RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11066
(70 letters)
>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 = 70.3 bits (173), Expect = 5e-18
Identities = 26/62 (41%), Positives = 44/62 (70%), Gaps = 1/62 (1%)
Query: 5 MLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGAN-FDKLRS 63
+L+ELA E+P V F+KVDVDE+ ++A Y + S+PTF+F K+ +V++ GA+ ++L
Sbjct: 31 VLEELAEEYPKVKFVKVDVDENPELAEEYGVRSIPTFLFFKNGKEVDRVVGADPKEELEE 90
Query: 64 TV 65
+
Sbjct: 91 FL 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 = 68.8 bits (169), Expect = 3e-17
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 5 MLQELASEFP-DVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA-NFDKLR 62
++LA E+ DV F KVD DE+ D+A Y + PT F K+ KV + GA D L
Sbjct: 39 EYEKLAQEYKDDVKFAKVDADENPDLASEYGVRGFPTIKFFKNGKKVSDYVGARTKDDLV 98
Query: 63 STVLAN 68
+ + +
Sbjct: 99 AFIKKH 104
>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 = 57.7 bits (140), Expect = 7e-13
Identities = 23/54 (42%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 5 MLQELASEFP-DVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGAN 57
+L+ELA E+ V F+K++VDE+ DIA Y I S+PT + K+ +V++ GA
Sbjct: 35 ILEELAKEYEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLFKNGKEVDRSVGAL 88
>gnl|CDD|239282 cd02984, TRX_PICOT, TRX domain, PICOT (for PKC-interacting cousin
of TRX) subfamily; PICOT is a protein that interacts
with protein kinase C (PKC) theta, a calcium
independent PKC isoform selectively expressed in
skeletal muscle and T lymphocytes. PICOT contains an
N-terminal TRX-like domain, which does not contain the
catalytic CXXC motif, followed by one to three
glutaredoxin domains. The TRX-like domain is required
for interaction with PKC theta. PICOT inhibits the
activation of c-Jun N-terminal kinase and the
transcription factors, AP-1 and NF-kB, induced by PKC
theta or T-cell activating stimuli.
Length = 97
Score = 55.4 bits (134), Expect = 4e-12
Identities = 21/65 (32%), Positives = 40/65 (61%)
Query: 1 MSLVMLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDK 60
M+ V + FP V+FL ++ +E +I+ ++I+++PTFVF ++ V++ SGA+ +
Sbjct: 32 MNQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTFVFFRNGTIVDRVSGADPKE 91
Query: 61 LRSTV 65
L V
Sbjct: 92 LAKKV 96
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 55.3 bits (133), Expect = 5e-12
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 7 QELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDKLRST 64
+E + E+ +VF+KVDVDE ++A +I+SMPTF K+ + V+ GAN + L+
Sbjct: 41 EECSKEYTKMVFVKVDVDELSEVAEKENITSMPTFKVFKNGSVVDTLLGANDEALKQL 98
>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 = 38.7 bits (91), Expect = 1e-05
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 7 QELASEF---PDVVFLKVDVDESEDIAMAYDISSMPTF-VFVKSTAKVEQFSG 55
++LA E VV KVD + D+ Y + PT +F + + ++ G
Sbjct: 38 EKLAKELKGDGKVVVAKVDCTANNDLCSEYGVRGYPTIKLFPNGSKEPVKYEG 90
>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 = 38.0 bits (89), Expect = 3e-05
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 8 ELASEF---PDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA 56
+LA E PD+V KVD +D+A + +S PT F K + G
Sbjct: 37 KLAKELKKDPDIVLAKVDATAEKDLASRFGVSGFPTIKFFPKGKKPVDYEGG 88
>gnl|CDD|239247 cd02949, TRX_NTR, TRX domain, novel NADPH thioredoxin reductase
(NTR) family; composed of fusion proteins found only in
oxygenic photosynthetic organisms containing both TRX
and NTR domains. The TRX domain functions as a protein
disulfide reductase via the reversible oxidation of an
active center dithiol present in a CXXC motif, while
the NTR domain functions as a reductant to oxidized
TRX. The fusion protein is bifunctional, showing both
TRX and NTR activities, but it is not an independent
NTR/TRX system. In plants, the protein is found
exclusively in shoots and mature leaves and is
localized in the chloroplast. It is involved in plant
protection against oxidative stress.
Length = 97
Score = 36.7 bits (85), Expect = 9e-05
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 5 MLQELASEFPDVV-FLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSG 55
+L ++ EF V F+++D+DE ++IA A I PT F K V++ SG
Sbjct: 34 ILNKVIDEFDGAVHFVEIDIDEDQEIAEAAGIMGTPTVQFFKDKELVKEISG 85
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 36.3 bits (84), Expect = 3e-04
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 8 ELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA 56
L + ++V VD E ++A + + PT F V +SG
Sbjct: 77 MLKEKKSEIVLASVDATEEMELAQEFGVRGYPTIKFFNKGNPVN-YSGG 124
>gnl|CDD|239283 cd02985, TRX_CDSP32, TRX family, chloroplastic drought-induced
stress protein of 32 kD (CDSP32); CDSP32 is composed of
two TRX domains, a C-terminal TRX domain which contains
a redox active CXXC motif and an N-terminal TRX-like
domain which contains an SXXS sequence instead of the
redox active motif. CDSP32 is a stress-inducible TRX,
i.e., it acts as a TRX by reducing protein disulfides
and is induced by environmental and oxidative stress
conditions. It plays a critical role in plastid defense
against oxidative damage, a role related to its function
as a physiological electron donor to BAS1, a plastidic
2-cys peroxiredoxin. Plants lacking CDSP32 exhibit
decreased photosystem II photochemical efficiencies and
chlorophyll retention compared to WT controls, as well
as an increased proportion of BAS1 in its overoxidized
monomeric form.
Length = 103
Score = 35.2 bits (81), Expect = 3e-04
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 8 ELASEFPDVVFLKVDVDESEDIAMAY----DISSMPTFVFVKSTAKVEQFSGANFDKLRS 63
+L+ DVVFL V+ DE+ D M I +P F+F K K+ + G D+L
Sbjct: 39 KLSRTCNDVVFLLVNGDEN-DSTMELCRREKIIEVPHFLFYKDGEKIHEEEGIGPDELIG 97
Query: 64 TVL 66
VL
Sbjct: 98 DVL 100
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 35.8 bits (83), Expect = 5e-04
Identities = 12/42 (28%), Positives = 18/42 (42%)
Query: 16 VVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGAN 57
KV+ D +A + + S+PT K V+ F GA
Sbjct: 76 FKLAKVNCDAEPMVAAQFGVQSIPTVYAFKDGQPVDGFQGAQ 117
>gnl|CDD|239255 cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd
and Phd-like proteins (PhLP), characterized as
cytosolic regulators of G protein functions. Phd and
PhLPs specifically bind G protein betagamma
(Gbg)-subunits with high affinity, resulting in the
solubilization of Gbg from the plasma membrane and
impeding G protein-mediated signal transduction by
inhibiting the formation of a functional G protein
trimer (G protein alphabetagamma). Phd also inhibits
the GTPase activity of G protein alpha. Phd can be
phosphorylated by protein kinase A and G
protein-coupled receptor kinase 2, leading to its
inactivation. Phd was originally isolated from the
retina, where it is highly expressed and has been
implicated to play an important role in light
adaptation. It is also found in the pineal gland,
liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain. Also included in this family is a PhLP
characterized as a viral inhibitor of apoptosis
(IAP)-associated factor, named VIAF, that functions in
caspase activation during apoptosis.
Length = 113
Score = 34.1 bits (79), Expect = 0.001
Identities = 15/56 (26%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDKL 61
L+ELA+++P+ F+K++ +++ + DI +PT + K+ ++ G F++L
Sbjct: 46 LEELAAKYPETKFVKINAEKAF-LVNYLDIKVLPTLLVYKNGELIDNIVG--FEEL 98
>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 = 33.4 bits (77), Expect = 0.001
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 6 LQELASEFPD-VVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA 56
L+ LA E+ V KV+ D IA + + ++PT + V+ F GA
Sbjct: 34 LERLAEEYQGQFVLAKVNCDAQPQIAQQFGVQALPTVYLFAAGQPVDGFQGA 85
>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 = 33.4 bits (77), Expect = 0.002
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 7 QELASEF---PDVVFLKVDVDESE-DIAMAYDISSMPTFV-FVKSTAKVEQFSGA 56
++LA+ F DVV KVD DE+ D+A Y +S PT F K + + ++ G
Sbjct: 41 EKLAAVFANEDDVVIAKVDADEANKDLAKKYGVSGFPTLKFFPKGSTEPVKYEGG 95
>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 = 33.1 bits (76), Expect = 0.002
Identities = 17/32 (53%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 12 EFPD---VVFLKVDVDESEDIAMAYDISSMPT 40
EFPD VV+ KVD D+ DIA Y I+ PT
Sbjct: 50 EFPDAGKVVWGKVDCDKESDIADRYRINKYPT 81
>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 = 32.3 bits (74), Expect = 0.009
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 7 QELASEFPDVVFLKVDVDESEDIAMAYDISSMPTF-VFVKSTAKVEQFSGA 56
EL + P + KVD E +D+A Y +S PT +F V ++G
Sbjct: 45 DELKKKGPPIKLAKVDATEEKDLAQKYGVSGYPTLKIFRNGEDSVSDYNGP 95
Score = 28.1 bits (63), Expect = 0.27
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 5 MLQELASEF----PDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVE 51
+ +ELA ++ DVV K+D ++ +++ PT FV + K E
Sbjct: 385 IYEELAEKYKDAESDVVIAKMDATAND--VPPFEVEGFPTIKFVPAGKKSE 433
>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 = 30.4 bits (68), Expect = 0.017
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 5 MLQELASEFPDVVFLKVDVDESEDIAMA---YDISSMPTFVFVKSTAKV 50
+L ELA V F VDVDE + Y + +PT V V
Sbjct: 18 VLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVFGPGIGV 66
>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 = 30.7 bits (70), Expect = 0.017
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 8 ELASEF----PDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA-NFDKLR 62
+LA +F P V KVD + ++ + + PT + K KV+++ G + D L+
Sbjct: 40 QLAKKFNNENPSVKIAKVDCTQHRELCSEFQVRGYPTLLLFKDGEKVDKYKGTRDLDSLK 99
Query: 63 STV 65
V
Sbjct: 100 EFV 102
>gnl|CDD|239271 cd02973, TRX_GRX_like, Thioredoxin (TRX)-Glutaredoxin (GRX)-like
family; composed of archaeal and bacterial proteins
that show similarity to both TRX and GRX, including the
C-terminal TRX-fold subdomain of Pyrococcus furiosus
protein disulfide oxidoreductase (PfPDO). All members
contain a redox-active CXXC motif and may function as
PDOs. The archaeal proteins Mj0307 and Mt807 show
structures more similar to GRX, but activities more
similar to TRX. Some members of the family are similar
to PfPDO in that they contain a second CXXC motif
located in a second TRX-fold subdomain at the
N-terminus; the superimposable N- and C-terminal TRX
subdomains form a compact structure. PfPDO is
postulated to be the archaeal counterpart of bacterial
DsbA and eukaryotic protein disulfide isomerase (PDI).
The C-terminal CXXC motif of PfPDO is required for its
oxidase, reductase and isomerase activities. Also
included in the family is the C-terminal TRX-fold
subdomain of the N-terminal domain (NTD) of bacterial
AhpF, which has a similar fold as PfPDO with two
TRX-fold subdomains but without the second CXXC motif.
Length = 67
Score = 30.2 bits (69), Expect = 0.017
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 4 VMLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVF 43
+A+ P++ +D E D+A Y + S+P V
Sbjct: 19 QAANRIAALNPNISAEMIDAAEFPDLADEYGVMSVPAIVI 58
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 30.7 bits (70), Expect = 0.027
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSG 55
L ELA +FPD F+K+ S Y ++PT + ++ V+QF G
Sbjct: 124 LSELARKFPDTKFVKII---STQCIPNYPDKNLPTILVYRNGDIVKQFIG 170
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 30.6 bits (68), Expect = 0.029
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 5 MLQELASEFP-DVVFLKVDV-DESEDIAMAY--DISSMPTFVFVKSTAKVEQFSGANF 58
+L+ELA E+ DV + V+V DE+ D+A + + S+PT + K +V++ G
Sbjct: 53 LLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVAVRSIPTLLLFKDGKEVDRLVGGKV 110
>gnl|CDD|239263 cd02965, HyaE, HyaE family; HyaE is also called HupG and HoxO.
They are proteins serving a critical role in the
assembly of multimeric [NiFe] hydrogenases, the enzymes
that catalyze the oxidation of molecular hydrogen to
enable microorganisms to utilize hydrogen as the sole
energy source. The E. coli HyaE protein is a chaperone
that specifically interacts with the twin-arginine
translocation (Tat) signal peptide of the [NiFe]
hydrogenase-1 beta subunit precursor. Tat signal
peptides target precursor proteins to the Tat protein
export system, which facilitates the transport of fully
folded proteins across the inner membrane. HyaE may be
involved in regulating the traffic of [NiFe]
hydrogenase-1 on the Tat transport pathway.
Length = 111
Score = 30.0 bits (68), Expect = 0.033
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 4 VMLQELASEFPDVVFLKVDVDESED-IAMAYDISSMPTFVFVK 45
V+L EL FP V E +A + + P +F +
Sbjct: 49 VVLPELLKAFPGRFRAAVVGRADEQALAARFGVLRTPALLFFR 91
>gnl|CDD|133998 PHA02125, PHA02125, thioredoxin-like protein.
Length = 75
Score = 29.6 bits (66), Expect = 0.039
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMA--YDISSMPTFVFVKSTAKVEQFSG 55
+ + +V + VDVD E + + + I S+PT V + ++F+G
Sbjct: 13 CKMVKPMLANVEYTYVDVDTDEGVELTAKHHIRSLPTLVNTSTL---DRFTG 61
>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 = 29.1 bits (65), Expect = 0.062
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 1 MSLVMLQELASEFPD-VVFLKVDVDESEDIAMAYDISSMPTFV 42
+ +++E+A E D V ++V E+ AM Y I ++P V
Sbjct: 16 AAKRVVEEVAKEMGDAVEVEYINVMENPQKAMEYGIMAVPAIV 58
>gnl|CDD|239287 cd02989, Phd_like_TxnDC9, Phosducin (Phd)-like family,
Thioredoxin (TRX) domain containing protein 9 (TxnDC9)
subfamily; composed of predominantly uncharacterized
eukaryotic proteins, containing a TRX-like domain
without the redox active CXXC motif. The gene name for
the human protein is TxnDC9. The two characterized
members are described as Phd-like proteins, PLP1 of
Saccharomyces cerevisiae and PhLP3 of Dictyostelium
discoideum. Gene disruption experiments show that both
PLP1 and PhLP3 are non-essential proteins. Unlike Phd
and most Phd-like proteins, members of this group do
not contain the Phd N-terminal helical domain which is
implicated in binding to the G protein betagamma
subunit.
Length = 113
Score = 29.1 bits (66), Expect = 0.071
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDKL 61
L+ LA + + F+KV+ +++ + +I +PT + K+ V++ G F++L
Sbjct: 44 LEILAKKHLETKFIKVNAEKAPFLVEKLNIKVLPTVILFKNGKTVDRIVG--FEEL 97
>gnl|CDD|203636 pfam07449, HyaE, Hydrogenase-1 expression protein HyaE. This
family contains bacterial hydrogenase-1 expression
proteins approximately 120 residues long. This includes
the E. coli protein HyaE, and the homologous proteins
HoxO of R. eutropha and HupG of R. leguminosarum.
Deletion of the hoxO gene in R. eutropha led to
complete loss of the uptake [NiFe] hydrogenase
activity, suggesting that it has a critical role in
hydrogenase assembly.
Length = 107
Score = 28.9 bits (65), Expect = 0.091
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 4 VMLQELASEFPDVVFLKVDVDESED-IAMAYDISSMPTFVFVK 45
V+L EL FP V E E+ + + + P+ +F +
Sbjct: 48 VVLPELLRAFPQRFRQAVVAREQEEALGDRFGVRRFPSLLFFR 90
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 27.7 bits (62), Expect = 0.27
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 15 DVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGA 56
V F+KV+ + +++ + I S+PT + K+ V+ +GA
Sbjct: 84 KVRFVKVNTEAERELSARFRIRSIPTIMIFKNGQVVDMLNGA 125
>gnl|CDD|239322 cd03024, DsbA_FrnE, DsbA family, FrnE subfamily; FrnE is a
DsbA-like protein containing a CXXC motif. It is
presumed to be a thiol oxidoreductase involved in
polyketide biosynthesis, specifically in the production
of the aromatic antibiotics frenolicin and nanaomycins.
Length = 201
Score = 27.5 bits (62), Expect = 0.41
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 22 DVDESEDIAMAYDISSMPTFVF 43
+V E A IS +P FVF
Sbjct: 160 EVRADEARARQLGISGVPFFVF 181
>gnl|CDD|239246 cd02948, TRX_NDPK, TRX domain, TRX and NDP-kinase (NDPK) fusion
protein family; most members of this group are fusion
proteins which contain one redox active TRX domain
containing a CXXC motif and three NDPK domains, and are
characterized as intermediate chains (ICs) of axonemal
outer arm dynein. Dyneins are molecular motors that
generate force against microtubules to produce cellular
movement, and are divided into two classes: axonemal and
cytoplasmic. They are supramolecular complexes
consisting of three protein groups classified according
to size: dynein heavy, intermediate and light chains.
Axonemal dyneins form two structures, the inner and
outer arms, which are attached to doublet microtubules
throughout the cilia and flagella. The human homolog is
the sperm-specific Sptrx-2, presumed to be a component
of the human sperm axoneme architecture. Included in
this group is another human protein, TRX-like protein 2,
a smaller fusion protein containing one TRX and one NDPK
domain, which is also associated with microtubular
structures. The other members of this group are
hypothetical insect proteins containing a TRX domain and
outer arm dynein light chains (14 and 16kDa) of
Chlamydomonas reinhardtii. Using standard assays, the
fusion proteins have shown no TRX enzymatic activity.
Length = 102
Score = 26.5 bits (59), Expect = 0.63
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 33 YDISSMPTFVFVKSTAKVEQFSGANFDKLRSTVL 66
Y PTF+F K+ V GAN L T+
Sbjct: 67 YRGKCEPTFLFYKNGELVAVIRGANAPLLNKTIT 100
>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 = 26.4 bits (59), Expect = 0.80
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 25/65 (38%)
Query: 5 MLQELASEF--PDVVFLKVDVDESE-----------------------DIAMAYDISSMP 39
L+ LA E+ V + V+VD+ + ++A AY + +P
Sbjct: 40 ELEALAKEYKDDGVEVVGVNVDDDDPAAVKAFLKKYGITFPVLLDPDGELAKAYGVRGLP 99
Query: 40 TFVFV 44
T +
Sbjct: 100 TTFLI 104
>gnl|CDD|225355 COG2761, FrnE, Predicted dithiol-disulfide isomerase involved in
polyketide biosynthesis [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 225
Score = 26.6 bits (59), Expect = 0.81
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 22 DVDESEDIAMAYDISSMPTFVF 43
V + E A I +PTFVF
Sbjct: 169 AVRQDEAAAQEMGIRGVPTFVF 190
>gnl|CDD|183168 PRK11509, PRK11509, hydrogenase-1 operon protein HyaE;
Provisional.
Length = 132
Score = 26.5 bits (58), Expect = 0.85
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 4 VMLQELASEFPDVVF--LKVDVDESEDIAMAYDISSMP-TFVFV 44
VM+ EL EFPD + D+++SE I + + P T VF
Sbjct: 56 VMIGELLREFPDYTWQVAIADLEQSEAIGDRFGVFRFPATLVFT 99
>gnl|CDD|203210 pfam05218, DUF713, Protein of unknown function (DUF713). This
family contains several proteins of unknown function
from C.elegans. The GO annotation suggests that this
protein is involved in nematode development and has a
positive regulation on growth rate.
Length = 182
Score = 26.6 bits (59), Expect = 0.96
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 5 MLQELASEFPDVVFLKV 21
LQEL F D +F+KV
Sbjct: 96 QLQELTEIFDDKLFIKV 112
>gnl|CDD|234353 TIGR03788, marine_srt_targ, marine proteobacterial sortase target
protein. Members of this protein family are restricted
to the Proteobacteria. Each contains a C-terminal
sortase-recognition motif, transmembrane domain, and
basic residues cluster at the the C-terminus, and is
encoded adjacent to a sortase gene. This protein is
frequently the only sortase target in its genome, which
is as unusual its occurrence in Gram-negative rather
than Gram-positive genomes. Many bacteria with this
system are marine. In addition to the LPXTG signal,
members carry a vault protein inter-alpha-trypsin
inhibitor domain (pfam08487) and a von Willebrand factor
type A domain (pfam00092).
Length = 596
Score = 25.8 bits (57), Expect = 1.7
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 40 TFVFVKSTAKVEQFSGANFDKLRSTVLAN 68
+F F+ ST +V++ F KL L +
Sbjct: 424 SFTFIGSTDEVQRKMSQLFAKLEQPALTD 452
>gnl|CDD|236956 PRK11697, PRK11697, putative two-component response-regulatory
protein YehT; Provisional.
Length = 238
Score = 25.6 bits (57), Expect = 2.3
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 14 PDVVFLKVD---VDESEDIAMAYDISSMPTFVFVKSTA 48
PDVVFL + + E + M D MP VFV TA
Sbjct: 48 PDVVFLDIQMPRISGLELVGM-LDPEHMPYIVFV--TA 82
>gnl|CDD|239273 cd02975, PfPDO_like_N, Pyrococcus furiosus protein disulfide
oxidoreductase (PfPDO)-like family, N-terminal TRX-fold
subdomain; composed of proteins with similarity to
PfPDO, a redox active thermostable protein believed to
be the archaeal counterpart of bacterial DsbA and
eukaryotic protein disulfide isomerase (PDI), which are
both involved in oxidative protein folding. PfPDO
contains two redox active CXXC motifs in two contiguous
TRX-fold subdomains. The active site in the N-terminal
TRX-fold subdomain is required for isomerase but not
for reductase activity of PfPDO. The exclusive presence
of PfPDO-like proteins in extremophiles may suggest
that they have a special role in adaptation to extreme
conditions.
Length = 113
Score = 25.0 bits (55), Expect = 2.3
Identities = 12/45 (26%), Positives = 23/45 (51%)
Query: 5 MLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAK 49
+L+EL+ + D DE ++ A Y + +PT +F++ K
Sbjct: 43 LLEELSELSDKLKLEIYDFDEDKEKAEKYGVERVPTTIFLQDGGK 87
>gnl|CDD|219398 pfam07394, DUF1501, Protein of unknown function (DUF1501). This
family contains a number of hypothetical bacterial
proteins of unknown function approximately 400 residues
long.
Length = 393
Score = 25.4 bits (56), Expect = 2.3
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 9/52 (17%)
Query: 2 SLVMLQELA------SEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKST 47
+ + ELA SE P+ L DE E Y + P F
Sbjct: 188 ARIAQYELAFRALMQSEAPEAFDLS---DEPEATRELYGRDAPPPGSFGARC 236
>gnl|CDD|219615 pfam07876, Dabb, Stress responsive A/B Barrel Domain. The
function of this family is unknown, but it is
upregulated in response to salt stress in Populus
balsamifera. It is also found at the C-terminus of an
fructose 1,6-bisphosphate aldolase from Hydrogenophilus
thermoluteolus. Arthrobacter nicotinovorans ORF106 is
found in the pA01 plasmid, which encodes genes for
molybdopterin uptake and degradation of plant alkaloid
nicotine. The structure of one has been solved and the
domain forms an a/b barrel dimer. Although there is a
clear duplication within the domain it is not obviously
detectable in the sequence.
Length = 96
Score = 25.0 bits (55), Expect = 2.5
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 3 LVMLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFV 42
L L+ L E P + ++V + S + Y + + F
Sbjct: 22 LEGLEALKGEIPGIKSIEVGRNVSPEGNQGYTHALVSEFE 61
>gnl|CDD|240250 PTZ00062, PTZ00062, glutaredoxin; Provisional.
Length = 204
Score = 25.1 bits (55), Expect = 2.7
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 8/60 (13%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDKLRSTV 65
L +FP + F V+ +A + F F +++ + G N L S +
Sbjct: 39 CNALVEDFPSLEFYVVN--------LADANNEYGVFEFYQNSQLINSLEGCNTSTLVSFI 90
>gnl|CDD|179545 PRK03147, PRK03147, thiol-disulfide oxidoreductase; Provisional.
Length = 173
Score = 25.3 bits (56), Expect = 2.8
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 21 VDVDESEDIAMAYDISSMPTFVFVKSTAKVEQ 52
V +D+ + AY + +PT + KV +
Sbjct: 122 VAIDKGRQVIDAYGVGPLPTTFLIDKDGKVVK 153
>gnl|CDD|224658 COG1744, Med, Uncharacterized ABC-type transport system,
periplasmic component/surface lipoprotein [General
function prediction only].
Length = 345
Score = 25.4 bits (56), Expect = 2.8
Identities = 8/17 (47%), Positives = 15/17 (88%)
Query: 6 LQELASEFPDVVFLKVD 22
L+++A+E+PDV F+ +D
Sbjct: 112 LEKVAAEYPDVKFVIID 128
>gnl|CDD|200131 TIGR01804, BADH, glycine betaine aldehyde dehydrogenase. Under
osmotic stress, betaine aldehyde dehydrogenase oxidizes
glycine betaine aldehyde into the osmoprotectant glycine
betaine, via the second of two oxidation steps from
exogenously supplied choline or betaine aldehyde. This
choline-glycine betaine synthesis pathway can be found
in gram-positive and gram-negative bacteria. In
Escherichia coli, betaine aldehyde dehydrogenase (betB)
is osmotically co-induced with choline dehydrogenase
(betA) in the presence of choline. These dehydrogenases
are located in a betaine gene cluster with the upstream
choline transporter (betT) and transcriptional regulator
(betI). Similar to E.coli, betaine synthesis in
Staphylococcus xylosus is also influenced by osmotic
stress and the presence of choline with genes localized
in a functionally equivalent gene cluster. Organization
of the betaine gene cluster in Sinorhizobium meliloti
and Bacillus subtilis differs from that of E.coli by the
absence of upstream choline transporter and
transcriptional regulator homologues. Additionally,
B.subtilis co-expresses a type II alcohol dehydrogenase
with betaine aldehyde dehydrogenase instead of choline
dehydrogenase as in E.coli, St.xylosus, and Si.meliloti.
Betaine aldehyde dehydrogenase is a member of the
aldehyde dehydrogenase family (pfam00171) [Cellular
processes, Adaptations to atypical conditions].
Length = 467
Score = 25.2 bits (55), Expect = 3.0
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 8 ELASEFPDVVFLKVDVDESEDIAM------AYDISSMPTFVFVKSTAKVEQFSGANFDKL 61
EL + P +VF D++ + D AM A + S T VFV K E+F ++
Sbjct: 242 ELGGKSPLIVFDDADLESAVDGAMLGNFFSAGQVCSNGTRVFVHKKIK-ERFLARLVERT 300
Query: 62 RSTVLAN 68
L +
Sbjct: 301 ERIKLGD 307
>gnl|CDD|99985 cd03814, GT1_like_2, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria and eukaryotes.
Length = 364
Score = 25.3 bits (56), Expect = 3.1
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 12/43 (27%)
Query: 5 MLQELASEFPDVVFL-KVDVDESEDIAMAY---DISSMPTFVF 43
L + +P+V FL +D E++A AY D+ FVF
Sbjct: 238 ARARLEARYPNVHFLGFLD---GEELAAAYASADV-----FVF 272
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 24.6 bits (53), Expect = 3.5
Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 5 MLQELASEFP-DVVFLKVDVDESEDIAMAYDISSMPTFVFVKS 46
+L E+A E+ + K+++D++ A Y I +PT + K+
Sbjct: 42 ILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKN 84
>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 = 25.0 bits (55), Expect = 3.5
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 15 DVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVE 51
+ V L VD + Y + +P FVF+ E
Sbjct: 54 NFVMLNVDNPKWLPEIDRYRVDGIPHFVFLDREGNEE 90
>gnl|CDD|153376 cd07364, PCA_45_Dioxygenase_B, Subunit B of the Class III
extradiol dioxygenase, Protocatechuate 4,5-dioxygenase,
which catalyzes the oxidization and subsequent
ring-opening of protocatechuate. Protocatechuate
4,5-dioxygenase (LigAB) catalyzes the oxidization and
subsequent ring-opening of protocatechuate (or
3,4-dihydroxybenzoic acid, PCA), an intermediate in the
breakdown of lignin and other compounds.
Protocatechuate 4,5-dioxygenase is an aromatic ring
opening dioxygenase belonging to the class III
extradiol enzyme family, a group of enyzmes that
cleaves aromatic rings between a hydroxylated carbon
and an adjacent non-hydroxylated carbon using a
non-heme Fe(II). LigAB is composed of two subunits,
designated A and B, which form a tetramer composed of
two copies of each subunit. The B subunit (LigB) is the
catalytic subunit of LigAB.
Length = 277
Score = 24.7 bits (54), Expect = 4.0
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 14 PDVVFLKVDVDESEDIAMAYDISSMPTFV 42
PDV + + D A A+D+ +PTF
Sbjct: 49 PDVAIIVYN-----DHASAFDLDIIPTFA 72
>gnl|CDD|233769 TIGR02187, GlrX_arch, Glutaredoxin-like domain protein. This
family of archaeal proteins contains a C-terminal domain
with homology to bacterial and eukaryotic glutaredoxins,
including a CPYC motif. There is an N-terminal domain
which has even more distant homology to glutaredoxins.
The name "glutaredoxin" may be inappropriate in the
sense of working in tandem with glutathione and
glutathione reductase which may not be present in the
archaea. The overall domain structure appears to be
related to bacterial alkylhydroperoxide reductases, but
the homology may be distant enough that the function of
this family is wholly different.
Length = 215
Score = 24.7 bits (54), Expect = 4.0
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 4 VMLQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANFDK 60
+M + A ++ ++ +E+ D+A Y + S+P V K VE+F GA ++
Sbjct: 153 LMAHKFALANDKILGEMIEANENPDLAEKYGVMSVPKIVINKG---VEEFVGAYPEE 206
>gnl|CDD|236224 PRK08297, PRK08297, L-lysine aminotransferase; Provisional.
Length = 443
Score = 24.9 bits (55), Expect = 4.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 3 LVMLQELASEFPDVV 17
L L+ELA+EFP VV
Sbjct: 359 LARLEELAAEFPAVV 373
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 24.7 bits (55), Expect = 4.8
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 7 QELASEFPDVVFLKVDVDE 25
+ELA FP+ L++D D
Sbjct: 444 EELAELFPEARILRIDRDT 462
>gnl|CDD|133434 cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA-
and pagL-like glycosidases. Bacillus subtilis GlvA and
Clostridium acetobutylicum pagL are
6-phospho-alpha-glucosidase, catalyzing the hydrolysis
of alpha-glucopyranoside bonds to release glucose from
oligosaccharides. The substrate specificities of other
members of this subgroup are unknown. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP_PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases, which
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. Members of this
subfamily are part of the NAD(P)-binding Rossmann fold
superfamily, which includes a wide variety of protein
families including the NAD(P)-binding domains of
alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and
NAD-binding potassium channel domains, among others.
Length = 437
Score = 24.5 bits (54), Expect = 5.3
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 1 MSLVMLQELASEFP--DVVFLKVDVDESEDIAMAYDI---SSMPTFVFVKSTAKVEQFSG 55
SL+ +E +FP ++V +D + E +A A I + P FV +T E F+
Sbjct: 18 KSLLDRKE---DFPLRELVLYDIDAERQEKVAEAVKILFKENYPEIKFVYTTDPEEAFTD 74
Query: 56 ANF 58
A+F
Sbjct: 75 ADF 77
>gnl|CDD|131490 TIGR02437, FadB, fatty oxidation complex, alpha subunit FadB.
Members represent alpha subunit of multifunctional
enzyme complex of the fatty acid degradation cycle.
Activities include: enoyl-CoA hydratase (EC 4.2.1.17),
dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8),
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35),
3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A
representative is E. coli FadB. This model excludes the
FadJ family represented by SP:P77399 [Fatty acid and
phospholipid metabolism, Degradation].
Length = 714
Score = 24.4 bits (53), Expect = 5.4
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 8 ELASEFPDV---VFLKVDVDESEDIAMAYDISSMPTFVFVKSTAKVEQFSGANF 58
E E P V V +V+ ED +A + S++ + K+ + E F G +F
Sbjct: 398 EAVVENPKVKAAVLAEVEQHVREDAILASNTSTISISLLAKALKRPENFCGMHF 451
>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 = 23.4 bits (51), Expect = 8.3
Identities = 8/41 (19%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 6 LQELASEFPDVVFLKVDVDESEDIAMAYDISSMPTFVFVKS 46
L+++ ++ +V F E ++ Y + ++PT V +
Sbjct: 53 LKKMPKDWLNVPF---GDKERNELLRLYGVKAIPTLVLLDK 90
>gnl|CDD|107348 cd06353, PBP1_BmpA_Med_like, Periplasmic binding domain of the
basic membrane lipoprotein Med in Bacillus and its
close homologs from other bacteria and Archaea.
Periplasmic binding domain of the basic membrane
lipoprotein Med in Bacillus and its close homologs from
other bacteria and Archaea. Med, a cell-surface
localized protein, which regulates the competence
transcription factor gene comK in Bacillus subtilis,
lacks the DNA binding domain when compared with
structures of transcription regulators from the LacI
family. Nevertheless, Med has significant overall
sequence homology to various periplasmic
substrate-binding proteins. Moreover, the structure of
Med shows a striking similarity to PnrA, a periplasmic
nucleoside binding protein of an ATP-binding cassette
transport system. Members of this group contain the
type I periplasmic sugar-binding protein-like fold.
Length = 258
Score = 23.7 bits (52), Expect = 8.9
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 7 QELASEFPDVVFL 19
++A E+PDV F
Sbjct: 73 LKVAKEYPDVKFE 85
>gnl|CDD|131789 TIGR02742, TrbC_Ftype, type-F conjugative transfer system pilin
assembly protein TrbC. This protein is an essential
component of the F-type conjugative pilus assembly
system for the transfer of plasmid DNA. The N-terminal
portion of these proteins are heterogeneous and are not
covered by this model.
Length = 130
Score = 23.5 bits (51), Expect = 9.8
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 33 YDISSMPTFVFVKSTAKVEQ---FSGANFDKLRSTV 65
+DI+++P FV VK +++D + V
Sbjct: 67 FDITAVPAFVVVKDGLACLPEQPCPESDYDVVYGNV 102
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 0.130 0.339
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: 3,389,939
Number of extensions: 249628
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 388
Number of HSP's successfully gapped: 61
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
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 (21.8 bits)
S2: 53 (24.2 bits)