RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13814
(75 letters)
>gnl|CDD|239314 cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily;
composed of PRXs containing only one conserved cysteine,
which serves as the peroxidatic cysteine. They are
homodimeric thiol-specific antioxidant (TSA) proteins
that confer a protective role in cells by reducing and
detoxifying hydrogen peroxide, peroxynitrite, and
organic hydroperoxides. As with all other PRXs, a
cysteine sulfenic acid intermediate is formed upon
reaction of 1-cys PRX with its substrates. Having no
resolving cysteine, the oxidized enzyme is resolved by
an external small-molecule or protein reductant such as
thioredoxin or glutaredoxin. Similar to typical 2-cys
PRX, 1-cys PRX forms a functional dimeric unit with a
B-type interface, as well as a decameric structure which
is stabilized in the reduced form of the enzyme. Other
oligomeric forms, tetramers and hexamers, have also been
reported. Mammalian 1-cys PRX is localized cellularly in
the cytosol and is expressed at high levels in brain,
eye, testes and lung. The seed-specific plant 1-cys PRXs
protect tissues from reactive oxygen species during
desiccation and are also called rehydrins.
Length = 203
Score = 84.9 bits (211), Expect = 1e-22
Identities = 30/73 (41%), Positives = 47/73 (64%), Gaps = 7/73 (9%)
Query: 3 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKL 62
DI+ Y + PF II D +R++A L ++D + + L TVRAV+II PD+K++L
Sbjct: 79 DIEEYT---GVEIPFPIIADPDREVAKLLGMIDPDAGSTL----TVRAVFIIDPDKKIRL 131
Query: 63 SIVYPASTGRSVE 75
+ YPA+TGR+ +
Sbjct: 132 ILYYPATTGRNFD 144
>gnl|CDD|223527 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 56.5 bits (137), Expect = 1e-11
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 13 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 72
G F +I D ++A +L E + +R +II PD ++ +V P + GR
Sbjct: 95 GKIKFPMIADPKGEIARAYGVLHPE------EGLALRGTFIIDPDGVIRHILVNPLTIGR 148
Query: 73 SV 74
+V
Sbjct: 149 NV 150
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 53.7 bits (129), Expect = 1e-10
Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 10/70 (14%)
Query: 10 DIKGDF----PFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIV 65
DI+ F PF +I D +++LA + +L+DE + TVR V+II P++ ++ I
Sbjct: 81 DIEERFGIKIPFPVIADIDKELAREYNLIDENSGA------TVRGVFIIDPNQIVRWMIY 134
Query: 66 YPASTGRSVE 75
YPA TGR+++
Sbjct: 135 YPAETGRNID 144
>gnl|CDD|239269 cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the
different classes of PRXs including many proteins
originally known as bacterioferritin comigratory
proteins (BCP), based on their electrophoretic mobility
before their function was identified. PRXs are
thiol-specific antioxidant (TSA) proteins also known as
TRX peroxidases and alkyl hydroperoxide reductase C22
(AhpC) proteins. They confer a protective antioxidant
role in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either TRX, glutathione,
trypanothione and AhpF. They are distinct from other
peroxidases in that they have no cofactors such as
metals or prosthetic groups. The first step of
catalysis, common to all PRXs, is the nucleophilic
attack by the catalytic cysteine (also known as the
peroxidatic cysteine) on the peroxide leading to
cleavage of the oxygen-oxygen bond and the formation of
a cysteine sulfenic acid intermediate. The second step
of the reaction, the resolution of the intermediate,
distinguishes the different types of PRXs. The presence
or absence of a second cysteine (the resolving cysteine)
classifies PRXs as either belonging to the 2-cys or
1-cys type. The resolving cysteine of 2-cys PRXs is
either on the same chain (atypical) or on the second
chain (typical) of a functional homodimer. Structural
and motif analysis of this growing family supports the
need for a new classification system. The peroxidase
activity of PRXs is regulated in vivo by irreversible
cysteine over-oxidation into a sulfinic acid,
phosphorylation and limited proteolysis.
Length = 140
Score = 49.9 bits (120), Expect = 2e-09
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 13 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 72
G F ++ D + + A +L E++ + RA +II PD K++ V P TGR
Sbjct: 78 GGLNFPLLSDPDGEFAKAYGVLIEKSAGGG---LAARATFIIDPDGKIRYVEVEPLPTGR 134
Query: 73 SVE 75
+ E
Sbjct: 135 NAE 137
>gnl|CDD|237297 PRK13189, PRK13189, peroxiredoxin; Provisional.
Length = 222
Score = 49.2 bits (118), Expect = 7e-09
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 14 DFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRS 73
+ F II D+ ++A KL ++ N TVRAV+II P ++ + YP GR+
Sbjct: 97 EIEFPIIADDRGEIAKKLGMISPGKGTN-----TVRAVFIIDPKGIIRAILYYPQEVGRN 151
Query: 74 VE 75
++
Sbjct: 152 MD 153
>gnl|CDD|183885 PRK13191, PRK13191, putative peroxiredoxin; Provisional.
Length = 215
Score = 43.3 bits (102), Expect = 1e-06
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 10 DIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPAS 69
++K + PF II D ++A +L ++ E+ TVRAV+I+ ++L + YP
Sbjct: 91 NLKVEVPFPIIADPMGNVAKRLGMIHAESSTA-----TVRAVFIVDDKGTVRLILYYPME 145
Query: 70 TGRSVE 75
GR+++
Sbjct: 146 IGRNID 151
>gnl|CDD|239313 cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys PRX
subfamily; PRXs are thiol-specific antioxidant (TSA)
proteins, which confer a protective role in cells
through its peroxidase activity by reducing hydrogen
peroxide, peroxynitrite, and organic hydroperoxides. The
functional unit of typical 2-cys PRX is a homodimer. A
unique intermolecular redox-active disulfide center is
utilized for its activity. Upon reaction with peroxides,
its peroxidatic cysteine is oxidized into a sulfenic
acid intermediate which is resolved by bonding with the
resolving cysteine from the other subunit of the
homodimer. This intermolecular disulfide bond is then
reduced by thioredoxin, tryparedoxin or AhpF. Typical
2-cys PRXs, like 1-cys PRXs, form decamers which are
stabilized by reduction of the active site cysteine.
Typical 2-cys PRX interacts through beta strands at one
edge of the monomer (B-type interface) to form the
functional homodimer, and uses an A-type interface
(similar to the dimeric interface in atypical 2-cys PRX
and PRX5) at the opposite end of the monomer to form the
stable decameric (pentamer of dimers) structure.
Length = 173
Score = 35.6 bits (83), Expect = 5e-04
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 13 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 72
G F ++ D + ++ +LDEE L R +II P+ ++ V GR
Sbjct: 91 GKINFPLLADPKKKISRDYGVLDEEEGVAL------RGTFIIDPEGIIRHITVNDLPVGR 144
Query: 73 SVE 75
SV+
Sbjct: 145 SVD 147
>gnl|CDD|106544 PRK13599, PRK13599, putative peroxiredoxin; Provisional.
Length = 215
Score = 34.3 bits (78), Expect = 0.002
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 16 PFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVE 75
PF +I D+ ++ +L ++ N TVRAV+I+ ++L + YP GR+V+
Sbjct: 92 PFPVIADDLGKVSNQLGMIHPGKGTN-----TVRAVFIVDDKGTIRLIMYYPQEVGRNVD 146
>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 = 32.6 bits (75), Expect = 0.005
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 3 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLK 61
K + + FP ++ D + ++A +L+EE + +R ++I PD K++
Sbjct: 72 SHKKFAEKLGLPFP--LLSDPDGEVAKAYGVLNEE------EGLALRTTFVIDPDGKIR 122
>gnl|CDD|239315 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
comigratory protein (BCP) subfamily; composed of
thioredoxin-dependent thiol peroxidases, widely
expressed in pathogenic bacteria, that protect cells
against toxicity from reactive oxygen species by
reducing and detoxifying hydroperoxides. The protein was
named BCP based on its electrophoretic mobility before
its function was known. BCP shows substrate selectivity
toward fatty acid hydroperoxides rather than hydrogen
peroxide or alkyl hydroperoxides. BCP contains the
peroxidatic cysteine but appears not to possess a
resolving cysteine (some sequences, not all, contain a
second cysteine but its role is still unknown). Unlike
other PRXs, BCP exists as a monomer. The plant homolog
of BCP is PRX Q, which is expressed only in leaves and
is cellularly localized in the chloroplasts and the
guard cells of stomata. Also included in this subfamily
is the fungal nuclear protein, Dot5p (for disrupter of
telomere silencing protein 5), which functions as an
alkyl-hydroperoxide reductase during post-diauxic
growth.
Length = 140
Score = 30.6 bits (70), Expect = 0.035
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 12 KGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLS 63
K PF ++ D + LA + E+ K + R+ ++I PD K+
Sbjct: 77 KYGLPFPLLSDPDGKLAKAYGVWGEKKK---KYMGIERSTFLIDPDGKIVKV 125
>gnl|CDD|224146 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 29.9 bits (68), Expect = 0.055
Identities = 12/50 (24%), Positives = 24/50 (48%)
Query: 12 KGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLK 61
K F ++ DE+ ++A + E+ E R+ ++I PD K++
Sbjct: 84 KHGLTFPLLSDEDGEVAEAYGVWGEKKMYGKEYMGIERSTFVIDPDGKIR 133
>gnl|CDD|183050 PRK11241, gabD, succinate-semialdehyde dehydrogenase I;
Provisional.
Length = 482
Score = 28.3 bits (63), Expect = 0.25
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 3 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYI 53
DIK L++ G+ PF + D + D AV+ L + +N +T + +Y+
Sbjct: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGALA-SKFRNAGQTCVCANRLYV 297
>gnl|CDD|211789 TIGR03137, AhpC, peroxiredoxin. This peroxiredoxin (AhpC,
alkylhydroperoxide reductase subunit C) is one subunit
of a two-subunit complex with subunit F(TIGR03140).
Usually these are found as an apparent operon. The gene
has been characterized in Bacteroides fragilis where it
is important in oxidative stress defense. This gene
contains two invariant cysteine residues, one near the
N-terminus and one near the C-terminus, each followed
immediately by a proline residue [Cellular processes,
Detoxification, Cellular processes, Adaptations to
atypical conditions].
Length = 187
Score = 27.8 bits (62), Expect = 0.34
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 17 FAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVE 75
+ ++GD L +L EE + R ++I P+ ++ ++ GR
Sbjct: 94 YPMLGDPTGVLTRNFGVLIEE------AGLADRGTFVIDPEGVIQAVEIHDNGIGRDAS 146
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 26.4 bits (58), Expect = 1.2
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 13 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 72
G ++ D+ + +A +L+EE + R ++II P L+ V GR
Sbjct: 98 GTMAIPMLADKTKSIARSYGVLEEEQ------GVAYRGLFIIDPKGMLRQITVNDMPVGR 151
Query: 73 SVE 75
+VE
Sbjct: 152 NVE 154
>gnl|CDD|239268 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical
proteins that show sequence similarity to PRXs. Members
of this group contain a CXXC motif, similar to TRX. The
second cysteine in the motif corresponds to the
peroxidatic cysteine of PRX, however, these proteins do
not contain the other two residues of the catalytic
triad of PRX. PRXs confer a protective antioxidant role
in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF. TRXs alter the
redox state of target proteins by catalyzing the
reduction of their disulfide bonds via the CXXC motif
using reducing equivalents derived from either NADPH or
ferredoxins.
Length = 149
Score = 25.4 bits (56), Expect = 2.4
Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 17/73 (23%)
Query: 12 KGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVR-----------------AVYII 54
PF + D +R L L L+ +N A+ V++I
Sbjct: 77 GKFLPFPVYADPDRKLYRALGLVRSLPWSNTPRALWKNAAIGFRGNDEGDGLQLPGVFVI 136
Query: 55 GPDRKLKLSIVYP 67
GPD + + V
Sbjct: 137 GPDGTILFAHVDR 149
>gnl|CDD|184426 PRK13968, PRK13968, putative succinate semialdehyde dehydrogenase;
Provisional.
Length = 462
Score = 25.6 bits (56), Expect = 2.6
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 4 IKNYCLDIKGDFPFAIIGDENRDLAVK 30
+K L++ G PF ++ D + +LAVK
Sbjct: 228 LKKCVLELGGSDPFIVLNDADLELAVK 254
>gnl|CDD|188173 TIGR01852, lipid_A_lpxA,
acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine
O-acyltransferase. This model describes LpxA, an
enzyme for the biosynthesis of lipid A, a component
oflipopolysaccharide (LPS) in the outer membrane outer
leaflet of most Gram-negative bacteria. Some
differences are found between lipid A of different
species, but this protein represents the first step
(from UDP-N-acetyl-D-glucosamine) and appears to be
conserved in function. Proteins from this family
contain many copies of the bacterial transferase
hexapeptide repeat (pfam00132) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 254
Score = 25.3 bits (56), Expect = 2.8
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 15 FPFAIIGDENRDLAVK 30
FP A+IG +DL K
Sbjct: 56 FPGAVIGGVPQDLKYK 71
>gnl|CDD|223973 COG1043, LpxA, Acyl-[acyl carrier protein].
Length = 260
Score = 25.3 bits (56), Expect = 3.0
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 15 FPFAIIGDENRDL 27
FPFA IG++ +DL
Sbjct: 61 FPFASIGEDPQDL 73
>gnl|CDD|235390 PRK05289, PRK05289, UDP-N-acetylglucosamine acyltransferase;
Provisional.
Length = 262
Score = 25.1 bits (56), Expect = 3.5
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 15 FPFAIIGDENRDL 27
FPFA IG++ +DL
Sbjct: 60 FPFASIGEDPQDL 72
>gnl|CDD|181602 PRK08979, PRK08979, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 572
Score = 25.2 bits (55), Expect = 3.6
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 11 IKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAIT 47
++ D P I+G ++ L L LLDE + N E AI
Sbjct: 314 VRVDIP--IVGSADKVLDSMLALLDESGETNDEAAIA 348
>gnl|CDD|143460 cd07142, ALDH_F2BC, Arabidosis aldehyde dehydrogenase family 2 B4,
B7, C4-like. Included in this CD is the Arabidosis
aldehyde dehydrogenase family 2 members B4 and B7
(EC=1.2.1.3), which are mitochondrial homotetramers
that oxidize acetaldehyde and glycolaldehyde, but not
L-lactaldehyde. Also in this group, is the Arabidosis
cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme
involved in the oxidation of sinapalehyde and
coniferaldehyde.
Length = 476
Score = 24.8 bits (54), Expect = 4.9
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 2 SDIKNYCLDIKGDFPFAIIGDENRDLAVKL 31
S++K L++ G PF + D + D AV+L
Sbjct: 243 SNLKPVTLELGGKSPFIVCEDADVDKAVEL 272
>gnl|CDD|100042 cd03351, LbH_UDP-GlcNAc_AT, UDP-N-acetylglucosamine
O-acyltransferase (UDP-GlcNAc acyltransferase):
Proteins in this family catalyze the transfer of
(R)-3-hydroxymyristic acid from its acyl carrier
protein thioester to UDP-GlcNAc. It is the first enzyme
in the lipid A biosynthetic pathway and is also
referred to as LpxA. Lipid A is essential for the
growth of Escherichia coli and related bacteria. It is
also essential for maintaining the integrity of the
outer membrane. UDP-GlcNAc acyltransferase is a
homotrimer of left-handed parallel beta helix (LbH)
subunits. Each subunit contains an N-terminal LbH
region with 9 turns, each containing three imperfect
tandem repeats of a hexapeptide repeat motif
(X-[STAV]-X-[LIV]-[GAED]-X), and a C-terminal
alpha-helical region.
Length = 254
Score = 24.3 bits (54), Expect = 6.8
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 15 FPFAIIGDENRDL 27
FPFA IG+ +DL
Sbjct: 57 FPFASIGEAPQDL 69
>gnl|CDD|224148 COG1227, PPX1, Inorganic pyrophosphatase/exopolyphosphatase
[Energy production and conversion].
Length = 311
Score = 24.2 bits (53), Expect = 8.0
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 7 YCLDIKGDF--PFAIIGDENRDLAVKLDLLDEENKNNLETA 45
Y L+ G+F +G+ N + A LD E +E+
Sbjct: 25 YLLNAYGEFEAKAVRLGEPNLETAFVLDYFGVEAPKLVESV 65
>gnl|CDD|220801 pfam10543, ORF6N, ORF6N domain. This domain was identified by
Iyer and colleagues.
Length = 87
Score = 23.7 bits (52), Expect = 8.0
Identities = 8/42 (19%), Positives = 15/42 (35%)
Query: 11 IKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVY 52
+G F F + G+E ++L + + T R
Sbjct: 41 PEGKFYFELTGEELKELRSQFVTSKISGRARKPYLFTERGAA 82
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
0.318 0.139 0.390
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,772,303
Number of extensions: 294678
Number of successful extensions: 293
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 30
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)