RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5679
(149 letters)
>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 = 90.3 bits (225), Expect = 1e-24
Identities = 31/93 (33%), Positives = 58/93 (62%), Gaps = 1/93 (1%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREF 110
++F++ I+ PV+ F+ P CG CK + P + ++E V+FVK++V+ E+A E+
Sbjct: 1 EEFEELIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDE-NPELAEEY 59
Query: 111 EVQAVPTVIGFRNGDPVDTVVGNADQDVIQTLV 143
V+++PT + F+NG VD VVG ++ ++ +
Sbjct: 60 GVRSIPTFLFFKNGKEVDRVVGADPKEELEEFL 92
>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 = 71.9 bits (177), Expect = 3e-17
Identities = 35/99 (35%), Positives = 59/99 (59%), Gaps = 5/99 (5%)
Query: 51 DDFKQTI-RGRNPVLAYFFKPSCGFCKQLEPKISTVS-ETTSGVEFVKINV-ENGGGEIA 107
+F +TI PVL F+ P CG CK + P + ++ E V+FVK+NV EN +IA
Sbjct: 4 ANFDETIASSDKPVLVDFWAPWCGPCKMIAPILEELAKEYEGKVKFVKLNVDENP--DIA 61
Query: 108 REFEVQAVPTVIGFRNGDPVDTVVGNADQDVIQTLVSKL 146
++ ++++PT++ F+NG VD VG + ++ L++K
Sbjct: 62 AKYGIRSIPTLLLFKNGKEVDRSVGALPKAALKQLINKN 100
>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 = 67.6 bits (166), Expect = 1e-15
Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINV-ENGGGEIAREFEVQAVPTVI 119
PVL F+ P CG CK L P+ +++ V+F K++ EN ++A E+ V+ PT+
Sbjct: 20 PVLVDFYAPWCGPCKALAPEYEKLAQEYKDDVKFAKVDADENP--DLASEYGVRGFPTIK 77
Query: 120 GFRNGDPVDTVVGNADQDVIQTLVSKL 146
F+NG V VG +D + + K
Sbjct: 78 FFKNGKKVSDYVGARTKDDLVAFIKKH 104
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 66.6 bits (163), Expect = 8e-14
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINVENGGGEIAREFEVQAVPTVIG 120
PVL F+ P CG CKQL P + ++ G + K+N + +A +F VQ++PTV
Sbjct: 45 PVLVDFWAPWCGPCKQLTPTLEKLAAEYKGKFKLAKVNCDAEPM-VAAQFGVQSIPTVYA 103
Query: 121 FRNGDPVDTVVGNADQDVIQTLVSKLSQK 149
F++G PVD G + ++ + K+
Sbjct: 104 FKDGQPVDGFQGAQPESQLRQFLDKVLPA 132
>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 = 62.2 bits (152), Expect = 1e-13
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEP---KISTVSETTSGVEFVKINVENGGGEIA 107
D+F + ++ VL F+ P CG CK L P K++ + V K++ ++
Sbjct: 6 DNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTA-NNDLC 64
Query: 108 REFEVQAVPTVIGFRNGD 125
E+ V+ PT+ F NG
Sbjct: 65 SEYGVRGYPTIKLFPNGS 82
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 60.7 bits (147), Expect = 6e-13
Identities = 27/90 (30%), Positives = 50/90 (55%), Gaps = 1/90 (1%)
Query: 52 DFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREFE 111
+F+ T+ V+ F+ CG CK++ P S+ + + FVK++V+ E+A +
Sbjct: 10 EFESTLSQNELVIVDFYAEWCGPCKRIAPFYEECSKEYTKMVFVKVDVDE-LSEVAEKEN 68
Query: 112 VQAVPTVIGFRNGDPVDTVVGNADQDVIQT 141
+ ++PT F+NG VDT++G D+ + Q
Sbjct: 69 ITSMPTFKVFKNGSVVDTLLGANDEALKQL 98
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 56.1 bits (134), Expect = 6e-11
Identities = 29/100 (29%), Positives = 49/100 (49%), Gaps = 3/100 (3%)
Query: 36 LIQAVQMAYLIIEKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEF 94
L + A + PVL F+ P C C+ P + ++E G VE
Sbjct: 8 LGELATAASFEELDGAPLSLSELKGKPVLVDFWAPWCPPCRAEAPLLEELAEEYGGDVEV 67
Query: 95 VKINVENGGGEIAREFE--VQAVPTVIGFRNGDPVDTVVG 132
V +NV++ ++A EF V+++PT++ F++G VD +VG
Sbjct: 68 VAVNVDDENPDLAAEFGVAVRSIPTLLLFKDGKEVDRLVG 107
>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 = 54.6 bits (132), Expect = 1e-10
Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 51 DDFKQTI--RGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINVENGGGEIA 107
+F+Q + + PV+ F+ P K+L P + ++E G K+N + +IA
Sbjct: 1 QNFQQVLQESTQVPVVVDFWAPRSPPSKELLPLLERLAEEYQGQFVLAKVNCDAQP-QIA 59
Query: 108 REFEVQAVPTVIGFRNGDPVDTVVGNADQDVIQTLVS 144
++F VQA+PTV F G PVD G ++ ++ ++
Sbjct: 60 QQFGVQALPTVYLFAAGQPVDGFQGAQPEEQLRQMLD 96
>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 = 52.7 bits (127), Expect = 6e-10
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 7/83 (8%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEP---KISTVSETTSGVEFVKINV-ENGGGEI 106
+F + + VL F+ P CG CK L P K++ + + K++ ++
Sbjct: 4 SNFDEIVLSNKDVLVEFYAPWCGHCKNLAPEYEKLAKELKKDPDIVLAKVDATAE--KDL 61
Query: 107 AREFEVQAVPTVIGFRNGD-PVD 128
A F V PT+ F G PVD
Sbjct: 62 ASRFGVSGFPTIKFFPKGKKPVD 84
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 55.1 bits (133), Expect = 9e-10
Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 6/101 (5%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKIS----TVSETTSGVEFVKINVENGGGEI 106
F + I VL F+ P CG CK+L P+ + E S + ++ E+
Sbjct: 40 STFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASVDAT-EEMEL 98
Query: 107 AREFEVQAVPTVIGFRNGDPVDTVVGNADQDVIQTLVSKLS 147
A+EF V+ PT+ F G+PV+ G D I + + KL+
Sbjct: 99 AQEFGVRGYPTIKFFNKGNPVN-YSGGRTADGIVSWIKKLT 138
Score = 31.3 bits (71), Expect = 0.15
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENG-GGEIA-REFEVQAVPTVI 119
VL + P CG CK LEP + + E + + + NG E EF A PT++
Sbjct: 377 DVLLEIYAPWCGHCKNLEPVYNELGEKYKDNDSIIVAKMNGTANETPLEEFSWSAFPTIL 436
Query: 120 GFRNG 124
+ G
Sbjct: 437 FVKAG 441
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 52.4 bits (126), Expect = 2e-09
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINVENGGGEIARE 109
+ + ++ PV+ F+ P CG C+ P V+ SG V FVK+N E E++
Sbjct: 43 ETLDKLLQDDLPVVIDFWAPWCGPCRNFAPIFEDVAAERSGKVRFVKVNTE-AERELSAR 101
Query: 110 FEVQAVPTVIGFRNGDPVDTVVG 132
F ++++PT++ F+NG VD + G
Sbjct: 102 FRIRSIPTIMIFKNGQVVDMLNG 124
>gnl|CDD|239255 cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd and
Phd-like proteins (PhLP), characterized as cytosolic
regulators of G protein functions. Phd and PhLPs
specifically bind G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane and impeding G
protein-mediated signal transduction by inhibiting the
formation of a functional G protein trimer (G protein
alphabetagamma). Phd also inhibits the GTPase activity
of G protein alpha. Phd can be phosphorylated by protein
kinase A and G protein-coupled receptor kinase 2,
leading to its inactivation. Phd was originally isolated
from the retina, where it is highly expressed and has
been implicated to play an important role in light
adaptation. It is also found in the pineal gland, liver,
spleen, striated muscle and the brain. The C-terminal
domain of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain. Also
included in this family is a PhLP characterized as a
viral inhibitor of apoptosis (IAP)-associated factor,
named VIAF, that functions in caspase activation during
apoptosis.
Length = 113
Score = 51.0 bits (123), Expect = 3e-09
Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 63 VLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQAVPTVIGFR 122
V+ +F++P CK L+ + ++ +FVKIN E + +++ +PT++ ++
Sbjct: 27 VVVHFYEPGFPRCKILDSHLEELAAKYPETKFVKINAEKAF--LVNYLDIKVLPTLLVYK 84
Query: 123 NGDPVDTVVG 132
NG+ +D +VG
Sbjct: 85 NGELIDNIVG 94
>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 = 49.9 bits (120), Expect = 7e-09
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 51 DDFKQTIRG-RNPVLAYFFKPSCGFCKQLEP---KISTVSETTSGVEFVKINVENGGGEI 106
+F + + + VL F+ P CG CK L P K++ V V K++ + ++
Sbjct: 8 SNFDKVVGDDKKDVLVEFYAPWCGHCKNLAPEYEKLAAVFANEDDVVIAKVDADEANKDL 67
Query: 107 AREFEVQAVPTVIGFRNG--DPVD 128
A+++ V PT+ F G +PV
Sbjct: 68 AKKYGVSGFPTLKFFPKGSTEPVK 91
>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 = 52.0 bits (125), Expect = 1e-08
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 7/84 (8%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKIS----TVSETTSGVEFVKIN-VENGGGE 105
D+F I+ VL F+ P CG CK L P+ + + ++ K++ E +
Sbjct: 9 DNFDDFIKSHEFVLVEFYAPWCGHCKSLAPEYEKAADELKKKGPPIKLAKVDATEE--KD 66
Query: 106 IAREFEVQAVPTVIGFRNGDPVDT 129
+A+++ V PT+ FRNG+ +
Sbjct: 67 LAQKYGVSGYPTLKIFRNGEDSVS 90
Score = 37.3 bits (87), Expect = 0.001
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 9/81 (11%)
Query: 63 VLAYFFKPSCGFCKQLEPKI----STVSETTSGVEFVKIN-VENGGGEIAREFEVQAVPT 117
VL F+ P CG CK L P + S V K++ N FEV+ PT
Sbjct: 367 VLVEFYAPWCGHCKNLAPIYEELAEKYKDAESDVVIAKMDATAND----VPPFEVEGFPT 422
Query: 118 VIGFRNGDPVDTVVGNADQDV 138
+ G + V + D+ +
Sbjct: 423 IKFVPAGKKSEPVPYDGDRTL 443
>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 = 48.0 bits (115), Expect = 3e-08
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVS-ETTSGVEFVKINVENGGGEIAREFEVQAVPTVIG 120
++ +F+ P CKQ+ ++ E V F+ I E EI+ +FE+ AVPT +
Sbjct: 16 LLVLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAE-ELPEISEKFEITAVPTFVF 74
Query: 121 FRNGDPVDTVVG 132
FRNG VD V G
Sbjct: 75 FRNGTIVDRVSG 86
>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 = 47.3 bits (113), Expect = 7e-08
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 5/94 (5%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEP---KISTVSETTSGVEFVKINVENGGGE-I 106
+DF++ ++ VL F+ P CG CK+++P K +T + ++ + +
Sbjct: 8 EDFRKFLKKEKHVLVMFYAPWCGHCKKMKPEFTKAATELKEDGKGVLAAVDCTKPEHDAL 67
Query: 107 AREFEVQAVPTVIGFRNGDPVDTV-VGNADQDVI 139
E+ V+ PT F NG V+ +D+I
Sbjct: 68 KEEYNVKGFPTFKYFENGKFVEKYEGERTAEDII 101
>gnl|CDD|239287 cd02989, Phd_like_TxnDC9, Phosducin (Phd)-like family, Thioredoxin
(TRX) domain containing protein 9 (TxnDC9) subfamily;
composed of predominantly uncharacterized eukaryotic
proteins, containing a TRX-like domain without the redox
active CXXC motif. The gene name for the human protein
is TxnDC9. The two characterized members are described
as Phd-like proteins, PLP1 of Saccharomyces cerevisiae
and PhLP3 of Dictyostelium discoideum. Gene disruption
experiments show that both PLP1 and PhLP3 are
non-essential proteins. Unlike Phd and most Phd-like
proteins, members of this group do not contain the Phd
N-terminal helical domain which is implicated in binding
to the G protein betagamma subunit.
Length = 113
Score = 47.6 bits (114), Expect = 7e-08
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 1/89 (1%)
Query: 44 YLIIEKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGG 103
Y + +F + ++ V+ +F+ P CK ++ + +++ +F+K+N E
Sbjct: 6 YREVSDEKEFFEIVKSSERVVCHFYHPEFFRCKIMDKHLEILAKKHLETKFIKVNAEK-A 64
Query: 104 GEIAREFEVQAVPTVIGFRNGDPVDTVVG 132
+ + ++ +PTVI F+NG VD +VG
Sbjct: 65 PFLVEKLNIKVLPTVILFKNGKTVDRIVG 93
>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 = 46.2 bits (109), Expect = 1e-07
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 64 LAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGG--EIAREFEVQAVPTVIGF 121
L F+ P C FC+ L P ++ ++ GV+F ++V+ + + + V VPT++ F
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVF 60
Query: 122 RNGDPV 127
G V
Sbjct: 61 GPGIGV 66
>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 = 47.3 bits (113), Expect = 1e-07
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 23/92 (25%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSE--------TTSG-----VEFVK--------INVE 100
PVL YF+ C C+ P ++ ++ SG F++ IN
Sbjct: 22 PVLVYFWATWCPVCRFTSPTVNQLAADYPVVSVALRSGDDGAVARFMQKKGYGFPVINDP 81
Query: 101 NGGGEIAREFEVQAVPTVIGFRNGDPVDTVVG 132
+ G I+ + V P ++ G V G
Sbjct: 82 D--GVISARWGVSVTPAIVIVDPGGIVFVTTG 111
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 46.6 bits (111), Expect = 1e-07
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 17/88 (19%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTS----GVEFVKINVEN------------GGGE 105
PVL F P C +CK+L ++ + + +NV++ E
Sbjct: 7 PVLVVFTDPDCPYCKKLHKELLKDPDVQEYLKDNFVVIYVNVDDSKEVTDFDGETLSEKE 66
Query: 106 IAREFEVQAVPTVIGF-RNGDPVDTVVG 132
+AR++ V+ PT++ +G V + G
Sbjct: 67 LARKYGVRGTPTIVFLDGDGKEVARLPG 94
>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 = 46.0 bits (110), Expect = 2e-07
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 63 VLAYFFKPSCGFCKQLEPKISTVSETTSGVE---FVKINVENGGGEIAREFEVQAVPTVI 119
VL F+ P CG CK L P ++E G + K++ ++ EF V PT++
Sbjct: 21 VLVEFYAPWCGHCKALAPIYEELAEKLKGDDNVVIAKMDATA--NDVPSEFVVDGFPTIL 78
Query: 120 GFRNGDPVDTVVGNADQDV 138
F GD + + D+ +
Sbjct: 79 FFPAGDKSNPIKYEGDRTL 97
>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 = 43.9 bits (104), Expect = 1e-06
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 52 DFKQTIRGRNPV-LAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINVENGGG-EIAR 108
+F + + N L F+ P CG CK L+P+ + ++ G V+ ++ + +
Sbjct: 9 NFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEYAKAAKELDGLVQVAAVDCDEDKNKPLCG 68
Query: 109 EFEVQAVPTVIGFRNGDPV 127
++ VQ PT+ FR
Sbjct: 69 KYGVQGFPTLKVFRPPKKA 87
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTV-SETTSGVEFVKINVENGGGEIAREFEVQAVPTVIG 120
+L + P+CG C+ L+P ++ V E V FV+I+++ EIA + PTV
Sbjct: 15 LILVLYTSPTCGPCRTLKPILNKVIDEFDGAVHFVEIDIDE-DQEIAEAAGIMGTPTVQF 73
Query: 121 FRNGDPVDTVVG 132
F++ + V + G
Sbjct: 74 FKDKELVKEISG 85
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 42.4 bits (99), Expect = 6e-06
Identities = 26/94 (27%), Positives = 49/94 (52%), Gaps = 4/94 (4%)
Query: 42 MAYLIIEKIDDFKQT--IRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKIN 98
M+ II DD T ++ +L F+ CG CK + P + +++ G + K+N
Sbjct: 1 MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLN 60
Query: 99 VENGGGEIAREFEVQAVPTVIGFRNGDPVDTVVG 132
++ G A ++ ++ +PT++ F+NG+ T VG
Sbjct: 61 IDQNPG-TAPKYGIRGIPTLLLFKNGEVAATKVG 93
>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 = 40.5 bits (95), Expect = 3e-05
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 47 IEKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTV----SETTSGVEFVKINVENG 102
+ +DD + +R + L F+ P CG CK+LEP + V + S V K++
Sbjct: 2 VLDLDDSFKDVRKEDIWLVDFYAPWCGHCKKLEPVWNEVGAELKSSGSPVRVGKLDATAY 61
Query: 103 GGEIAREFEVQAVPTVIGFRNG 124
IA EF V+ PT+ +
Sbjct: 62 SS-IASEFGVRGYPTIKLLKGD 82
>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 = 39.2 bits (92), Expect = 8e-05
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 10/99 (10%)
Query: 51 DDFKQTIRGRNPVLAYFFKPSCGFCKQLEP---KISTVSETT-SGVEFVKIN--VENGGG 104
D+F I N FF P CG CK+L P +++ V+ K++
Sbjct: 8 DNFDHHIAEGN-HFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAKVDCTQHR--- 63
Query: 105 EIAREFEVQAVPTVIGFRNGDPVDTVVGNADQDVIQTLV 143
E+ EF+V+ PT++ F++G+ VD G D D ++ V
Sbjct: 64 ELCSEFQVRGYPTLLLFKDGEKVDKYKGTRDLDSLKEFV 102
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 51 DDFKQTIRGR------NPVLAYFF--KPSCGFCKQLEPKISTVSETTSGVEFVKINVENG 102
D+ ++ ++ NPV F K C +C+ + + +SE + ++ + +
Sbjct: 5 DEDRKALKEEFFKEMKNPVDLVVFSSKEGCQYCEVTKQLLEELSELSDKLKLEIYDFDED 64
Query: 103 GGEIAREFEVQAVPTVI 119
E A ++ V+ VPT I
Sbjct: 65 K-EKAEKYGVERVPTTI 80
>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 = 37.4 bits (87), Expect = 4e-04
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 48 EKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSE--TTSGVEFVKINVENGGGE 105
+I+ + R L + P C FC+ +E ++E S V+ K N + E
Sbjct: 9 AEIEALAKGERRNQSTLVVLYAPWCPFCQAMEASYEELAEKLAGSNVKVAKFNADGEQRE 68
Query: 106 IARE-FEVQAVPTVIGF 121
A+E ++++ PT++ F
Sbjct: 69 FAKEELQLKSFPTILFF 85
>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 = 37.4 bits (87), Expect = 0.001
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 12/86 (13%)
Query: 51 DDFKQTIRGR------NPVLAYFF----KPSCGFCKQLEPKISTVSETTSGVEFVKINVE 100
++ ++ ++ NPV F K C +CK+ E + +SE + ++ + +
Sbjct: 3 EEDREILKELFLKELKNPVEIVVFTDNDKEGCQYCKETEQLLEELSEVSPKLKLEIYDFD 62
Query: 101 NGGG-EIAREFEVQAVPTVIGFRNGD 125
E A ++ V+ VPT I
Sbjct: 63 TPEDKEEAEKYGVERVPTTI-ILEEG 87
>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 = 35.3 bits (82), Expect = 0.002
Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 28/101 (27%)
Query: 58 RGRNPVLAYFFKPSCGFCKQLEPKISTVSETTS--GVEFVKINVENGG------------ 103
+G+ VL F+ C C+ P++ +++ GVE V +NV++
Sbjct: 18 KGK-VVLVNFWASWCPPCRAEMPELEALAKEYKDDGVEVVGVNVDDDDPAAVKAFLKKYG 76
Query: 104 ----------GEIAREFEVQAVPT--VIGFRNGDPVDTVVG 132
GE+A+ + V+ +PT +I R+G VG
Sbjct: 77 ITFPVLLDPDGELAKAYGVRGLPTTFLID-RDGRIRARHVG 116
>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 = 32.6 bits (75), Expect = 0.017
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGE--IAREFEVQAVPTVI 119
L F+ P CG CK L P+ ++ G+ VK+ + +A+++ V+ PT+
Sbjct: 20 VWLVEFYAPWCGHCKNLAPEWKKAAKALKGI--VKVGAVDADVHQSLAQQYGVRGFPTIK 77
Query: 120 GFRNG--DPVD 128
F G P D
Sbjct: 78 VFGAGKNSPQD 88
>gnl|CDD|239283 cd02985, TRX_CDSP32, TRX family, chloroplastic drought-induced
stress protein of 32 kD (CDSP32); CDSP32 is composed of
two TRX domains, a C-terminal TRX domain which contains
a redox active CXXC motif and an N-terminal TRX-like
domain which contains an SXXS sequence instead of the
redox active motif. CDSP32 is a stress-inducible TRX,
i.e., it acts as a TRX by reducing protein disulfides
and is induced by environmental and oxidative stress
conditions. It plays a critical role in plastid defense
against oxidative damage, a role related to its function
as a physiological electron donor to BAS1, a plastidic
2-cys peroxiredoxin. Plants lacking CDSP32 exhibit
decreased photosystem II photochemical efficiencies and
chlorophyll retention compared to WT controls, as well
as an increased proportion of BAS1 in its overoxidized
monomeric form.
Length = 103
Score = 32.1 bits (73), Expect = 0.029
Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 47 IEKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGG-- 104
+E++D+ + +GR VL + K G ++ P + +S T + V F+ +N +
Sbjct: 3 VEELDEALKKAKGRLVVLEFALK-HSGPSVKIYPTMVKLSRTCNDVVFLLVNGDENDSTM 61
Query: 105 EIAREFEVQAVPTVIGFRNGDPVDTVVG 132
E+ R ++ VP + +++G+ + G
Sbjct: 62 ELCRREKIIEVPHFLFYKDGEKIHEEEG 89
>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 = 32.0 bits (73), Expect = 0.033
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 67 FFKPSCGFCKQLEP---KISTVSETTSGVEFVKINVENGGGEIAREFEVQAVPTVIGFRN 123
F+ P C C+QL+P + + S+ G+ K++V G R F V A+PT+ ++
Sbjct: 23 FYAPWCPACQQLQPEWEEFADWSDDL-GINVAKVDVTQEPGLSGR-FFVTALPTIYHAKD 80
Query: 124 GDPVDTVVGNADQDVIQTLVSK 145
G G D++ + + + +
Sbjct: 81 GV-FRRYQGPRDKEDLISFIEE 101
>gnl|CDD|233990 TIGR02740, TraF-like, TraF-like protein. This protein is related
to the F-type conjugation system pilus assembly proteins
TraF (TIGR02739)and TrbB (TIGR02738) both of which
exhibit a thioredoxin fold. The protein represented by
this model has the same length and architecture as TraF,
but lacks the CXXC-motif found in TrbB and believed to
be responsible for the disulfide isomerase activity of
that protein.
Length = 271
Score = 32.4 bits (74), Expect = 0.057
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 11/66 (16%)
Query: 63 VLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGG----------GEIAREFEV 112
L +FFK C +C Q P + + G+E + ++V+ G A++ ++
Sbjct: 169 GLFFFFKSDCPYCHQQAPILQAFEDRY-GIEVLPVSVDGGPLPGFPNARPDAGQAQQLKI 227
Query: 113 QAVPTV 118
+ VP V
Sbjct: 228 RTVPAV 233
>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 = 31.5 bits (72), Expect = 0.067
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 16/79 (20%)
Query: 59 GRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG----VEFVKINV------------ENG 102
G+ P+L F +P C +C +L+ + V IN+
Sbjct: 13 GKKPLLLLFSQPGCPYCDKLKRDYLNDPAVQAYIRAHFVVVYINIDGDKEVTDFDGEALS 72
Query: 103 GGEIAREFEVQAVPTVIGF 121
E+AR++ V+ PTVI
Sbjct: 73 EKELARKYRVRFTPTVIFL 91
>gnl|CDD|218740 pfam05768, DUF836, Glutaredoxin-like domain (DUF836). These
proteins are related to the pfam00462 family.
Length = 76
Score = 30.3 bits (69), Expect = 0.079
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 63 VLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENG 102
L + KP C C+ + ++ + E G + +I++++
Sbjct: 1 TLTLYGKPGCHLCEGAKEVLAEL-EAALGFDLERIDIDDD 39
>gnl|CDD|223767 COG0695, GrxC, Glutaredoxin and related proteins [Posttranslational
modification, protein turnover, chaperones].
Length = 80
Score = 30.0 bits (68), Expect = 0.15
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 18/60 (30%)
Query: 69 KPSCGFCKQ----LEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQA-----VPTVI 119
KP C +CK+ L+ K GV++ +I+V++ E ARE + VP +
Sbjct: 8 KPGCPYCKRAKRLLDRK---------GVDYEEIDVDDDEPEEAREMVKRGKGQRTVPQIF 58
>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 = 30.2 bits (68), Expect = 0.18
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 49 KIDDFKQTIRGRN-PVLAYFFKPSCGFCKQLEPKISTVSETTSGVE-FVKINVEN 101
++D + + P++ K CG CK L+PK + E + FV +N+E+
Sbjct: 7 TLEDGIKEAKDSGKPLMLLIHKTWCGACKALKPKFAESKEISELSHNFVMVNLED 61
>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 = 30.4 bits (69), Expect = 0.22
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 62 PVLAYFFKPSCGFCKQLEP 80
V+ F P C +C++LE
Sbjct: 79 RVVYVFTDPDCPYCRKLEK 97
>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 = 29.7 bits (67), Expect = 0.22
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 64 LAYFFKPSCGFCKQLEPKI-STVSETTSGVEFVKINV 99
+ FF P C +C EP++ + GV V
Sbjct: 1 IVEFFDPLCPYCYLFEPELEKLLYADDGGVRVVYRPF 37
>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 = 29.2 bits (66), Expect = 0.32
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 57 IRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSG-VEFVKINVENGGGEIAREFEVQAV 115
+ + P L F+ P CG C+ L P++ + G V+ ++ + + ++A
Sbjct: 16 LNRKEPWLVDFYAPWCGPCQALLPELRKAARALKGKVKVGSVDCQKYESLCQQA-NIRAY 74
Query: 116 PTVIGF 121
PT+ +
Sbjct: 75 PTIRLY 80
>gnl|CDD|239285 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily;
Phd is a cytosolic regulator of G protein functions. It
specifically binds G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane. This impedes the formation
of a functional G protein trimer (G protein
alphabetagamma), thereby inhibiting G protein-mediated
signal transduction. Phd also inhibits the GTPase
activity of G protein alpha. Phd can be phosphorylated
by protein kinase A and G protein-coupled receptor
kinase 2, leading to its inactivation. Phd was
originally isolated from the retina, where it is highly
expressed and has been implicated to play an important
role in light adaptation. It is also found in the pineal
gland, liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain.
Length = 175
Score = 29.6 bits (67), Expect = 0.42
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQAVPTVIGF 121
V+ + ++P C L + ++ V+F KI G EF+ A+P ++ +
Sbjct: 85 TVVVHIYEPGIPGCAALNSSLLCLAAEYPAVKFCKIRASATGAS--DEFDTDALPALLVY 142
Query: 122 RNGDPVDTVVGNADQ 136
+ G+ + V +
Sbjct: 143 KGGELIGNFVRVTED 157
>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 = 28.7 bits (65), Expect = 0.68
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 67 FFKPSCGFCKQLEPKI 82
FF +CG+CK+L P++
Sbjct: 12 FFDYNCGYCKKLAPEL 27
>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 = 29.2 bits (65), Expect = 0.76
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 60 RNPVLAYFFKPSCGFCKQLEPKISTVSE--TTSGVEFVKINVENGGGEIAR-EFEVQAVP 116
+ L + P C FC+ +E ++E SGV+ K + E A+ E ++ + P
Sbjct: 371 KEAWLVVLYAPWCPFCQAMEASYLELAEKLAGSGVKVAKFRADGDQKEFAKQELQLGSFP 430
Query: 117 TVIGF 121
T++ F
Sbjct: 431 TILFF 435
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 29.1 bits (65), Expect = 0.96
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 79 EPKISTVSETTSGVEFVKINV-ENGGGEIAREFEVQAVPT-VIGFRNGDPVDTVVGN 133
E K + +G+++ K+ V + GG +A+ + P+ I ++GD V G+
Sbjct: 103 EKKDGDFQKWYAGLDYPKLPVLTDNGGTLAQSLNISVYPSWAIIGKDGDVQRIVKGS 159
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 29.0 bits (65), Expect = 1.0
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSE--TTSGVEFVKINVENGGGEIAR-EFEVQAVPTV 118
P L + P C FC+ +E ++E SGV+ K + E A+ E ++ + PT+
Sbjct: 367 PWLVVLYAPWCPFCQAMEASYEELAEKLAGSGVKVAKFRADGDQKEFAKQELQLGSFPTI 426
Query: 119 IGF 121
+ F
Sbjct: 427 LLF 429
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 28.8 bits (64), Expect = 1.1
Identities = 14/63 (22%), Positives = 27/63 (42%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQAVPTVIGF 121
P F+ P C C+++ P +++ G V +A+ F ++ PT++ F
Sbjct: 54 PWFVKFYAPWCSHCRKMAPAWERLAKALKGQVNVADLDATRALNLAKRFAIKGYPTLLLF 113
Query: 122 RNG 124
G
Sbjct: 114 DKG 116
>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 = 27.7 bits (62), Expect = 1.2
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 26/85 (30%)
Query: 61 NPVLAYFFKPSCGFCKQLEPKISTVSETTS--GVEFVKINVENGG--------------- 103
VL YF+ C C+ P++ + E VE V ++++
Sbjct: 2 KVVLLYFWASWCPPCRAFTPELKELYEKLKKPKVEIVYVSLDRDEEEWKKYLKKMPKDWL 61
Query: 104 ---------GEIAREFEVQAVPTVI 119
E+ R + V+A+PT++
Sbjct: 62 NVPFGDKERNELLRLYGVKAIPTLV 86
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 28.3 bits (63), Expect = 1.2
Identities = 18/94 (19%), Positives = 33/94 (35%), Gaps = 19/94 (20%)
Query: 47 IEKIDDFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSET----TSGVEFVKINVE-- 100
I+ DD K +L F C +C++ + + V +N+
Sbjct: 29 IDVFDDNKSISPNDKYLLLMFESNGCSYCERFKKDLKNVKRLREYLKEHFSAYYLNISYS 88
Query: 101 -----NGGG--------EIAREFEVQAVPTVIGF 121
G E+A++F V++ PT + F
Sbjct: 89 KPVLFKVGDKEEKMSTEELAQKFAVRSTPTFVFF 122
>gnl|CDD|222346 pfam13728, TraF, F plasmid transfer operon protein. TraF protein
undergoes proteolytic processing associated with export.
The 19 amino acids at the amino terminus of the
polypeptides appear to constitute a typical membrane
leader peptide - not included in this family, while the
remainder of the molecule is predicted to be primarily
hydrophilic in character. F plasmid TraF and TraH are
required for F pilus assembly and F plasmid transfer,
and they are both localised to the outer membrane in the
presence of the complete F transfer region, especially
TraV, the putative anchor.
Length = 215
Score = 28.3 bits (64), Expect = 1.3
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 11/66 (16%)
Query: 64 LAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGE----------IAREFEVQ 113
L +F++ C +C+ P + ++ G + ++V+ G A+ V+
Sbjct: 124 LFFFYRGDCPYCQAQAPILQAFAD-KYGFSVIPVSVDGGPLPGFPNNRVDTGQAQRLGVK 182
Query: 114 AVPTVI 119
P +
Sbjct: 183 TTPALF 188
>gnl|CDD|183512 PRK12412, PRK12412, pyridoxal kinase; Reviewed.
Length = 268
Score = 28.4 bits (63), Expect = 1.6
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 24 RAALPPRAHL--PNLIQAVQMAYLIIEKIDDFKQ 55
R L P+A + PNL +A Q++ + I ++D K+
Sbjct: 126 RDVLVPKALVVTPNLFEAYQLSGVKINSLEDMKE 159
>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 = 26.7 bits (59), Expect = 2.3
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 4/75 (5%)
Query: 52 DFKQTIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGG--GEIARE 109
DF + F+ P C C L P ++ GV ++I N G + R
Sbjct: 10 DFDAAVNSGEIWFVNFYSPRCSHCHDLAPTWREFAKEMDGV--IRIGAVNCGDDRMLCRS 67
Query: 110 FEVQAVPTVIGFRNG 124
V + P++ F +G
Sbjct: 68 QGVNSYPSLYVFPSG 82
>gnl|CDD|177928 PLN02291, PLN02291, phospho-2-dehydro-3-deoxyheptonate aldolase.
Length = 474
Score = 27.4 bits (61), Expect = 2.9
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 30 RAHLPNLIQAVQMAYLIIEKIDD 52
R LP+LI+AV+ A I+ + D
Sbjct: 343 RVKLPHLIRAVRRAGQIVTWVSD 365
>gnl|CDD|220297 pfam09581, Spore_III_AF, Stage III sporulation protein AF
(Spore_III_AF). This family represents the stage III
sporulation protein AF (Spore_III_AF) of the bacterial
endospore formation program, which exists in some but
not all members of the Firmicutes (formerly called
low-GC Gram-positives). The C-terminal region of these
proteins is poorly conserved.
Length = 185
Score = 27.3 bits (61), Expect = 3.0
Identities = 10/66 (15%), Positives = 22/66 (33%), Gaps = 2/66 (3%)
Query: 76 KQLEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQAVPTVIGFRNGDPVDTVVGNAD 135
KQLE ++ + GV+ + VE + F+++ V + +
Sbjct: 86 KQLEKQVEKKLKEEYGVKVKDVEVEIDEDLESNNFDIKEV--NVTLKEESKEKQKSKVEP 143
Query: 136 QDVIQT 141
+
Sbjct: 144 VVIDTQ 149
>gnl|CDD|237526 PRK13837, PRK13837, two-component VirA-like sensor kinase;
Provisional.
Length = 828
Score = 27.3 bits (61), Expect = 3.7
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 24 RAALPPRAHLPNLIQAVQMAYLIIEKIDDF 53
++ +I A A LII++I F
Sbjct: 480 ARHSRAARYIDEIISAGARARLIIDQILAF 509
>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 = 26.7 bits (59), Expect = 3.9
Identities = 9/40 (22%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 64 LAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGG 103
L +F++ +C +C Q P + S+ G+ +++ G
Sbjct: 54 LVFFYQSTCPYCHQFAPVLKRFSQQF-GLPVYAFSLDGQG 92
>gnl|CDD|217204 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase,
carbamoyl-P binding domain.
Length = 140
Score = 26.3 bits (59), Expect = 4.7
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 46 IIEKIDDFKQTIRGRNPVLA------YFFKPS 71
+++ + K+ + +P+LA FF+PS
Sbjct: 17 LLDLAAELKKKPKSGSPLLAGKTLALLFFEPS 48
>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 = 25.2 bits (56), Expect = 5.2
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 21/63 (33%)
Query: 67 FFKPSCGFC----------KQLEPKISTVSETTSGVEFVKINVENGGGEIAREFEVQAVP 116
F P+C +C L P IS +E EF ++A E+ V +VP
Sbjct: 6 FVSPTCPYCPDAVQAANRIAALNPNIS--AEMIDAAEF---------PDLADEYGVMSVP 54
Query: 117 TVI 119
++
Sbjct: 55 AIV 57
>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 = 25.3 bits (56), Expect = 5.3
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 23/68 (33%)
Query: 69 KPSCGFCKQ----LEPKISTVSETTSGVEFVKINVENGGGEIAR---EFEVQAVPTVI-- 119
KP C +CK L+ + G+ F +++V+ + ++VP V+
Sbjct: 7 KPDCPYCKATKRFLDER---------GIPFEEVDVDEDPEALEELKKLNGYRSVPVVVIG 57
Query: 120 -----GFR 122
GFR
Sbjct: 58 DEHLSGFR 65
>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 = 25.8 bits (57), Expect = 6.0
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 57 IRGRNPVLAYFFKPSCGFCKQLEPKISTV 85
I P L +F P+C CK+L P I ++
Sbjct: 18 ISPGRPTLLFFLSPTCPVCKKLLPVIRSI 46
>gnl|CDD|236422 PRK09234, fbiC, FO synthase; Reviewed.
Length = 843
Score = 26.5 bits (59), Expect = 6.1
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 23 ARAALPPRAHL---PNLIQAVQMAYLIIEKIDDF 53
AR L P+ + PNL+ + A L+ IDD+
Sbjct: 300 ARLVLGPKMRIQAPPNLVSGDECAALLGAGIDDW 333
>gnl|CDD|215931 pfam00462, Glutaredoxin, Glutaredoxin.
Length = 60
Score = 24.8 bits (55), Expect = 6.4
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 18/69 (26%)
Query: 66 YFFKPSCGFCKQ----LEPKISTVSETTSGVEFVKINVENGGG---EIAREFEVQAVPTV 118
F KP+C FCK+ L+ GV+F +I+V+ E+ VP V
Sbjct: 3 LFTKPTCPFCKRAKRLLDSL---------GVKFEEIDVDEDPEIREELKELSGWPTVPQV 53
Query: 119 IGFRNGDPV 127
F +G+ +
Sbjct: 54 --FIDGEHI 60
>gnl|CDD|215902 pfam00403, HMA, Heavy-metal-associated domain.
Length = 62
Score = 24.9 bits (55), Expect = 6.9
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 71 SCGFCKQLEPKISTVSETTSGVEFVKINVENG 102
+C C + K+ GV V +++E G
Sbjct: 8 TCAGCAK---KVEKALSKLPGVSSVSVDLETG 36
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 26.6 bits (59), Expect = 7.2
Identities = 10/46 (21%), Positives = 22/46 (47%)
Query: 56 TIRGRNPVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVEN 101
+ +P+ ++ PS + +L+ IS S + F+ + +EN
Sbjct: 72 ALFNSDPIKLKYYNPSISWFDKLKNLISNDSSKLNCSMFIAVIIEN 117
>gnl|CDD|225755 COG3214, COG3214, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 400
Score = 26.2 bits (58), Expect = 7.4
Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 2/43 (4%)
Query: 8 AAAHVTFHNSGGKLSARAALPPRAHLPNLIQAVQMAYLIIEKI 50
A A + G L+ + L I + L I+ I
Sbjct: 8 ADARRIALAAQGLLAPPRRAASKRDLLATISR--LGLLQIDSI 48
>gnl|CDD|173585 PTZ00394, PTZ00394, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 670
Score = 26.4 bits (58), Expect = 7.5
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 113 QAVPTVIGFRNGDPVDTVVGNADQDV 138
+ P ++G R D V+ D+
Sbjct: 210 KGSPLMVGIRRTDDRGCVMKLQTYDL 235
>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 = 25.3 bits (56), Expect = 7.6
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 105 EIAREFEVQAVPTVIGFRNGDPVDTVVG 132
+A F V P ++ FR+G V + G
Sbjct: 74 ALAARFGVLRTPALLFFRDGRYVGVLAG 101
>gnl|CDD|236306 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated.
Length = 257
Score = 26.2 bits (58), Expect = 8.0
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 105 EIAREFEVQAVPTVIG 120
R FE AVPT+IG
Sbjct: 77 SFGRSFEAFAVPTIIG 92
>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 = 25.6 bits (56), Expect = 9.0
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 62 PVLAYFFKPSCGFCKQLEPKISTVSETTSGVEFVKINVENGGGEIAREF 110
P L F PSC C +L P I +++ E + + +G R F
Sbjct: 76 PTLLMFTAPSCPVCDKLFPIIKSIARAE---ETDVVMISDGTPAEHRRF 121
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
0.320 0.135 0.388
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: 7,553,142
Number of extensions: 677649
Number of successful extensions: 662
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 79
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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 (21.8 bits)
S2: 54 (24.6 bits)