RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7943
(142 letters)
>gnl|CDD|233282 TIGR01130, ER_PDI_fam, protein disulfide isomerase, eukaryotic.
This model represents eukaryotic protein disulfide
isomerases retained in the endoplasmic reticulum (ER)
and closely related forms. Some members have been
assigned alternative or additional functions such as
prolyl 4-hydroxylase and
dolichyl-diphosphooligosaccharide-protein
glycotransferase. Members of this family have at least
two protein-disulfide domains, each similar to
thioredoxin but with the redox-active disulfide in the
motif PWCGHCK, and an ER retention signal at the extreme
C-terminus (KDEL, HDEL, and similar motifs).
Length = 462
Score = 150 bits (382), Expect = 1e-44
Identities = 57/117 (48%), Positives = 75/117 (64%), Gaps = 8/117 (6%)
Query: 25 DGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVD 84
+ VLVLT+DNF I+ H+ +LVEFYAPWCGHCK L PEY KAA +L G IKLAKVD
Sbjct: 1 EDVLVLTKDNFDDFIKSHEFVLVEFYAPWCGHCKSLAPEYEKAADELKKKGPPIKLAKVD 60
Query: 85 ATQHTALAEQYGVRGYPTLKFFKKRSIIEYGEVTSVEYCYQRNWHKRAVTSVIIRKT 141
AT+ LA++YGV GYPTLK F+ GE + +Y R+ + + +++
Sbjct: 61 ATEEKDLAQKYGVSGYPTLKIFRN------GEDSVSDYNGPRD--ADGIVKYMKKQS 109
Score = 92.4 bits (230), Expect = 6e-23
Identities = 40/97 (41%), Positives = 53/97 (54%), Gaps = 8/97 (8%)
Query: 23 EEDGVLVLTQDNFQSSI--EKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKL 80
+E V VL NF + E D +LVEFYAPWCGHCK L P Y + A + D+ +
Sbjct: 344 DEGPVKVLVGKNFDEIVLDETKD-VLVEFYAPWCGHCKNLAPIYEELAEKYKDAESDVVI 402
Query: 81 AKVDATQHTALAEQYGVRGYPTLKFF---KKRSIIEY 114
AK+DAT + + V G+PT+KF KK + Y
Sbjct: 403 AKMDATAND--VPPFEVEGFPTIKFVPAGKKSEPVPY 437
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 138 bits (349), Expect = 1e-39
Identities = 56/116 (48%), Positives = 72/116 (62%), Gaps = 4/116 (3%)
Query: 4 LSLLFLLISPL--VVFADDVTE--EDGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQ 59
LS LFLL+ L VF + V VLT F I +++ +LV+FYAPWCGHCK+
Sbjct: 7 LSSLFLLLILLAFAVFGSAEEHFISEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKR 66
Query: 60 LVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRSIIEYG 115
L PEY KAA L +I LA VDAT+ LA+++GVRGYPT+KFF K + + Y
Sbjct: 67 LAPEYKKAAKMLKEKKSEIVLASVDATEEMELAQEFGVRGYPTIKFFNKGNPVNYS 122
Score = 61.7 bits (150), Expect = 4e-12
Identities = 36/117 (30%), Positives = 57/117 (48%), Gaps = 18/117 (15%)
Query: 8 FLLISPLVVFADDV---------------TEEDG-VLVLTQDNFQSSIEKHDH-ILVEFY 50
F + L+ F DV E+DG V V+ + F+ + K D +L+E Y
Sbjct: 324 FDSVEALIEFFKDVEAGKVEKSIKSEPIPEEQDGPVKVVVGNTFEEIVFKSDKDVLLEIY 383
Query: 51 APWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFK 107
APWCGHCK L P Y++ + + I +AK++ T + E++ +PT+ F K
Sbjct: 384 APWCGHCKNLEPVYNELGEKYKDNDS-IIVAKMNGTANETPLEEFSWSAFPTILFVK 439
>gnl|CDD|200074 TIGR01126, pdi_dom, protein disulfide-isomerase domain. This model
describes a domain of eukaryotic protein disulfide
isomerases, generally found in two copies. The high
cutoff for total score reflects the expectation of
finding both copies. The domain is similar to
thioredoxin but the redox-active disulfide region motif
is APWCGHCK [Protein fate, Protein folding and
stabilization].
Length = 102
Score = 124 bits (314), Expect = 4e-38
Identities = 46/86 (53%), Positives = 57/86 (66%), Gaps = 2/86 (2%)
Query: 30 LTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHT 89
LT NF + + +LVEFYAPWCGHCK L PEY K A +L D DI LAKVDAT
Sbjct: 1 LTASNFDEIVLSNKDVLVEFYAPWCGHCKNLAPEYEKLAKELKKDP-DIVLAKVDATAEK 59
Query: 90 ALAEQYGVRGYPTLKFFKK-RSIIEY 114
LA ++GV G+PT+KFF K + ++Y
Sbjct: 60 DLASRFGVSGFPTIKFFPKGKKPVDY 85
>gnl|CDD|239259 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 = 123 bits (311), Expect = 1e-37
Identities = 44/89 (49%), Positives = 57/89 (64%), Gaps = 3/89 (3%)
Query: 28 LVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQ 87
+ LT DNF ++ +LVEFYAPWCGHCK L PEY K A +L DG + +AKVD T
Sbjct: 1 VELTDDNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDG-KVVVAKVDCTA 59
Query: 88 HTALAEQYGVRGYPTLKFFKK--RSIIEY 114
+ L +YGVRGYPT+K F + ++Y
Sbjct: 60 NNDLCSEYGVRGYPTIKLFPNGSKEPVKY 88
>gnl|CDD|239299 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 = 112 bits (282), Expect = 3e-33
Identities = 43/84 (51%), Positives = 53/84 (63%), Gaps = 4/84 (4%)
Query: 26 GVLVLTQDNFQSSIEKHDHI-LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVD 84
V+ LT NF + D + LVEFYAPWCGHCK L PE+ KAA L +K+ VD
Sbjct: 1 DVVELTDSNFDKKVLNSDDVWLVEFYAPWCGHCKNLAPEWKKAAKALKG---IVKVGAVD 57
Query: 85 ATQHTALAEQYGVRGYPTLKFFKK 108
A H +LA+QYGVRG+PT+K F
Sbjct: 58 ADVHQSLAQQYGVRGFPTIKVFGA 81
>gnl|CDD|215704 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 = 112 bits (282), Expect = 3e-33
Identities = 44/84 (52%), Positives = 55/84 (65%), Gaps = 4/84 (4%)
Query: 26 GVLVLTQDNFQSSIEK-HDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVD 84
V VLT +NF + K +LV+FYAPWCG CK L PEY K A + D+K AKVD
Sbjct: 1 VVKVLTDENFDEEVAKSDKPVLVDFYAPWCGPCKALAPEYEKLAQEYKD---DVKFAKVD 57
Query: 85 ATQHTALAEQYGVRGYPTLKFFKK 108
A ++ LA +YGVRG+PT+KFFK
Sbjct: 58 ADENPDLASEYGVRGFPTIKFFKN 81
>gnl|CDD|239295 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 = 110 bits (277), Expect = 1e-32
Identities = 42/84 (50%), Positives = 60/84 (71%), Gaps = 3/84 (3%)
Query: 27 VLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDAT 86
V+ LT ++F+ ++K H+LV FYAPWCGHCK++ PE++KAA +L DG LA VD T
Sbjct: 2 VVHLTDEDFRKFLKKEKHVLVMFYAPWCGHCKKMKPEFTKAATELKEDGK-GVLAAVDCT 60
Query: 87 --QHTALAEQYGVRGYPTLKFFKK 108
+H AL E+Y V+G+PT K+F+
Sbjct: 61 KPEHDALKEEYNVKGFPTFKYFEN 84
>gnl|CDD|239296 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 = 108 bits (273), Expect = 6e-32
Identities = 47/100 (47%), Positives = 61/100 (61%), Gaps = 5/100 (5%)
Query: 26 GVLVLTQDNFQSSIEK-HDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVD 84
V+ LT NF + +LVEFYAPWCGHCK L PEY K A A + D+ +AKVD
Sbjct: 1 NVVELTDSNFDKVVGDDKKDVLVEFYAPWCGHCKNLAPEYEKLAAVFANE-DDVVIAKVD 59
Query: 85 ATQ-HTALAEQYGVRGYPTLKFFKKRSI--IEYGEVTSVE 121
A + + LA++YGV G+PTLKFF K S ++Y +E
Sbjct: 60 ADEANKDLAKKYGVSGFPTLKFFPKGSTEPVKYEGGRDLE 99
>gnl|CDD|239303 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 = 99.7 bits (249), Expect = 3e-28
Identities = 41/82 (50%), Positives = 55/82 (67%), Gaps = 1/82 (1%)
Query: 26 GVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDA 85
GVL LT+DNF I + +H V+F+APWCGHCK+L P + + A + + +K+AKVD
Sbjct: 1 GVLELTEDNFDHHIAEGNH-FVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVDC 59
Query: 86 TQHTALAEQYGVRGYPTLKFFK 107
TQH L ++ VRGYPTL FK
Sbjct: 60 TQHRELCSEFQVRGYPTLLLFK 81
>gnl|CDD|239300 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 = 92.4 bits (230), Expect = 3e-25
Identities = 41/85 (48%), Positives = 55/85 (64%), Gaps = 6/85 (7%)
Query: 27 VLVLTQDNFQSSIEKHDHI-LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV-- 83
V LT NF + ++ LVEFYAPWCGHCK L PEY+KAA +L DG +++A V
Sbjct: 2 VYELTPKNFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEYAKAAKEL--DGL-VQVAAVDC 58
Query: 84 DATQHTALAEQYGVRGYPTLKFFKK 108
D ++ L +YGV+G+PTLK F+
Sbjct: 59 DEDKNKPLCGKYGVQGFPTLKVFRP 83
>gnl|CDD|239298 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 = 91.0 bits (226), Expect = 8e-25
Identities = 32/75 (42%), Positives = 52/75 (69%), Gaps = 1/75 (1%)
Query: 41 KHDHI-LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRG 99
+ + I LV+FYAPWCGHCK+L P +++ +L + G +++ K+DAT ++++A ++GVRG
Sbjct: 13 RKEDIWLVDFYAPWCGHCKKLEPVWNEVGAELKSSGSPVRVGKLDATAYSSIASEFGVRG 72
Query: 100 YPTLKFFKKRSIIEY 114
YPT+K K Y
Sbjct: 73 YPTIKLLKGDLAYNY 87
>gnl|CDD|239302 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 = 90.4 bits (225), Expect = 1e-24
Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 4/82 (4%)
Query: 27 VLVLTQDNFQSS-IEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDA 85
V+ LT ++F + + + LV+FYAPWCG C+ L+PE KAA L +K+ VD
Sbjct: 3 VITLTPEDFPELVLNRKEPWLVDFYAPWCGPCQALLPELRKAARALK---GKVKVGSVDC 59
Query: 86 TQHTALAEQYGVRGYPTLKFFK 107
++ +L +Q +R YPT++ +
Sbjct: 60 QKYESLCQQANIRAYPTIRLYP 81
>gnl|CDD|239245 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 = 83.8 bits (208), Expect = 4e-22
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 33 DNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALA 92
+ F+ I+ ++V+F+APWCG CK + P + LA + +K KVD ++ LA
Sbjct: 1 EEFEELIKSAKPVVVDFWAPWCGPCKAIAPVLEE----LAEEYPKVKFVKVDVDENPELA 56
Query: 93 EQYGVRGYPTLKFFKK 108
E+YGVR PT FFK
Sbjct: 57 EEYGVRSIPTFLFFKN 72
>gnl|CDD|239293 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 = 82.2 bits (204), Expect = 2e-21
Identities = 37/99 (37%), Positives = 56/99 (56%), Gaps = 6/99 (6%)
Query: 27 VLVLTQDNFQSSI-EKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDA 85
V V+ NF + + +LVEFYAPWCGHCK L P Y + A +L D ++ +AK+DA
Sbjct: 2 VKVVVGKNFDEVVLDSDKDVLVEFYAPWCGHCKALAPIYEELAEKLKGDD-NVVIAKMDA 60
Query: 86 TQHTALAEQYGVRGYPTLKFFKKRSI---IEYGEVTSVE 121
T + + ++ V G+PT+ FF I+Y ++E
Sbjct: 61 TAND-VPSEFVVDGFPTILFFPAGDKSNPIKYEGDRTLE 98
>gnl|CDD|200072 TIGR01068, thioredoxin, thioredoxin. Several proteins, such as
protein disulfide isomerase, have two or more copies of
a domain closely related to thioredoxin. This model is
designed to recognize authentic thioredoxin, a small
protein that should be hit exactly once by This model.
Any protein that hits once with a score greater than the
second (per domain) trusted cutoff may be taken as
thioredoxin [Energy metabolism, Electron transport].
Length = 101
Score = 80.8 bits (200), Expect = 7e-21
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 4/80 (5%)
Query: 30 LTQDNFQSSIEKHDH-ILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQH 88
LT NF +I D +LV+F+APWCG CK + P + A + +K K++ ++
Sbjct: 1 LTDANFDETIASSDKPVLVDFWAPWCGPCKMIAPILEELAKEY---EGKVKFVKLNVDEN 57
Query: 89 TALAEQYGVRGYPTLKFFKK 108
+A +YG+R PTL FK
Sbjct: 58 PDIAAKYGIRSIPTLLLFKN 77
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 71.6 bits (175), Expect = 4e-16
Identities = 35/124 (28%), Positives = 67/124 (54%), Gaps = 18/124 (14%)
Query: 6 LLFLLISPLVVF---ADDVT-------EEDGVLVLTQDNFQ-----SSIEKHDHILVEFY 50
+ F++++ ++F AD+ T + + +++L NF+ S+ V+FY
Sbjct: 1 MKFIILACCILFGLIADEATNVKLDAEDANALVLLNDKNFEKLTQASTGATTGPWFVKFY 60
Query: 51 APWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRS 110
APWC HC+++ P + + A L + +A +DAT+ LA+++ ++GYPTL F K
Sbjct: 61 APWCSHCRKMAPAWERLAKALKG---QVNVADLDATRALNLAKRFAIKGYPTLLLFDKGK 117
Query: 111 IIEY 114
+ +Y
Sbjct: 118 MYQY 121
>gnl|CDD|239294 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 = 66.6 bits (163), Expect = 3e-15
Identities = 31/104 (29%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 26 GVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQL---ATDGHDIKLAK 82
++ LT N ++ + +LV FYA WC + L P + +AA ++ D + K
Sbjct: 2 EIVSLTSGNIDDILQSAELVLVNFYADWCRFSQMLHPIFEEAAAKIKEEFPDAGKVVWGK 61
Query: 83 VDATQHTALAEQYGVRGYPTLKFFKKRSIIEYGEVTSVEYCYQR 126
VD + + +A++Y + YPTLK F+ G + EY QR
Sbjct: 62 VDCDKESDIADRYRINKYPTLKLFR------NGMMMKREYRGQR 99
>gnl|CDD|239290 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 = 65.4 bits (160), Expect = 9e-15
Identities = 34/86 (39%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 25 DGVLVLTQDNFQSSI-EKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV 83
D V+VL +F S++ LVEFYA WCGHC+ P + K A L +++A V
Sbjct: 1 DPVIVLDAASFNSALLGSPSAWLVEFYASWCGHCRAFAPTWKKLARDLRKWRPVVRVAAV 60
Query: 84 DATQHT--ALAEQYGVRGYPTLKFFK 107
D AL +GV GYPTL++F
Sbjct: 61 DCADEENVALCRDFGVTGYPTLRYFP 86
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 63.4 bits (154), Expect = 4e-14
Identities = 26/85 (30%), Positives = 50/85 (58%), Gaps = 4/85 (4%)
Query: 29 VLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQH 88
V +Q F+S++ +++ ++V+FYA WCG CK++ P Y + + + + KVD +
Sbjct: 5 VTSQAEFESTLSQNELVIVDFYAEWCGPCKRIAPFYE----ECSKEYTKMVFVKVDVDEL 60
Query: 89 TALAEQYGVRGYPTLKFFKKRSIIE 113
+ +AE+ + PT K FK S+++
Sbjct: 61 SEVAEKENITSMPTFKVFKNGSVVD 85
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 65.5 bits (160), Expect = 2e-13
Identities = 37/88 (42%), Positives = 48/88 (54%), Gaps = 9/88 (10%)
Query: 20 DVTEEDGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIK 79
DVTE + Q+ QSS + +LV+F+APWCG CKQL P K A A K
Sbjct: 27 DVTEAN----FEQEVIQSS--REVPVLVDFWAPWCGPCKQLTPTLEKLA---AEYKGKFK 77
Query: 80 LAKVDATQHTALAEQYGVRGYPTLKFFK 107
LAKV+ +A Q+GV+ PT+ FK
Sbjct: 78 LAKVNCDAEPMVAAQFGVQSIPTVYAFK 105
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 62.0 bits (150), Expect = 2e-13
Identities = 34/98 (34%), Positives = 53/98 (54%), Gaps = 10/98 (10%)
Query: 25 DGVLVLTQDNFQSSIEKHDHI-LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV 83
D ++ LT D+F + + K D LV+F+A WCG CK + P + A + + +AK+
Sbjct: 3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGK---LTVAKL 59
Query: 84 DATQHTALAEQYGVRGYPTLKFFKKRSIIEYGEVTSVE 121
+ Q+ A +YG+RG PTL FK GEV + +
Sbjct: 60 NIDQNPGTAPKYGIRGIPTLLLFKN------GEVAATK 91
>gnl|CDD|239292 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 = 57.8 bits (140), Expect = 6e-12
Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 27 VLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHD--IKLAKVD 84
V+ LT N+ +E ++EFYAPWC C+QL PE+ + A D I +AKVD
Sbjct: 3 VVELTDSNWTLVLE--GEWMIEFYAPWCPACQQLQPEWE----EFADWSDDLGINVAKVD 56
Query: 85 ATQHTALAEQYGVRGYPTL 103
TQ L+ ++ V PT+
Sbjct: 57 VTQEPGLSGRFFVTALPTI 75
>gnl|CDD|239254 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 = 56.9 bits (138), Expect = 1e-11
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 33 DNFQSSIEKHDH--ILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTA 90
NFQ +++ ++V+F+AP K+L+P + A + LAKV+
Sbjct: 1 QNFQQVLQESTQVPVVVDFWAPRSPPSKELLPLLERLAEE---YQGQFVLAKVNCDAQPQ 57
Query: 91 LAEQYGVRGYPTLKFFKK 108
+A+Q+GV+ PT+ F
Sbjct: 58 IAQQFGVQALPTVYLFAA 75
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 56.6 bits (137), Expect = 3e-11
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 31 TQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTA 90
T + ++ ++++F+APWCG C+ P + A A ++ KV+
Sbjct: 41 TGETLDKLLQDDLPVVIDFWAPWCGPCRNFAPIFEDVA---AERSGKVRFVKVNTEAERE 97
Query: 91 LAEQYGVRGYPTLKFFKK 108
L+ ++ +R PT+ FK
Sbjct: 98 LSARFRIRSIPTIMIFKN 115
>gnl|CDD|239291 cd02993, PDI_a_APS_reductase, PDIa family, 5'-Adenylylsulfate (APS)
reductase subfamily; composed of plant-type APS
reductases containing a C-terminal redox active TRX
domain and an N-terminal reductase domain which is part
of a superfamily that includes N type ATP PPases. APS
reductase catalyzes the reduction of activated sulfate
to sulfite, a key step in the biosynthesis of
sulfur-containing metabolites. Sulfate is first
activated by ATP sulfurylase, forming APS, which can be
phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate
(PAPS). Depending on the organism, either APS or PAPS
can be used for sulfate reduction. Prokaryotes and fungi
use PAPS, whereas plants use both APS and PAPS. Since
plant-type APS reductase uses glutathione (GSH) as its
electron donor, the C-terminal domain may function like
glutaredoxin, a GSH-dependent member of the TRX
superfamily. The flow of reducing equivalents goes from
GSH -> C-terminal TRX domain -> N-terminal reductase
domain -> APS. Plant-type APS reductase shows no
homology to that of dissimilatory sulfate-reducing
bacteria, which is an iron-sulfur flavoenzyme. Also
included in the alignment is EYE2 from Chlamydomonas
reinhardtii, a protein required for eyespot assembly.
Length = 109
Score = 52.1 bits (125), Expect = 1e-09
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV--DATQHTALAEQYGVRGYPTL 103
LV YAPWC C+ + Y + A +LA G ++K+AK D Q E+ ++ +PT+
Sbjct: 25 LVVLYAPWCPFCQAMEASYEELAEKLA--GSNVKVAKFNADGEQREFAKEELQLKSFPTI 82
Query: 104 KFFKKRS--IIEY 114
FF K S I+Y
Sbjct: 83 LFFPKNSRQPIKY 95
>gnl|CDD|238829 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 = 50.8 bits (121), Expect = 2e-09
Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAE---QYGVRGYPT 102
LV FYAPWC C+ L P ++ AL +K VD + AL + +YGV G PT
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLN----KGVKFEAVDVDEDPALEKELKRYGVGGVPT 56
Query: 103 LKFFKKRSIIEYG 115
L F ++YG
Sbjct: 57 LVVFGPGIGVKYG 69
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 51.4 bits (122), Expect = 3e-09
Identities = 20/64 (31%), Positives = 28/64 (43%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLK 104
+LV+F+APWC C+ P + A + D + + D A VR PTL
Sbjct: 35 VLVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVAVRSIPTLL 94
Query: 105 FFKK 108
FK
Sbjct: 95 LFKD 98
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 48.2 bits (115), Expect = 3e-08
Identities = 22/83 (26%), Positives = 31/83 (37%), Gaps = 15/83 (18%)
Query: 40 EKHDHILVEFYAPWCGHCKQLVPEYSK-AALQLATDGHDIKLAKVDA------------- 85
+LV F P C +CK+L E K +Q + + V+
Sbjct: 3 GNGKPVLVVFTDPDCPYCKKLHKELLKDPDVQEYLKDN-FVVIYVNVDDSKEVTDFDGET 61
Query: 86 TQHTALAEQYGVRGYPTLKFFKK 108
LA +YGVRG PT+ F
Sbjct: 62 LSEKELARKYGVRGTPTIVFLDG 84
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 50.6 bits (121), Expect = 4e-08
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAK--VDATQHTALAEQYGVRGYPTL 103
LV YAPWC C+ + Y + A +LA G +K+AK D Q ++ + +PT+
Sbjct: 369 LVVLYAPWCPFCQAMEASYEELAEKLA--GSGVKVAKFRADGDQKEFAKQELQLGSFPTI 426
Query: 104 KFFKKRS--IIEYG 115
F K S I+Y
Sbjct: 427 LLFPKNSSRPIKYP 440
>gnl|CDD|239282 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 = 47.7 bits (114), Expect = 5e-08
Identities = 16/70 (22%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSKAALQLATDGH-DIKLAKVDATQHTALAEQYGVRGYPTL 103
+++ F+APW CKQ+ ++ +LA + + ++A + ++E++ + PT
Sbjct: 17 LVLHFWAPWAEPCKQM----NQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTF 72
Query: 104 KFFKKRSIIE 113
FF+ +I++
Sbjct: 73 VFFRNGTIVD 82
>gnl|CDD|239301 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 = 47.5 bits (113), Expect = 5e-08
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 27 VLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDAT 86
++ L + +F +++ + V FY+P C HC L P + + A ++ DG I++ V+
Sbjct: 3 IVTLDRGDFDAAVNSGEIWFVNFYSPRCSHCHDLAPTWREFAKEM--DG-VIRIGAVNCG 59
Query: 87 QHTALAEQYGVRGYPTLKFFK 107
L GV YP+L F
Sbjct: 60 DDRMLCRSQGVNSYPSLYVFP 80
>gnl|CDD|239251 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 = 46.8 bits (112), Expect = 1e-07
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 45 ILVEFYAPWCGHCKQLVPE-YSKAALQLATDGHDIKLAKVDATQ----HTALAEQYGVRG 99
+ V+F A WC CK +S +Q A D+ L + D T+ TAL +++GV G
Sbjct: 14 VFVDFTADWCVTCKVNEKVVFSDPEVQAALK-KDVVLLRADWTKNDPEITALLKRFGVFG 72
Query: 100 YPTLKFFKKRSIIE 113
PT F+ E
Sbjct: 73 PPTYLFYGPGGEPE 86
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 48.1 bits (115), Expect = 2e-07
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 41 KHDHILVEFYAPWCGHCKQLVPE-YSKAALQLATDGHDIKLAKVDAT----QHTALAEQY 95
K ++++FYA WC CK+ +S +Q A D+ L + D T TAL ++
Sbjct: 473 KAKPVMLDFYADWCVTCKENEKYTFSDPQVQQAL--QDVVLLQADVTANDPAITALLKRL 530
Query: 96 GVRGYPTLKFF 106
GV G PT FF
Sbjct: 531 GVFGVPTYLFF 541
>gnl|CDD|239247 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 = 44.8 bits (106), Expect = 4e-07
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLK 104
ILV + +P CG C+ L P +K + + ++D + +AE G+ G PT++
Sbjct: 16 ILVLYTSPTCGPCRTLKPILNKVIDEF---DGAVHFVEIDIDEDQEIAEAAGIMGTPTVQ 72
Query: 105 FFKKRSIIE 113
FFK + +++
Sbjct: 73 FFKDKELVK 81
>gnl|CDD|232970 TIGR00424, APS_reduc, 5'-adenylylsulfate reductase,
thioredoxin-independent. This enzyme, involved in the
assimilation of inorganic sulfate, is closely related to
the thioredoxin-dependent PAPS reductase of Bacteria
(CysH) and Saccharomyces cerevisiae. However, it has its
own C-terminal thioredoxin-like domain and is not
thioredoxin-dependent. Also, it has a substrate
preference for 5'-adenylylsulfate (APS) over
3'-phosphoadenylylsulfate (PAPS) so the pathway does not
require an APS kinase (CysC) to convert APS to PAPS.
Arabidopsis thaliana appears to have three isozymes, all
able to complement E. coli CysH mutants (even in
backgrounds lacking thioredoxin or APS kinase) but
likely localized to different compartments in
Arabidopsis [Central intermediary metabolism, Sulfur
metabolism].
Length = 463
Score = 46.9 bits (111), Expect = 6e-07
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 20 DVTEEDGVLVLTQ---DNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGH 76
D+ + + V+ L++ +N E+ + LV YAPWC C+ + Y + A +LA G
Sbjct: 346 DIFDSNNVVSLSRPGIENLLKLEERKEAWLVVLYAPWCPFCQAMEASYLELAEKLAGSGV 405
Query: 77 DIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRS 110
+ + D Q ++ + +PT+ FF K S
Sbjct: 406 KVAKFRADGDQKEFAKQELQLGSFPTILFFPKHS 439
>gnl|CDD|239248 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 = 42.7 bits (101), Expect = 7e-06
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKF 105
LVEFYA WC C+++ P+ +K Q D + + VD + ++Y V G P F
Sbjct: 24 LVEFYADWCTVCQEMAPDVAKLK-QKYGDQVNFVMLNVDNPKWLPEIDRYRVDGIPHFVF 82
Query: 106 FKKRSIIE 113
+ E
Sbjct: 83 LDREGNEE 90
>gnl|CDD|239297 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 = 41.6 bits (98), Expect = 8e-06
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 41 KHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDAT-QHTALAEQYGVRG 99
+ D+ V FYA WC P ++ L++ I+ ++ + +L +YGV G
Sbjct: 17 REDYTAVLFYASWCPFSASFRPHFNA----LSSMFPQIRHLAIEESSIKPSLLSRYGVVG 72
Query: 100 YPTLKFFKKRSIIEY 114
+PT+ F + Y
Sbjct: 73 FPTILLFNSTPRVRY 87
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 42.5 bits (101), Expect = 2e-05
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 23/75 (30%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSK---------AALQLATDGHDIKLAKVDAT----QHTAL 91
++++ YA WC CK E+ K AL D L + D T + AL
Sbjct: 477 VMLDLYADWCVACK----EFEKYTFSDPQVQQALA------DTVLLQADVTANNAEDVAL 526
Query: 92 AEQYGVRGYPTLKFF 106
+ Y V G PT+ FF
Sbjct: 527 LKHYNVLGLPTILFF 541
>gnl|CDD|239264 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 = 38.4 bits (90), Expect = 2e-04
Identities = 27/101 (26%), Positives = 36/101 (35%), Gaps = 21/101 (20%)
Query: 35 FQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDI--------KLAKVDAT 86
S K +LV F+A WC C+ +PE A + DG ++ A V A
Sbjct: 12 VSLSDLKGKVVLVNFWASWCPPCRAEMPELEALAKEYKDDGVEVVGVNVDDDDPAAVKAF 71
Query: 87 -------------QHTALAEQYGVRGYPTLKFFKKRSIIEY 114
LA+ YGVRG PT + I
Sbjct: 72 LKKYGITFPVLLDPDGELAKAYGVRGLPTTFLIDRDGRIRA 112
>gnl|CDD|239363 cd03065, PDI_b_Calsequestrin_N, PDIb family, Calsequestrin
subfamily, N-terminal TRX-fold domain; Calsequestrin is
the major calcium storage protein in the sarcoplasmic
reticulum (SR) of skeletal and cardiac muscle. It stores
calcium ions in sufficient quantities (up to 20 mM) to
allow repetitive contractions and is essential to
maintain movement, respiration and heart beat. A
missense mutation in human cardiac calsequestrin is
associated with catecholamine-induced polymorphic
ventricular tachycardia (CPVT), a rare disease
characterized by seizures or sudden death in response to
physiologic or emotional stress. Calsequestrin is a
highly acidic protein with up to 50 calcium binding
sites formed simply by the clustering of two or more
acidic residues. The monomer contains three redox
inactive TRX-fold domains. Calsequestrin is condensed as
a linear polymer in the SR lumen and is
membrane-anchored through binding with intra-membrane
proteins triadin, junctin and ryanodine receptor (RyR)
Ca2+ release channel. In addition to its role as a
calcium ion buffer, calsequestrin also regulates the
activity of the RyR channel, coordinating the release of
calcium ions from the SR with the loading of the calcium
store. The N-terminal TRX-fold domain (or domain I)
mediates front-to-front dimer interaction, an important
feature in the formation of calsequestrin polymers.
Length = 120
Score = 38.2 bits (89), Expect = 2e-04
Identities = 28/118 (23%), Positives = 52/118 (44%), Gaps = 26/118 (22%)
Query: 24 EDGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAA----------LQLAT 73
+D V+ L + N++ ++K+D + + ++ P E K A L+LA
Sbjct: 8 KDRVIDLNEKNYKQVLKKYDVLCLLYHEP---------VESDKEAQKQFQMEELVLELAA 58
Query: 74 ---DGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRSIIEY-GEV---TSVEYCY 124
+ I VD+ + +A++ G+ ++ FK +IEY GE T VE+
Sbjct: 59 QVLEDKGIGFGLVDSKKDAKVAKKLGLDEEDSIYVFKDDEVIEYDGEFAADTLVEFLL 116
>gnl|CDD|239260 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 = 36.2 bits (84), Expect = 0.002
Identities = 27/117 (23%), Positives = 51/117 (43%), Gaps = 13/117 (11%)
Query: 3 RLSLLFLLISPLVVFADDVTEEDG---VLVLTQDNFQSSIEKHDHI--LVEFYAPWCGHC 57
RL LL+LL+ +V G + T + +E+ + LVEF+ W C
Sbjct: 3 RLGLLYLLLCIVVYLLAPQPLYMGPEHIKYFTPKTLEEELERDKRVTWLVEFFTTWSPEC 62
Query: 58 KQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGV------RGYPTLKFFKK 108
P +++ +L+ + +K K+D + +AE++ V + PT+ F+
Sbjct: 63 VNFAPVFAELSLKYNNNN--LKFGKIDIGRFPNVAEKFRVSTSPLSKQLPTIILFQG 117
>gnl|CDD|239270 cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like
proteins, including DsbC, DsbG, glutathione (GSH)
S-transferase kappa (GSTK),
2-hydroxychromene-2-carboxylate (HCCA) isomerase, an
oxidoreductase (FrnE) presumed to be involved in
frenolicin biosynthesis, a 27-kDa outer membrane
protein, and similar proteins. Members of this family
contain a redox active CXXC motif (except GSTK and HCCA
isomerase) imbedded in a TRX fold, and an alpha helical
insert of about 75 residues (shorter in DsbC and DsbG)
relative to TRX. DsbA is involved in the oxidative
protein folding pathway in prokaryotes, catalyzing
disulfide bond formation of proteins secreted into the
bacterial periplasm. DsbC and DsbG function as protein
disulfide isomerases and chaperones to correct
non-native disulfide bonds formed by DsbA and prevent
aggregation of incorrectly folded proteins.
Length = 98
Score = 34.3 bits (79), Expect = 0.004
Identities = 21/90 (23%), Positives = 28/90 (31%), Gaps = 35/90 (38%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAK----------------------- 82
+VEF+ P C +C PE K L D +++
Sbjct: 1 IVEFFDPLCPYCYLFEPELEKL---LYADDGGVRVVYRPFPLLGGMPPNSLAAARAALAA 57
Query: 83 ---------VDATQHTALAEQYGVRGYPTL 103
+A TALA GV G PT
Sbjct: 58 AAQGKFEALHEALADTALARALGVTGTPTF 87
>gnl|CDD|239271 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 = 32.2 bits (74), Expect = 0.013
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 44 HILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTL 103
+I V F +P C +C P+ +AA ++A +I +DA + LA++YGV P +
Sbjct: 2 NIEV-FVSPTCPYC----PDAVQAANRIAALNPNISAEMIDAAEFPDLADEYGVMSVPAI 56
>gnl|CDD|239321 cd03023, DsbA_Com1_like, DsbA family, Com1-like subfamily;
composed of proteins similar to Com1, a 27-kDa outer
membrane-associated immunoreactive protein originally
found in both acute and chronic disease strains of the
pathogenic bacteria Coxiella burnetti. It contains a
CXXC motif, assumed to be imbedded in a DsbA-like
structure. Its homology to DsbA suggests that the
protein is a protein disulfide oxidoreductase. The role
of such a protein in pathogenesis is unknown.
Length = 154
Score = 33.3 bits (77), Expect = 0.018
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 43 DHILVEFYAPWCGHCKQLVPE 63
D +VEF+ CG+CK+L PE
Sbjct: 6 DVTIVEFFDYNCGYCKKLAPE 26
>gnl|CDD|239249 cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX,
containing a redox active CXXC motif, encoded by a
genetic locus (sox operon) involved in thiosulfate
oxidation. Sulfur bacteria oxidize sulfur compounds to
provide reducing equivalents for carbon dioxide fixation
during autotrophic growth and the respiratory electron
transport chain. It is unclear what the role of SoxW is,
since it has been found to be dispensable in the
oxidation of thiosulfate to sulfate. SoxW is
specifically kept in the reduced state by SoxV, which is
essential in thiosulfate oxidation.
Length = 125
Score = 32.7 bits (75), Expect = 0.024
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 13/75 (17%)
Query: 45 ILVEFYAPWCGHCKQL---------VPEYSKA---ALQLATDGHDI-KLAKVDATQHTAL 91
+L+ F P C +C +L V Y +A + + DG +A L
Sbjct: 17 LLLLFSQPGCPYCDKLKRDYLNDPAVQAYIRAHFVVVYINIDGDKEVTDFDGEALSEKEL 76
Query: 92 AEQYGVRGYPTLKFF 106
A +Y VR PT+ F
Sbjct: 77 ARKYRVRFTPTVIFL 91
>gnl|CDD|239309 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 = 32.3 bits (74), Expect = 0.032
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 16/82 (19%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLAT------DGHDIKLAK-VDATQHT--------- 89
LV F+A WC C+ P ++ A G D +A+ + +
Sbjct: 24 LVYFWATWCPVCRFTSPTVNQLAADYPVVSVALRSGDDGAVARFMQKKGYGFPVINDPDG 83
Query: 90 ALAEQYGVRGYPTLKFFKKRSI 111
++ ++GV P + I
Sbjct: 84 VISARWGVSVTPAIVIVDPGGI 105
>gnl|CDD|233769 TIGR02187, GlrX_arch, Glutaredoxin-like domain protein. This
family of archaeal proteins contains a C-terminal domain
with homology to bacterial and eukaryotic glutaredoxins,
including a CPYC motif. There is an N-terminal domain
which has even more distant homology to glutaredoxins.
The name "glutaredoxin" may be inappropriate in the
sense of working in tandem with glutathione and
glutathione reductase which may not be present in the
archaea. The overall domain structure appears to be
related to bacterial alkylhydroperoxide reductases, but
the homology may be distant enough that the function of
this family is wholly different.
Length = 215
Score = 32.8 bits (75), Expect = 0.033
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 37 SSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYG 96
S+++ I V F P C +C V A + A I ++A ++ LAE+YG
Sbjct: 129 QSLDEPVRIEV-FVTPTCPYCPYAV----LMAHKFALANDKILGEMIEANENPDLAEKYG 183
Query: 97 VRGYP 101
V P
Sbjct: 184 VMSVP 188
Score = 28.6 bits (64), Expect = 0.94
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 53 WCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRSII 112
+C +QL+ E S+ + +L + +D D + AE+YGV PT ++
Sbjct: 36 YCKETEQLLEELSEVSPKLKLEIYDF-----DTPEDKEEAEKYGVERVPTTIILEEGKDG 90
Query: 113 E 113
Sbjct: 91 G 91
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 32.9 bits (75), Expect = 0.033
Identities = 27/124 (21%), Positives = 48/124 (38%), Gaps = 16/124 (12%)
Query: 1 MRRLSLLFLLISPLVVFADDVTEEDGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQL 60
+ R+ L+ LLI L + A E + D+ +S ++L+ F + C +C++
Sbjct: 1 VMRVLLIVLLIISLFLSACKSNNEKRSNIDVFDDNKSISPNDKYLLLMFESNGCSYCERF 60
Query: 61 ---------VPEYSKAALQ----LATDGHDIKLA---KVDATQHTALAEQYGVRGYPTLK 104
+ EY K + + K + LA+++ VR PT
Sbjct: 61 KKDLKNVKRLREYLKEHFSAYYLNISYSKPVLFKVGDKEEKMSTEELAQKFAVRSTPTFV 120
Query: 105 FFKK 108
FF K
Sbjct: 121 FFDK 124
>gnl|CDD|222448 pfam13905, Thioredoxin_8, Thioredoxin-like. Thioredoxins are small
enzymes that participate in redox reactions, via the
reversible oxidation of an active centre disulfide bond.
Length = 94
Score = 31.9 bits (73), Expect = 0.034
Identities = 17/82 (20%), Positives = 25/82 (30%), Gaps = 23/82 (28%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSKAALQ-----------------------LATDGHDIKLA 81
+L+ F+A WC C+ PE + + L D
Sbjct: 4 VLLYFWASWCPPCRAFTPELKELYEKLKKPKVEIVYVSLDRDEEEWKKYLKKMPKDWLNV 63
Query: 82 KVDATQHTALAEQYGVRGYPTL 103
+ L YGV+ PTL
Sbjct: 64 PFGDKERNELLRLYGVKAIPTL 85
>gnl|CDD|239261 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 = 32.0 bits (73), Expect = 0.040
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTL 103
L++ + WC C + P + + +L G + +A V+A LA + G P +
Sbjct: 28 LIKITSDWCFSCIHIEPVWKEVIQELEPLG--VGIATVNAGHERRLARKLGAHSVPAI 83
>gnl|CDD|133998 PHA02125, PHA02125, thioredoxin-like protein.
Length = 75
Score = 31.1 bits (70), Expect = 0.043
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 9/55 (16%)
Query: 49 FYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTL 103
F A WC +CK + P + + VD + L ++ +R PTL
Sbjct: 5 FGAEWCANCKMVKPMLANV---------EYTYVDVDTDEGVELTAKHHIRSLPTL 50
>gnl|CDD|239246 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 = 31.2 bits (71), Expect = 0.065
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 45 ILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLK 104
+V+ Y WCG CK +V + K +L + A +A L ++Y + PT
Sbjct: 20 TVVDVYQEWCGPCKAVVSLFKKIKNEL--GDDLLHFATAEADTIDTL-KRYRGKCEPTFL 76
Query: 105 FFKKRSIIE 113
F+K ++
Sbjct: 77 FYKNGELVA 85
>gnl|CDD|221091 pfam11355, DUF3157, Protein of unknown function (DUF3157). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 197
Score = 31.6 bits (72), Expect = 0.082
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 1 MRRLSLLFLLISPLVVFADD---VTEEDGVLVLTQDNF 35
M+ +LL LL+ FA D VT EDG V D+F
Sbjct: 1 MKSYALLALLLLASSAFAADVATVTLEDGAQVRLNDDF 38
>gnl|CDD|239263 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 = 30.4 bits (69), Expect = 0.14
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 81 AKVDATQHTALAEQYGVRGYPTLKFFKK 108
A V ALA ++GV P L FF+
Sbjct: 65 AVVGRADEQALAARFGVLRTPALLFFRD 92
>gnl|CDD|239262 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 = 30.7 bits (70), Expect = 0.15
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 25/89 (28%)
Query: 44 HILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV-------------------- 83
+ + F A WC C+ P+ + +L +G + ++ V
Sbjct: 19 TVGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFEIVFVSRDRSEESFNEYFSEMPPWL 78
Query: 84 -----DATQHTALAEQYGVRGYPTLKFFK 107
D L +Q+ V G PTL K
Sbjct: 79 AVPFEDEELRELLEKQFKVEGIPTLVVLK 107
>gnl|CDD|182802 PRK10877, PRK10877, protein disulfide isomerase II DsbC;
Provisional.
Length = 232
Score = 30.4 bits (69), Expect = 0.22
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 68 ALQLATDGHDIKLA--KVDATQHTALAEQYGVRGYPTL 103
A A G D+ A VD H AL Q+GV+G P +
Sbjct: 169 AFDDAMKGKDVSPASCDVDIADHYALGVQFGVQGTPAI 206
>gnl|CDD|239273 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 = 29.7 bits (67), Expect = 0.26
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 53 WCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQYGVRGYPTLKFFKKRS 110
+C KQL+ E S+ + +L KL D + AE+YGV PT F +
Sbjct: 36 YCEVTKQLLEELSELSDKL-------KLEIYDFDEDKEKAEKYGVERVPTTIFLQDGG 86
>gnl|CDD|239265 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 = 29.7 bits (67), Expect = 0.28
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 16/65 (24%)
Query: 46 LVEFYAPWCGHCKQLVP--------EYSKAALQLATDGHDIKLAKVDATQHTALAEQYGV 97
L+ F +P C CK+L+P E + LA+DG + +H +++G+
Sbjct: 25 LLFFLSPTCPVCKKLLPVIRSIARAEADWLDVVLASDG--------EKAEHQRFLKKHGL 76
Query: 98 RGYPT 102
+P
Sbjct: 77 EAFPY 81
>gnl|CDD|239304 cd03006, PDI_a_EFP1_N, PDIa family, N-terminal EFP1 subfamily; EFP1
is a binding partner protein of thyroid oxidase (ThOX),
also called Duox. ThOX proteins are responsible for the
generation of hydrogen peroxide, a crucial substrate of
thyroperoxidase, which functions to iodinate
thyroglobulin and synthesize thyroid hormones. EFP1 was
isolated through a yeast two-hybrid method using the
EF-hand fragment of dog Duox1 as a bait. It could be one
of the partners in the assembly of a multiprotein
complex constituting the thyroid hydrogen peroxide
generating system. EFP1 contains two TRX domains related
to the redox active TRX domains of protein disulfide
isomerase (PDI). This subfamily is composed of the
N-terminal TRX domain of EFP1, which contains a CXXS
sequence in place of the typical CXXC motif, similar to
ERp44. The CXXS motif allows the formation of stable
mixed disulfides, crucial for the ER-retention function
of ERp44.
Length = 113
Score = 29.0 bits (65), Expect = 0.37
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 46 LVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDA-TQHTALAEQYGVRGYPTLK 104
LV +YAPW + E+ + A +L+ + ++ +Q +P +
Sbjct: 33 LVMYYAPWDAQSQAARQEFEQVAQKLSD---QVLFVAINCWWPQGKCRKQKHFFYFPVIH 89
Query: 105 FFKKR--SIIEYGEVTSVEY 122
+ + I G + +
Sbjct: 90 LYYRSRGPIEYKGPMRAPYM 109
>gnl|CDD|239318 cd03020, DsbA_DsbC_DsbG, DsbA family, DsbC and DsbG subfamily;
V-shaped homodimeric proteins containing a redox active
CXXC motif imbedded in a TRX fold. They function as
protein disulfide isomerases and chaperones in the
bacterial periplasm to correct non-native disulfide
bonds formed by DsbA and prevent aggregation of
incorrectly folded proteins. DsbC and DsbG are kept in
their reduced state by the cytoplasmic membrane protein
DsbD, which utilizes the TRX/TRX reductase system in the
cytosol as a source of reducing equivalents. DsbG differ
from DsbC in that it has a more limited substrate
specificity, and it may preferentially act later in the
folding process to catalyze disulfide rearrangements in
folded or partially folded proteins. Also included in
the alignment is the predicted protein TrbB, whose gene
was sequenced from the enterohemorrhagic E. coli type IV
pilus gene cluster, which is required for efficient
plasmid transfer.
Length = 197
Score = 29.6 bits (67), Expect = 0.41
Identities = 19/100 (19%), Positives = 27/100 (27%), Gaps = 38/100 (38%)
Query: 42 HDHILVEFYAPWCGHCKQLVPE--------------YS--------------------KA 67
++ F P C +C++L E
Sbjct: 77 GKRVVYVFTDPDCPYCRKLEKELKPNADGVTVRIFPVPILGLPDSTAKAAAIWCAKDRAK 136
Query: 68 ALQLATDGHDI--KLAKVDAT--QHTALAEQYGVRGYPTL 103
A A G + A D + AL Q GV G PT+
Sbjct: 137 AWTDAMSGGKVPPPAASCDNPVAANLALGRQLGVNGTPTI 176
>gnl|CDD|239307 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 = 29.2 bits (66), Expect = 0.42
Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 24/84 (28%)
Query: 44 HILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKV-------------------- 83
+ + F A WC C+ P+ + +L G + ++ +
Sbjct: 20 TVGLYFSASWCPPCRAFTPKLVEFYEKLKESGKNFEIVFISWDRDEESFNDYFSKMPWLA 79
Query: 84 ----DATQHTALAEQYGVRGYPTL 103
D + + L + + G PTL
Sbjct: 80 VPFSDRERRSRLNRTFKIEGIPTL 103
>gnl|CDD|110233 pfam01216, Calsequestrin, Calsequestrin.
Length = 350
Score = 29.9 bits (67), Expect = 0.43
Identities = 25/101 (24%), Positives = 51/101 (50%), Gaps = 5/101 (4%)
Query: 24 EDGVLVLTQDNFQSSIEKHDHILVEFYAPWCG-HCKQLVPEYSKAALQLAT---DGHDIK 79
+D V+ LT+ N++ ++K++ + + ++ P Q E + L+LA + +
Sbjct: 10 KDRVISLTEKNYKQVLKKYEVLALLYHEPVSDDKASQRQFEMEELILELAAQVLEDKGVG 69
Query: 80 LAKVDATQHTALAEQYGVRGYPTLKFFKKRSIIEY-GEVTS 119
VD+ + A+A++ G+ +L FK IEY GE ++
Sbjct: 70 FGLVDSEKDAAVAKKLGLDEEDSLYVFKGDETIEYDGEFSA 110
>gnl|CDD|239274 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small
monomeric protein with a conserved redox active CXXC
motif within a TRX fold, characterized by a glutaredoxin
(GRX)-like sequence and TRX-like activity profile. In
vitro, it displays protein disulfide reductase activity
that is dependent on TRX reductase, not glutathione
(GSH). It is part of the NrdHIEF operon, where NrdEF
codes for class Ib ribonucleotide reductase (RNR-Ib), an
efficient enzyme at low oxygen levels. Under these
conditions when GSH is mostly conjugated to spermidine,
NrdH can still function and act as a hydrogen donor for
RNR-Ib. It has been suggested that the NrdHEF system may
be the oldest RNR reducing system, capable of
functioning in a microaerophilic environment, where GSH
was not yet available. NrdH from Corynebacterium
ammoniagenes can form domain-swapped dimers, although it
is unknown if this happens in vivo. Domain-swapped
dimerization, which results in the blocking of the TRX
reductase binding site, could be a mechanism for
regulating the oxidation state of the protein.
Length = 73
Score = 28.0 bits (63), Expect = 0.59
Identities = 16/64 (25%), Positives = 21/64 (32%), Gaps = 14/64 (21%)
Query: 47 VEFYA-PWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQ----YGVRGYP 101
V Y P C +CK K L D I +VD + E+ G R P
Sbjct: 2 VTVYTKPDCPYCKAT-----KRFL----DERGIPFEEVDVDEDPEALEELKKLNGYRSVP 52
Query: 102 TLKF 105
+
Sbjct: 53 VVVI 56
>gnl|CDD|203636 pfam07449, HyaE, Hydrogenase-1 expression protein HyaE. This
family contains bacterial hydrogenase-1 expression
proteins approximately 120 residues long. This includes
the E. coli protein HyaE, and the homologous proteins
HoxO of R. eutropha and HupG of R. leguminosarum.
Deletion of the hoxO gene in R. eutropha led to complete
loss of the uptake [NiFe] hydrogenase activity,
suggesting that it has a critical role in hydrogenase
assembly.
Length = 107
Score = 28.1 bits (63), Expect = 0.78
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 81 AKVDATQHTALAEQYGVRGYPTLKFFKK 108
A V Q AL +++GVR +P+L FF+
Sbjct: 64 AVVAREQEEALGDRFGVRRFPSLLFFRD 91
>gnl|CDD|222442 pfam13899, Thioredoxin_7, Thioredoxin-like. Thioredoxins are
small enzymes that participate in redox reactions, via
the reversible oxidation of an active centre disulfide
bond.
Length = 81
Score = 27.3 bits (61), Expect = 1.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 45 ILVEFYAPWCGHCKQL 60
+LV+F A WC C+ L
Sbjct: 20 LLVDFGADWCPTCQAL 35
>gnl|CDD|233372 TIGR01355, cyt_deam_dimer, cytidine deaminase, homodimeric. This
homodimeric zinc metalloprotein is found in Arabidopis
and some Proteobacteria. A related, homotetrameric form
with a much smaller subunit is found most bacteria and
in animals. Both types may act on deoxycytidine as well
as cytidine [Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 283
Score = 28.6 bits (64), Expect = 1.0
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 15/63 (23%)
Query: 40 EKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKL------AKVDATQHTALAE 93
E+ + L +AP CGHC+Q + E A IK+ K D + + L +
Sbjct: 88 ERGLNDLAVSFAP-CGHCRQFLNEIRNA--------SSIKILLPDPHNKRDMSLQSYLPD 138
Query: 94 QYG 96
++G
Sbjct: 139 RFG 141
>gnl|CDD|131251 TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family. This
glutaredoxin-like protein family contains the conserved
CxxC motif and includes the Clostridium pasteurianum
protein YruB which has been cloned from a rubredoxin
operon. Somewhat related to NrdH, it is unknown whether
this protein actually interacts with
glutathione/glutathione reducatase, or, like NrdH, some
other reductant system.
Length = 74
Score = 27.0 bits (60), Expect = 1.2
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 14/62 (22%)
Query: 47 VEFYA-PWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTALAEQ----YGVRGYP 101
V+ Y PWC CK+ K L I ++D + +A E+ G RG P
Sbjct: 2 VKVYTTPWCPPCKKA-----KEYLT----SKGIAFEEIDVEKDSAAREEVLKVLGQRGVP 52
Query: 102 TL 103
+
Sbjct: 53 VI 54
>gnl|CDD|131785 TIGR02738, TrbB, type-F conjugative transfer system pilin
assembly thiol-disulfide isomerase TrbB. This protein
is part of a large group of proteins involved in
conjugative transfer of plasmid DNA, specifically the
F-type system. This protein has been predicted to
contain a thioredoxin fold, contains a conserved pair
of cysteines and has been shown to function as a thiol
disulfide isomerase by complementation of an Ecoli DsbA
defect. The protein is believed to be involved in pilin
assembly. The protein is closely related to TraF
(TIGR02739) which is somewhat longer, lacks the
cysteine motif and is apparently not functional as a
disulfide bond isomerase.
Length = 153
Score = 27.8 bits (62), Expect = 1.4
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 1 MRRLSLLFLLISPLVVFADDVTEEDGVLVLTQDNFQSSIEK--------HDHILVEFYAP 52
M R L+ LL+ + A + E + Q ++ D+ LV FY
Sbjct: 1 MLRKLLIVLLLLAGLAQASTLDEITNLWAPPQGLTAATDNAPQGRHANQDDYALVFFYQS 60
Query: 53 WCGHCKQLVP 62
C +C Q P
Sbjct: 61 TCPYCHQFAP 70
>gnl|CDD|215931 pfam00462, Glutaredoxin, Glutaredoxin.
Length = 60
Score = 26.3 bits (59), Expect = 1.7
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 14/64 (21%)
Query: 52 PWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHT----ALAEQYGVRGYPTLKFFK 107
P C CK+ K L D +K ++D + L E G P + F
Sbjct: 7 PTCPFCKRA-----KRLL----DSLGVKFEEIDVDEDPEIREELKELSGWPTVPQV-FID 56
Query: 108 KRSI 111
I
Sbjct: 57 GEHI 60
>gnl|CDD|239257 cd02959, ERp19, Endoplasmic reticulum protein 19 (ERp19) family;
ERp19 is also known as ERp18, a protein located in the
ER containing one redox active TRX domain. Denaturation
studies indicate that the reduced form is more stable
than the oxidized form, suggesting that the protein is
involved in disulfide bond formation. In vitro, ERp19
has been shown to possess thiol-disulfide oxidase
activity which is dependent on the presence of both
active site cysteines. Although described as protein
disulfide isomerase (PDI)-like, the protein does not
complement for PDI activity. ERp19 shows a wide tissue
distribution but is most abundant in liver, testis,
heart and kidney.
Length = 117
Score = 27.1 bits (60), Expect = 2.2
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 45 ILVEFYAPWCGHCKQLVPEY--SKAALQLATD 74
+++ + WCG CK L P++ SK +L+ +
Sbjct: 22 LMLLIHKTWCGACKALKPKFAESKEISELSHN 53
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 27.5 bits (61), Expect = 2.4
Identities = 24/132 (18%), Positives = 41/132 (31%), Gaps = 29/132 (21%)
Query: 12 SPLVVFADDVTEEDGVLVLTQ---DNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAA 68
SP ++ A T + L ++K L++F+A WC C + E K A
Sbjct: 23 SPKILDAGTATVPHTLSTLKTADNRPASVYLKKDKPTLIKFWASWCPLCLSELGETEKWA 82
Query: 69 ----------LQLATDGH----------------DIKLAKVDATQHTALAEQYGVRGYPT 102
+ +A+ G D V LA+ + YP+
Sbjct: 83 QDAKFSSANLITVASPGFLHEKKDGDFQKWYAGLDYPKLPVLTDNGGTLAQSLNISVYPS 142
Query: 103 LKFFKKRSIIEY 114
K ++
Sbjct: 143 WAIIGKDGDVQR 154
>gnl|CDD|132263 TIGR03219, salicylate_mono, salicylate 1-monooxygenase. Members of
this protein family are salicylate 1-monooxygenase, also
called salicylate hydroxylase. This enzyme converts
salicylate to catechol, which is a common intermediate
in the degradation of a number of aromatic compounds
(phenol, toluene, benzoate, etc.). The gene for this
protein may occur in catechol degradation genes, such as
those of the meta-cleavage pathway.
Length = 414
Score = 27.5 bits (61), Expect = 3.0
Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 36 QSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDATQHTA 90
QSS+ + D F H + + + K A Q+ ++++ D T++
Sbjct: 99 QSSVHRAD-----FLDALLKHLPEGIASFGKRATQIEEQAEEVQVLFTDGTEYRC 148
>gnl|CDD|150341 pfam09641, DUF2026, Protein of unknown function (DUF2026). This
protein of approx. 100 residues is found in bacteria. It
contains up to five alpha helices and up to seven beta
strands and is probably monomeric. Its function is
unknown. It is cited as a major prophage head protein,
so might generally be of viral origin.
Length = 204
Score = 27.1 bits (60), Expect = 3.1
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 24 EDGVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAA 68
ED LV +D F +E H +++F AP + PE A
Sbjct: 70 EDDQLVSAEDAFHMWVEADGH-VIDFMAP-------IFPEAFAAR 106
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion
helps coordinate the alcohol, followed by deprotonation
of a histidine (His-51), the ribose of NAD, a serine
(Ser-48), then the alcohol, which allows the transfer
of a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H) binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding.
Length = 365
Score = 27.4 bits (61), Expect = 3.2
Identities = 7/17 (41%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 43 DHILVEFYAPWCGHCKQ 59
D + + + P CG CKQ
Sbjct: 79 DKV-IPLFGPQCGKCKQ 94
>gnl|CDD|119372 cd06539, CIDE_N_A, CIDE_N domain of CIDE-A proteins. The CIDE_N
(cell death-inducing DFF45-like effector, N-terminal)
domain is found at the N-terminus of the CIDE (cell
death-inducing DFF45-like effector) proteins. These
proteins are associated with the chromatin condensation
and DNA fragmentation events of apoptosis; the CIDE_N
domain is thought to regulate the activity of the
CAD/DFF40, ICAD/DFF45, and CIDE nucleases during
apoptosis. The CIDE protein family includes 3 members:
CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence
similarity with DFF40 and DFF45, the CIDE proteins were
initially characterized as mitochondrial activators of
apoptosis. However, strong metabolic phenotypes of mice
lacking CIDE-A and CIDE-B indicated that this family
may play critical roles in energy balance.
Length = 78
Score = 25.7 bits (56), Expect = 4.4
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 14 LVVFADDVT---EEDGVLVLTQDNFQSSIEKHDHILV 47
LV+ + VT EEDG +V T++ FQ ++ + H +V
Sbjct: 34 LVITSGLVTLVLEEDGTVVDTEEFFQ-TLGDNTHFMV 69
>gnl|CDD|218651 pfam05600, DUF773, Protein of unknown function (DUF773). This
family contains several eukaryotic sequences which are
thought to be CDK5 activator-binding proteins, however,
the function of this family is unknown.
Length = 506
Score = 26.6 bits (59), Expect = 5.0
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 55 GHCKQLVPEYSKAALQLATDGHDIK-LAKVDATQHTALAEQYGVRG 99
C+QL E + D K A Q+ A +Q G++G
Sbjct: 134 AKCQQLQQELERKE-------EDCKRSAADSREQYYAACKQLGIKG 172
>gnl|CDD|239308 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 = 26.0 bits (58), Expect = 5.6
Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 5/30 (16%)
Query: 30 LTQDNFQSSIEKHDHILVEFYAPWCGHCKQ 59
LT + K L+ +A WC C++
Sbjct: 18 LTSADL-----KGKPYLLNVWASWCAPCRE 42
>gnl|CDD|129481 TIGR00385, dsbE, periplasmic protein thiol:disulfide
oxidoreductases, DsbE subfamily. Involved in the
biogenesis of c-type cytochromes as well as in
disulfide bond formation in some periplasmic proteins
[Protein fate, Protein folding and stabilization].
Length = 173
Score = 25.9 bits (57), Expect = 6.6
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 46 LVEFYAPWCGHCK---QLVPEYSKAAL 69
L+ +A WC C+ + E +K L
Sbjct: 67 LLNVWASWCPPCRAEHPYLNELAKQGL 93
>gnl|CDD|239305 cd03007, PDI_a_ERp29_N, PDIa family, endoplasmic reticulum protein
29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident
protein expressed in high levels in secretory cells. It
forms homodimers and higher oligomers in vitro and in
vivo. It contains a redox inactive TRX-like domain at
the N-terminus, which is homologous to the redox active
TRX (a) domains of PDI, and a C-terminal helical domain
similar to the C-terminal domain of P5. The expression
profile of ERp29 suggests a role in secretory protein
production distinct from that of PDI. It has also been
identified as a member of the thyroglobulin folding
complex. The Drosophila homolog, Wind, is the product of
windbeutel, an essential gene in the development of
dorsal-ventral patterning. Wind is required for correct
targeting of Pipe, a Golgi-resident type II
transmembrane protein with homology to
2-O-sulfotransferase.
Length = 116
Score = 25.6 bits (56), Expect = 7.8
Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 9/89 (10%)
Query: 26 GVLVLTQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHDIKLAKVDA 85
G + L F I K + LV+F + K +++ A A+ D+ +A+V
Sbjct: 2 GCVDLDTVTFYKVIPKFKYSLVKFDTAYPYGEKH--EAFTRLAESSASATDDLLVAEVGI 59
Query: 86 TQH-----TALAEQYGV--RGYPTLKFFK 107
+ L E+Y + YP + F
Sbjct: 60 KDYGEKLNMELGERYKLDKESYPVIYLFH 88
>gnl|CDD|171518 PRK12463, PRK12463, chorismate synthase; Reviewed.
Length = 390
Score = 26.2 bits (57), Expect = 8.0
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 31 TQDNFQSSIEKHDHILVEFYAPWCGHCKQLVPEYSKAALQLATDGHD-IKLAKVDATQHT 89
T++ FQ+SIE+ D V P G + V + A + G D ++L + + TQH
Sbjct: 329 TKEAFQASIERSDSCAV----PAAGVVAESVVAWELAHALVEQFGKDRMELIQQNITQHN 384
Query: 90 ALAEQY 95
A+++
Sbjct: 385 KYAKEF 390
>gnl|CDD|227598 COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn
finger [General function prediction only].
Length = 309
Score = 25.9 bits (57), Expect = 8.6
Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 4 LSLLFLLISPLVVFAD--DVTEEDGVL--VLTQDNFQSSIEKHDHILVEFYAPWCGHCKQ 59
+LF++I L F+ + + G L +T ++ +I + +C C
Sbjct: 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNI 117
Query: 60 LVPEYSK 66
P S
Sbjct: 118 YKPPRSH 124
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.408
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,077,134
Number of extensions: 611646
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 674
Number of HSP's successfully gapped: 97
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.6 bits)