RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022560
(295 letters)
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 612 bits (1580), Expect = 0.0
Identities = 244/295 (82%), Positives = 274/295 (92%), Gaps = 5/295 (1%)
Query: 1 MFPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTR 60
MFPDAVEVQALVR+KGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTR
Sbjct: 168 MFPDAVEVQALVRNKGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTR 227
Query: 61 SEIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGC 120
+E+PVVQVDPVFEGL+GG GSLVKWNP+ANV GN++WNFLRTMDVP+NSLH+QGY+SIGC
Sbjct: 228 AEVPVVQVDPVFEGLDGGPGSLVKWNPLANVTGNEVWNFLRTMDVPVNSLHAQGYVSIGC 287
Query: 121 EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIKQEDAAVNGNGNGAGNASEAVADIF 180
EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIK+ED NG N + AVADIF
Sbjct: 288 EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIKEED-----NGAANDNGNAAVADIF 342
Query: 181 NSQNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVG 240
NSQN+V L+R G+ENL +L++R+EPWLVVLYAPWC FCQAME SY ELA+KLAG+GVKV
Sbjct: 343 NSQNVVALSRAGIENLLKLENRKEPWLVVLYAPWCPFCQAMEASYEELAEKLAGSGVKVA 402
Query: 241 KFRADGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFVDALR 295
KFRADGDQKE+AKQ+LQLGSFPTIL FPK+SS+PIKYPSE+RDVDSL++FV++LR
Sbjct: 403 KFRADGDQKEFAKQELQLGSFPTILLFPKNSSRPIKYPSEKRDVDSLLSFVNSLR 457
>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 = 580 bits (1496), Expect = 0.0
Identities = 251/297 (84%), Positives = 278/297 (93%), Gaps = 8/297 (2%)
Query: 1 MFPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTR 60
MFPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGL+AWITGQRKDQSPGTR
Sbjct: 173 MFPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLKAWITGQRKDQSPGTR 232
Query: 61 SEIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGC 120
SEIPVVQVDPVFEGL+GGVGSLVKWNPVANV+G D+WNFLRTMDVP+N+LH+QGY+SIGC
Sbjct: 233 SEIPVVQVDPVFEGLDGGVGSLVKWNPVANVEGKDVWNFLRTMDVPVNTLHAQGYVSIGC 292
Query: 121 EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIKQE--DAAVNGNGNGAGNASEAVAD 178
EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIK+E D AVNGNG S+AVAD
Sbjct: 293 EPCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIKEETLDGAVNGNG------SDAVAD 346
Query: 179 IFNSQNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVK 238
IF+S N+V+L+R G+ENL +L+ R+E WLVVLYAPWC FCQAME SY+ELA+KLAG+GVK
Sbjct: 347 IFDSNNVVSLSRPGIENLLKLEERKEAWLVVLYAPWCPFCQAMEASYLELAEKLAGSGVK 406
Query: 239 VGKFRADGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFVDALR 295
V KFRADGDQKE+AKQ+LQLGSFPTILFFPKHSS+PIKYPSE+RDVDSLM+FV+ LR
Sbjct: 407 VAKFRADGDQKEFAKQELQLGSFPTILFFPKHSSRPIKYPSEKRDVDSLMSFVNLLR 463
>gnl|CDD|233701 TIGR02055, APS_reductase, thioredoxin-dependent adenylylsulfate APS
reductase. This model describes recently identified
adenosine 5'-phosphosulfate (APS) reductase activity
found in sulfate-assimilatory prokaryotes, thus
separating it from the traditionally described
phosphoadenosine 5'-phosphosulfate (PAPS) reductases
found in bacteria and fungi. Homologous to PAPS
reductase in enterobacteria, cyanobacteria, and yeast,
APS reductase here clusters with, and demonstrates
greater homology to plant APS reductase. Additionally,
the presence of two conserved C-terminal motifs
(CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate
specificity and serves as a FeS cluster [Central
intermediary metabolism, Sulfur metabolism].
Length = 191
Score = 201 bits (512), Expect = 1e-64
Identities = 73/149 (48%), Positives = 95/149 (63%), Gaps = 9/149 (6%)
Query: 2 FPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTRS 61
P + V+ V+ GL FY ECC +RKV PL+RAL G+ AWITG R+DQSP TR+
Sbjct: 52 SPPPLTVEEQVKEYGLNLFYRSVPHECCGIRKVEPLKRALAGVSAWITGLRRDQSP-TRA 110
Query: 62 EIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCE 121
+ P +++D LVK NP+A+ D+W ++ ++P N LH +GY SIGCE
Sbjct: 111 QAPFLEID--------EAFGLVKINPLADWTSEDVWEYIADNELPYNPLHDRGYPSIGCE 162
Query: 122 PCTRPVLPGQHEREGRWWWEDAKAKECGL 150
PCTRPV PG+ R GRWWWE+A KECGL
Sbjct: 163 PCTRPVAPGEDPRAGRWWWEEAAKKECGL 191
>gnl|CDD|234997 PRK02090, PRK02090, phosphoadenosine phosphosulfate reductase;
Provisional.
Length = 241
Score = 201 bits (514), Expect = 3e-64
Identities = 75/155 (48%), Positives = 96/155 (61%), Gaps = 13/155 (8%)
Query: 2 FPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLRAWITGQRKDQSPGTRS 61
PDA + R GL+ + ECCR+RKV PL RAL GL AWITG R++QS TR+
Sbjct: 100 RPDASAAEQEARYGGLWEQSVEDRDECCRIRKVEPLNRALAGLDAWITGLRREQSG-TRA 158
Query: 62 EIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCE 121
+PV+++D G K NP+A+ D+W +L+ D+P + L QGY SIGCE
Sbjct: 159 NLPVLEID----------GGRFKINPLADWTNEDVWAYLKEHDLPYHPLVDQGYPSIGCE 208
Query: 122 PCTRPVLPGQHEREGRWWWEDAKAKECGLHKGNIK 156
PCTRPV PG+ ER GR WW K KECGLH+GN+
Sbjct: 209 PCTRPVEPGEDERAGR-WWGGLK-KECGLHEGNLP 241
>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 = 191 bits (487), Expect = 4e-62
Identities = 73/108 (67%), Positives = 90/108 (83%)
Query: 184 NLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFR 243
+VTL+R +E LA+ + R + LVVLYAPWC FCQAME SY ELA+KLAG+ VKV KF
Sbjct: 2 AVVTLSRAEIEALAKGERRNQSTLVVLYAPWCPFCQAMEASYEELAEKLAGSNVKVAKFN 61
Query: 244 ADGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFV 291
ADG+Q+E+AK++LQL SFPTILFFPK+S +PIKYPSE+RDVDSL+ FV
Sbjct: 62 ADGEQREFAKEELQLKSFPTILFFPKNSRQPIKYPSEQRDVDSLLMFV 109
>gnl|CDD|223253 COG0175, CysH, 3'-phosphoadenosine 5'-phosphosulfate
sulfotransferase (PAPS reductase)/FAD synthetase and
related enzymes [Amino acid transport and metabolism /
Coenzyme metabolism].
Length = 261
Score = 149 bits (379), Expect = 7e-44
Identities = 60/142 (42%), Positives = 83/142 (58%), Gaps = 11/142 (7%)
Query: 16 GLFSFYEDGHQECCRVRKVRPLRRALKGL--RAWITGQRKDQSPGTRSEIPVVQVDPVFE 73
G + + CC +RKV PL+RAL AW TG R+D+SP TR+++PVV D F
Sbjct: 111 GGKLWEPSVERWCCDIRKVEPLKRALDEYGFDAWFTGLRRDESP-TRAKLPVVSFDSEFG 169
Query: 74 GLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPCTRPVLP-GQH 132
++ NP+A+ D+W ++ ++P N L+ QGY SIGC PCTRPV P +
Sbjct: 170 ES-------IRVNPLADWTELDVWLYILANNLPYNPLYDQGYRSIGCWPCTRPVEPLAED 222
Query: 133 EREGRWWWEDAKAKECGLHKGN 154
ER GRW E A+ ECGLH+ +
Sbjct: 223 ERAGRWEGELAEKTECGLHRAD 244
>gnl|CDD|201832 pfam01507, PAPS_reduct, Phosphoadenosine phosphosulfate reductase
family. This domain is found in phosphoadenosine
phosphosulfate (PAPS) reductase enzymes or PAPS
sulfotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP). It is also
found in NodP nodulation protein P from Rhizobium which
has ATP sulfurylase activity (sulfate adenylate
transferase).
Length = 173
Score = 133 bits (336), Expect = 2e-38
Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 14/127 (11%)
Query: 2 FPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALK--GLRAWITGQRKDQSPGT 59
P+ + + S Y + CCR+RKV PL+RALK G AW TG R+D+SP +
Sbjct: 59 LPEDSFAEGINPEGIPSSLY----RRCCRLRKVEPLKRALKELGFDAWFTGLRRDESP-S 113
Query: 60 RSEIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIG 119
R+++P+V +D F + +K P+ N D+W ++ +VP N L+ QGY SIG
Sbjct: 114 RAKLPIVSIDGDFPKV-------IKVFPLLNWTETDVWQYILANNVPYNPLYDQGYRSIG 166
Query: 120 CEPCTRP 126
C PCT P
Sbjct: 167 CYPCTGP 173
>gnl|CDD|129526 TIGR00434, cysH, phosophoadenylyl-sulfate reductase (thioredoxin).
This enzyme, involved in the assimilation of inorganic
sulfate, is designated cysH in Bacteria and MET16 in
Saccharomyces cerevisiae. Synonyms include
phosphoadenosine phosphosulfate reductase, PAPS
reductase, and PAPS reductase, thioredoxin-dependent. In
a reaction requiring reduced thioredoxin and NADPH, it
converts 3(prime)-phosphoadenylylsulfate (PAPS) to
sulfite and adenosine 3(prime),5(prime) diphosphate
(PAP). A related family of plant enzymes, scoring below
the trusted cutoff, differs in having a thioredoxin-like
C-terminal domain, not requiring thioredoxin, and in
having a preference for 5(prime)-adenylylsulfate (APS)
over PAPS [Central intermediary metabolism, Sulfur
metabolism].
Length = 212
Score = 127 bits (320), Expect = 1e-35
Identities = 52/134 (38%), Positives = 74/134 (55%), Gaps = 15/134 (11%)
Query: 21 YEDGHQECCRVRKVRPLRRALKGL--RAWITGQRKDQSPGTRSEIPVVQVDPVFEGLEGG 78
+E + +RKV P+ RALK L AW TG R+DQ P +R+ + ++ +D F
Sbjct: 90 WEQDPNKYDYLRKVEPMHRALKELHASAWFTGLRRDQGP-SRANLSILNIDEKFG----- 143
Query: 79 VGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPCTRPVLPGQHEREGRW 138
++K P+ + D++ ++ ++P N LH QGY SIG TRPV G+ ER GRW
Sbjct: 144 ---ILKVLPLIDWTWKDVYQYIDAHNLPYNPLHDQGYPSIGDYHSTRPVKEGEDERAGRW 200
Query: 139 WWEDAKAK-ECGLH 151
KAK ECGLH
Sbjct: 201 ---KGKAKTECGLH 211
>gnl|CDD|238846 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. A highly modified
version of the P loop, the fingerprint peptide of
mononucleotide-binding proteins, is present in the
active site of the protein, which appears to be a
positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) .
Length = 173
Score = 112 bits (281), Expect = 2e-30
Identities = 43/121 (35%), Positives = 57/121 (47%), Gaps = 10/121 (8%)
Query: 1 MFPDAVEVQALVRSKGLFSFYEDGHQECCRVRKVRPLRRALKGLR--AWITGQRKDQSPG 58
+ P + L F + CCR+ KV PLRRALK L AWITG R+D+S
Sbjct: 61 VRPPDSPAEGLALGLKGFPLPSPDRRWCCRILKVEPLRRALKELGVVAWITGIRRDESAR 120
Query: 59 TRSEIPVVQVDPVFEGLEGGVGSLVKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISI 118
V D G G ++K NP+ + D+W +L +P N L+ QGY SI
Sbjct: 121 RALLPVVWTDD--------GKGGILKVNPLLDWTYEDVWAYLARHGLPYNPLYDQGYRSI 172
Query: 119 G 119
G
Sbjct: 173 G 173
>gnl|CDD|131112 TIGR02057, PAPS_reductase, phosphoadenosine phosphosulfate
reductase, thioredoxin dependent. Requiring thioredoxin
as an electron donor, phosphoadenosine phosphosulfate
reductase catalyzes the reduction of
3'-phosphoadenylylsulfate (PAPS) to sulfite and
phospho-adenosine-phosphate (PAP). Found in
enterobacteria, cyanobacteria, and yeast, PAPS reductase
is related to a group of plant (TIGR00424) and bacterial
(TIGR02055) enzymes preferring 5'-adenylylsulfate (APS)
over PAPS as a substrate for reduction to sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 226
Score = 107 bits (268), Expect = 7e-28
Identities = 48/124 (38%), Positives = 68/124 (54%), Gaps = 15/124 (12%)
Query: 31 VRKVRPLRRALKGLR--AWITGQRKDQSPGTRSEIPVVQVDPVFEGLEGGVGSLVKWNPV 88
+ KV P++RALK L AW TG+R+DQ R+ +PV+++D ++K NP+
Sbjct: 115 IAKVEPMQRALKELNASAWFTGRRRDQG-SARANLPVIEID--------EQNGILKVNPL 165
Query: 89 ANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPCTRPVLPGQHEREGRWWWEDAKAK-E 147
+ ++ +L +VP N L QGY SIG TR V G+ ER GRW K K E
Sbjct: 166 IDWTFEQVYQYLDAHNVPYNPLLDQGYRSIGDYHSTRKVKEGEDERAGRWK---GKLKTE 222
Query: 148 CGLH 151
CG+H
Sbjct: 223 CGIH 226
>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 = 87.3 bits (217), Expect = 9e-22
Identities = 35/107 (32%), Positives = 54/107 (50%), Gaps = 7/107 (6%)
Query: 186 VTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNG-VKVGKFRA 244
V L +N L + LV YAPWC C+A+ Y +LA +L G+G V V K
Sbjct: 1 VELTD---DNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDC 57
Query: 245 DGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFV 291
+ ++ ++ +PTI FP S +P+KY R ++SL+ F+
Sbjct: 58 TANNDLCSEYGVR--GYPTIKLFPNGSKEPVKYEGP-RTLESLVEFI 101
>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 = 78.1 bits (193), Expect = 2e-18
Identities = 36/86 (41%), Positives = 50/86 (58%), Gaps = 3/86 (3%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAG-NGVKVGKFRADGDQKEYAKQKLQLGSFPTIL 265
LV YAPWC C+ + Y +LA A + V + K AD K+ AK K + FPT+
Sbjct: 22 LVEFYAPWCGHCKNLAPEYEKLAAVFANEDDVVIAKVDADEANKDLAK-KYGVSGFPTLK 80
Query: 266 FFPKHSSKPIKYPSERRDVDSLMAFV 291
FFPK S++P+KY RD++ L+ FV
Sbjct: 81 FFPKGSTEPVKY-EGGRDLEDLVKFV 105
>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 = 72.2 bits (178), Expect = 4e-16
Identities = 36/87 (41%), Positives = 49/87 (56%), Gaps = 6/87 (6%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAG-NGVKVGKFRADGDQKEYAKQKLQLGSFPTIL 265
LV YAPWC C+A+ Y ELA+KL G + V + K D + + + G FPTIL
Sbjct: 22 LVEFYAPWCGHCKALAPIYEELAEKLKGDDNVVIAKM--DATANDVPSEFVVDG-FPTIL 78
Query: 266 FFPK-HSSKPIKYPSERRDVDSLMAFV 291
FFP S PIKY + R ++ L+ F+
Sbjct: 79 FFPAGDKSNPIKYEGD-RTLEDLIKFI 104
>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 = 70.8 bits (174), Expect = 1e-15
Identities = 39/107 (36%), Positives = 56/107 (52%), Gaps = 5/107 (4%)
Query: 185 LVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRA 244
++TL L +R+EPWLV YAPWC CQA+ + A L G VKVG
Sbjct: 3 VITLTPEDFPELVL--NRKEPWLVDFYAPWCGPCQALLPELRKAARALKGK-VKVGSV-- 57
Query: 245 DGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFV 291
D + E Q+ + ++PTI +P ++SK Y RD DS++ F+
Sbjct: 58 DCQKYESLCQQANIRAYPTIRLYPGNASKYHSYNGWHRDADSILEFI 104
>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 = 69.2 bits (170), Expect = 4e-15
Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 204 EPWLVVLYAPWCQFCQAMEGSYVELADKLAGNG-VKVGKFRADGDQKEYAKQKLQLGSFP 262
+ LV YAPWC C+ + Y +LA +L + + + K A ++ ++ + FP
Sbjct: 14 KDVLVEFYAPWCGHCKNLAPEYEKLAKELKKDPDIVLAKVDATAEKDLASRFGVS--GFP 71
Query: 263 TILFFPKHSSKPIKYPSERRDVDSLMAFVD 292
TI FFPK KP+ Y RD+++++ FV+
Sbjct: 72 TIKFFPK-GKKPVDYEGG-RDLEAIVEFVN 99
>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 = 70.1 bits (172), Expect = 2e-13
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTILF 266
LV YAPWC C+ + Y ELA+K V + D + +++ FPTI F
Sbjct: 368 LVEFYAPWCGHCKNLAPIYEELAEKYKDAESDVVIAKMDATANDVPPFEVE--GFPTIKF 425
Query: 267 FPKHS-SKPIKYPSERRDVDSLMAFVD 292
P S+P+ Y + R ++ F+
Sbjct: 426 VPAGKKSEPVPYDGD-RTLEDFSKFIA 451
Score = 47.4 bits (113), Expect = 4e-06
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNG--VKVGKFRADGDQKEYAKQKLQLGSFPTI 264
LV YAPWC C+++ Y + AD+L G +K+ K A ++K+ A QK + +PT+
Sbjct: 22 LVEFYAPWCGHCKSLAPEYEKAADELKKKGPPIKLAKVDAT-EEKDLA-QKYGVSGYPTL 79
Query: 265 LFFPKHSSKPIKY 277
F Y
Sbjct: 80 KIFRNGEDSVSDY 92
>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 = 61.5 bits (150), Expect = 3e-12
Identities = 32/91 (35%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 204 EPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPT 263
+P LV YAPWC C+A+ Y +LA + + VK K AD + + A + + FPT
Sbjct: 19 KPVLVDFYAPWCGPCKALAPEYEKLAQEYKDD-VKFAKVDAD-ENPDLASE-YGVRGFPT 75
Query: 264 ILFFPKHSSKPIKYPSERRDVDSLMAFVDAL 294
I FF K Y R D L+AF+
Sbjct: 76 IKFFKN-GKKVSDY-VGARTKDDLVAFIKKH 104
>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 = 60.4 bits (147), Expect = 7e-12
Identities = 27/80 (33%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 203 QEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFP 262
+ WLV YAPWC C+ + + + A L G VKVG AD Q + ++ FP
Sbjct: 18 DDVWLVEFYAPWCGHCKNLAPEWKKAAKALKGI-VKVGAVDADVHQSLAQQYGVR--GFP 74
Query: 263 TILFFPKHSSKPIKYPSERR 282
TI F + P Y R
Sbjct: 75 TIKVFGAGKNSPQDYQGGRT 94
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 63.2 bits (154), Expect = 3e-11
Identities = 31/86 (36%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNG-VKVGKFRADGDQKEYAKQKLQLGSFPTIL 265
L+ +YAPWC C+ +E Y EL +K N + V K +G E ++ +FPTIL
Sbjct: 379 LLEIYAPWCGHCKNLEPVYNELGEKYKDNDSIIVAKM--NGTANETPLEEFSWSAFPTIL 436
Query: 266 FFPKHSSKPIKYPSERRDVDSLMAFV 291
F PI Y E R V+ FV
Sbjct: 437 FVKAGERTPIPYEGE-RTVEGFKEFV 461
Score = 51.3 bits (123), Expect = 2e-07
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLA--GNGVKVGKFRADGDQKEYAKQKLQLGSFPTI 264
LV YAPWC C+ + Y + A L + + + A + E A Q+ + +PTI
Sbjct: 53 LVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASVDATEEM-ELA-QEFGVRGYPTI 110
Query: 265 LFFPKHSSKPIKYPSERRDVDSLMAFVDAL 294
FF K P+ Y R D +++++ L
Sbjct: 111 KFFNK--GNPVNYSGG-RTADGIVSWIKKL 137
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 53.1 bits (127), Expect = 3e-08
Identities = 36/124 (29%), Positives = 51/124 (41%), Gaps = 7/124 (5%)
Query: 169 AGNASEAVADIFNSQNLVTLNRTGMENL--ARLDHRQEPWLVVLYAPWCQFCQAMEGSYV 226
A A+ D ++ LV LN E L A PW V YAPWC C+ M ++
Sbjct: 16 ADEATNVKLDAEDANALVLLNDKNFEKLTQASTGATTGPWFVKFYAPWCSHCRKMAPAWE 75
Query: 227 ELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDS 286
LA L G +V D + ++ + +PT+L F K +Y R +
Sbjct: 76 RLAKALKG---QVNVADLDATRALNLAKRFAIKGYPTLLLF--DKGKMYQYEGGDRSTEK 130
Query: 287 LMAF 290
L AF
Sbjct: 131 LAAF 134
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 6/87 (6%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKL--AGNGVKVGKFRADGDQKEYAKQKLQLGSFPTI 264
V +APWC C+ + ++ +LA K VK+ K D Q + Q+ +PT+
Sbjct: 20 FVKFFAPWCGHCKRLAPTWEQLAKKFNNENPSVKIAK--VDCTQHRELCSEFQVRGYPTL 77
Query: 265 LFFPKHSSKPIKYPSERRDVDSLMAFV 291
L F K K KY RD+DSL FV
Sbjct: 78 LLF-KDGEKVDKY-KGTRDLDSLKEFV 102
>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 = 48.2 bits (115), Expect = 2e-07
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 199 LDHRQEP-WLVVLYAPWCQFCQAMEGSYVELADKLAGNG--VKVGKFRADGDQKEYAKQK 255
D R+E WLV YAPWC C+ +E + E+ +L +G V+VGK D +
Sbjct: 10 KDVRKEDIWLVDFYAPWCGHCKKLEPVWNEVGAELKSSGSPVRVGKL--DATAYSSIASE 67
Query: 256 LQLGSFPTILFF 267
+ +PTI
Sbjct: 68 FGVRGYPTIKLL 79
>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 = 44.6 bits (106), Expect = 3e-06
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 194 ENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNG------VKVGKFRADGD 247
E+ + +++ LV+ YAPWC C+ M+ + + A +L +G V K D
Sbjct: 8 EDFRKFLKKEKHVLVMFYAPWCGHCKKMKPEFTKAATELKEDGKGVLAAVDCTKPEHDAL 67
Query: 248 QKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERR 282
++EY + FPT +F KY ER
Sbjct: 68 KEEYNVK-----GFPTFKYFENGKFV-EKYEGERT 96
>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 = 44.7 bits (106), Expect = 4e-06
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 10/91 (10%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTILF 266
LV YAPWC C+ ++ Y + A +L G V+V D D+ + K + FPT+
Sbjct: 22 LVEFYAPWCGHCKNLKPEYAKAAKELDGL-VQVAAVDCDEDKNKPLCGKYGVQGFPTLKV 80
Query: 267 FP------KHSSKPIKYPSERRDVDSLMAFV 291
F KH+ + + +++ FV
Sbjct: 81 FRPPKKASKHAVEDYNGERSAK---AIVDFV 108
>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 = 41.4 bits (98), Expect = 3e-05
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 194 ENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAK 253
E L +P +V +APWC C+A+ ELA++ VK K D + E A
Sbjct: 1 EEFEELIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEE--YPKVKFVKVDVD-ENPELA- 56
Query: 254 QKLQLGSFPTILFF 267
++ + S PT LFF
Sbjct: 57 EEYGVRSIPTFLFF 70
>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 = 40.0 bits (93), Expect = 7e-05
Identities = 24/62 (38%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQK-EYAKQKLQLGSFPTIL 265
LV+ YAPWC FCQA+ ELA GVK D D E ++ +G PT++
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNK--GVKFEAVDVDEDPALEKELKRYGVGGVPTLV 58
Query: 266 FF 267
F
Sbjct: 59 VF 60
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 28/108 (25%), Positives = 51/108 (47%), Gaps = 8/108 (7%)
Query: 183 QNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKF 242
+VTL+R + + E W V Y+P C C + ++ E A ++ G +++G
Sbjct: 1 PEIVTLDRGDFD---AAVNSGEIWFVNFYSPRCSHCHDLAPTWREFAKEMDGV-IRIGAV 56
Query: 243 RADGDQKEYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAF 290
GD + + + + S+P++ FP P KY + R +SL+ F
Sbjct: 57 NC-GDDRMLCRSQ-GVNSYPSLYVFPS-GMNPEKYYGD-RSKESLVKF 100
>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 = 40.0 bits (94), Expect = 1e-04
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 204 EPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPT 263
+P LV +APWC C+ + ELA + G VK K D + + A K + S PT
Sbjct: 15 KPVLVDFWAPWCGPCKMIAPILEELAKEYEG-KVKFVKLNVD-ENPDIA-AKYGIRSIPT 71
Query: 264 ILFFPK 269
+L F
Sbjct: 72 LLLFKN 77
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 206 WLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTIL 265
W++ YAPWC CQ ++ + E AD G+ V K D Q+ + + + PTI
Sbjct: 19 WMIEFYAPWCPACQQLQPEWEEFADWSDDLGINVAK--VDVTQEPGLSGRFFVTALPTIY 76
Query: 266 FFPKHSSKPI--KYPSERRDVDSLMAFV 291
H+ + +Y RD + L++F+
Sbjct: 77 ----HAKDGVFRRYQGP-RDKEDLISFI 99
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 38.0 bits (87), Expect = 0.001
Identities = 20/61 (32%), Positives = 30/61 (49%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTILF 266
LV +APWC C+A ELA++ G+ V D + A+ + + S PT+L
Sbjct: 36 LVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVAVRSIPTLLL 95
Query: 267 F 267
F
Sbjct: 96 F 96
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 35.9 bits (83), Expect = 0.005
Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 15/86 (17%)
Query: 207 LVVLYAPWCQFCQAMEG---SYVELADKLAGNGV-----------KVGKFRADGDQKEYA 252
LVV P C +C+ + ++ + L N V +KE A
Sbjct: 9 LVVFTDPDCPYCKKLHKELLKDPDVQEYLKDNFVVIYVNVDDSKEVTDFDGETLSEKELA 68
Query: 253 KQKLQLGSFPTILFFPKHSSKPIKYP 278
+K + PTI+F + + P
Sbjct: 69 -RKYGVRGTPTIVFLDGDGKEVARLP 93
>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 = 35.4 bits (82), Expect = 0.007
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKL---AGNGVKVGKFRADGDQKEYAKQKLQLGSFPT 263
LV YA WC+F Q + + E A K+ + KV + D D++ + ++ +PT
Sbjct: 22 LVNFYADWCRFSQMLHPIFEEAAAKIKEEFPDAGKVVWGKVDCDKESDIADRYRINKYPT 81
Query: 264 I-LFFPKHSSKPIKYPSERRDVDSLMAFV 291
+ LF K +Y + R V++L FV
Sbjct: 82 LKLFRNGMMMK-REYRGQ-RSVEALAEFV 108
>gnl|CDD|181465 PRK08557, PRK08557, hypothetical protein; Provisional.
Length = 417
Score = 37.4 bits (87), Expect = 0.007
Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 13/101 (12%)
Query: 28 CCRVRKVRPLRRALKGLRAW-----ITGQRKDQSPGTRSEIPVVQVDPVFEGLEGGVGSL 82
C K+ PL+ LK I G RK +S TR+ + +E G +
Sbjct: 262 CNSACKLMPLKEYLKKKYGNKKVLTIDGSRKYES-FTRANLD-------YERKSGFIDFQ 313
Query: 83 VKWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPC 123
P+ + DIW+++ D+ N L+ +G+ IGC C
Sbjct: 314 TNVFPILDWNSLDIWSYIYLNDILYNPLYDKGFERIGCYLC 354
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 37.0 bits (86), Expect = 0.011
Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 15/106 (14%)
Query: 197 ARLDHRQEPWLVVLYAPWCQFCQAMEG---SYVELADKLAGNGVKVGKFRAD----GDQK 249
A + + +P ++ YA WC C+ E S ++ L V +AD
Sbjct: 468 ALAEAKAKPVMLDFYADWCVTCKENEKYTFSDPQVQQALQD----VVLLQADVTANDPAI 523
Query: 250 EYAKQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFVDALR 295
++L + PT LFF S+P D AF++ L
Sbjct: 524 TALLKRLGVFGVPTYLFFGPQGSEPEILT-GFLTAD---AFLEHLE 565
>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 = 34.3 bits (79), Expect = 0.016
Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 178 DIFNSQNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGV 237
D F+ + +T ++ EN ++P+L+ + + WC C +E + E+ +L GV
Sbjct: 1 DSFDYKYSLTFSQ--YENEIVPKSFKKPYLIKITSDWCFSCIHIEPVWKEVIQELEPLGV 58
Query: 238 KVGKFRADGDQKEYAKQKLQLGSFPTIL 265
+ + + +KL S P I+
Sbjct: 59 GIAT--VNAGHERRLARKLGAHSVPAIV 84
>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 = 33.1 bits (76), Expect = 0.030
Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 10/99 (10%)
Query: 196 LARLDHRQEP--WLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRAD-GDQKEYA 252
L V+ YA WC F + + + L+ ++ + K
Sbjct: 9 ALDLMAFNREDYTAVLFYASWCPFSASFRPHF----NALSSMFPQIRHLAIEESSIKPSL 64
Query: 253 KQKLQLGSFPTILFFPKHSSKPIKYPSERRDVDSLMAFV 291
+ + FPTIL F +S+ ++Y + R +DSL AF
Sbjct: 65 LSRYGVVGFPTILLF--NSTPRVRY-NGTRTLDSLAAFY 100
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 32.4 bits (75), Expect = 0.21
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 159 DAAVNGNGNGAGNAS-EAVADIFNSQNLVT-LNRTGMENLARL 199
D +VNG G AGNA+ E + + T ++ + ++R
Sbjct: 220 DGSVNGLGERAGNAATEDLVAALEGLGIDTGIDLEKLLEISRY 262
>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 = 0.25
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 205 PWLVVLYAPWCQFCQAMEGSYVELADK 231
P LV YA WC CQ M +L K
Sbjct: 22 PTLVEFYADWCTVCQEMAPDVAKLKQK 48
>gnl|CDD|212823 cd11890, MIA, Melanoma Inhibitory Activity protein. MIA is a
single domain protein that adopts a Src Homology 3 (SH3)
domain-like fold; it contains an additional antiparallel
beta sheet and two disulfide bonds compared to classical
SH3 domains. MIA is secreted from malignant melanoma
cells and it plays an important role in melanoma
development and invasion. MIA is expressed by
chondrocytes in normal tissues and may be important in
the cartilage cell phenotype. Unlike classical SH3
domains, MIA does not bind proline-rich ligands. It
binds peptide ligands with sequence similarity to type
III human fibronectin repeats.
Length = 98
Score = 30.2 bits (68), Expect = 0.35
Identities = 21/66 (31%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 211 YAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFPTILFFPKH 270
AP C+F G V + KL G G GD Y +Q +LG FP+ +
Sbjct: 23 MAPDCRFIPIQRGQVVYVFSKLKGRGRLFWGGSVQGDY--YGEQAARLGYFPSSIVQEDQ 80
Query: 271 SSKPIK 276
KP K
Sbjct: 81 YLKPGK 86
>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 = 0.40
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 200 DHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKV 239
D + + LV +A WC C+A LA + +GV+V
Sbjct: 16 DLKGKVVLVNFWASWCPPCRAEMPELEALAKEYKDDGVEV 55
>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 = 29.9 bits (68), Expect = 0.41
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 203 QEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSFP 262
Q P +V +AP + + LA++ G V + + D + Q+ + + P
Sbjct: 12 QVPVVVDFWAPRSPPSKELLPLLERLAEEYQGQFVLA---KVNCDAQPQIAQQFGVQALP 68
Query: 263 TILFF 267
T+ F
Sbjct: 69 TVYLF 73
>gnl|CDD|239260 cd02962, TMX2, TMX2 family; composed of proteins similar to human
TMX2, a 372-amino acid TRX-related transmembrane
protein, identified and characterized through the
cloning of its cDNA from a human fetal library. It
contains a TRX domain but the redox active CXXC motif is
replaced with SXXC. Sequence analysis predicts that TMX2
may be a Type I membrane protein, with its C-terminal
half protruding on the luminal side of the endoplasmic
reticulum (ER). In addition to the TRX domain,
transmembrane region and ER-retention signal, TMX2 also
contains a Myb DNA-binding domain repeat signature and a
dileucine motif in the tail.
Length = 152
Score = 30.8 bits (70), Expect = 0.42
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 182 SQNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGK 241
+++ +E D R WLV + W C + EL+ K N +K GK
Sbjct: 27 PEHIKYFTPKTLEEELERDKRVT-WLVEFFTTWSPECVNFAPVFAELSLKYNNNNLKFGK 85
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 31.6 bits (72), Expect = 0.43
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 202 RQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAKQKLQLGSF 261
R+ P LV +APWC C+ + + +LA + G K+ K D + A Q + S
Sbjct: 42 REVPVLVDFWAPWCGPCKQLTPTLEKLAAEYKG-KFKLAKVNCDAEP-MVAAQ-FGVQSI 98
Query: 262 PTILFF 267
PT+ F
Sbjct: 99 PTVYAF 104
>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 = 29.9 bits (68), Expect = 0.43
Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 12/87 (13%)
Query: 196 LARLDHRQEPWLVVLYAPWCQFCQAMEGSYV----ELADKLAGNGVKVGKFRAD---GDQ 248
LA+ + +P V A WC C+ E V E+ L + V + RAD D
Sbjct: 4 LAQALAQGKPVFVDFTADWCVTCKVNE-KVVFSDPEVQAALKKDVVLL---RADWTKNDP 59
Query: 249 KEYA-KQKLQLGSFPTILFFPKHSSKP 274
+ A ++ + PT LF+
Sbjct: 60 EITALLKRFGVFGPPTYLFYGPGGEPE 86
>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 = 29.9 bits (68), Expect = 0.60
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 206 WLVVLYAPWCQFCQAMEGSYVELADKLAG--NGVKVGKFRADGDQKEYAK--QKLQLGSF 261
WLV YA WC C+A ++ +LA L V+V D +E + + +
Sbjct: 22 WLVEFYASWCGHCRAFAPTWKKLARDLRKWRPVVRVA--AVDCADEENVALCRDFGVTGY 79
Query: 262 PTILFFP 268
PT+ +FP
Sbjct: 80 PTLRYFP 86
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 30.0 bits (68), Expect = 0.60
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 193 MENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNG--VKVGKFRADGDQKE 250
E L +L P ++ +APWC C+ + ++A + +G VKV ++E
Sbjct: 42 GETLDKLLQDDLPVVIDFWAPWCGPCRNFAPIFEDVAAERSGKVRFVKVNT----EAERE 97
Query: 251 YAKQKLQLGSFPTILFF 267
+ + ++ S PTI+ F
Sbjct: 98 LSAR-FRIRSIPTIMIF 113
>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 = 29.2 bits (66), Expect = 0.66
Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 6/78 (7%)
Query: 194 ENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYV--ELADKLAGNGVKVGKFRADGDQKEY 251
E LA+ +P LV A WC CQA++ ++ LA V + R D ++
Sbjct: 8 EALAKAREEGKPLLVDFGADWCPTCQALDRDFLSDPRVKALAEKFVLL---RVDVTTRDP 64
Query: 252 AKQKLQLGSFPTILFFPK 269
G P ++F
Sbjct: 65 NLLLDGQG-VPHVVFLDP 81
>gnl|CDD|239304 cd03006, PDI_a_EFP1_N, PDIa family, N-terminal EFP1 subfamily; EFP1
is a binding partner protein of thyroid oxidase (ThOX),
also called Duox. ThOX proteins are responsible for the
generation of hydrogen peroxide, a crucial substrate of
thyroperoxidase, which functions to iodinate
thyroglobulin and synthesize thyroid hormones. EFP1 was
isolated through a yeast two-hybrid method using the
EF-hand fragment of dog Duox1 as a bait. It could be one
of the partners in the assembly of a multiprotein
complex constituting the thyroid hydrogen peroxide
generating system. EFP1 contains two TRX domains related
to the redox active TRX domains of protein disulfide
isomerase (PDI). This subfamily is composed of the
N-terminal TRX domain of EFP1, which contains a CXXS
sequence in place of the typical CXXC motif, similar to
ERp44. The CXXS motif allows the formation of stable
mixed disulfides, crucial for the ER-retention function
of ERp44.
Length = 113
Score = 29.0 bits (65), Expect = 1.0
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 193 MENLARLDHRQ---EPWLVVLYAPWCQFCQAMEGSYVELADKLA 233
L + + E LV+ YAPW QA + ++A KL+
Sbjct: 16 KGQLDYAEELRTDAEVSLVMYYAPWDAQSQAARQEFEQVAQKLS 59
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 30.7 bits (70), Expect = 1.1
Identities = 29/100 (29%), Positives = 53/100 (53%), Gaps = 12/100 (12%)
Query: 28 CCRVRKVRPLRRALK--GLRAWIT--GQRKDQSPGTRSEIPVVQVDPVFEGLEGGVGSLV 83
CC+V K+ P+ RA+K + +T GQRK +S +R++ P V +P V + +
Sbjct: 325 CCKVCKLGPITRAIKENFPKGCLTFVGQRKYES-FSRAKSPRVWRNPW-------VPNQI 376
Query: 84 KWNPVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPC 123
+P+ + ++W ++ +P N L+ +G+ IGC C
Sbjct: 377 GASPIQDWTALEVWLYIFWRKLPYNPLYERGFDRIGCWLC 416
>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 = 28.8 bits (65), Expect = 1.1
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKEYAK 253
L+ +A WC C+A EL +KL V++ D D++E+ K
Sbjct: 5 LLYFWASWCPPCRAFTPELKELYEKLKKPKVEIVYVSLDRDEEEWKK 51
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 29.1 bits (66), Expect = 1.4
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 208 VVLYAPWCQFCQAMEGSYVELADKLAGNGVKVGKFRADGDQKE 250
V+++ P + ELA+ L G+KV DG Q+E
Sbjct: 31 VLIFCPSKKMLD-------ELAELLRKPGIKVAALHGDGSQEE 66
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 29.6 bits (67), Expect = 1.7
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 280 ERRDVDSLMAFVDAL 294
RRD+ SLMA +DAL
Sbjct: 189 FRRDMPSLMALLDAL 203
>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 = 28.4 bits (64), Expect = 2.4
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 202 RQEPWLVVLYAPWCQFCQAMEGSYVELAD 230
+P LV +A WC C+ + +LA
Sbjct: 19 SGKPVLVYFWATWCPVCRFTSPTVNQLAA 47
>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 = 28.7 bits (65), Expect = 3.3
Identities = 21/86 (24%), Positives = 28/86 (32%), Gaps = 22/86 (25%)
Query: 207 LVVLYAPWCQFCQAMEGSYVELADKLAGNGVKV------GKF-------RADGDQKEYAK 253
L Y C +CQA ADK G V G R D Q
Sbjct: 124 LFFFYRGDCPYCQAQAPILQAFADK---YGFSVIPVSVDGGPLPGFPNNRVDTGQ----A 176
Query: 254 QKLQLGSFPTILFFPKHSS--KPIKY 277
Q+L + + P + + KP+ Y
Sbjct: 177 QRLGVKTTPALFLVDPKTGKVKPVAY 202
>gnl|CDD|235310 PRK04750, ubiB, putative ubiquinone biosynthesis protein UbiB;
Reviewed.
Length = 537
Score = 29.1 bits (66), Expect = 3.4
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 32 RKVRPLRRALKGLRAWITGQRKDQSPGTRSEIPVVQVDPVF 72
R RPLR + L W+ + KD+ G R + + ++ P+F
Sbjct: 27 RLTRPLRLWRRSLF-WMPNRHKDKPRGERLRLALEELGPIF 66
>gnl|CDD|236300 PRK08576, PRK08576, hypothetical protein; Provisional.
Length = 438
Score = 28.5 bits (64), Expect = 4.3
Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 9/97 (9%)
Query: 29 CRVRKVRPLRRALKGLR--AWITGQRKDQSPGTRSEIPVVQVDPVFEGLEGGVGSLVKWN 86
C KV L A++ L + G R +S R P PV E LV
Sbjct: 314 CTKLKVEALEEAIRELEDGLLVVGDRDGESA-RRRLRP-----PVVERKTNFGKILVV-M 366
Query: 87 PVANVKGNDIWNFLRTMDVPINSLHSQGYISIGCEPC 123
P+ G + ++ + +N L+ +G+ +GC C
Sbjct: 367 PIKFWSGAMVQLYILMNGLELNPLYYKGFYRLGCYIC 403
>gnl|CDD|240484 cd12904, SPRY_BSPRY, SPRY domain in Ro-Ret family. This domain,
named BSPRY, has been identified in the Ro-Ret family,
since the protein is composed of a B-box, an
alpha-helical coiled coil and a SPRY domain. The gene
for BSPRY resides on human chromosome 9 and is
specifically expressed in testis. The function of BSPRY
is not known, but several related proteins of the
RING-Box-coiled-coil (RBCC) family have been implicated
in cell transformation.
Length = 170
Score = 27.9 bits (62), Expect = 4.7
Identities = 14/51 (27%), Positives = 20/51 (39%)
Query: 187 TLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYVELADKLAGNGV 237
+L R G N ARL + W+ Y +F + +EL GV
Sbjct: 75 SLERKGSGNEARLGYNANSWVFSRYDGDFRFSHNGQHVPLELLRGPKRIGV 125
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 28.6 bits (65), Expect = 4.9
Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 19/94 (20%)
Query: 183 QNLVTLNRTGMENLARLDHRQEPWLVVLYAPWCQFCQAMEGSYV----ELADKLAGNGVK 238
+ + L++ LA + +P ++ LYA WC C+ E Y ++ LA +
Sbjct: 458 KTVAELDQA----LAEAKGKGKPVMLDLYADWCVACKEFE-KYTFSDPQVQQALADTVL- 511
Query: 239 VGKFRAD-----GDQKEYAKQKLQLGSFPTILFF 267
+AD + K + PTILFF
Sbjct: 512 ---LQADVTANNAEDVALLKH-YNVLGLPTILFF 541
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 28.0 bits (63), Expect = 6.5
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 147 ECGLHKGNIKQEDAAVNGNGNGAGNAS-EAVADI 179
+ G Q + VNG G AGNA+ E V
Sbjct: 210 LAAVEAG-ADQVEGTVNGIGERAGNAALEEVVLA 242
>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 = 26.8 bits (60), Expect = 6.9
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 208 VVLY---APWCQFCQAMEGSYVELADKLAGNGVKV 239
VVL+ + C + +L ++ GV+V
Sbjct: 28 VVLFFYPKDFTPVCTTELPALADLYEEFKKLGVEV 62
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 27.3 bits (61), Expect = 8.8
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 159 DAAVNGNGNGAGNAS-EAVA 177
D VNG G AGNA+ E +
Sbjct: 210 DGTVNGLGERAGNAALEELV 229
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 0.136 0.430
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: 14,856,343
Number of extensions: 1373329
Number of successful extensions: 1176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1139
Number of HSP's successfully gapped: 66
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
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: 59 (26.5 bits)