RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17681
(148 letters)
>gnl|CDD|239257 cd02959, ERp19, Endoplasmic reticulum protein 19 (ERp19) family;
ERp19 is also known as ERp18, a protein located in the
ER containing one redox active TRX domain. Denaturation
studies indicate that the reduced form is more stable
than the oxidized form, suggesting that the protein is
involved in disulfide bond formation. In vitro, ERp19
has been shown to possess thiol-disulfide oxidase
activity which is dependent on the presence of both
active site cysteines. Although described as protein
disulfide isomerase (PDI)-like, the protein does not
complement for PDI activity. ERp19 shows a wide tissue
distribution but is most abundant in liver, testis,
heart and kidney.
Length = 117
Score = 141 bits (356), Expect = 2e-44
Identities = 56/116 (48%), Positives = 82/116 (70%)
Query: 29 HINWKSLDAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISD 88
HI+W +L+ G++ AK SGKPLM+LIHK++C AC L PKFA S EI+EL+ F MVN+ D
Sbjct: 2 HIHWVTLEDGIKEAKDSGKPLMLLIHKTWCGACKALKPKFAESKEISELSHNFVMVNLED 61
Query: 89 DEEPQDPKYAPDGDYVPRILYFGPQGEPKSQVFNAKSPQVYRHYYYDVPSIVQAMK 144
DEEP+D +++PDG Y+PRIL+ P G+ ++ N K Y+++Y + ++MK
Sbjct: 62 DEEPKDEEFSPDGGYIPRILFLDPSGDVHPEIINKKGNPNYKYFYSSAAQVTESMK 117
>gnl|CDD|239258 cd02960, AGR, Anterior Gradient (AGR) family; members of this
family are similar to secreted proteins encoded by the
cement gland-specific genes XAG-1 and XAG-2, expressed
in the anterior region of dorsal ectoderm of Xenopus.
They are implicated in the formation of the cement gland
and the induction of forebrain fate. The human homologs,
hAG-2 and hAG-3, are secreted proteins associated with
estrogen-positive breast tumors. Yeast two-hybrid
studies identified the metastasis-associated C4.4a
protein and dystroglycan as binding partners, indicating
possible roles in the development and progression of
breast cancer. hAG-2 has also been implicated in
prostate cancer. Its gene was cloned as an
androgen-inducible gene and it was shown to be
overexpressed in prostate cancer cells at the mRNA and
protein levels. AGR proteins contain one conserved
cysteine corresponding to the first cysteine in the CXXC
motif of TRX. They show high sequence similarity to
ERp19.
Length = 130
Score = 76.4 bits (188), Expect = 9e-19
Identities = 45/125 (36%), Positives = 66/125 (52%), Gaps = 4/125 (3%)
Query: 25 GFGGHINW-KSLDAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAP-KFE 82
G+G I W ++ + GL AK S KPLMV+ H C L FA EI +LA F
Sbjct: 1 GWGDDIIWVQTYEEGLYKAKKSNKPLMVIHHLEDCPHSQALKKAFAEHKEIQKLAQEDFI 60
Query: 83 MVNISDDEEPQDPKYAPDGDYVPRILYFGPQGEPKSQVFNAKSPQVYRHYYYDVPSIVQA 142
M+N+ E D +PDG YVPRI++ P ++ + S ++Y + D+P +++
Sbjct: 61 MLNLV--HETTDKNLSPDGQYVPRIMFVDPSLTVRADITGRYSNRLYTYEPADIPLLIEN 118
Query: 143 MKSAL 147
MK AL
Sbjct: 119 MKKAL 123
>gnl|CDD|222442 pfam13899, Thioredoxin_7, Thioredoxin-like. Thioredoxins are small
enzymes that participate in redox reactions, via the
reversible oxidation of an active centre disulfide bond.
Length = 81
Score = 71.5 bits (176), Expect = 2e-17
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 3/83 (3%)
Query: 31 NWKS-LDAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDD 89
+W LD L A+ GKPL+V +C C L F + P + LA KF ++ + D
Sbjct: 1 DWVQDLDEALAKAREEGKPLLVDFGADWCPTCQALDRDFLSDPRVKALAEKFVLLRV--D 58
Query: 90 EEPQDPKYAPDGDYVPRILYFGP 112
+DP DG VP +++ P
Sbjct: 59 VTTRDPNLLLDGQGVPHVVFLDP 81
>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 = 37.9 bits (89), Expect = 2e-04
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 39 LQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDDEEPQ 93
+ S KP++V +C C ++P E+AE PK + V + DE P+
Sbjct: 3 FEELIKSAKPVVVDFWAPWCGPCKAIAPVLE---ELAEEYPKVKFVKVDVDENPE 54
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 37.4 bits (87), Expect = 4e-04
Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 13/104 (12%)
Query: 42 AKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAE-LAPKFE--MVNISDDEEPQDPKYA 98
AK +GKP++V+ C C +L + P++ E L F VN+ D +E D
Sbjct: 1 AKGNGKPVLVVFTDPDCPYCKKLHKELLKDPDVQEYLKDNFVVIYVNVDDSKEVTDFDGE 60
Query: 99 PDG----------DYVPRILYFGPQGEPKSQVFNAKSPQVYRHY 132
P I++ G+ +++ P+ +
Sbjct: 61 TLSEKELARKYGVRGTPTIVFLDGDGKEVARLPGYLPPEEFLKL 104
>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 = 36.9 bits (86), Expect = 0.001
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 3/91 (3%)
Query: 39 LQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDDE-EPQDPKY 97
+ A ++GKP +V + +C C E++P A + F M+N+ + + P+ +Y
Sbjct: 13 PEVALSNGKPTLVEFYADWCTVCQEMAPDVAKLKQKYGDQVNFVMLNVDNPKWLPEIDRY 72
Query: 98 APDGDYVPRILYFGPQGEPKSQVFNAKSPQV 128
DG +P ++ +G + Q + QV
Sbjct: 73 RVDG--IPHFVFLDREGNEEGQSIGLQPKQV 101
>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 = 35.4 bits (82), Expect = 0.002
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 46 GKPLMVLIHKSYCAACHELSPKFAASPEIAE--LAPKFEMVNISDDEEPQDPK 96
GK +++ S+C C +P+ E+ E PK E+V +S D + ++ K
Sbjct: 1 GKVVLLYFWASWCPPCRAFTPELK---ELYEKLKKPKVEIVYVSLDRDEEEWK 50
>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 = 34.6 bits (79), Expect = 0.002
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 50 MVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDDEEPQDPKYAPDGDYVPRILY 109
+VL + +C C L P A + + KFE V++ +D + VP ++
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGV-KFEAVDVDEDPALEKELKRYGVGGVPTLVV 59
Query: 110 FGPQG 114
FGP
Sbjct: 60 FGPGI 64
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 36.0 bits (82), Expect = 0.002
Identities = 19/101 (18%), Positives = 36/101 (35%), Gaps = 10/101 (9%)
Query: 41 AAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDDEEPQDPKYAPD 100
++ GKP++V +C C +P E + VN+ D+ ++
Sbjct: 27 LSELKGKPVLVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVA 86
Query: 101 GDYVPRILYF----------GPQGEPKSQVFNAKSPQVYRH 131
+P +L F G + PK + +A + R
Sbjct: 87 VRSIPTLLLFKDGKEVDRLVGGKVLPKEALIDALGELLARL 127
>gnl|CDD|234717 PRK00293, dipZ, thiol:disulfide interchange protein precursor;
Provisional.
Length = 571
Score = 34.0 bits (79), Expect = 0.021
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 31 NWKSLDAGLQAAKTSGKPLMVLIHKSYCAACHE 63
LD L AK GKP+M+ ++ +C AC E
Sbjct: 459 TVAELDQALAEAKGKGKPVMLDLYADWCVACKE 491
>gnl|CDD|239251 cd02953, DsbDgamma, DsbD gamma family; DsbD gamma is the C-terminal
periplasmic domain of the bacterial protein DsbD. It
contains a CXXC motif in a TRX fold and shuttles the
reducing potential from the membrane domain (DsbD beta)
to the N-terminal periplasmic domain (DsbD alpha). DsbD
beta, a transmembrane domain comprising of eight
helices, acquires its reducing potential from the
cytoplasmic thioredoxin. DsbD alpha transfers the
acquired reducing potential from DsbD gamma to target
proteins such as the periplasmic protein disulphide
isomerases, DsbC and DsbG. This flow of reducing
potential from the cytoplasm through DsbD allows DsbC
and DsbG to act as isomerases in the oxidizing
environment of the bacterial periplasm. DsbD also
transfers reducing potential from the cytoplasm to
specific reductases in the periplasm which are involved
in the maturation of cytochromes.
Length = 104
Score = 29.5 bits (67), Expect = 0.30
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 16/95 (16%)
Query: 36 DAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAE-LAPKFEMV--NISDDEEP 92
+A L A GKP+ V +C C + PE+ L ++ + + +
Sbjct: 1 EAALAQALAQGKPVFVDFTADWCVTCKVNEKVVFSDPEVQAALKKDVVLLRADWTKN--- 57
Query: 93 QDP-------KYAPDGDYVPRILYFGPQGEPKSQV 120
DP ++ G P L++GP GEP+
Sbjct: 58 -DPEITALLKRFGVFG--PPTYLFYGPGGEPEPLR 89
>gnl|CDD|239307 cd03009, TryX_like_TryX_NRX, Tryparedoxin (TryX)-like family,
TryX and nucleoredoxin (NRX) subfamily; TryX and NRX
are thioredoxin (TRX)-like protein disulfide
oxidoreductases that alter the redox state of target
proteins via the reversible oxidation of an active
center CXXC motif. TryX is involved in the regulation
of oxidative stress in parasitic trypanosomatids by
reducing TryX peroxidase, which in turn catalyzes the
reduction of hydrogen peroxide and organic
hydroperoxides. TryX derives reducing equivalents from
reduced trypanothione, a polyamine peptide conjugate
unique to trypanosomatids, which is regenerated by the
NADPH-dependent flavoprotein trypanothione reductase.
Vertebrate NRX is a 400-amino acid nuclear protein with
one redox active TRX domain containing a CPPC active
site motif followed by one redox inactive TRX-like
domain. Mouse NRX transcripts are expressed in all
adult tissues but is restricted to the nervous system
and limb buds in embryos. Plant NRX, longer than the
vertebrate NRX by about 100-200 amino acids, is a
nuclear protein containing a redox inactive TRX-like
domain between two redox active TRX domains. Both
vertebrate and plant NRXs show thiol oxidoreductase
activity in vitro. Their localization in the nucleus
suggests a role in the redox regulation of nuclear
proteins such as transcription factors.
Length = 131
Score = 28.4 bits (64), Expect = 0.73
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 46 GKPLMVLIHKSYCAACHELSPKFAAS-PEIAELAPKFEMVNISDDEE 91
GK + + S+C C +PK ++ E FE+V IS D +
Sbjct: 18 GKTVGLYFSASWCPPCRAFTPKLVEFYEKLKESGKNFEIVFISWDRD 64
>gnl|CDD|224250 COG1331, COG1331, Highly conserved protein containing a
thioredoxin domain [Posttranslational modification,
protein turnover, chaperones].
Length = 667
Score = 29.3 bits (66), Expect = 0.90
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 30 INWK--SLDAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPK-FEMVNI 86
++W +A AK KP+++ I S C CH ++ + PEIA + + F V +
Sbjct: 26 VDWYPWGEEA-FAKAKEEDKPILLSIGYSTCHWCHVMAHESFEDPEIAAILNENFVPVKV 84
Query: 87 SDDEEP 92
+E P
Sbjct: 85 DREERP 90
>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 = 27.1 bits (60), Expect = 1.8
Identities = 20/80 (25%), Positives = 27/80 (33%), Gaps = 14/80 (17%)
Query: 45 SGKPLMVLIHKSYCAACHELSPKFAASPEIAELAPKFEMVNISDDEEPQDPKYAPDGDYV 104
S + ++VL C C L P + I E V I DE+ + + A
Sbjct: 12 SDRLILVLYTSPTCGPCRTLKPIL--NKVIDEFDGAVHFVEIDIDEDQEIAEAA------ 63
Query: 105 PRILYFGPQGEPKSQVFNAK 124
G G P Q F K
Sbjct: 64 ------GIMGTPTVQFFKDK 77
>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 = 27.3 bits (61), Expect = 1.9
Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 13/88 (14%)
Query: 40 QAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEI-AELAPKFEM--VNISDDEEPQDPK 96
+AA KPL++L + C C +L + P + A + F + +NI D+E D
Sbjct: 8 EAAADGKKPLLLLFSQPGCPYCDKLKRDYLNDPAVQAYIRAHFVVVYINIDGDKEVTDFD 67
Query: 97 YAP----------DGDYVPRILYFGPQG 114
+ P +++ P+G
Sbjct: 68 GEALSEKELARKYRVRFTPTVIFLDPEG 95
>gnl|CDD|239262 cd02964, TryX_like_family, Tryparedoxin (TryX)-like family;
composed of TryX and related proteins including
nucleoredoxin (NRX), rod-derived cone viability factor
(RdCVF) and the nematode homolog described as a 16-kD
class of TRX. Most members of this family, except
RdCVF, are protein disulfide oxidoreductases containing
an active site CXXC motif, similar to TRX.
Length = 132
Score = 27.2 bits (61), Expect = 2.5
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 46 GKPLMVLIHKSYCAACHELSPKFAAS-PEIAELAPKFEMVNISDDEEPQD 94
GK + + S+C C +PK ++ E FE+V +S D +
Sbjct: 17 GKTVGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFEIVFVSRDRSEES 66
>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 = 26.4 bits (59), Expect = 2.9
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 45 SGKPLMVLIHKSYCAACHELSPKFAASPEIA-ELAPKFEMVNISDDEEPQDP-KYAPDGD 102
S KP++V + +C C L+P++ ++A E + + DE P +Y G
Sbjct: 17 SDKPVLVDFYAPWCGPCKALAPEYE---KLAQEYKDDVKFAKVDADENPDLASEYGVRG- 72
Query: 103 YVPRILYFGPQGEPKSQV 120
P I +F + V
Sbjct: 73 -FPTIKFFKNGKKVSDYV 89
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 27.4 bits (61), Expect = 3.3
Identities = 10/50 (20%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 44 TSGKPLMVLIHKSYCAACHELSPKF-AASPEIAELAPKFEMVNISDDEEP 92
T + ++V + +C C L+P++ A+ + E + + ++ EE
Sbjct: 47 TENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASVDATEEM 96
>gnl|CDD|239256 cd02958, UAS, UAS family; UAS is a domain of unknown function.
Most members of this family are uncharacterized
proteins with similarity to FAS-associated factor 1
(FAF1) and ETEA because of the presence of a UAS domain
N-terminal to a ubiquitin-associated UBX domain. FAF1
is a longer protein, compared to the other members of
this family, having additional N-terminal domains, a
ubiquitin-associated UBA domain and a nuclear targeting
domain. FAF1 is an apoptotic signaling molecule that
acts downstream in the Fas signal transduction pathway.
It interacts with the cytoplasmic domain of Fas, but
not to a Fas mutant that is deficient in signal
transduction. ETEA is the protein product of a highly
expressed gene in T-cells and eosinophils of atopic
dermatitis patients. The presence of the
ubiquitin-associated UBX domain in the proteins of this
family suggests the possibility of their involvement in
ubiquitination. Recently, FAF1 has been shown to
interact with valosin-containing protein (VCP), which
is involved in the ubiquitin-proteosome pathway. Some
members of this family are uncharacterized proteins
containing only a UAS domain.
Length = 114
Score = 26.0 bits (58), Expect = 4.8
Identities = 9/44 (20%), Positives = 17/44 (38%)
Query: 34 SLDAGLQAAKTSGKPLMVLIHKSYCAACHELSPKFAASPEIAEL 77
S + Q AK+ K L+V + L+ ++ + E
Sbjct: 5 SFEDAKQEAKSEKKWLLVYLQSEDEFDSQVLNRDLWSNESVKEF 48
>gnl|CDD|227556 COG5231, VMA13, Vacuolar H+-ATPase V1 sector, subunit H [Energy
production and conversion].
Length = 432
Score = 26.8 bits (59), Expect = 5.5
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 7/42 (16%)
Query: 56 SYCAACHELSPKFAASPEIAELAPK-------FEMVNISDDE 90
C AC ++ ASPEI + K ++N DD+
Sbjct: 373 WICVACSDIFQLVRASPEINAVLSKYGVKEIIMNLINHDDDD 414
>gnl|CDD|214887 smart00889, EFG_IV, Elongation factor G, domain IV. Translation
elongation factors are responsible for two main
processes during protein synthesis on the ribosome. EF1A
(or EF-Tu) is responsible for the selection and binding
of the cognate aminoacyl-tRNA to the A-site (acceptor
site) of the ribosome. EF2 (or EF-G) is responsible for
the translocation of the peptidyl-tRNA from the A-site
to the P-site (peptidyl-tRNA site) of the ribosome,
thereby freeing the A-site for the next aminoacyl-tRNA
to bind. Elongation factors are responsible for
achieving accuracy of translation and both EF1A and EF2
are remarkably conserved throughout evolution.
Elongation factor EF2 (EF-G) is a G-protein. It brings
about the translocation of peptidyl-tRNA and mRNA
through a ratchet-like mechanism: the binding of GTP-EF2
to the ribosome causes a counter-clockwise rotation in
the small ribosomal subunit; the hydrolysis of GTP to
GDP by EF2 and the subsequent release of EF2 causes a
clockwise rotation of the small subunit back to the
starting position. This twisting action destabilises
tRNA-ribosome interactions, freeing the tRNA to
translocate along the ribosome upon GTP-hydrolysis by
EF2. EF2 binding also affects the entry and exit channel
openings for the mRNA, widening it when bound to enable
the mRNA to translocate along the ribosome. EF2 has five
domains. This entry represents domain IV found in EF2
(or EF-G) of both prokaryotes and eukaryotes. The
EF2-GTP-ribosome complex undergoes extensive structural
rearrangement for tRNA-mRNA movement to occur. Domain
IV, which extends from the 'body' of the EF2 molecule
much like a lever arm, appears to be essential for the
structural transition to take place.
Length = 120
Score = 25.6 bits (57), Expect = 7.1
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 96 KYAPDGDYVPRILYFGPQGEPKSQVFNAKSPQ--VYRHYYYDVPSIVQAMKSALN 148
+ DG Y IL P F+ + + Y +P++ + + AL
Sbjct: 22 QSGGDGQYARVILEVEPLERGSGFEFDDTIVGGVIPKEY---IPAVEKGFREALE 73
>gnl|CDD|223038 PHA03302, PHA03302, envelope glycoprotein L; Provisional.
Length = 253
Score = 26.2 bits (58), Expect = 7.2
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 82 EMVNISDDEEPQDPKY---APDGDYVPRILYFGPQGEPKSQV 120
E + S+D+ P P +GD I Y P GE +S +
Sbjct: 45 ETFSRSEDDSPLRPLIQAPHRNGDLSSLIRYRPPTGELRSPI 86
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor,
cyanobacterial RpoD-like family. This family includes a
number of closely related sigma-70 (TIGR02937) factors
in the cyanobacteria. All appear most closely related to
the essential sigma-70 factor RpoD, and some score above
trusted to the RpoD C-terminal domain model (TIGR02393).
Length = 298
Score = 26.1 bits (58), Expect = 7.7
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 63 ELSPKFAASPEIAELAPKFEM 83
ELS K +P AE+A E+
Sbjct: 169 ELSQKLGRTPSEAEIAEALEL 189
>gnl|CDD|239261 cd02963, TRX_DnaJ, TRX domain, DnaJ domain containing protein
family; composed of uncharacterized proteins of about
500-800 amino acids, containing an N-terminal DnaJ
domain followed by one redox active TRX domain. DnaJ is
a member of the 40 kDa heat-shock protein (Hsp40)
family of molecular chaperones, which regulate the
activity of Hsp70s. TRX is involved in the redox
regulation of many protein substrates through the
reduction of disulfide bonds. TRX has been implicated
to catalyse the reduction of Hsp33, a chaperone holdase
that binds to unfolded protein intermediates. The
presence of DnaJ and TRX domains in members of this
family suggests that they could be involved in a
redox-regulated chaperone network.
Length = 111
Score = 25.4 bits (56), Expect = 7.7
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 43 KTSGKPLMVLIHKSYCAACHELSPKFA-ASPEIAELAPKFEMVNISDDEE 91
K+ KP ++ I +C +C + P + E+ L VN +
Sbjct: 21 KSFKKPYLIKITSDWCFSCIHIEPVWKEVIQELEPLGVGIATVNAGHERR 70
>gnl|CDD|239301 cd03003, PDI_a_ERdj5_N, PDIa family, N-terminal ERdj5 subfamily;
ERdj5, also known as JPDI and macrothioredoxin, is a
protein containing an N-terminal DnaJ domain and four
redox active TRX domains. This subfamily is comprised
of the first TRX domain of ERdj5 located after the DnaJ
domain at the N-terminal half of the protein. ERdj5 is
a ubiquitous protein localized in the endoplasmic
reticulum (ER) and is abundant in secretory cells. It's
transcription is induced during ER stress. It interacts
with BiP through its DnaJ domain in an ATP-dependent
manner. BiP, an ER-resident member of the Hsp70
chaperone family, functions in ER-associated
degradation and protein translocation.
Length = 101
Score = 25.2 bits (55), Expect = 8.2
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 34 SLDAG-LQAAKTSGKPLMVLIHKSYCAACHELSP---KFA 69
+LD G AA SG+ V + C+ CH+L+P +FA
Sbjct: 5 TLDRGDFDAAVNSGEIWFVNFYSPRCSHCHDLAPTWREFA 44
>gnl|CDD|222879 PHA02563, PHA02563, DNA polymerase; Provisional.
Length = 630
Score = 25.9 bits (57), Expect = 9.9
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 67 KFAASPEIAELAPKFEM----VNISDDEEPQDPKYAPDGDYV 104
KFA +P+ P + IS+ EE ++P Y P ++
Sbjct: 416 KFALNPDNTGKVPYLDDNGRLDLISNGEENKEPNYIPIAAFI 457
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 0.136 0.420
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,548,812
Number of extensions: 659430
Number of successful extensions: 648
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 37
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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: 54 (24.4 bits)