RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3969
(86 letters)
>gnl|CDD|239328 cd03030, GRX_SH3BGR, Glutaredoxin (GRX) family, SH3BGR (SH3
domain binding glutamic acid-rich protein) subfamily; a
recently-identified subfamily composed of SH3BGR and
similar proteins possessing significant sequence
similarity to GRX, but without a redox active CXXC
motif. The SH3BGR gene was cloned in an effort to
identify genes mapping to chromosome 21, which could be
involved in the pathogenesis of congenital heart
disease affecting Down syndrome newborns. Several human
SH3BGR-like (SH3BGRL) genes have been identified since,
mapping to different locations in the chromosome. Of
these, SH3BGRL3 was identified as a tumor necrosis
factor (TNF) alpha inhibitory protein and was also
named TIP-B1. Upregulation of expression of SH3BGRL3 is
associated with differentiation. It has been suggested
that it functions as a regulator of
differentiation-related signal transduction pathways.
Length = 92
Score = 79.2 bits (196), Expect = 3e-21
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 8/73 (10%)
Query: 10 TVRGVKGVKKRQQRVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNP 69
+ G +KKRQQ VL L++K I++ +DI+ E +++M++N P
Sbjct: 8 SSSGSTEIKKRQQEVLGFLEAKKIEFEEVDISM--NEENRQWMRENVPNE------NGKP 59
Query: 70 LPPQIFNEEDYCG 82
LPPQIFN ++YCG
Sbjct: 60 LPPQIFNGDEYCG 72
>gnl|CDD|218321 pfam04908, SH3BGR, SH3-binding, glutamic acid-rich protein.
Length = 92
Score = 76.0 bits (187), Expect = 6e-20
Identities = 31/73 (42%), Positives = 44/73 (60%), Gaps = 10/73 (13%)
Query: 10 TVRGVKGVKKRQQRVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNP 69
+ G +KK+QQRVLMILD+ I + +DIT+ E ++ +M++N P
Sbjct: 9 SSSGSPEIKKKQQRVLMILDANKIPFDEVDITK--DEEQRRWMRENPP--------NGAP 58
Query: 70 LPPQIFNEEDYCG 82
LPPQIFNE+ YCG
Sbjct: 59 LPPQIFNEDQYCG 71
>gnl|CDD|239017 cd02066, GRX_family, Glutaredoxin (GRX) family; composed of GRX,
approximately 10 kDa in size, and proteins containing a
GRX or GRX-like domain. GRX is a glutathione (GSH)
dependent reductase, catalyzing the disulfide reduction
of target proteins such as ribonucleotide reductase. It
contains a redox active CXXC motif in a TRX fold and
uses a similar dithiol mechanism employed by TRXs for
intramolecular disulfide bond reduction of protein
substrates. Unlike TRX, GRX has preference for mixed
GSH disulfide substrates, in which it uses a monothiol
mechanism where only the N-terminal cysteine is
required. The flow of reducing equivalents in the GRX
system goes from NADPH -> GSH reductase -> GSH -> GRX
-> protein substrates. By altering the redox state of
target proteins, GRX is involved in many cellular
functions including DNA synthesis, signal transduction
and the defense against oxidative stress. Different
classes are known including human GRX1 and GRX2, as
well as E. coli GRX1 and GRX3, which are members of
this family. E. coli GRX2, however, is a 24-kDa protein
that belongs to the GSH S-transferase (GST) family.
Length = 72
Score = 51.7 bits (125), Expect = 1e-10
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 14 VKGVKKRQQRVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNPLPPQ 73
K +R +L+S I++ IDI E +E +++ S P PQ
Sbjct: 6 SKSTCPYCKRAKRLLESLGIEFEEIDILED--GELREELKELSGW----------PTVPQ 53
Query: 74 IFNEEDYCG 82
IF ++ G
Sbjct: 54 IFINGEFIG 62
>gnl|CDD|239510 cd03418, GRX_GRXb_1_3_like, Glutaredoxin (GRX) family, GRX
bacterial class 1 and 3 (b_1_3)-like subfamily;
composed of bacterial GRXs, approximately 10 kDa in
size, and proteins containing a GRX or GRX-like domain.
GRX is a glutathione (GSH) dependent reductase,
catalyzing the disulfide reduction of target proteins
such as ribonucleotide reductase. It contains a redox
active CXXC motif in a TRX fold and uses a similar
dithiol mechanism employed by TRXs for intramolecular
disulfide bond reduction of protein substrates. Unlike
TRX, GRX has preference for mixed GSH disulfide
substrates, in which it uses a monothiol mechanism
where only the N-terminal cysteine is required. The
flow of reducing equivalents in the GRX system goes
from NADPH -> GSH reductase -> GSH -> GRX -> protein
substrates. By altering the redox state of target
proteins, GRX is involved in many cellular functions
including DNA synthesis, signal transduction and the
defense against oxidative stress. Different classes are
known including E. coli GRX1 and GRX3, which are
members of this subfamily.
Length = 75
Score = 32.2 bits (74), Expect = 0.005
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 28 LDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNPLPPQIF 75
LD K +DY ID+ G +E M S TV PQIF
Sbjct: 20 LDKKGVDYEEIDVD--GDPALREEMINRSGGR---RTV------PQIF 56
>gnl|CDD|215931 pfam00462, Glutaredoxin, Glutaredoxin.
Length = 60
Score = 30.1 bits (69), Expect = 0.023
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 23 RVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNPLPPQIF 75
R +LDS + + ID+ E +E +++ S TV PQ+F
Sbjct: 14 RAKRLLDSLGVKFEEIDVDE--DPEIREELKELSGW----PTV------PQVF 54
>gnl|CDD|223767 COG0695, GrxC, Glutaredoxin and related proteins
[Posttranslational modification, protein turnover,
chaperones].
Length = 80
Score = 30.4 bits (69), Expect = 0.029
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 10/53 (18%)
Query: 23 RVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNPLPPQIF 75
R +LD K +DY ID+ + E +E +++ TV PQIF
Sbjct: 16 RAKRLLDRKGVDYEEIDVDDDEPEEAREMVKRGKGQR----TV------PQIF 58
>gnl|CDD|222110 pfam13409, GST_N_2, Glutathione S-transferase, N-terminal domain.
This family is closely related to pfam02798.
Length = 68
Score = 29.9 bits (68), Expect = 0.041
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKAT 59
+RV + L+ K + Y + ++ + E + N
Sbjct: 6 RRVRLALELKGLPYEIEEVPLDPWDKPPELLALNPLGK 43
>gnl|CDD|233766 TIGR02181, GRX_bact, Glutaredoxin, GrxC family. Glutaredoxins
are thioltransferases (disulfide reductases) which
utilize glutathione and NADPH as cofactors. Oxidized
glutathione is regenerated by glutathione reductase.
Together these components compose the glutathione
system. Glutaredoxins utilize the CXXC motif common to
thioredoxins and are involved in multiple cellular
processes including protection from redox stress,
reduction of critical enzymes such as ribonucleotide
reductase and the generation of reduced sulfur for iron
sulfur cluster formation. Glutaredoxins are capable of
reduction of mixed disulfides of glutathione as well as
the formation of glutathione mixed disulfides. This
family of glutaredoxins includes the E. coli protein
GrxC (Grx3) which appears to have a secondary role in
reducing ribonucleotide reductase (in the absence of
GrxA) possibly indicating a role in the reduction of
other protein disulfides [Energy metabolism, Electron
transport].
Length = 79
Score = 29.1 bits (66), Expect = 0.079
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 12/48 (25%)
Query: 28 LDSKNIDYTVIDITEPGKENEKEFMQQNSKATPSDSTVKSNPLPPQIF 75
L SK + +T I + G ++ M Q S TV PQIF
Sbjct: 19 LSSKGVTFTEIRVD--GDPALRDEMMQRSGRR----TV------PQIF 54
>gnl|CDD|238319 cd00570, GST_N_family, Glutathione S-transferase (GST) family,
N-terminal domain; a large, diverse group of cytosolic
dimeric proteins involved in cellular detoxification by
catalyzing the conjugation of glutathione (GSH) with a
wide range of endogenous and xenobiotic alkylating
agents, including carcinogens, therapeutic drugs,
environmental toxins and products of oxidative stress.
In addition, GSTs also show GSH peroxidase activity and
are involved in the synthesis of prostaglandins and
leukotrienes. This family, also referred to as soluble
GSTs, is the largest family of GSH transferases and is
only distantly related to the mitochondrial GSTs (GSTK
subfamily, a member of the DsbA family). Soluble GSTs
bear no structural similarity to microsomal GSTs (MAPEG
family) and display additional activities unique to
their group, such as catalyzing thiolysis, reduction
and isomerization of certain compounds. The GST fold
contains an N-terminal TRX-fold domain and a C-terminal
alpha helical domain, with an active site located in a
cleft between the two domains. Based on sequence
similarity, different classes of GSTs have been
identified, which display varying tissue distribution,
substrate specificities and additional specific
activities. In humans, GSTs display polymorphisms which
may influence individual susceptibility to diseases
such as cancer, arthritis, allergy and sclerosis. Some
GST family members with non-GST functions include
glutaredoxin 2, the CLIC subfamily of anion channels,
prion protein Ure2p, crystallins, metaxin 2 and
stringent starvation protein A.
Length = 71
Score = 28.7 bits (65), Expect = 0.094
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEFMQQN 55
RV + L+ K + Y ++ + G+ ++EF+ N
Sbjct: 13 LRVRLALEEKGLPYELVPVD-LGEGEQEEFLALN 45
>gnl|CDD|225272 COG2409, COG2409, Predicted drug exporters of the RND superfamily
[General function prediction only].
Length = 937
Score = 29.3 bits (66), Expect = 0.21
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 12/61 (19%)
Query: 24 VLMILDSKNIDYTVIDITEPGKENEKEFMQQNS----KATPSDSTVKSNPLPPQIFNEED 79
+ L + DY + ++ ++ + +A + ST S LPP+ F D
Sbjct: 632 RIAALFGLSTDYEIFLLSR--------QREELAAAMGQAFDTASTDDSFYLPPEAFANGD 683
Query: 80 Y 80
+
Sbjct: 684 F 684
>gnl|CDD|239349 cd03051, GST_N_GTT2_like, GST_N family, Saccharomyces cerevisiae
GTT2-like subfamily; composed of predominantly
uncharacterized proteins with similarity to the S.
cerevisiae GST protein, GTT2. GSTs are cytosolic
dimeric proteins involved in cellular detoxification by
catalyzing the conjugation of glutathione (GSH) with a
wide range of endogenous and xenobiotic alkylating
agents, including carcinogens, therapeutic drugs,
environmental toxins and products of oxidative stress.
GSTs also show GSH peroxidase activity and are involved
in the synthesis of prostaglandins and leukotrienes.
The GST fold contains an N-terminal TRX-fold domain and
a C-terminal alpha helical domain, with an active site
located in a cleft between the two domains. GTT2, a
homodimer, exhibits GST activity with standard
substrates. Strains with deleted GTT2 genes are viable
but exhibit increased sensitivity to heat shock.
Length = 74
Score = 28.0 bits (63), Expect = 0.22
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEF 51
+RV + L K ID ++ + E
Sbjct: 13 RRVRIFLAEKGIDVPLVTVDLAAGEQRSPE 42
>gnl|CDD|239334 cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown
subfamily; uncharacterized proteins containing a CXXC
motif with similarity to thioredoxin (TRX)-fold arsenic
reductases, ArsC. Proteins containing a redox active
CXXC motif like TRX and glutaredoxin (GRX) function as
protein disulfide oxidoreductases, altering the redox
state of target proteins via the reversible oxidation
of the active site dithiol. ArsC catalyzes the
reduction of arsenate [As(V)] to arsenite [As(III)],
using reducing equivalents derived from glutathione via
GRX, through a single catalytic cysteine.
Length = 111
Score = 28.4 bits (64), Expect = 0.27
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 28 LDSKNIDYTVIDITE--PGKENEKEFMQQ 54
LD +DYT IDI E P KE K+++++
Sbjct: 19 LDEHGVDYTAIDIVEEPPSKEELKKWLEK 47
>gnl|CDD|239353 cd03055, GST_N_Omega, GST_N family, Class Omega subfamily; GSTs
are cytosolic dimeric proteins involved in cellular
detoxification by catalyzing the conjugation of
glutathione (GSH) with a wide range of endogenous and
xenobiotic alkylating agents, including carcinogens,
therapeutic drugs, environmental toxins and products of
oxidative stress. The GST fold contains an N-terminal
TRX-fold domain and a C-terminal alpha helical domain,
with an active site located in a cleft between the two
domains. Class Omega GSTs show little or no
GSH-conjugating activity towards standard GST
substrates. Instead, they catalyze the GSH dependent
reduction of protein disulfides, dehydroascorbate and
monomethylarsonate, activities which are more
characteristic of glutaredoxins. They contain a
conserved cysteine equivalent to the first cysteine in
the CXXC motif of glutaredoxins, which is a redox
active residue capable of reducing GSH mixed disulfides
in a monothiol mechanism. Polymorphisms of the class
Omega GST genes may be associated with the development
of some types of cancer and the age-at-onset of both
Alzheimer's and Parkinson's diseases.
Length = 89
Score = 27.3 bits (61), Expect = 0.51
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 22 QRVLMILDSKNIDYTVIDI 40
QR ++L +KNI + VI+I
Sbjct: 31 QRARLVLAAKNIPHEVINI 49
>gnl|CDD|205595 pfam13417, GST_N_3, Glutathione S-transferase, N-terminal domain.
Length = 75
Score = 26.8 bits (60), Expect = 0.55
Identities = 7/38 (18%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEFMQQNSKAT 59
++V + L K + Y +++ P + E + N
Sbjct: 11 RKVRLALREKGLPYEEVEV--PPGDKPPELLALNPLGK 46
>gnl|CDD|223698 COG0625, Gst, Glutathione S-transferase [Posttranslational
modification, protein turnover, chaperones].
Length = 211
Score = 26.7 bits (59), Expect = 1.3
Identities = 6/34 (17%), Positives = 18/34 (52%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEFMQQN 55
++V + L+ K + Y ++ + ++ +F+ N
Sbjct: 13 RKVRLALEEKGLPYEIVLVDLDAEQKPPDFLALN 46
>gnl|CDD|220346 pfam09692, Arb1, Argonaute siRNA chaperone (ARC) complex subunit
Arb1. Arb1 is required for histone H3 Lys9 (H3-K9)
methylation, heterochromatin, assembly and siRNA
generation in fission yeast.
Length = 394
Score = 26.2 bits (58), Expect = 2.3
Identities = 3/22 (13%), Positives = 7/22 (31%)
Query: 35 YTVIDITEPGKENEKEFMQQNS 56
+ V+ I P + +
Sbjct: 274 FEVVAIHLPSEAVRAFYQTVAP 295
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 26.2 bits (58), Expect = 2.7
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 41 TEPGKENEKEFMQQNSKAT---PSDSTVKSNPLPPQIF 75
T GK EKEF++ S + P++ + P +I+
Sbjct: 366 TGTGKVAEKEFIETYSLSVVKIPTNKPIIRIDYPDKIY 403
>gnl|CDD|239274 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small
monomeric protein with a conserved redox active CXXC
motif within a TRX fold, characterized by a
glutaredoxin (GRX)-like sequence and TRX-like activity
profile. In vitro, it displays protein disulfide
reductase activity that is dependent on TRX reductase,
not glutathione (GSH). It is part of the NrdHIEF
operon, where NrdEF codes for class Ib ribonucleotide
reductase (RNR-Ib), an efficient enzyme at low oxygen
levels. Under these conditions when GSH is mostly
conjugated to spermidine, NrdH can still function and
act as a hydrogen donor for RNR-Ib. It has been
suggested that the NrdHEF system may be the oldest RNR
reducing system, capable of functioning in a
microaerophilic environment, where GSH was not yet
available. NrdH from Corynebacterium ammoniagenes can
form domain-swapped dimers, although it is unknown if
this happens in vivo. Domain-swapped dimerization,
which results in the blocking of the TRX reductase
binding site, could be a mechanism for regulating the
oxidation state of the protein.
Length = 73
Score = 24.9 bits (55), Expect = 3.1
Identities = 6/27 (22%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 28 LDSKNIDYTVIDITEPGKENEKEFMQQ 54
LD + I + +D+ E E +++
Sbjct: 20 LDERGIPFEEVDVDE--DPEALEELKK 44
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 25.7 bits (57), Expect = 3.3
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 6 KISNTVRGVKGVKKRQQRVLMILDSKN--IDY 35
I + +K V R + V + K +DY
Sbjct: 310 DILAGLETLKPVPGRMELVNI--GGKLVIVDY 339
>gnl|CDD|215378 PLN02702, PLN02702, L-idonate 5-dehydrogenase.
Length = 364
Score = 25.5 bits (56), Expect = 4.3
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 69 PLPPQIFNEEDYCGVFRY 86
PL P E D GVFRY
Sbjct: 294 PLTPAAAREVDVVGVFRY 311
>gnl|CDD|226919 COG4545, COG4545, Glutaredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 85
Score = 24.4 bits (53), Expect = 5.7
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 28 LDSKNIDYTVIDITEPGKENEKEFM 52
L+ N+DY ++ITE N K F+
Sbjct: 22 LERLNVDYDFVEITESMA-NLKRFL 45
>gnl|CDD|235720 PRK06156, PRK06156, hypothetical protein; Provisional.
Length = 520
Score = 24.9 bits (55), Expect = 5.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 28 LDSKNIDYTVIDITEPGKENEK 49
LD +N+D V++I G ++K
Sbjct: 90 LDYRNVDNRVLEIGLGGSGSDK 111
>gnl|CDD|201157 pfam00327, Ribosomal_L30, Ribosomal protein L30p/L7e. This
family includes prokaryotic L30 and eukaryotic L7.
Length = 52
Score = 23.2 bits (51), Expect = 8.8
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 11 VRGVKGVKKRQQRVLMILDSKNIDYTVI 38
+R + G +Q++ L +L + I+ TV
Sbjct: 7 IRSIIGRPPKQKKTLKLLGLRKINQTVF 34
>gnl|CDD|233310 TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase. This
model describes D-Ala--D-Ala ligase, an enzyme that
makes a required precursor of the bacterial cell wall.
It also describes some closely related proteins
responsible for resistance to glycopeptide antibiotics
such as vancomycin. The mechanism of glyopeptide
antibiotic resistance involves the production of
D-alanine-D-lactate (VanA and VanB families) or
D-alanine-D-serine (VanC). The seed alignment contains
only chromosomally encoded D-ala--D-ala ligases, but a
number of antibiotic resistance proteins score above
the trusted cutoff of this model [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 315
Score = 24.5 bits (54), Expect = 9.2
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 22 QRVLMILDSKNIDYTVIDITEPGKENEKEFMQQ 54
VL L D +DI + G K+ Q
Sbjct: 21 AAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQL 53
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
0.312 0.132 0.370
Gapped
Lambda K H
0.267 0.0795 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,166,950
Number of extensions: 314445
Number of successful extensions: 278
Number of sequences better than 10.0: 1
Number of HSP's gapped: 275
Number of HSP's successfully gapped: 31
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)