RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1894
(228 letters)
>gnl|CDD|239511 cd03419, GRX_GRXh_1_2_like, Glutaredoxin (GRX) family, GRX human
class 1 and 2 (h_1_2)-like subfamily; composed of
proteins similar to human 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 human GRX1 and GRX2, which are members
of this subfamily. Also included in this subfamily are
the N-terminal GRX domains of proteins similar to human
thioredoxin reductase 1 and 3.
Length = 82
Score = 89.9 bits (224), Expect = 1e-23
Identities = 30/55 (54%), Positives = 39/55 (70%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
+++FSKSYCPYCK AK + ++L V P VELD +DG IQD L E+TG R+ P
Sbjct: 1 PVVVFSKSYCPYCKRAKSLLKELGVKPAVVELDQHEDGSEIQDYLQELTGQRTVP 55
>gnl|CDD|233765 TIGR02180, GRX_euk, Glutaredoxin. 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
model represents eukaryotic glutaredoxins and includes
sequences from fungi, plants and metazoans as well as
viruses.
Length = 84
Score = 76.9 bits (190), Expect = 1e-18
Identities = 31/56 (55%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLKVTP--KTVELDHRDDGDSIQDVLLEITGARSQP 71
+++FSKSYCPYCK AK++ KL V P + VELD +G IQD L EITG R+ P
Sbjct: 1 VVVFSKSYCPYCKKAKEILAKLNVKPAYEVVELDQLSNGSEIQDYLEEITGQRTVP 56
>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 = 55.9 bits (136), Expect = 6e-11
Identities = 21/55 (38%), Positives = 37/55 (67%), Gaps = 3/55 (5%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
K+++FSKS CPYCK AK + + L + + E+D +DG+ +++ L E++G + P
Sbjct: 1 KVVVFSKSTCPYCKRAKRLLESLGI--EFEEIDILEDGE-LREELKELSGWPTVP 52
>gnl|CDD|215931 pfam00462, Glutaredoxin, Glutaredoxin.
Length = 60
Score = 54.8 bits (133), Expect = 2e-10
Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
+++F+K CP+CK AK + L V + +++ D+ I++ L E++G + P
Sbjct: 1 VVLFTKPTCPFCKRAKRLLDSLGVKFEEIDV---DEDPEIREELKELSGWPTVP 51
>gnl|CDD|223767 COG0695, GrxC, Glutaredoxin and related proteins
[Posttranslational modification, protein turnover,
chaperones].
Length = 80
Score = 47.3 bits (113), Expect = 1e-07
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
+ I++K CPYCK AK + + V + +++D D+ + ++++ G R+ P
Sbjct: 2 NVTIYTKPGCPYCKRAKRLLDRKGVDYEEIDVDD-DEPEEAREMVKRGKGQRTVP 55
>gnl|CDD|233771 TIGR02189, GlrX-like_plant, Glutaredoxin-like family. This
family of glutaredoxin-like proteins is aparrently
limited to plants. Multiple isoforms are found in A.
thaliana and O.sativa.
Length = 99
Score = 45.9 bits (109), Expect = 8e-07
Identities = 17/63 (26%), Positives = 33/63 (52%)
Query: 9 VQDLIASEKILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGAR 68
V+ +++ + ++IFS+S C C + K + L V P E+D G I++ L + +
Sbjct: 1 VRRMVSEKAVVIFSRSSCCMCHVVKRLLLTLGVNPAVHEIDKEPAGKDIENALSRLGCSP 60
Query: 69 SQP 71
+ P
Sbjct: 61 AVP 63
>gnl|CDD|165343 PHA03050, PHA03050, glutaredoxin; Provisional.
Length = 108
Score = 42.3 bits (99), Expect = 2e-05
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 5 SKQFVQDLIASEKILIFSKSYCPYCKMAKDVFQKLKVTP---KTVELDHRDDGDSIQDVL 61
+++FVQ +A+ K+ IF K CP+C+ A D+ K + V++ + ++D
Sbjct: 2 AEEFVQQRLANNKVTIFVKFTCPFCRNALDILNKFSFKRGAYEIVDIKEFKPENELRDYF 61
Query: 62 LEITGARSQP 71
+ITG R+ P
Sbjct: 62 EQITGGRTVP 71
>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 = 39.1 bits (92), Expect = 9e-05
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
++ +++K CPYCK K + + + V++D + + L ++ G RS P
Sbjct: 1 EVTVYTKPDCPYCKATKRFLDERGIPFEEVDVDEDPEA---LEELKKLNGYRSVP 52
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDD 53
K+ I++K CPYC AK + K V + +++D
Sbjct: 1 KVEIYTKPNCPYCVRAKALLDKKGVDYEEIDVDGDPA 37
>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 = 37.6 bits (88), Expect = 5e-04
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
+ I++K YCPYC AK + VT + + D +++D +++ +G R+ P
Sbjct: 1 VTIYTKPYCPYCTRAKALLSSKGVTFTEIRV---DGDPALRDEMMQRSGRRTVP 51
>gnl|CDD|239327 cd03029, GRX_hybridPRX5, Glutaredoxin (GRX) family, PRX5 hybrid
subfamily; composed of hybrid proteins containing
peroxiredoxin (PRX) and GRX domains, which is found in
some pathogenic bacteria and cyanobacteria. PRXs are
thiol-specific antioxidant (TSA) proteins that 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. GRX is a glutathione (GSH) dependent reductase,
catalyzing the disulfide reduction of target proteins.
PRX-GRX hybrid proteins from Haemophilus influenza and
Neisseria meningitis exhibit GSH-dependent peroxidase
activity. The flow of reducing equivalents in the
catalytic cycle of the hybrid protein goes from NADPH
-> GSH reductase -> GSH -> GRX domain of hybrid -> PRX
domain of hybrid -> peroxide substrate.
Length = 72
Score = 36.7 bits (85), Expect = 7e-04
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 16 EKILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
E + +F+K CP+C AK Q+ ++ + + L G S++ V TGA + P
Sbjct: 1 ESVSLFTKPGCPFCARAKAALQENGISYEEIPLGKDITGRSLRAV----TGAMTVP 52
>gnl|CDD|233042 TIGR00598, rad14, DNA repair protein. All proteins in this family
for which functions are known are used for the
recognition of DNA damage as part of nucleotide excision
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 172
Score = 35.9 bits (83), Expect = 0.006
Identities = 27/93 (29%), Positives = 54/93 (58%), Gaps = 7/93 (7%)
Query: 113 ITPNRAMSDFLLKQSDLEG----LKVIKRRSPYENE-PPISVYWRKDVEAKAIQVWGSKE 167
+T A ++LLK DL+ L+ I +++P+ + +Y + VE +A++VWGS+E
Sbjct: 35 LTKTEAKEEYLLKDCDLDKREPLLRRIVKKNPHNPRWGDMKLYLKLQVEKRALEVWGSEE 94
Query: 168 RLLQERLKNELERKYQQQHIFTMKRKLRDYRRE 200
L +E+ + E ++ ++ F ++KL++ RR
Sbjct: 95 ALDEEKERREESKEEMKEKKF--EKKLKELRRA 125
>gnl|CDD|131251 TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family.
This glutaredoxin-like protein family contains the
conserved CxxC motif and includes the Clostridium
pasteurianum protein YruB which has been cloned from a
rubredoxin operon. Somewhat related to NrdH, it is
unknown whether this protein actually interacts with
glutathione/glutathione reducatase, or, like NrdH, some
other reductant system.
Length = 74
Score = 32.7 bits (75), Expect = 0.022
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
K+ +++ +CP CK AK+ + E+D D + ++V L++ G R P
Sbjct: 1 KVKVYTTPWCPPCKKAKEYLTSKGI--AFEEIDVEKDSAAREEV-LKVLGQRGVP 52
>gnl|CDD|183036 PRK11200, grxA, glutaredoxin 1; Provisional.
Length = 85
Score = 32.7 bits (75), Expect = 0.027
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 16 EKILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGD 55
++IF + CPYC AK++ +KL + RDD D
Sbjct: 1 MFVVIFGRPGCPYCVRAKELAEKLS--------EERDDFD 32
>gnl|CDD|131245 TIGR02190, GlrX-dom, Glutaredoxin-family domain. This C-terminal
domain with homology to glutaredoxin is fused to an
N-terminal peroxiredoxin-like domain.
Length = 79
Score = 32.5 bits (74), Expect = 0.029
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 14 ASEKILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDVLLEITGARSQP 71
E +++F+K CP+C AK ++ + + L + G S++ +TGA + P
Sbjct: 6 KPESVVVFTKPGCPFCAKAKATLKEKGYDFEEIPLGNDARGRSLR----AVTGATTVP 59
>gnl|CDD|227474 COG5145, RAD14, DNA excision repair protein [DNA replication,
recombination, and repair].
Length = 292
Score = 33.4 bits (76), Expect = 0.069
Identities = 24/102 (23%), Positives = 55/102 (53%), Gaps = 6/102 (5%)
Query: 112 FITPNRAMSDFLLKQSDLEG---LKVIKRRSPYENE-PPISVYWRKDVEAKAIQVWGSKE 167
+T SD+LL +L+ + +++ +P++ + +Y R++VE AI+ WGS E
Sbjct: 153 LLTKTECKSDYLLTDPELKDQELFRRLQKPNPHKGTWSKMHLYLREEVEQFAIKKWGSLE 212
Query: 168 RLLQERLKNELERKYQQQHIFTMKRKLRDYRREQGSLADQKM 209
L +E+ + E + +++ ++K+++ RR+ + +M
Sbjct: 213 ELDREKQRREKMKDDRKEKKL--EKKIKELRRKTRTSNYSRM 252
>gnl|CDD|218740 pfam05768, DUF836, Glutaredoxin-like domain (DUF836). These
proteins are related to the pfam00462 family.
Length = 76
Score = 30.3 bits (69), Expect = 0.18
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRD-DGDSI 57
+ ++ K C C+ AK+V +L+ +L+ D D D
Sbjct: 1 TLTLYGKPGCHLCEGAKEVLAELEAALG-FDLERIDIDDDEE 41
>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 = 29.6 bits (66), Expect = 0.26
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGD 55
+++F +CP+C+ + V +L + K V+ + D +
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDE 38
>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 = 29.4 bits (67), Expect = 0.38
Identities = 7/35 (20%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 6 KQFVQDLIASEKILI-FSKSYCPYCKMAKDVFQKL 39
++F + + +++ +++ F +C CK V ++L
Sbjct: 1 EEFEELIKSAKPVVVDFWAPWCGPCKAIAPVLEEL 35
>gnl|CDD|131255 TIGR02200, GlrX_actino, Glutaredoxin-like protein. This family
of glutaredoxin-like proteins is limited to the
Actinobacteria and contains the conserved CxxC motif.
Length = 77
Score = 29.4 bits (66), Expect = 0.39
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDG 54
I ++ ++C YC KL + V+++ +
Sbjct: 1 TITVYGTTWCGYCAQLMRTLDKLGAAYEWVDIEEDEGA 38
>gnl|CDD|239325 cd03027, GRX_DEP, Glutaredoxin (GRX) family, Dishevelled, Egl-10,
and Pleckstrin (DEP) subfamily; composed of
uncharacterized proteins containing a GRX domain and
additional domains DEP and DUF547, both of which have
unknown functions. GRX is a glutathione (GSH)
dependent reductase containing a redox active CXXC
motif in a TRX fold. It has preference for mixed GSH
disulfide substrates, in which it uses a monothiol
mechanism where only the N-terminal cysteine is
required. By altering the redox state of target
proteins, GRX is involved in many cellular functions.
Length = 73
Score = 28.5 bits (64), Expect = 0.59
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELD-HRDDGDSIQDVLLEITGARSQP 71
++ I+S+ C C + ++ + + +D + L E TG+ P
Sbjct: 2 RVTIYSRLGCEDCTAVRLFLREKGLPYVEINIDIFP----ERKAELEERTGSSVVP 53
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 28.9 bits (65), Expect = 0.70
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 17 KILIFSKSYCPYC-KMAKDVFQKLKVTPKT 45
+++F+ CPYC K+ K++ + V
Sbjct: 8 VLVVFTDPDCPYCKKLHKELLKDPDVQEYL 37
>gnl|CDD|216433 pfam01323, DSBA, DSBA-like thioredoxin domain. This family
contains a diverse set of proteins with a
thioredoxin-like structure pfam00085. This family also
includes 2-hydroxychromene-2-carboxylate (HCCA)
isomerase enzymes catalyze one step in prokaryotic
polyaromatic hydrocarbon (PAH) catabolic pathways. This
family also contains members with functions other than
HCCA isomerisation, such as Kappa family GSTs, whose
similarity to HCCA isomerases was not previously
recognised. Some member sequences have been annotated
as a dioxygenases, dehydrogenases, and putative
glycerol-3-phosphate transfer proteins, but are most
likely HCCA isomerase enzymes.
Length = 191
Score = 29.7 bits (67), Expect = 0.91
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 4/77 (5%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHR----DDGDSIQDVLLEITGARSQPSD 73
+ F CP+C +AK+ +KL V++ +R I +V + +
Sbjct: 2 VDEFFDFLCPFCYLAKERLEKLAARYGDVKVVYRPFPLAGAKKIGNVGPSNLPVKLKYMM 61
Query: 74 NDLEEKPKAEKKILEIP 90
DLE L P
Sbjct: 62 ADLERWAALYGIPLRFP 78
>gnl|CDD|129505 TIGR00411, redox_disulf_1, small redox-active disulfide protein
1. This protein is homologous to a family of proteins
that includes thioredoxins, glutaredoxins,
protein-disulfide isomerases, and others, some of which
have several such domains. The sequence of this protein
at the redox-active disufide site, CPYC, matches
glutaredoxins rather than thioredoxins, although its
overall sequence seems closer to thioredoxins. It is
suggested to be a ribonucleotide-reducing system
component distinct from thioredoxin or glutaredoxin
[Unknown function, General].
Length = 82
Score = 27.9 bits (62), Expect = 1.2
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLK 40
KI +F+ CPYC AK V +++
Sbjct: 2 KIELFTSPTCPYCPAAKRVVEEVA 25
>gnl|CDD|239249 cd02951, SoxW, SoxW family; SoxW is a bacterial periplasmic TRX,
containing a redox active CXXC motif, encoded by a
genetic locus (sox operon) involved in thiosulfate
oxidation. Sulfur bacteria oxidize sulfur compounds to
provide reducing equivalents for carbon dioxide
fixation during autotrophic growth and the respiratory
electron transport chain. It is unclear what the role
of SoxW is, since it has been found to be dispensable
in the oxidation of thiosulfate to sulfate. SoxW is
specifically kept in the reduced state by SoxV, which
is essential in thiosulfate oxidation.
Length = 125
Score = 28.4 bits (64), Expect = 1.4
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 18 ILIFSKSYCPYC-KMAKDVFQKLKVTP 43
+L+FS+ CPYC K+ +D V
Sbjct: 18 LLLFSQPGCPYCDKLKRDYLNDPAVQA 44
>gnl|CDD|236963 PRK11720, PRK11720, galactose-1-phosphate uridylyltransferase;
Provisional.
Length = 346
Score = 29.1 bits (66), Expect = 1.8
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 17/48 (35%)
Query: 161 QVWGSKERLLQERLKNELERKYQQQHIFTMKRKLRDYRREQGS--LAD 206
Q+W + L NE ER+ + Q R Y E GS L D
Sbjct: 168 QIWAN------SFLPNEAEREDRLQ---------RAYFAEHGSPLLVD 200
>gnl|CDD|224565 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
modification, protein turnover, chaperones].
Length = 244
Score = 28.7 bits (64), Expect = 2.0
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 3 PASKQFVQ--DLIASEKILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRD 52
+ V + A ++ F CPYCK A +K + V L R+
Sbjct: 71 TPDGKDVVLGNPYAPVTVVEFFDYTCPYCKEAFPELKKKYIDDGKVRLVLRE 122
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 28.9 bits (65), Expect = 2.2
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 100 RVDLSVSSTERNFITP 115
RVD VSST++NF+ P
Sbjct: 263 RVDAVVSSTDKNFMVP 278
>gnl|CDD|239270 cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like
proteins, including DsbC, DsbG, glutathione (GSH)
S-transferase kappa (GSTK),
2-hydroxychromene-2-carboxylate (HCCA) isomerase, an
oxidoreductase (FrnE) presumed to be involved in
frenolicin biosynthesis, a 27-kDa outer membrane
protein, and similar proteins. Members of this family
contain a redox active CXXC motif (except GSTK and HCCA
isomerase) imbedded in a TRX fold, and an alpha helical
insert of about 75 residues (shorter in DsbC and DsbG)
relative to TRX. DsbA is involved in the oxidative
protein folding pathway in prokaryotes, catalyzing
disulfide bond formation of proteins secreted into the
bacterial periplasm. DsbC and DsbG function as protein
disulfide isomerases and chaperones to correct
non-native disulfide bonds formed by DsbA and prevent
aggregation of incorrectly folded proteins.
Length = 98
Score = 27.4 bits (61), Expect = 2.4
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 18 ILIFSKSYCPYCKMA-KDVFQKLKVTPKTVELDHRD 52
I+ F CPYC + ++ + L V + +R
Sbjct: 1 IVEFFDPLCPYCYLFEPELEKLLYADDGGVRVVYRP 36
>gnl|CDD|177519 PHA03075, PHA03075, glutaredoxin-like protein; Provisional.
Length = 123
Score = 27.3 bits (61), Expect = 4.0
Identities = 5/23 (21%), Positives = 13/23 (56%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLK 40
+++F K C C+ + ++L+
Sbjct: 5 LILFGKPLCSVCESISEALKELE 27
>gnl|CDD|224471 COG1554, ATH1, Trehalose and maltose hydrolases (possible
phosphorylases) [Carbohydrate transport and metabolism].
Length = 772
Score = 28.5 bits (64), Expect = 4.0
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 186 HIFTMK---RKLRDYRREQGSLADQKMAEKAGLFGLLYP 221
+FT R L YR A + A+K GL G LYP
Sbjct: 364 LLFTDPEVARNLLLYRYNTLPGAKEN-AKKYGLKGALYP 401
>gnl|CDD|131238 TIGR02183, GRXA, Glutaredoxin, GrxA 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
model includes the E. coli glyutaredoxin GrxA which
appears to have primary responsibility for the
reduction of ribonucleotide reductase.
Length = 86
Score = 26.3 bits (58), Expect = 4.5
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKLK 40
++IF + CPYC AK + +KL
Sbjct: 2 VVIFGRPGCPYCVRAKQLAEKLA 24
>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 = 27.2 bits (61), Expect = 4.8
Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 7 QFVQDLIAS-EKILIFSKSYCPYCKMAKDVFQKLK 40
+ +++ + K+LIF CP KM ++ + L+
Sbjct: 19 ELLKEHLKKGGKVLIF----CPSKKMLDELAELLR 49
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 27.5 bits (61), Expect = 5.1
Identities = 7/22 (31%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 18 ILIFSKSYCPYC-KMAKDVFQK 38
+L+F + C YC + KD+
Sbjct: 46 LLMFESNGCSYCERFKKDLKNV 67
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 27.6 bits (62), Expect = 5.1
Identities = 9/64 (14%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 152 RKDVEAKAIQVWGSKERLLQERLKNELERKYQQQHIFTMKRKLRDYR----REQGSLADQ 207
+ + ++ K++ ++ ++ + + Q+H+ + K+ R EQ + +
Sbjct: 212 KAEAAEAEQELLREKQKEEEQMMEAQ--ERSYQEHVKQLIEKMEAEREKLLAEQERMLEH 269
Query: 208 KMAE 211
K+ E
Sbjct: 270 KLQE 273
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.5 bits (62), Expect = 6.7
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 8/52 (15%)
Query: 152 RKDVEAKAIQVWGSKERLLQ--ERLKNELERKYQQQHIFTMKRKLRDYRREQ 201
+++E KA + E LL+ E+LK ELE K ++ + KL + ++
Sbjct: 529 ERELEQKAEEA----EALLKEAEKLKEELEEKKEKLQE--EEDKLLEEAEKE 574
>gnl|CDD|183262 PRK11657, dsbG, disulfide isomerase/thiol-disulfide oxidase;
Provisional.
Length = 251
Score = 27.2 bits (61), Expect = 6.9
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 14 ASEKILIFSKSYCPYCKM 31
A + +F+ CPYCK
Sbjct: 117 APRIVYVFADPNCPYCKQ 134
>gnl|CDD|216765 pfam01888, CbiD, CbiD. CbiD is essential for cobalamin
biosynthesis in both S. typhimurium and B. megaterium,
no functional role has been ascribed to the protein. The
CbiD protein has a putative S-AdoMet binding site. It is
possible that CbiD might have the same role as CobF in
undertaking the C-1 methylation and deacylation
reactions required during the ring contraction process.
Length = 261
Score = 27.0 bits (60), Expect = 7.1
Identities = 8/51 (15%), Positives = 17/51 (33%), Gaps = 3/51 (5%)
Query: 172 ERLKNELERKYQQQH---IFTMKRKLRDYRREQGSLADQKMAEKAGLFGLL 219
L +++ + +F Y R+Q + D + A G +
Sbjct: 184 ASLAQQIDVAAASGYQRLVFVPGNIGEKYARQQFGVPDDAFVQMANFVGFM 234
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 27.2 bits (60), Expect = 8.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 100 RVDLSVSSTERNFITP 115
R+D V S ++NFI P
Sbjct: 213 RIDAVVQSLDKNFIVP 228
>gnl|CDD|226493 COG4004, COG4004, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 96
Score = 26.0 bits (57), Expect = 8.0
Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 8/89 (8%)
Query: 52 DDGDSIQDVLLEITGARSQPSDNDLEEKPKAEKKILEIPVEAVAKPRIRVDLSVSSTERN 111
D D I L E+ S+ D + P + +EI E ++ V+ + + +
Sbjct: 12 PDPDRIMRGLSELGWTVSEEGDRIVASSPGISR--IEIKPE---NKKLLVNTTDYTDDET 66
Query: 112 FITPNRAMSDFLLK---QSDLEGLKVIKR 137
+ + +DFL K + E K++K+
Sbjct: 67 KLQTAKTYNDFLEKLTGYTAKERKKMMKK 95
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 26.4 bits (57), Expect = 8.8
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 18 ILIFSKSYCPYCKMAKDVFQKL-KVTPKTVELDHRDDGDSIQDVLLE 63
++ F +CP C+ + ++L + VE+ + D D+ E
Sbjct: 36 LVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAE 82
>gnl|CDD|239335 cd03037, GST_N_GRX2, GST_N family, Glutaredoxin 2 (GRX2)
subfamily; composed of bacterial proteins similar to E.
coli GRX2, an atypical GRX with a molecular mass of
about 24kD, compared with other GRXs which are 9-12kD
in size. GRX2 adopts a GST fold containing an
N-terminal thioredoxin-fold domain and a C-terminal
alpha helical domain. It contains a redox active CXXC
motif located in the N-terminal domain but is not able
to reduce ribonucleotide reductase like other GRXs.
However, it catalyzes GSH-dependent protein disulfide
reduction of other substrates efficiently. GRX2 is
thought to function primarily in catalyzing the
reversible glutathionylation of proteins in cellular
redox regulation including stress responses.
Length = 71
Score = 25.0 bits (55), Expect = 9.2
Identities = 9/44 (20%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 17 KILIFSKSYCPYCKMAKDVFQKLKVTPKTVELDHRDDGDSIQDV 60
K+ I+ +CP+C A+ + + + + L + D+ I+ +
Sbjct: 2 KLYIYE--HCPFCVKARMIAGLKNIPVEQIILQNDDEATPIRMI 43
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
0.316 0.133 0.373
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,615,556
Number of extensions: 1110830
Number of successful extensions: 1242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1239
Number of HSP's successfully gapped: 74
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
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: 57 (25.8 bits)