (30%), Positives = 55/93 (59%), Gaps = 5/93 (5%) Query: 4 LKVDTKSFDSEVLECSN----PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDI 59 ++V+T S VL + VVVDF+A+WC PC ++P + +A++ D V K+D+ Sbjct: 2 VEVETVSDLDLVLSAAEAGDKLVVVDFYATWCGPCKAIAPKFEKLAEKYPD-VVFLKVDV 60 Query: 60 EESSEISTRYQISSIPTLILFKDGKVIDRMMPG 92 +E E++ + + ++PT + +K G+ +D ++ Sbjct: 61 DELEEVAKEFNVKAMPTFVFYKGGEEVDEVVGA 93 >gnl|CDD|48553 cd03004, PDI_a_ERdj5_C, PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Also included in the alignment is the single complete TRX domain of an uncharacterized protein from Tetraodon nigroviridis, which also contains a DnaJ domain at its N-terminus.. Length = 104 Score = 66.4 bits (162), Expect = 2e-12 Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 1/96 (1%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR 68 + F VL P +VDF+A WC PC L P + A L KVK+ +D ++ + + Sbjct: 9 EDFPELVLNRKEPWLVDFYAPWCGPCQALLPELRKAARALKGKVKVGSVDCQKYESLCQQ 68 Query: 69 YQISSIPTLILFKDGKVIDRMMPGASSQSD-IIEWI 103 I + PT+ L+ G +D I+E+I Sbjct: 69 ANIRAYPTIRLYPGNASKYHSYNGWHRDADSILEFI 104 >gnl|CDD|48547 cd02998, PDI_a_ERp38, PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5. The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase (PDI) cDNA. The G1 protein is constitutively expressed in all major organs of the plant and its expression is induced by treatment with tunicamycin, indicating that it may be a glucose-regulated protein. The G1 homolog in the eukaryotic social amoeba Dictyostelium discoideum is also described as a P5-like protein, which is located in the endoplasmic reticulum (ER) despite the absence of an ER-retrieval signal. G1 homologs from Aspergillus niger and Neurospora crassa have also been characterized, and are named TIGA and ERp38, respectively. Also included in the alignment is an atypical PDI from Leishmania donovani containing a single a domain, and the C-terminal a domain of a P5-like protein from Entamoeba histolytica.. Length = 105 Score = 64.8 bits (158), Expect = 5e-12 Identities = 29/105 (27%), Positives = 54/105 (51%), Gaps = 3/105 (2%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELA--DKVKITKLDI 59 + +++ +FD V + V+V+F+A WC C L+P + +A A D V I K+D Sbjct: 1 NVVELTDSNFDKVVGDDKKDVLVEFYAPWCGHCKNLAPEYEKLAAVFANEDDVVIAKVDA 60 Query: 60 EES-SEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 +E+ +++ +Y +S PTL F G G D+++++ Sbjct: 61 DEANKDLAKKYGVSGFPTLKFFPKGSTEPVKYEGGRDLEDLVKFV 105 >gnl|CDD|35412 KOG0191, KOG0191, KOG0191, Thioredoxin/protein disulfide isomerase [Posttranslational modification, protein turnover, chaperones]. Length = 383 Score = 64.0 bits (155), Expect = 8e-12 Identities = 29/79 (36%), Positives = 45/79 (56%) Query: 6 VDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI 65 + SF +L+ +P +V+F+A WC C KL+P +A L KVKI +D +E ++ Sbjct: 34 LTLDSFFDFLLKDDSPWLVEFYAPWCGHCKKLAPTYKKLAKALKGKVKIGAVDCDEHKDL 93 Query: 66 STRYQISSIPTLILFKDGK 84 +Y I PTL +F+ GK Sbjct: 94 CEKYGIQGFPTLKVFRPGK 112 Score = 55.6 bits (133), Expect = 3e-09 Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 2/98 (2%) Query: 11 FDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELA--DKVKITKLDIEESSEISTR 68 FD V + +V+F+A WC C KL+P + +A L + V++ K+D +++R Sbjct: 154 FDETVKDSDADWLVEFYAPWCGHCKKLAPEWEKLAKLLKSKENVELGKIDATVHKSLASR 213 Query: 69 YQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWILSR 106 ++ PTL LF G+ G I+ ++ + Sbjct: 214 LEVRGYPTLKLFPPGEEDIYYYSGLRDSDSIVSFVEKK 251 Score = 32.1 bits (72), Expect = 0.034 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 3/86 (3%) Query: 6 VDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADE---LADKVKITKLDIEES 62 + + LE V F+A WC C +P+ +D A+ K+K KLD Sbjct: 274 FLDTAEFLDSLEKKKNKFVKFYAPWCGHCGGFAPVYEDKAELGYPDLSKIKAAKLDCALL 333 Query: 63 SEISTRYQISSIPTLILFKDGKVIDR 88 + + + PT+ L+ GK Sbjct: 334 KSLCQKAIVRGYPTIKLYNYGKNPSN 359 >gnl|CDD|48554 cd03005, PDI_a_ERp46, 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.. Length = 102 Score = 63.7 bits (155), Expect = 9e-12 Identities = 31/104 (29%), Positives = 54/104 (51%), Gaps = 6/104 (5%) Query: 3 ALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADEL---ADKVKITKLDI 59 L++ +FD + E V F+A WC C +L+P + +A + VKI K+D Sbjct: 2 VLELTEDNFDHHIAE--GNHFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVDC 59 Query: 60 EESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 + E+ + +Q+ PTL+LFKDG+ +D+ G + E++ Sbjct: 60 TQHRELCSEFQVRGYPTLLLFKDGEKVDK-YKGTRDLDSLKEFV 102 >gnl|CDD|48550 cd03001, PDI_a_P5, 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.. Length = 103 Score = 63.3 bits (154), Expect = 1e-11 Identities = 26/95 (27%), Positives = 45/95 (47%) Query: 10 SFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRY 69 +FD +VL + +V+F+A WC C L+P A L VK+ +D + ++ +Y Sbjct: 9 NFDKKVLNSDDVWLVEFYAPWCGHCKNLAPEWKKAAKALKGIVKVGAVDADVHQSLAQQY 68 Query: 70 QISSIPTLILFKDGKVIDRMMPGASSQSDIIEWIL 104 + PT+ +F GK + G + I+ L Sbjct: 69 GVRGFPTIKVFGAGKNSPQDYQGGRTAKAIVSAAL 103 >gnl|CDD|35411 KOG0190, KOG0190, KOG0190, Protein disulfide isomerase (prolyl 4-hydroxylase beta subunit) [Posttranslational modification, protein turnover, chaperones]. Length = 493 Score = 63.0 bits (153), Expect = 1e-11 Identities = 30/103 (29%), Positives = 56/103 (54%), Gaps = 5/103 (4%) Query: 4 LKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIE 60 L + +F E + V+V+F+A WC C L+P + A EL ++ VK+ K+D Sbjct: 28 LVLTKDNFK-ETINGHEFVLVEFYAPWCGHCKALAPEYEKAATELKEEGSPVKLAKVDAT 86 Query: 61 ESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 E S+++++Y++ PTL +F++G+ G I++W+ Sbjct: 87 EESDLASKYEVRGYPTLKIFRNGRSAQD-YNGPREADGIVKWL 128 Score = 49.6 bits (118), Expect = 2e-07 Identities = 21/76 (27%), Positives = 41/76 (53%) Query: 9 KSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR 68 K+FD VL+ V+V+F+A WC C L+PI +++A++ D + ++ ++ Sbjct: 374 KNFDDIVLDEGKDVLVEFYAPWCGHCKALAPIYEELAEKYKDDENVVIAKMDATANDVPS 433 Query: 69 YQISSIPTLILFKDGK 84 ++ PT++ F G Sbjct: 434 LKVDGFPTILFFPAGH 449 >gnl|CDD|36126 KOG0908, KOG0908, KOG0908, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]. Length = 288 Score = 63.0 bits (153), Expect = 2e-11 Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 2/75 (2%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 VVVDF ASWC PC +++PI D+A++ V K+D++E + ++++PT I F+ Sbjct: 24 VVVDFTASWCGPCKRIAPIFSDLANKYPGAV-FLKVDVDECRGTAATNGVNAMPTFIFFR 82 Query: 82 DGKVIDRMMPGASSQ 96 +G ID + GA + Sbjct: 83 NGVKID-QIQGADAS 96 >gnl|CDD|30872 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]. Length = 127 Score = 59.1 bits (141), Expect = 2e-10 Identities = 29/72 (40%), Positives = 52/72 (72%), Gaps = 3/72 (4%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDI-EESSEISTRYQ--ISSIPTL 77 PV+VDFWA WC PC +P+++++A+E V++ +++ +E+ +++ + + SIPTL Sbjct: 34 PVLVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVAVRSIPTL 93 Query: 78 ILFKDGKVIDRM 89 +LFKDGK +DR+ Sbjct: 94 LLFKDGKEVDRL 105 >gnl|CDD|48544 cd02995, PDI_a_PDI_a'_C, PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are 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. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins, while PDI shows a wider substrate specificity. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. EFP1 is a binding partner protein of thyroid oxidase, which is responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones.. Length = 104 Score = 58.2 bits (141), Expect = 5e-10 Identities = 32/102 (31%), Positives = 56/102 (54%), Gaps = 4/102 (3%) Query: 5 KVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELA--DKVKITKLDIEES 62 V K+FD VL+ V+V+F+A WC C L+PI +++A++L D V I K+D Sbjct: 4 VVVGKNFDEVVLDSDKDVLVEFYAPWCGHCKALAPIYEELAEKLKGDDNVVIAKMDATA- 62 Query: 63 SEISTRYQISSIPTLILFKDG-KVIDRMMPGASSQSDIIEWI 103 +++ + + + PT++ F G K G + D+I++I Sbjct: 63 NDVPSEFVVDGFPTILFFPAGDKSNPIKYEGDRTLEDLIKFI 104 >gnl|CDD|48545 cd02996, PDI_a_ERp44, 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.. Length = 108 Score = 57.6 bits (139), Expect = 8e-10 Identities = 33/108 (30%), Positives = 62/108 (57%), Gaps = 7/108 (6%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADEL------ADKVKIT 55 + + + + D ++L+ + V+V+F+A WCR L PI ++ A ++ A KV Sbjct: 2 EIVSLTSGNID-DILQSAELVLVNFYADWCRFSQMLHPIFEEAAAKIKEEFPDAGKVVWG 60 Query: 56 KLDIEESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 K+D ++ S+I+ RY+I+ PTL LF++G ++ R G S + E++ Sbjct: 61 KVDCDKESDIADRYRINKYPTLKLFRNGMMMKREYRGQRSVEALAEFV 108 >gnl|CDD|39478 KOG4277, KOG4277, KOG4277, Uncharacterized conserved protein, contains thioredoxin domain [General function prediction only]. Length = 468 Score = 56.3 bits (135), Expect = 2e-09 Identities = 31/82 (37%), Positives = 41/82 (50%), Gaps = 5/82 (6%) Query: 24 VDFWASWCRPCVKLSPIIDDIADELAD---KVKITKLDIEESSEISTRYQISSIPTLILF 80 VDF+A WC C KL PI D++ EL D +K+ KLD I+ + I PT+ F Sbjct: 48 VDFYAPWCAHCKKLEPIWDEVGHELKDIGLPIKVGKLDATRFPAIANEFGIQGYPTIKFF 107 Query: 81 KDGKVIDRMMPGASSQSDIIEW 102 K ID G + IIE+ Sbjct: 108 KGDHAIDYR--GGREKDAIIEF 127 >gnl|CDD|48551 cd03002, PDI_a_MPD1_like, 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.. Length = 109 Score = 55.7 bits (134), Expect = 3e-09 Identities = 28/107 (26%), Positives = 49/107 (45%), Gaps = 6/107 (5%) Query: 4 LKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESS 63 ++ K+FD V + +V+F+A WC C L P A EL V++ +D +E Sbjct: 3 YELTPKNFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEYAKAAKELDGLVQVAAVDCDEDK 62 Query: 64 --EISTRYQISSIPTLILFKDGKVIDRMMP----GASSQSDIIEWIL 104 + +Y + PTL +F+ K + G S I++++L Sbjct: 63 NKPLCGKYGVQGFPTLKVFRPPKKASKHAVEDYNGERSAKAIVDFVL 109 >gnl|CDD|48511 cd02962, TMX2, TMX2 family; composed of proteins similar to human TMX2, a 372-amino acid TRX-related transmembrane protein, identified and characterized through the cloning of its cDNA from a human fetal library. It contains a TRX domain but the redox active CXXC motif is replaced with SXXC. Sequence analysis predicts that TMX2 may be a Type I membrane protein, with its C-terminal half protruding on the luminal side of the endoplasmic reticulum (ER). In addition to the TRX domain, transmembrane region and ER-retention signal, TMX2 also contains a Myb DNA-binding domain repeat signature and a dileucine motif in the tail.. Length = 152 Score = 55.3 bits (133), Expect = 3e-09 Identities = 21/90 (23%), Positives = 48/90 (53%), Gaps = 7/90 (7%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELA-DKVKITKLDIEESSEISTRYQISS------IP 75 +V+F+ +W CV +P+ +++ + + +K K+DI ++ ++++S+ +P Sbjct: 51 LVEFFTTWSPECVNFAPVFAELSLKYNNNNLKFGKIDIGRFPNVAEKFRVSTSPLSKQLP 110 Query: 76 TLILFKDGKVIDRMMPGASSQSDIIEWILS 105 T+ILF+ GK + R S+ + + S Sbjct: 111 TIILFQGGKEVARRPYYNDSKGRAVPFTFS 140 >gnl|CDD|48515 cd02966, TlpA_like_family, 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.. Length = 116 Score = 54.5 bits (131), Expect = 7e-09 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 25/95 (26%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADK-VKITKLDIEES----------------- 62 V+V+FWASWC PC P ++ +A E D V++ +++++ Sbjct: 21 VVLVNFWASWCPPCRAEMPELEALAKEYKDDGVEVVGVNVDDDDPAAVKAFLKKYGITFP 80 Query: 63 ------SEISTRYQISSIPTLILF-KDGKVIDRMM 90 E++ Y + +PT L +DG++ R + Sbjct: 81 VLLDPDGELAKAYGVRGLPTTFLIDRDGRIRARHV 115 >gnl|CDD|48498 cd02949, TRX_NTR, TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.. Length = 97 Score = 54.2 bits (130), Expect = 7e-09 Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 1/87 (1%) Query: 17 ECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPT 76 E ++V + + C PC L PI++ + DE V ++DI+E EI+ I PT Sbjct: 11 ESDRLILVLYTSPTCGPCRTLKPILNKVIDEFDGAVHFVEIDIDEDQEIAEAAGIMGTPT 70 Query: 77 LILFKDGKVIDRMMPGASSQSDIIEWI 103 + FKD K + + + G +S+ E+I Sbjct: 71 VQFFKD-KELVKEISGVKMKSEYREFI 96 >gnl|CDD|48549 cd03000, PDI_a_TMX3, PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase.. Length = 104 Score = 53.8 bits (129), Expect = 1e-08 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 5/83 (6%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELAD---KVKITKLDIEESSEISTRYQISSIPTLIL 79 +VDF+A WC C KL P+ +++ EL V++ KLD S I++ + + PT+ L Sbjct: 19 LVDFYAPWCGHCKKLEPVWNEVGAELKSSGSPVRVGKLDATAYSSIASEFGVRGYPTIKL 78 Query: 80 FKDGKVIDRMMPGASSQSDIIEW 102 K + G ++ DI+E+ Sbjct: 79 LKGDLAYN--YRGPRTKDDIVEF 99 >gnl|CDD|48546 cd02997, PDI_a_PDIR, 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.. Length = 104 Score = 52.6 bits (126), Expect = 2e-08 Identities = 27/106 (25%), Positives = 48/106 (45%), Gaps = 6/106 (5%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADKVKI--TKLDI 59 + + + F + L+ V+V F+A WC C K+ P A EL + K +D Sbjct: 1 DVVHLTDEDFR-KFLKKEKHVLVMFYAPWCGHCKKMKPEFTKAATELKEDGKGVLAAVDC 59 Query: 60 EESSE--ISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 + + Y + PT F++GK +++ G + DIIE++ Sbjct: 60 TKPEHDALKEEYNVKGFPTFKYFENGKFVEK-YEGERTAEDIIEFM 104 >gnl|CDD|36130 KOG0912, KOG0912, KOG0912, Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones, Energy production and conversion]. Length = 375 Score = 52.6 bits (126), Expect = 2e-08 Identities = 32/103 (31%), Positives = 59/103 (57%), Gaps = 6/103 (5%) Query: 6 VDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELAD-----KVKITKLDIE 60 + +++ DS +L+ + V V+F+A WCR L PI ++ A + KV K+D + Sbjct: 1 LTSENIDS-ILDSNELVFVNFYADWCRFSQMLKPIFEEAAAKFKQEFPEGKVVWGKVDCD 59 Query: 61 ESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 + +I+ +Y I+ PTL +F++G+++ R G S +IE+I Sbjct: 60 KEDDIADKYHINKYPTLKVFRNGEMMKREYRGQRSVEALIEFI 102 >gnl|CDD|36129 KOG0911, KOG0911, KOG0911, Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]. Length = 227 Score = 50.3 bits (120), Expect = 1e-07 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 1/68 (1%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILF 80 +V+ FWA W K + D E + KL+ EE EIS + ++P + F Sbjct: 19 LLVLHFWAIWAVVQ-KQMDQVFDHLAEYFKNAQFLKLEAEEFPEISNLIAVEAVPYFVFF 77 Query: 81 KDGKVIDR 88 G+ +DR Sbjct: 78 FLGEKVDR 85 >gnl|CDD|48560 cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.. Length = 123 Score = 49.9 bits (119), Expect = 2e-07 Identities = 27/114 (23%), Positives = 48/114 (42%), Gaps = 21/114 (18%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIAD--------------- 46 +A +D + FD E L PV+V FWA+WC C SP ++ +A Sbjct: 4 TATTLDGEQFDLESLS-GKPVLVYFWATWCPVCRFTSPTVNQLAADYPVVSVALRSGDDG 62 Query: 47 ELADKVKITKLDI----EESSEISTRYQISSIPTLILFKDGKVIDRMMPGASSQ 96 +A ++ + IS R+ +S P +++ G ++ G +S+ Sbjct: 63 AVARFMQKKGYGFPVINDPDGVISARWGVSVTPAIVIVDPGGIVFVTT-GVTSE 115 >gnl|CDD|36132 KOG0914, KOG0914, KOG0914, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]. Length = 265 Score = 49.2 bits (117), Expect = 3e-07 Identities = 21/73 (28%), Positives = 43/73 (58%), Gaps = 7/73 (9%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELA-DKVKITKLDIEESSEISTRYQISS------IP 75 +++F+A W CV+ SP+ +++ + + +K K+DI +++ +++IS +P Sbjct: 148 LIEFFACWSPKCVRFSPVFAELSIKYNNNLLKFGKVDIGRFPDVAAKFRISLSPGSRQLP 207 Query: 76 TLILFKDGKVIDR 88 T ILF+ GK + R Sbjct: 208 TYILFQKGKEVSR 220 >gnl|CDD|48543 cd02994, PDI_a_TMX, 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.. Length = 101 Score = 48.8 bits (116), Expect = 3e-07 Identities = 24/82 (29%), Positives = 47/82 (57%), Gaps = 3/82 (3%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELAD-KVKITKLDIEESSEISTRYQISSIPTLILFK 81 +++F+A WC C +L P ++ AD D + + K+D+ + +S R+ ++++PT+ K Sbjct: 20 MIEFYAPWCPACQQLQPEWEEFADWSDDLGINVAKVDVTQEPGLSGRFFVTALPTIYHAK 79 Query: 82 DGKVIDRMMPGASSQSDIIEWI 103 DG + R G + D+I +I Sbjct: 80 DG--VFRRYQGPRDKEDLISFI 99 >gnl|CDD|48541 cd02992, PDI_a_QSOX, 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.. Length = 114 Score = 45.6 bits (108), Expect = 3e-06 Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 5/85 (5%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELAD---KVKITKLD 58 + +D SF+S +L + +V+F+ASWC C +P +A +L V++ +D Sbjct: 2 PVIVLDAASFNSALLGSPSAWLVEFYASWCGHCRAFAPTWKKLARDLRKWRPVVRVAAVD 61 Query: 59 --IEESSEISTRYQISSIPTLILFK 81 EE+ + + ++ PTL F Sbjct: 62 CADEENVALCRDFGVTGYPTLRYFP 86 >gnl|CDD|48502 cd02953, DsbDgamma, 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.. Length = 104 Score = 44.8 bits (106), Expect = 5e-06 Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 8/91 (8%) Query: 21 PVVVDFWASWCRPCVKLSPII---DDIADELADKVKITKLDI----EESSEISTRYQISS 73 PV VDF A WC C ++ ++ L V + + D E + + R+ + Sbjct: 13 PVFVDFTADWCVTCKVNEKVVFSDPEVQAALKKDVVLLRADWTKNDPEITALLKRFGVFG 72 Query: 74 IPTLILFKDGKVI-DRMMPGASSQSDIIEWI 103 PT + + G +PG + + +E + Sbjct: 73 PPTYLFYGPGGEPEPLRLPGFLTADEFLEAL 103 >gnl|CDD|48494 cd01659, TRX_superfamily, 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.. Length = 69 Score = 44.1 bits (103), Expect = 7e-06 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI---STRYQISSIPTLIL 79 +V F+A WC C L P++ ++A VK +D++E + RY + +PTL++ Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALL-NKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVV 59 Query: 80 FKDGKVI 86 F G + Sbjct: 60 FGPGIGV 66 >gnl|CDD|48548 cd02999, PDI_a_ERp44_like, PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER.. Length = 100 Score = 43.3 bits (102), Expect = 1e-05 Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 6/67 (8%) Query: 20 NPVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESS---EISTRYQISSIPT 76 + V F+ASWC P + ++ I L IEESS + +RY + PT Sbjct: 19 DYTAVLFYASWCPFSASFRPHFNALSSMFPQ---IRHLAIEESSIKPSLLSRYGVVGFPT 75 Query: 77 LILFKDG 83 ++LF Sbjct: 76 ILLFNST 82 >gnl|CDD|48559 cd03010, TlpA_like_DsbE, 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.. Length = 127 Score = 43.2 bits (102), Expect = 2e-05 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%) Query: 1 MSALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADE 47 + AL K+ S L+ P +++ WASWC PC + P++ +A + Sbjct: 8 LPALPGPDKTLTSADLK-GKPYLLNVWASWCAPCREEHPVLMALARQ 53 >gnl|CDD|48538 cd02989, Phd_like_TxnDC9, 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.. Length = 113 Score = 41.7 bits (98), Expect = 4e-05 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 8/85 (9%) Query: 7 DTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIEESS 63 D K F V VV F+ P I+D + LA K K K++ E++ Sbjct: 11 DEKEFFEIVKSSER-VVCHFY----HPEFFRCKIMDKHLEILAKKHLETKFIKVNAEKAP 65 Query: 64 EISTRYQISSIPTLILFKDGKVIDR 88 + + I +PT+ILFK+GK +DR Sbjct: 66 FLVEKLNIKVLPTVILFKNGKTVDR 90 >gnl|CDD|48506 cd02957, Phd_like, 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.. Length = 113 Score = 41.7 bits (98), Expect = 4e-05 Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 15/110 (13%) Query: 6 VDTKSFDSEVLECSN--PVVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIE 60 + +K F EV + S VVV F+ P I+D +ELA K K K++ E Sbjct: 9 ISSKEFLEEVTKASKGTRVVVHFY----EPGFPRCKILDSHLEELAAKYPETKFVKINAE 64 Query: 61 ESSEISTRYQISSIPTLILFKDGKVIDRM-----MPGASSQSDIIEWILS 105 ++ + I +PTL+++K+G++ID + + G ++ +E L+ Sbjct: 65 KAF-LVNYLDIKVLPTLLVYKNGELIDNIVGFEELGGDDFTTEDLEKFLA 113 >gnl|CDD|36942 KOG1731, KOG1731, KOG1731, FAD-dependent sulfhydryl oxidase/quiescin and related proteins [Cell cycle control, cell division, chromosome partitioning]. Length = 606 Score = 41.5 bits (97), Expect = 5e-05 Identities = 25/114 (21%), Positives = 50/114 (43%), Gaps = 8/114 (7%) Query: 2 SALKVDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELAD---KVKITKLD 58 +++D +F++ V +V+F+ SWC C +P A +L V++ +D Sbjct: 40 PIIELDVDTFNAAVFGSRKAKLVEFYNSWCGHCRAFAPTFKKFAKDLEKWRPVVRVAAVD 99 Query: 59 --IEESSEISTRYQISSIPTLILFKDG---KVIDRMMPGASSQSDIIEWILSRV 107 EE+ ++ + +S PTL F K + G S+I + ++ + Sbjct: 100 CADEENVKLCREFSVSGYPTLRYFPPDSQNKTDGSDVSGPVIPSEIRDQLIRTL 153 >gnl|CDD|33957 COG4232, COG4232, Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]. Length = 569 Score = 41.4 bits (97), Expect = 5e-05 Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 8/90 (8%) Query: 21 PVVVDFWASWCRPCVKLSPII---DDIADELAD----KVKITKLDIEESSEISTRYQISS 73 PV++DF+A WC C + + L D + +T D + + R + Sbjct: 476 PVMLDFYADWCVTCKENEKYTFSDPQVQQALQDVVLLQADVTAND-PAITALLKRLGVFG 534 Query: 74 IPTLILFKDGKVIDRMMPGASSQSDIIEWI 103 +PT + F ++ G + +E + Sbjct: 535 VPTYLFFGPQGSEPEILTGFLTADAFLEHL 564 >gnl|CDD|48499 cd02950, TxlA, 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.. Length = 142 Score = 40.6 bits (95), Expect = 1e-04 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 4/65 (6%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESS---EISTRYQISSIPTL 77 P +V+F+A WC C +++P + + + D+V L+++ EI RY++ IP Sbjct: 22 PTLVEFYADWCTVCQEMAPDVAKLKQKYGDQVNFVMLNVDNPKWLPEID-RYRVDGIPHF 80 Query: 78 ILFKD 82 + Sbjct: 81 VFLDR 85 >gnl|CDD|48513 cd02964, TryX_like_family, Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.. Length = 132 Score = 39.8 bits (93), Expect = 2e-04 Identities = 22/96 (22%), Positives = 41/96 (42%), Gaps = 29/96 (30%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVK------ITKLDIEES------------- 62 V + F ASWC PC +P + + ++L ++ K +++ EES Sbjct: 20 VGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFEIVFVSRDRSEESFNEYFSEMPPWLA 79 Query: 63 ---------SEISTRYQISSIPTLILFK-DGKVIDR 88 + ++++ IPTL++ K DG V+ Sbjct: 80 VPFEDEELRELLEKQFKVEGIPTLVVLKPDGDVVTT 115 >gnl|CDD|48497 cd02948, TRX_NDPK, 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.. Length = 102 Score = 39.1 bits (91), Expect = 3e-04 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEIST--RYQISSIPTLILF 80 VVD + WC PC + + I +EL D + E+ I T RY+ PT + + Sbjct: 21 VVDVYQEWCGPCKAVVSLFKKIKNELGD--DLLHFATAEADTIDTLKRYRGKCEPTFLFY 78 Query: 81 KDGKVIDRM 89 K+G+++ + Sbjct: 79 KNGELVAVI 87 >gnl|CDD|38624 KOG3414, KOG3414, KOG3414, Component of the U4/U6.U5 snRNP/mitosis protein DIM1 [RNA processing and modification, Cell cycle control, cell division, chromosome partitioning]. Length = 142 Score = 37.9 bits (88), Expect = 6e-04 Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 2/83 (2%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 VV+ F W C+K+ ++ IA+++++ I +DI+E + Y++ PT++ F Sbjct: 26 VVIRFGRDWDPTCMKMDELLSSIAEDVSNFAVIYLVDIDEVPDFVKMYELYDPPTVMFFF 85 Query: 82 DGKVIDRMMPGASSQSDIIEWIL 104 + K + + + ++ I + Sbjct: 86 NNKHM--KIDLGTGDNNKINFAF 106 >gnl|CDD|48512 cd02963, TRX_DnaJ, 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.. Length = 111 Score = 37.9 bits (88), Expect = 7e-04 Identities = 15/88 (17%), Positives = 39/88 (44%), Gaps = 3/88 (3%) Query: 4 LKVDTKSFDSEVLECSN--PVVVDFWASWCRPCVKLSPIIDDIADELAD-KVKITKLDIE 60 + +++E++ S P ++ + WC C+ + P+ ++ EL V I ++ Sbjct: 7 YSLTFSQYENEIVPKSFKKPYLIKITSDWCFSCIHIEPVWKEVIQELEPLGVGIATVNAG 66 Query: 61 ESSEISTRYQISSIPTLILFKDGKVIDR 88 ++ + S+P ++ +G+V Sbjct: 67 HERRLARKLGAHSVPAIVGIINGQVTFY 94 >gnl|CDD|48558 cd03009, TryX_like_TryX_NRX, Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the vertebrate NRX by about 100-200 amino acids, is a nuclear protein containing a redox inactive TRX-like domain between two redox active TRX domains. Both vertebrate and plant NRXs show thiol oxidoreductase activity in vitro. Their localization in the nucleus suggests a role in the redox regulation of nuclear proteins such as transcription factors.. Length = 131 Score = 36.4 bits (84), Expect = 0.002 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 28/96 (29%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVK------ITKLDIEES------------ 62 V + F ASWC PC +P + + ++L + K I+ EES Sbjct: 20 TVGLYFSASWCPPCRAFTPKLVEFYEKLKESGKNFEIVFISWDRDEESFNDYFSKMPWLA 79 Query: 63 ---------SEISTRYQISSIPTLILFK-DGKVIDR 88 S ++ ++I IPTLI+ DG+V+ Sbjct: 80 VPFSDRERRSRLNRTFKIEGIPTLIILDADGEVVTT 115 >gnl|CDD|36885 KOG1672, KOG1672, KOG1672, ATP binding protein [Posttranslational modification, protein turnover, chaperones, Energy production and conversion]. Length = 211 Score = 36.4 bits (84), Expect = 0.002 Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 8/87 (9%) Query: 6 VDTKSFDSEVLECSNPVVVDFWASWCRPCVKLSPIIDDIADELADK---VKITKLDIEES 62 K F EV + S VV F+ RP I+D + LA + + K++ E++ Sbjct: 72 ASEKDFFEEVKK-SEKVVCHFY----RPEFFRCKIMDKHLEILAKRHVETRFIKVNAEKA 126 Query: 63 SEISTRYQISSIPTLILFKDGKVIDRM 89 + T+ I +PT+ LFK+GK +D + Sbjct: 127 PFLVTKLNIKVLPTVALFKNGKTVDYV 153 >gnl|CDD|48537 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. 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.. Length = 192 Score = 35.6 bits (82), Expect = 0.003 Identities = 24/113 (21%), Positives = 51/113 (45%), Gaps = 11/113 (9%) Query: 2 SALKVDTKSFDSEVLECSN--PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDI 59 ++ + EV E S VVV + + L +++ ELA K TK Sbjct: 83 EVYEISKPDYVREVTEASKDTWVVVHLYKD----GIPLCRLLNQHLSELARKFPDTKFVK 138 Query: 60 EESSEISTRYQISSIPTLILFKDGKVIDRM-----MPGASSQSDIIEWILSRV 107 S++ Y ++PT++++++G ++ + G ++ + +EW+L +V Sbjct: 139 IISTQCIPNYPDKNLPTILVYRNGDIVKQFIGLLEFGGMNTTMEDLEWLLVQV 191 >gnl|CDD|48524 cd02975, PfPDO_like_N, Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.. Length = 113 Score = 34.5 bits (79), Expect = 0.006 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 3/69 (4%) Query: 17 ECSNPVVVDFW--ASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSI 74 E NPV + + C+ C ++++++ EL+DK+K+ D +E E + +Y + + Sbjct: 18 EMKNPVDLVVFSSKEGCQYCEVTKQLLEELS-ELSDKLKLEIYDFDEDKEKAEKYGVERV 76 Query: 75 PTLILFKDG 83 PT I +DG Sbjct: 77 PTTIFLQDG 85 >gnl|CDD|48534 cd02985, TRX_CDSP32, 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.. Length = 103 Score = 34.1 bits (78), Expect = 0.008 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 2/69 (2%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESS--EISTRYQISSIPTLIL 79 VV++F P VK+ P + ++ D V + E S E+ R +I +P + Sbjct: 18 VVLEFALKHSGPSVKIYPTMVKLSRTCNDVVFLLVNGDENDSTMELCRREKIIEVPHFLF 77 Query: 80 FKDGKVIDR 88 +KDG+ I Sbjct: 78 YKDGEKIHE 86 >gnl|CDD|48503 cd02954, DIM1, 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.. Length = 114 Score = 34.0 bits (78), Expect = 0.008 Identities = 16/65 (24%), Positives = 36/65 (55%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 VV+ F W C+++ ++ IA+++++ I +DI+E + + Y++ PT++ F Sbjct: 17 VVIRFGRDWDPVCMQMDEVLAKIAEDVSNFAVIYLVDIDEVPDFNKMYELYDPPTVMFFF 76 Query: 82 DGKVI 86 K + Sbjct: 77 RNKHM 81 >gnl|CDD|48552 cd03003, PDI_a_ERdj5_N, PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is comprised of the first TRX domain of ERdj5 located after the DnaJ domain at the N-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation.. Length = 101 Score = 33.4 bits (76), Expect = 0.014 Identities = 14/60 (23%), Positives = 30/60 (50%) Query: 24 VDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFKDG 83 V+F++ C C L+P + A E+ ++I ++ + + ++S P+L +F G Sbjct: 23 VNFYSPRCSHCHDLAPTWREFAKEMDGVIRIGAVNCGDDRMLCRSQGVNSYPSLYVFPSG 82 >gnl|CDD|176467 cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase (ASL)_like. This group contains ASL, prokaryotic-type 3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and related proteins. These proteins are members of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two steps in the de novo purine biosynthesis: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and; the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP). pCMLE catalyzes the cyclization of 3-carboxy-cis,cis-muconate (3CM) to 4-carboxy-muconolactone, in the beta-ketoadipate pathway. ASL deficiency has been linked to several pathologies including psychomotor retardation with autistic features, epilepsy and muscle wasting. Length = 381 Score = 32.9 bits (76), Expect = 0.018 Identities = 10/42 (23%), Positives = 20/42 (47%) Query: 24 VDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI 65 +D A+ +L I + A+E+ + ++D E +EI Sbjct: 15 LDVEAALAEAQAELGLIPKEAAEEIRAAADVFEIDAERIAEI 56 >gnl|CDD|36131 KOG0913, KOG0913, KOG0913, Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones, Energy production and conversion]. Length = 248 Score = 31.5 bits (71), Expect = 0.052 Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 3/85 (3%) Query: 23 VVDFWASWCRPCVKLSPIIDDIADELAD-KVKITKLDIEESSEISTRYQISSIPTLILFK 81 +++F A WC C L P +++ A D VK+ K+D+ + +S R+ ++++PT+ K Sbjct: 43 MIEFGAPWCPSCSDLIPHLENFATVSLDLGVKVAKVDVTTNPGLSGRFLVTALPTIYHVK 102 Query: 82 DGKVIDRMMPGASSQSDIIEWILSR 106 DG+ R GA ++D I + R Sbjct: 103 DGEF--RRYSGARDKNDFISFEEHR 125 >gnl|CDD|37712 KOG2501, KOG2501, KOG2501, Thioredoxin, nucleoredoxin and related proteins [General function prediction only]. Length = 157 Score = 30.3 bits (68), Expect = 0.11 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 29/96 (30%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKL-----DIEESS------------- 63 V + F A WC PC +PI+ D +EL D ++ D +E S Sbjct: 36 VGLYFSAHWCPPCRDFTPILKDFYEELKDNAAPFEVVFVSSDRDEESLDEYMLEHHGDWL 95 Query: 64 ----------EISTRYQISSIPTLILFK-DGKVIDR 88 ++S +Y++ IP L++ K DG V+ Sbjct: 96 AIPFGDDLIQKLSEKYEVKGIPALVILKPDGTVVTE 131 >gnl|CDD|30365 COG0015, PurB, Adenylosuccinate lyase [Nucleotide transport and metabolism]. Length = 438 Score = 30.2 bits (68), Expect = 0.12 Identities = 10/42 (23%), Positives = 17/42 (40%) Query: 24 VDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEI 65 + A+ R +L I + A E+ + D+E EI Sbjct: 24 LKVEAALARAQAELGVIPAEAAAEIDAAAAFAEFDLERIKEI 65 >gnl|CDD|144244 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA). Length = 124 Score = 29.9 bits (68), Expect = 0.15 Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 1/33 (3%) Query: 20 NPVVVDFWAS-WCRPCVKLSPIIDDIADELADK 51 VV+ F+ + C P + D+ +E Sbjct: 26 KWVVLFFYPKDFTPVCTTELPALADLYEEFKKL 58 >gnl|CDD|48501 cd02952, TRP14_like, Human TRX-related protein 14 (TRP14)-like family; composed of proteins similar to TRP14, a 14kD cytosolic protein that shows disulfide reductase activity in vitro with a different substrate specificity compared with another human cytosolic protein, TRX1. TRP14 catalyzes the reduction of small disulfide-containing peptides but does not reduce disulfides of ribonucleotide reductase, peroxiredoxin and methionine sulfoxide reductase, which are TRX1 substrates. TRP14 also plays a role in tumor necrosis factor (TNF)-alpha signaling pathways, distinct from that of TRX1. Its depletion promoted TNF-alpha induced activation of c-Jun N-terminal kinase and mitogen-activated protein kinases.. Length = 119 Score = 29.9 bits (67), Expect = 0.15 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 11/85 (12%) Query: 29 SWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR--------YQISSIPTLILF 80 SWC CVK P++ + + D+ + + +PTL+ + Sbjct: 38 SWCPDCVKAEPVVREALKAAPEDCVFIYCDVGDRPYWRDPNNPFRTDPKLTTGVPTLLRW 97 Query: 81 KDGKVIDRMMPGASSQSDIIEWILS 105 K + R++ Q+D++E Sbjct: 98 KTPQ---RLVEDECLQADLVEMFFE 119 >gnl|CDD|38635 KOG3425, KOG3425, KOG3425, Uncharacterized conserved protein [Function unknown]. Length = 128 Score = 28.0 bits (62), Expect = 0.53 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 8/64 (12%) Query: 29 SWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTR--------YQISSIPTLILF 80 SWC CV P+I++ + V + + ++++PTL+ + Sbjct: 43 SWCPDCVAAEPVINEALKHAPEDVHFVHVYVGNRPYWKDPANPFRKDPGILTAVPTLLRW 102 Query: 81 KDGK 84 K Sbjct: 103 KRQP 106 >gnl|CDD|73336 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. 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.. Length = 175 Score = 28.3 bits (63), Expect = 0.54 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 2/66 (3%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILF 80 VVV + C L+ + +A E VK K+ ++ S + ++P L+++ Sbjct: 85 TVVVHIYEPGIPGCAALNSSLLCLAAEYP-AVKFCKI-RASATGASDEFDTDALPALLVY 142 Query: 81 KDGKVI 86 K G++I Sbjct: 143 KGGELI 148 >gnl|CDD|48522 cd02973, TRX_GRX_like, Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacterial AhpF, which has a similar fold as PfPDO with two TRX-fold subdomains but without the second CXXC motif.. Length = 67 Score = 27.1 bits (60), Expect = 0.94 Identities = 9/40 (22%), Positives = 20/40 (50%), Gaps = 2/40 (5%) Query: 47 ELADKVKITKLDIEESSEISTRYQISSIPTLILFKDGKVI 86 L + +D E +++ Y + S+P +++ +GKV Sbjct: 26 ALNPNISAEMIDAAEFPDLADEYGVMSVPAIVI--NGKVE 63 >gnl|CDD|48516 cd02967, mauD, Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.. Length = 114 Score = 27.2 bits (60), Expect = 0.98 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 21/86 (24%) Query: 21 PVVVDFWASWCRPCVKLSPIIDDIADELADKVKIT-----------------KLDIEE-- 61 P ++ F + C C KL P+I IA AD + + L+ Sbjct: 23 PTLLFFLSPTCPVCKKLLPVIRSIARAEADWLDVVLASDGEKAEHQRFLKKHGLEAFPYV 82 Query: 62 -SSEISTRYQISSIPTLILF-KDGKV 85 S+E+ YQ+S +P +L + G + Sbjct: 83 LSAELGMAYQVSKLPYAVLLDEAGVI 108 >gnl|CDD|48561 cd03012, TlpA_like_DipZ_like, TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.. Length = 126 Score = 27.1 bits (60), Expect = 1.1 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADK 51 V++DFW C C+ P + D+ + D Sbjct: 26 VLLDFWTYCCINCLHTLPYLTDLEQKYKDD 55 >gnl|CDD|145883 pfam02966, DIM1, Mitosis protein DIM1. Length = 133 Score = 26.8 bits (60), Expect = 1.2 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 3/69 (4%) Query: 22 VVVDFWASWCRPCVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 VV+ F C+++ I+ IA++L++ I +DI+E + + Y++ T++ F Sbjct: 23 VVIRFGRDDDPVCMQMDEILAKIAEKLSNFAVIYLVDIDEVPDFNKMYELYDPSTVMFFF 82 Query: 82 DGKVIDRMM 90 K MM Sbjct: 83 RNK---HMM 88 >gnl|CDD|48535 cd02986, DLP, Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein 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 adopts a thioredoxin fold but does not contain the redox active CXXC motif.. Length = 114 Score = 26.8 bits (59), Expect = 1.3 Identities = 13/51 (25%), Positives = 28/51 (54%) Query: 34 CVKLSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFKDGK 84 C++L I+ + +L+ I +D+++ + + IS IP+ I F +G+ Sbjct: 29 CLQLDDILSKTSHDLSKMASIYLVDVDKVPVYTQYFDISYIPSTIFFFNGQ 79 >gnl|CDD|48527 cd02978, KaiB_like, KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensory domain with a TRX fold which is involved in the SasA-KaiC interaction. This domain shows high sequence similarity with KaiB. However, the KaiB structure does not show a classical TRX fold. The N-terminal half of KaiB shares the same beta-alpha-beta topology as TRX, but the topology of its C-terminal half diverges.. Length = 72 Score = 26.3 bits (58), Expect = 1.9 Identities = 7/42 (16%), Positives = 21/42 (50%) Query: 37 LSPIIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLI 78 L + + + L ++ +D+ + +++ +I + PTL+ Sbjct: 19 LQNLKRILEELLGGPYELEVIDVLKQPQLAEEDKIVATPTLV 60 >gnl|CDD|31522 COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]. Length = 667 Score = 25.7 bits (56), Expect = 2.6 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 3/53 (5%) Query: 21 PVVVDFWASWCRPC---VKLSPIIDDIADELADKVKITKLDIEESSEISTRYQ 70 P+++ S C C S +IA L + K+D EE ++ + Y Sbjct: 45 PILLSIGYSTCHWCHVMAHESFEDPEIAAILNENFVPVKVDREERPDVDSLYM 97 >gnl|CDD|37814 KOG2603, KOG2603, KOG2603, Oligosaccharyltransferase, gamma subunit [Posttranslational modification, protein turnover, chaperones]. Length = 331 Score = 25.3 bits (55), Expect = 3.5 Identities = 8/42 (19%), Positives = 20/42 (47%) Query: 40 IIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFK 81 + K+ +D +ES ++ + ++++P L+LF Sbjct: 93 WRYNSPFSNGTKLFFCMVDYDESPQVFQQLNLNNVPHLVLFS 134 >gnl|CDD|48514 cd02965, HyaE, HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway.. Length = 111 Score = 25.2 bits (55), Expect = 4.0 Identities = 7/55 (12%), Positives = 24/55 (43%), Gaps = 3/55 (5%) Query: 40 IIDDIADELADKVKITKLDIEESSEISTRYQISSIPTLILFKDGK---VIDRMMP 91 ++ ++ + + + + ++ R+ + P L+ F+DG+ V+ + Sbjct: 50 VLPELLKAFPGRFRAAVVGRADEQALAARFGVLRTPALLFFRDGRYVGVLAGIRD 104 >gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Length = 310 Score = 24.8 bits (54), Expect = 4.8 Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 1/24 (4%) Query: 35 VKLSPIIDDIADELADKVKITKLD 58 VKL+P I DI DE+A + D Sbjct: 166 VKLAPNITDI-DEIAKAAEEAGAD 188 >gnl|CDD|109567 pfam00516, GP120, Envelope glycoprotein GP120. The entry of HIV requires interaction of viral GP120 with CD4 and a chemokine receptor on the cell surface. Length = 493 Score = 25.1 bits (55), Expect = 4.9 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 7/28 (25%) Query: 20 NPVVV----DFWASW---CRPCVKLSPI 40 N +V D + W +PCVKL+P+ Sbjct: 58 NNMVEQAHEDIISLWDQSLKPCVKLTPL 85 >gnl|CDD|48568 cd03019, DsbA_DsbA, DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.. Length = 178 Score = 24.9 bits (54), Expect = 5.0 Identities = 10/63 (15%), Positives = 33/63 (52%), Gaps = 4/63 (6%) Query: 46 DELADKVKITKLDIEESSEISTRYQISSIPTLILFKDGK-VIDRMMPGASSQSDIIEWIL 104 D + + L + ++ +++ +Y+I+ +P ++ +GK V++ G +++ ++ Sbjct: 117 DAAYNSFSVKAL-VAKAEKLAKKYKITGVPAFVV--NGKYVVNPSAIGGDDTLQVLDELI 173 Query: 105 SRV 107 +V Sbjct: 174 EKV 176 >gnl|CDD|144184 pfam00494, SQS_PSY, Squalene/phytoene synthase. Length = 262 Score = 24.6 bits (54), Expect = 5.8 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 10/37 (27%) Query: 25 DFWA--SWCRPCVKLSPIIDDIADELAD-KVKITKLD 58 A ++CR DDI DE++D + +LD Sbjct: 22 AVAALYAFCR-------EADDIVDEVSDPLIGRARLD 51 >gnl|CDD|34621 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]. Length = 472 Score = 24.5 bits (53), Expect = 7.4 Identities = 8/28 (28%), Positives = 13/28 (46%) Query: 31 CRPCVKLSPIIDDIADELADKVKITKLD 58 CRP L P +D + EL + + + Sbjct: 401 CRPADLLEPELDKLKKELEELAIEEEEE 428 >gnl|CDD|73154 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.. Length = 177 Score = 24.4 bits (53), Expect = 7.4 Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%) Query: 22 VVVDFWA--SWCRPCVKLSPIIDDIADELADKVKITKLDI 59 + VD+ P ID++ +ELA +KLD+ Sbjct: 26 LCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDL 65 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.133 0.392 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,269,253 Number of extensions: 54674 Number of successful extensions: 240 Number of sequences better than 10.0: 1 Number of HSP's gapped: 214 Number of HSP's successfully gapped: 83 Length of query: 107 Length of database: 6,263,737 Length adjustment: 74 Effective length of query: 33 Effective length of database: 4,664,671 Effective search space: 153934143 Effective search space used: 153934143 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (23.7 bits)