RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3441
(100 letters)
>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 = 62.3 bits (152), Expect = 3e-14
Identities = 26/41 (63%), Positives = 30/41 (73%), Gaps = 2/41 (4%)
Query: 53 AVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
VVHL T + K LKKE VL+MFYAPWCG CK++KPEF
Sbjct: 1 DVVHL-TDEDFRKFLKKEK-HVLVMFYAPWCGHCKKMKPEF 39
>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 = 53.8 bits (130), Expect = 6e-11
Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 53 AVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
VV L T +K++ + + VL+ FYAPWCG CK L PE+
Sbjct: 1 NVVEL-TDSNFDKVVGDDKKDVLVEFYAPWCGHCKNLAPEY 40
>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 = 53.8 bits (130), Expect = 7e-11
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 53 AVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
VV L T +K + L+ FYAPWCG CK L PE+
Sbjct: 1 DVVEL-TDSNFDKKVLNSDDVWLVEFYAPWCGHCKNLAPEW 40
>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 = 53.4 bits (129), Expect = 9e-11
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 59 TPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
T ++L+K + VL+ FYAPWCG CK L PE+
Sbjct: 4 TDDNFDELVKDS-KDVLVEFYAPWCGHCKALAPEY 37
>gnl|CDD|239365 cd03067, PDI_b_PDIR_N, PDIb family, PDIR subfamily, N-terminal
TRX-like b domain; 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. The TRX-like b domain of PDIR is critical for
its chaperone activity.
Length = 112
Score = 52.1 bits (125), Expect = 3e-10
Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 1 MKVEVN---LPYVIKHYKDGEFNKNYERKETVSAFVNFLKDPK 40
+KV+ + P +KHYKDG+F+ Y R+ T + V FL+DP+
Sbjct: 70 LKVDPSSKPKPVELKHYKDGDFHTEYNRQLTFKSMVAFLRDPE 112
>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 = 52.0 bits (125), Expect = 4e-10
Identities = 19/40 (47%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 54 VVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
V L TP+ +K++ L+ FYAPWCG CK LKPE+
Sbjct: 2 VYEL-TPKNFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEY 40
>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 = 51.1 bits (123), Expect = 6e-10
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 54 VVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
VV + T + ++ + K +PVL+ FYAPWCG CK L PE+
Sbjct: 1 VVKVLTDENFDEEVAKSDKPVLVDFYAPWCGPCKALAPEY 40
>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 = 47.2 bits (113), Expect = 2e-08
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 64 NKLLKKETRPVLIMFYAPWCGFCKQLKP------EFLAGRDNL 100
++++ + VL+ FYAPWCG CK L P E L G DN+
Sbjct: 11 DEVVLDSDKDVLVEFYAPWCGHCKALAPIYEELAEKLKGDDNV 53
>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 = 45.7 bits (109), Expect = 9e-08
Identities = 14/24 (58%), Positives = 17/24 (70%)
Query: 70 ETRPVLIMFYAPWCGFCKQLKPEF 93
+ VL+ FYAPWCG CK L PE+
Sbjct: 12 SNKDVLVEFYAPWCGHCKNLAPEY 35
>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 = 43.4 bits (103), Expect = 6e-07
Identities = 17/40 (42%), Positives = 22/40 (55%)
Query: 54 VVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
V TP+ +L+ P L+ FYAPWCG C+ L PE
Sbjct: 2 SVITLTPEDFPELVLNRKEPWLVDFYAPWCGPCQALLPEL 41
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 45.1 bits (107), Expect = 7e-07
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 46 EEDESAQAVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
EE ++ V L T +K + E VL+ FYAPWCG CK+L PE+
Sbjct: 26 EEHFISEHVTVL-TDSTFDKFIT-ENEIVLVKFYAPWCGHCKRLAPEY 71
Score = 44.0 bits (104), Expect = 2e-06
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 14/77 (18%)
Query: 27 ETVSAFVNFLKDPKG----------DIPWEEDESAQAVVHLPTPQALNKLLKKETRPVLI 76
++V A + F KD + IP E+D + VV +++ K + VL+
Sbjct: 325 DSVEALIEFFKDVEAGKVEKSIKSEPIPEEQDGPVKVVVG----NTFEEIVFKSDKDVLL 380
Query: 77 MFYAPWCGFCKQLKPEF 93
YAPWCG CK L+P +
Sbjct: 381 EIYAPWCGHCKNLEPVY 397
>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 = 42.9 bits (102), Expect = 9e-07
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 67 LKKETRPVLIMFYAPWCGFCKQLKPEF 93
L K +PV++ F+APWCG CK + P
Sbjct: 6 LIKSAKPVVVDFWAPWCGPCKAIAPVL 32
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 74 VLIMFYAPWCGFCKQLKPEF 93
VL+ FYAPWCG CK L PE+
Sbjct: 21 VLVEFYAPWCGHCKSLAPEY 40
Score = 44.3 bits (105), Expect = 1e-06
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 11/73 (15%)
Query: 26 KETVSAFVNFLKDPKG-------DIPWEEDESAQAVVHLPTPQALNKLLKKETRPVLIMF 78
E + AFV D K IP +++ + +V + ++++ ET+ VL+ F
Sbjct: 316 SENLEAFVKDFLDGKLKPYLKSEPIPEDDEGPVKVLV----GKNFDEIVLDETKDVLVEF 371
Query: 79 YAPWCGFCKQLKP 91
YAPWCG CK L P
Sbjct: 372 YAPWCGHCKNLAP 384
>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 = 40.7 bits (96), Expect = 6e-06
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 59 TPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
T ++ + +PVL+ F+APWCG CK + P
Sbjct: 2 TDANFDETIASSDKPVLVDFWAPWCGPCKMIAPIL 36
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 40.5 bits (95), Expect = 1e-05
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 67 LKKETRPVLIMFYAPWCGFCKQLKPEFLA 95
K +PVL++F P C +CK+L E L
Sbjct: 1 AKGNGKPVLVVFTDPDCPYCKKLHKELLK 29
>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 = 40.1 bits (94), Expect = 1e-05
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 75 LIMFYAPWCGFCKQLKPEF 93
L+ FYAPWCG CK+L+P +
Sbjct: 19 LVDFYAPWCGHCKKLEPVW 37
>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 = 40.0 bits (94), Expect = 2e-05
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 73 PVLIMFYAPWCGFCKQLKP 91
+ F+APWCG CK+L P
Sbjct: 18 NHFVKFFAPWCGHCKRLAP 36
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 39.6 bits (93), Expect = 6e-05
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 59 TPQALNKLLKKETR--PVLIMFYAPWCGFCKQLKP 91
T + + + +R PVL+ F+APWCG CKQL P
Sbjct: 29 TEANFEQEVIQSSREVPVLVDFWAPWCGPCKQLTP 63
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 38.5 bits (90), Expect = 9e-05
Identities = 17/35 (48%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 59 TPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
T + L+KLL+ + PV+I F+APWCG C+ P F
Sbjct: 41 TGETLDKLLQDDL-PVVIDFWAPWCGPCRNFAPIF 74
>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 = 36.5 bits (85), Expect = 4e-04
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 70 ETRPVLIMFYAPWCGFCKQLKPE 92
+PVL+ F+A WC C+ P
Sbjct: 19 SGKPVLVYFWATWCPVCRFTSPT 41
>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 = 36.2 bits (84), Expect = 4e-04
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 75 LIMFYAPWCGFCKQLKPE 92
+I FYAPWC C+QL+PE
Sbjct: 20 MIEFYAPWCPACQQLQPE 37
Score = 25.0 bits (55), Expect = 5.0
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 7 LPYVIKHYKDGEFNKNYERKETVSAFVNFLKD 38
LP I H KDG F + Y+ ++F+++
Sbjct: 72 LP-TIYHAKDGVFRR-YQGPRDKEDLISFIEE 101
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 37.1 bits (86), Expect = 5e-04
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 22 NYERKETVSAFVNFLKDPKGDIPWEEDESAQAVVHLPTPQALNKLLKKETR--PVLIMFY 79
N + ++ +A N DI + +Q VV L + + LLK E R P L++ Y
Sbjct: 321 NIKEEDNGAANDN-GNAAVADI-FN----SQNVVAL-SRAGIENLLKLENRKEPWLVVLY 373
Query: 80 APWCGFCKQLKPEF 93
APWC FC+ ++ +
Sbjct: 374 APWCPFCQAMEASY 387
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 35.2 bits (81), Expect = 8e-04
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 55 VHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
VH+ T QA + + V++ FYA WCG CK++ P +
Sbjct: 2 VHIVTSQAEFESTLSQNELVIVDFYAEWCGPCKRIAPFY 40
>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 = 35.0 bits (81), Expect = 9e-04
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 62 ALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
AL+ + ++FYA WC F +P F
Sbjct: 9 ALDLMAFNREDYTAVLFYASWCPFSASFRPHF 40
>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 = 34.9 bits (81), Expect = 0.001
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 60 PQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEFLA 95
AL + L + +PV + F A WC CK + +
Sbjct: 1 EAALAQALA-QGKPVFVDFTADWCVTCKVNEKVVFS 35
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 36.1 bits (83), Expect = 0.001
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 49 ESAQAVVHLPTPQALNKLLKKETR----PVLIMFYAPWCGFCKQLKP 91
E A A+V L + KL + T P + FYAPWC C+++ P
Sbjct: 27 EDANALVLL-NDKNFEKLTQASTGATTGPWFVKFYAPWCSHCRKMAP 72
>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 = 34.8 bits (80), Expect = 0.001
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 62 ALNKLLKKETRPVLIMFYAPWCGFCKQLKP 91
AL KL + R +L+++ +P CG C+ LKP
Sbjct: 4 ALRKLYHESDRLILVLYTSPTCGPCRTLKP 33
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 34.9 bits (79), Expect = 0.002
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 65 KLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
L + + +PVL+ F+APWC C+ P
Sbjct: 26 SLSELKGKPVLVDFWAPWCPPCRAEAPLL 54
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 35.0 bits (81), Expect = 0.003
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 35 FLKDPKGDIPWEEDESAQAVVH------LPTPQALNKLLKKET-RPVLIMFYAPWCGFCK 87
P + E+AQ+V H + L++ L + +PV++ FYA WC CK
Sbjct: 431 VGVQPLQAKAFLNPEAAQSVSHGEFWQPISPLAELDQALAEAKAKPVMLDFYADWCVTCK 490
Query: 88 QLKP 91
+ +
Sbjct: 491 ENEK 494
>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 = 35.0 bits (80), Expect = 0.003
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 61 QALNKLLKKETR--PVLIMFYAPWCGFCKQLKPEFL 94
+ LLK E R L++ YAPWC FC+ ++ +L
Sbjct: 359 PGIENLLKLEERKEAWLVVLYAPWCPFCQAMEASYL 394
>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 = 32.6 bits (75), Expect = 0.005
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 60 PQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEFLA 95
+AL K ++E +P+L+ F A WC C+ L +FL+
Sbjct: 7 DEALAKA-REEGKPLLVDFGADWCPTCQALDRDFLS 41
>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 = 33.2 bits (76), Expect = 0.006
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 61 QALNKLLKKETR--PVLIMFYAPWCGFCKQLKPEF 93
+ L K E R L++ YAPWC FC+ ++ +
Sbjct: 9 AEIEALAKGERRNQSTLVVLYAPWCPFCQAMEASY 43
>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 = 32.6 bits (75), Expect = 0.007
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 59 TPQALNKLLK-KETRPVLIMFYAPWCGFCKQLK 90
+ + +LLK ++ +++ F+APW CKQ+
Sbjct: 1 SEEEFEELLKSDASKLLVLHFWAPWAEPCKQMN 33
>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 = 31.9 bits (72), Expect = 0.008
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 75 LIMFYAPWCGFCKQLKPEF 93
L++FYAPWC FC+ L+P
Sbjct: 1 LVLFYAPWCPFCQALRPVL 19
>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 = 33.1 bits (76), Expect = 0.011
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 6/68 (8%)
Query: 38 DPKGDIPWEEDESAQAVVH-----LPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPE 92
D KG + + LP A+ K + V+ +F P C +C++L+ E
Sbjct: 40 DAKGRKDDLTEARLAQLNAIDLSALPLDDAI-VYGKGNGKRVVYVFTDPDCPYCRKLEKE 98
Query: 93 FLAGRDNL 100
D +
Sbjct: 99 LKPNADGV 106
>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 = 31.9 bits (73), Expect = 0.015
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 64 NKLLKKETRPVLIMFYAPWCGFCKQLKP 91
L + PV++ F+AP K+L P
Sbjct: 5 QVLQESTQVPVVVDFWAPRSPPSKELLP 32
>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 = 32.1 bits (73), Expect = 0.016
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 65 KLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
K K +P++++ + WCG CK LKP+F
Sbjct: 13 KEAKDSGKPLMLLIHKTWCGACKALKPKF 41
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 32.1 bits (74), Expect = 0.026
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 13/64 (20%)
Query: 39 PKGDIPWEEDESAQAVVH------LPTPQALNKLL---KKETRPVLIMFYAPWCGFCKQL 89
P D + + + T L++ L K + +PV++ YA WC CK
Sbjct: 433 PLQDWAFGGAAAGAQTQAHLNFQRIKTVAELDQALAEAKGKGKPVMLDLYADWCVACK-- 490
Query: 90 KPEF 93
EF
Sbjct: 491 --EF 492
>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 = 31.5 bits (72), Expect = 0.031
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 72 RPVLIMFYAPWCGFCKQLKPE 92
+P L+ FYA WC C+++ P+
Sbjct: 21 KPTLVEFYADWCTVCQEMAPD 41
>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 = 30.9 bits (70), Expect = 0.042
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 64 NKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
+ L+ + L+M+YAPW + + EF
Sbjct: 22 AEELRTDAEVSLVMYYAPWDAQSQAARQEF 51
>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 = 30.7 bits (70), Expect = 0.046
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 53 AVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEF 93
V+ L + N L L+ FYA WCG C+ P +
Sbjct: 2 PVIVL-DAASFNSALLGSPSAWLVEFYASWCGHCRAFAPTW 41
>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 = 30.4 bits (69), Expect = 0.065
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 71 TRPVLIMFYAPWCGFCKQLKPEF 93
VL+ FYA WC F + L P F
Sbjct: 18 AELVLVNFYADWCRFSQMLHPIF 40
>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 = 30.3 bits (69), Expect = 0.071
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 72 RPVLIMFYAPWCGFCKQ 88
+ VL+ F+A WC C+
Sbjct: 20 KVVLVNFWASWCPPCRA 36
>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 = 30.0 bits (68), Expect = 0.072
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 72 RPVLIMFYAPWCGFCKQLKPE 92
+ VL+ F+A WC C+ PE
Sbjct: 2 KVVLLYFWASWCPPCRAFTPE 22
>gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein
MauD. This protein, MauD, appears critical to proper
formation of the small subunit of methylamine
dehydrogenase, which has both an unusual tryptophan
tryptophylquinone cofactor and multiple disulfide
bonds. MauD shares sequence similarity, including a
CPxC motif, with a number of thiol:disulfide
interchange proteins. In MauD mutants, the small
subunit apparently does not form properly and is
rapidly degraded [Protein fate, Protein folding and
stabilization, Energy metabolism, Amino acids and
amines].
Length = 189
Score = 30.2 bits (68), Expect = 0.11
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 72 RPVLIMFYAPWCGFCKQLKP 91
RP L+MF AP C C +L P
Sbjct: 75 RPTLLMFTAPSCPVCDKLFP 94
>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 = 29.3 bits (66), Expect = 0.15
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 71 TRPVLIMFYAPWCGFCKQLKPEF 93
+P LI + WC C ++P +
Sbjct: 24 KKPYLIKITSDWCFSCIHIEPVW 46
>gnl|CDD|220479 pfam09936, Methyltrn_RNA_4, SAM-dependent RNA methyltransferase.
This family has a Rossmanoid fold, with a deep trefoil
knot in its C-terminal region. It has structural
similarity to RNA methyltransferases, and is likely to
function as an S-adenosyl-L-methionine (SAM)-dependent
RNA 2'-O methyltransferase.
Length = 185
Score = 29.5 bits (67), Expect = 0.19
Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 14/81 (17%)
Query: 10 VIKHYKDG---EFNKNYERKETVSAF--VNFLKDPKGDIPWEEDE-------SAQAVVHL 57
++ H+++G E+N + RKE +S V+ L++ DI + SA+ +
Sbjct: 61 ILAHWQEGYGGEYNPD--RKEALSLVKVVSSLEEAIEDIEKRTGQRPLIVATSARKRPNT 118
Query: 58 PTPQALNKLLKKETRPVLIMF 78
+ + L K++++ +PVL++F
Sbjct: 119 ISYEELRKMIQEREKPVLLLF 139
>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 = 28.9 bits (65), Expect = 0.19
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 72 RPVLIMFYAPWCGFCKQLKP 91
RP L+ F +P C CK+L P
Sbjct: 22 RPTLLFFLSPTCPVCKKLLP 41
>gnl|CDD|239268 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family;
hypothetical proteins that show sequence similarity to
PRXs. Members of this group contain a CXXC motif,
similar to TRX. The second cysteine in the motif
corresponds to the peroxidatic cysteine of PRX,
however, these proteins do not contain the other two
residues of the catalytic triad of PRX. PRXs confer a
protective antioxidant role in cells through their
peroxidase activity in which hydrogen peroxide,
peroxynitrate, and organic hydroperoxides are reduced
and detoxified using reducing equivalents derived from
either thioredoxin, glutathione, trypanothione and
AhpF. TRXs alter the redox state of target proteins by
catalyzing the reduction of their disulfide bonds via
the CXXC motif using reducing equivalents derived from
either NADPH or ferredoxins.
Length = 149
Score = 29.2 bits (66), Expect = 0.20
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 70 ETRPVLIMFY-APWCGFC-------KQLKPEFLA 95
PV+++FY C FC +L PE A
Sbjct: 22 GEGPVVVVFYRGFGCPFCREYLRALSKLLPELDA 55
>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 = 29.0 bits (65), Expect = 0.29
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 14/75 (18%)
Query: 28 TVSAFVNFLKDPKGDIPWEEDESAQAVVHLPTP-----------QALNKLLKKETRPVLI 76
+ ++ +GD P A++ P P Q + + +PVL+
Sbjct: 12 AAALLWQLARNAEGDDP---KALPSALIGKPVPAFRLASLDEPGQFYTADVLTQGKPVLL 68
Query: 77 MFYAPWCGFCKQLKP 91
+A WC C+ P
Sbjct: 69 NVWASWCPPCRAEHP 83
>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 = 28.7 bits (65), Expect = 0.31
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 57 LPTPQALNKLLKKET---RPVLIMFYAPWCGFCKQLKPEFLA 95
LP +K L +P L+ +A WC C++ P +A
Sbjct: 8 LPALPGPDKTLTSADLKGKPYLLNVWASWCAPCREEHPVLMA 49
>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 = 28.3 bits (64), Expect = 0.39
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 74 VLIMFYAPWCGFCKQLKPE 92
++ F+ CG+CK+L PE
Sbjct: 8 TIVEFFDYNCGYCKKLAPE 26
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 28.1 bits (62), Expect = 0.40
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 51 AQAVVHLPTPQALNKLLKKETRPVLIMFYAPWCGFCKQLKP 91
+ ++HL T + + + K +L+ F+A WCG CK + P
Sbjct: 2 SDKIIHL-TDDSFDTDVLKADGAILVDFWAEWCGPCKMIAP 41
>gnl|CDD|131255 TIGR02200, GlrX_actino, Glutaredoxin-like protein. This family
of glutaredoxin-like proteins is limited to the
Actinobacteria and contains the conserved CxxC motif.
Length = 77
Score = 27.5 bits (61), Expect = 0.46
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 77 MFYAPWCGFCKQLK 90
++ WCG+C QL
Sbjct: 4 VYGTTWCGYCAQLM 17
>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 = 28.0 bits (63), Expect = 0.46
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 71 TRPVLIMFYAPWCGFCKQLKPEFL 94
+P+L++F P C +C +LK ++L
Sbjct: 14 KKPLLLLFSQPGCPYCDKLKRDYL 37
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 27.9 bits (62), Expect = 0.63
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 64 NKLLKKETRPVLIMFYAPWCGFCKQLKPE 92
NK + + +L+MF + C +C++ K +
Sbjct: 35 NKSISPNDKYLLLMFESNGCSYCERFKKD 63
>gnl|CDD|165324 PHA03026, PHA03026, hypothetical protein; Provisional.
Length = 421
Score = 28.0 bits (62), Expect = 0.79
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 6 NLPYVIKHYKDGEFNKNYERKETVSAFVNFLKDP--------KGDIPWEEDE 49
N+ ++ KD +K + K+ F+NFLKDP DI DE
Sbjct: 247 NMINALEGIKDNC-DKLCD-KDEAKEFINFLKDPHTQKIICDNADIDLPFDE 296
>gnl|CDD|182640 PRK10676, PRK10676, DNA-binding transcriptional regulator ModE;
Provisional.
Length = 263
Score = 27.7 bits (62), Expect = 0.93
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 59 TPQALNKLLKKETRPVLIMFYAPWCGFCKQLKPEFLAGRDN 99
T Q+ +L E + VL++ APW G + P DN
Sbjct: 162 TAQSAERLGLDEGKEVLVLIKAPWVGITQD--PAVAQAADN 200
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 27.3 bits (60), Expect = 1.4
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 34 NFLKDPKGDIPWEEDESAQAVVHLPTPQALNKLLKKETR 72
NF K+ GDIP E++ + P Q + +++K +R
Sbjct: 1466 NFAKEIVGDIPTEKNAHELNLTDTPNAQKVQRIIKNLSR 1504
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of a
conjugation cascade to attach Ub or Ubls, covalently to
substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 26.5 bits (59), Expect = 2.9
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 14/59 (23%)
Query: 7 LPYVIKHYK---------DGEFNKNYERKETVSAFVNFLKDPKGDIPWEE--DESAQAV 54
PY++ K +G+ Y+ K+ V L D EE +E+ +AV
Sbjct: 202 TPYIVILIKYLEKWRSAHNGQLPSTYKEKKEFRDLVRSLMRSNED---EENFEEAIKAV 257
>gnl|CDD|222610 pfam14228, MOR2-PAG1_mid, Cell morphogenesis central region. This
family is the conserved central region of proteins that
are involved in cell morphogenesis.
Length = 1120
Score = 26.1 bits (57), Expect = 4.3
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 5 VNLPYVI--KHYKDGEF-NKNYERKETVSAFVNFLKDPKGDIPWEEDESAQAVVHLPTPQ 61
VNL Y + +H + E + + E K+ V + + +++ +G + WE ++ LP+
Sbjct: 982 VNLLYSLAGRHLELYEVEHSDSENKQQVVSLIKYVQSKRGSMMWENEDPTLVRTELPSAA 1041
Query: 62 ALNKLLK 68
L+ L++
Sbjct: 1042 LLSALVQ 1048
>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 = 24.9 bits (55), Expect = 4.7
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 75 LIMFYAPWCGFCKQLKPEFLA 95
+ ++ P C +CK K FL
Sbjct: 2 VTVYTKPDCPYCKATK-RFLD 21
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine
sulfoxide reductase A/B protein; Provisional.
Length = 521
Score = 25.6 bits (56), Expect = 5.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 69 KETRPVLIMFYAPWCGFC 86
K+ +P LI F+A WC C
Sbjct: 54 KKDKPTLIKFWASWCPLC 71
>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 = 25.1 bits (55), Expect = 5.7
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 75 LIMFYAPWCGFCKQLKPEFLA 95
++ F+ P C +C +PE
Sbjct: 1 IVEFFDPLCPYCYLFEPELEK 21
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for
correct cell division in bacteria. It has ATP-dependent
zinc metalloprotease activity. It was formerly
designated cell division protein FtsH [Cellular
processes, Cell division, Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 495
Score = 25.3 bits (56), Expect = 6.6
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)
Query: 24 ERKETVSAFVNFLKDPK------GDIP 44
E KE + V+FLK+P IP
Sbjct: 62 EAKEELMEIVDFLKNPSKFTKLGAKIP 88
>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 = 25.1 bits (55), Expect = 7.3
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 76 IMFYAPWCGFCKQLKPEFLAGRDNL 100
I + P CG CKQ L R NL
Sbjct: 82 IPLFGPQCGKCKQC----LNPRPNL 102
>gnl|CDD|217663 pfam03659, Glyco_hydro_71, Glycosyl hydrolase family 71. Family of
alpha-1,3-glucanases.
Length = 386
Score = 25.3 bits (56), Expect = 7.7
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 7 LPYVIKHYKDGEFNKNYERKETVSA 31
LPY I YK G+ + +E +
Sbjct: 262 LPYYIDAYKAGKTSDATITEEKLVY 286
>gnl|CDD|223014 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 24.9 bits (55), Expect = 8.4
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 28 TVSAFVNFLKDPKG 41
VS ++FLK+P G
Sbjct: 692 IVSGVISFLKNPFG 705
>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 = 24.4 bits (53), Expect = 8.6
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 75 LIMFYAPWCGFCKQLKP 91
+ FY+P C C L P
Sbjct: 22 FVNFYSPRCSHCHDLAP 38
>gnl|CDD|216002 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase
(AhpC) and thiol specific antioxidant (TSA).
Length = 124
Score = 24.5 bits (54), Expect = 9.5
Identities = 5/23 (21%), Positives = 9/23 (39%), Gaps = 1/23 (4%)
Query: 72 RPVLIMFYAP-WCGFCKQLKPEF 93
+ V++ FY + C P
Sbjct: 26 KWVVLFFYPKDFTPVCTTELPAL 48
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 25.0 bits (55), Expect = 9.7
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 55 VHLPTPQALNKLLK 68
VH+ T +A N LLK
Sbjct: 126 VHMLTKEAFNALLK 139
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
0.319 0.138 0.431
Gapped
Lambda K H
0.267 0.0561 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,170,149
Number of extensions: 422022
Number of successful extensions: 529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 88
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
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 (21.7 bits)
S2: 53 (24.6 bits)