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)