RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13445
(115 letters)
>gnl|CDD|239262 cd02964, TryX_like_family, Tryparedoxin (TryX)-like family;
composed of TryX and related proteins including
nucleoredoxin (NRX), rod-derived cone viability factor
(RdCVF) and the nematode homolog described as a 16-kD
class of TRX. Most members of this family, except
RdCVF, are protein disulfide oxidoreductases containing
an active site CXXC motif, similar to TRX.
Length = 132
Score = 31.0 bits (71), Expect = 0.067
Identities = 9/20 (45%), Positives = 9/20 (45%)
Query: 16 KIVFFYSSGVWCHHCEQFLP 35
K V Y S WC C F P
Sbjct: 18 KTVGLYFSASWCPPCRAFTP 37
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 31.2 bits (71), Expect = 0.077
Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+V F++ WC C+Q P
Sbjct: 47 LVDFWAP--WCGPCKQLTP 63
>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 = 28.7 bits (65), Expect = 0.29
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+V FY+ WC HC+ P
Sbjct: 19 LVEFYAP--WCGHCKALAP 35
>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 = 29.4 bits (66), Expect = 0.30
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)
Query: 16 KIVFFYSSGVWCHHCEQFLP 35
+VFFY S C +C QF P
Sbjct: 53 ALVFFYQST--CPYCHQFAP 70
>gnl|CDD|239307 cd03009, TryX_like_TryX_NRX, Tryparedoxin (TryX)-like family,
TryX and nucleoredoxin (NRX) subfamily; TryX and NRX
are thioredoxin (TRX)-like protein disulfide
oxidoreductases that alter the redox state of target
proteins via the reversible oxidation of an active
center CXXC motif. TryX is involved in the regulation
of oxidative stress in parasitic trypanosomatids by
reducing TryX peroxidase, which in turn catalyzes the
reduction of hydrogen peroxide and organic
hydroperoxides. TryX derives reducing equivalents from
reduced trypanothione, a polyamine peptide conjugate
unique to trypanosomatids, which is regenerated by the
NADPH-dependent flavoprotein trypanothione reductase.
Vertebrate NRX is a 400-amino acid nuclear protein with
one redox active TRX domain containing a CPPC active
site motif followed by one redox inactive TRX-like
domain. Mouse NRX transcripts are expressed in all
adult tissues but is restricted to the nervous system
and limb buds in embryos. Plant NRX, longer than the
vertebrate NRX by about 100-200 amino acids, is a
nuclear protein containing a redox inactive TRX-like
domain between two redox active TRX domains. Both
vertebrate and plant NRXs show thiol oxidoreductase
activity in vitro. Their localization in the nucleus
suggests a role in the redox regulation of nuclear
proteins such as transcription factors.
Length = 131
Score = 28.4 bits (64), Expect = 0.56
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 16 KIVFFYSSGVWCHHCEQFLPSSVD 39
K V Y S WC C F P V+
Sbjct: 19 KTVGLYFSASWCPPCRAFTPKLVE 42
>gnl|CDD|99989 cd03819, GT1_WavL_like, This family is most closely related to the
GT1 family of glycosyltransferases. WavL in Vibrio
cholerae has been shown to be involved in the
biosynthesis of the lipopolysaccharide core.
Length = 355
Score = 28.0 bits (63), Expect = 0.98
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 6/40 (15%)
Query: 76 RDHIQSHLGDKPFVCEHCFSNFARLRRLKEHILRMHPELI 115
R + P N ARLRRL I +++
Sbjct: 49 RHIKLPFISKNPLRI---LLNVARLRRL---IREEKVDIV 82
>gnl|CDD|178773 PLN03234, PLN03234, cytochrome P450 83B1; Provisional.
Length = 499
Score = 28.1 bits (62), Expect = 1.1
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 76 RDHIQSHLGDKPFVCEHCFSNFARLRRLKEHILRMHP 112
+D +++ +GDK +V E N L+ + + LR+ P
Sbjct: 326 QDEVRNVIGDKGYVSEEDIPNLPYLKAVIKESLRLEP 362
>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 = 26.9 bits (60), Expect = 1.4
Identities = 7/19 (36%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+++F++S WC C F P
Sbjct: 5 LLYFWAS--WCPPCRAFTP 21
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 25.4 bits (56), Expect = 1.6
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 74 HMRDHIQSHLGDKPFVCEHCFSNFAR 99
++R H+++H G+KP+ C C +F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>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 = 26.4 bits (59), Expect = 1.7
Identities = 6/19 (31%), Positives = 10/19 (52%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+V F++ WC C+ P
Sbjct: 14 VVDFWAP--WCGPCKAIAP 30
>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 = 26.5 bits (59), Expect = 2.2
Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 2/20 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLPS 36
+V FY+ WC C+ LP
Sbjct: 23 LVDFYAP--WCGPCQALLPE 40
>gnl|CDD|239299 cd03001, PDI_a_P5, PDIa family, P5 subfamily; composed of
eukaryotic proteins similar to human P5, a PDI-related
protein with a domain structure of aa'b (where a and a'
are redox active TRX domains and b is a redox inactive
TRX-like domain). Like PDI, P5 is located in the
endoplasmic reticulum (ER) and displays both isomerase
and chaperone activities, which are independent of each
other. Compared to PDI, the isomerase and chaperone
activities of P5 are lower. The first cysteine in the
CXXC motif of both redox active domains in P5 is
necessary for isomerase activity. The P5 gene was first
isolated as an amplified gene from a
hydroxyurea-resistant hamster cell line. The zebrafish
P5 homolog has been implicated to play a critical role
in establishing left/right asymmetries in the embryonic
midline. Some members of this subfamily are P5-like
proteins containing only one redox active TRX domain.
Length = 103
Score = 26.1 bits (58), Expect = 2.5
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+V FY+ WC HC+ P
Sbjct: 22 LVEFYAP--WCGHCKNLAP 38
>gnl|CDD|224299 COG1381, RecO, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 251
Score = 26.9 bits (60), Expect = 2.5
Identities = 19/91 (20%), Positives = 27/91 (29%), Gaps = 12/91 (13%)
Query: 6 YGMNFRICY-------SKIVFFYSSGVWCHHCEQFLPSSVDDLLLHSRKCASAHRPDKSY 58
G N C S G C C + P DLLL + +
Sbjct: 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCARAAPKPEKDLLLLFGRFLLDLLNRLAL 209
Query: 59 NYVCCICDYKSYKKSHMRDHIQSHLGDKPFV 89
+ K K R ++ +LG+KP
Sbjct: 210 KA-----ETKQAAKRITRQLLKEYLGEKPLK 235
>gnl|CDD|178712 PLN03168, PLN03168, chalcone synthase; Provisional.
Length = 389
Score = 26.9 bits (59), Expect = 2.6
Identities = 11/44 (25%), Positives = 15/44 (34%), Gaps = 3/44 (6%)
Query: 32 QFLPSSVDDLLLHSRKCASAHRPDKSYNYVCCICDYKSYKKSHM 75
+FL S D + C + ICD +K HM
Sbjct: 29 EFLQSEYPDFFFNITNCG---EKEALKAKFKRICDKSGIRKRHM 69
>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 = 26.2 bits (58), Expect = 3.1
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 14 YSKIVFFYSSGVWCHHCEQFLPS 36
Y+ +V FY+ WC HC+ P
Sbjct: 19 YTTLVEFYAP--WCGHCKNLKPE 39
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 26.6 bits (58), Expect = 3.4
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 85 DKPFVCEHCFSNFARLRRLKEHILRMH 111
DKP+ CE C + L LK H H
Sbjct: 396 DKPYRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|180864 PRK07168, PRK07168, bifunctional uroporphyrinogen-III
methyltransferase/uroporphyrinogen-III synthase;
Reviewed.
Length = 474
Score = 26.5 bits (58), Expect = 3.5
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 64 ICDYKSYKKSHMRDHIQSHLGDK--PFVCEH 92
+ D+ Y SH D I ++G K P +CE+
Sbjct: 151 LTDHGKYNSSHNSDTIAYYMGIKNLPTICEN 181
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 26.3 bits (58), Expect = 4.2
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 85 DKPFVCEHCFSNFARLRRLKEH 106
K + CE C R +L+ H
Sbjct: 196 SKLYFCEFCLKFMKRKEQLQRH 217
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.0 bits (52), Expect = 5.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 60 YVCCICDYKSYKKSHMRDHIQSH 82
Y C C KS +R+H+++H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 25.3 bits (56), Expect = 5.6
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 15 SKIVFFYSSGVWCHHCEQFLPS 36
+ +V FY+S WC HC F P+
Sbjct: 21 AWLVEFYAS--WCGHCRAFAPT 40
>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 = 25.3 bits (56), Expect = 5.7
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 17 IVFFYSSGVWCHHCEQFLP 35
+V FY+ WC HC+ P
Sbjct: 17 LVEFYAP--WCGHCKNLAP 33
>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 = 24.8 bits (55), Expect = 7.9
Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 2/18 (11%)
Query: 18 VFFYSSGVWCHHCEQFLP 35
V FY+ WC HC+ P
Sbjct: 23 VEFYAP--WCGHCKALAP 38
>gnl|CDD|203088 pfam04780, DUF629, Protein of unknown function (DUF629). This
family represents a region of several plant proteins of
unknown function. A C2H2 zinc finger is predicted in
this region in some family members, but the spacing
between the cysteine residues is not conserved
throughout the family.
Length = 463
Score = 25.4 bits (56), Expect = 8.3
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 3/50 (6%)
Query: 46 RKCASAHRPDKSYNY-VCCICDYKSYKKSHMRDHI-QSHLGD-KPFVCEH 92
+ S R ++ + + +C C K ++H+ Q H KP
Sbjct: 43 EQVLSFARENRKWRFWMCRTCSKKFSSSEECKNHLEQEHAAKFKPSSEMD 92
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase. Members
of this family are the tRNA modification enzyme TruA,
tRNA pseudouridine(38-40) synthase. In a few species
(e.g. Bacillus anthracis), TruA is represented by two
paralogs [Protein synthesis, tRNA and rRNA base
modification].
Length = 227
Score = 25.4 bits (56), Expect = 9.0
Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 12/68 (17%)
Query: 44 HSRKCASAHRPDKSYNYV--CCICDYKSYKKSHMRDHIQSHLGDKPFVCEHCFSNFARLR 101
H+R AS Y Y+ Y MR K + +H FSNF++ +
Sbjct: 99 HARFSASKRH----YRYILYNHRHYYSPLDLEKMRA------AAKQLLGKHDFSNFSKAK 148
Query: 102 RLKEHILR 109
+R
Sbjct: 149 SKSRSPIR 156
>gnl|CDD|182951 PRK11085, PRK11085, magnesium/nickel/cobalt transporter CorA;
Provisional.
Length = 316
Score = 25.1 bits (55), Expect = 9.5
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 1 MVMSSYGMNF 10
+V SSYGMNF
Sbjct: 271 LVASSYGMNF 280
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
0.331 0.140 0.481
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,719,529
Number of extensions: 453861
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 679
Number of HSP's successfully gapped: 54
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.3 bits)