RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy159
(285 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 = 42.9 bits (102), Expect = 8e-06
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 171 LETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYS 227
E +++ + + V F+ C C I LE++ +E + VK+ ++P+LA+ Y
Sbjct: 3 FEELIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYP--KVKFVKVDVDENPELAEEYG 60
Query: 228 IKTFPALVYFRNG 240
+++ P ++F+NG
Sbjct: 61 VRSIPTFLFFKNG 73
Score = 33.7 bits (78), Expect = 0.018
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 66 LDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFVKM---ADPRYARKWG 122
++L++ + V V F+ + LE++ + + FVK+ +P A ++G
Sbjct: 3 FEELIKSAKPVVVDFWAPWCGPCKAIAPVLEEL--AEEYPKVKFVKVDVDENPELAEEYG 60
Query: 123 VTKLPAVVYFR 133
V +P ++F+
Sbjct: 61 VRSIPTFLFFK 71
>gnl|CDD|222416 pfam13848, Thioredoxin_6, Thioredoxin-like domain.
Length = 183
Score = 39.2 bits (92), Expect = 8e-04
Identities = 30/161 (18%), Positives = 63/161 (39%), Gaps = 17/161 (10%)
Query: 4 ISDTEAAAKYNIINLPSLVYFRKQ--VPLLYDGDL-FDEEKILTWLTSQDVFEIKNEIEE 60
D E A KY I P+++ FRK + Y G+ + + ++ + E
Sbjct: 28 TFDKEVAKKYGI-KEPTILLFRKFDEKQVTYPGEDKTTFDDLKKFIQKN----SLPLVGE 82
Query: 61 VNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDG-ETDNMDITFVKMAD-PRYA 118
++L E + + + F + D +++ K+ R+E++ ++ V R
Sbjct: 83 FTPENAEELFESGKPL-LLFIKKDSEETEKLKNRVEEVAKKFKGKINFATVDGKSFGRVL 141
Query: 119 RKWGVT--KLPAVVY---FRHRFPSIYRGDLSEEEEVLQWL 154
G++ LP +V H+ + S E + ++L
Sbjct: 142 EYLGLSSADLPVIVIVDSASHKKKYFPEDEFS-PESLKEFL 181
>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 = 36.0 bits (84), Expect = 0.003
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 166 ITRVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYG-IHMVKI---QDPQ 221
+T + +V++++ + V FY C C + EK+ E G + + K+ +
Sbjct: 3 LTDDNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTANND 62
Query: 222 LAKRYSIKTFPALVYFRNG--NPLIFEGE 248
L Y ++ +P + F NG P+ +EG
Sbjct: 63 LCSEYGVRGYPTIKLFPNGSKEPVKYEGP 91
>gnl|CDD|150361 pfam09673, TrbC_Ftype, Type-F conjugative transfer system pilin
assembly protein. This entry represents TrbC, a protein
that 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 is
heterogeneous.
Length = 113
Score = 31.4 bits (72), Expect = 0.17
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 76 VTVF--FYETDHKDSVKVLERLEKIDGETDNMDITFVKMADPRYARKWGVTKLPAVVYFR 133
V F K++ ++ L K + I DP R++ +T +PA V +
Sbjct: 26 PVVLRGFVNGSLKETAAAIQELVKKGDRDAGVQI------DPTLFRRYNITSVPAFVVVK 79
Score = 29.1 bits (66), Expect = 0.88
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 219 DPQLAKRYSIKTFPALVYFRNGNP 242
DP L +RY+I + PA V ++
Sbjct: 60 DPTLFRRYNITSVPAFVVVKDSPL 83
>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 = 30.3 bits (69), Expect = 0.26
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 181 LAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYSIKTFPALVYF 237
L ++F+ C Q+ + E++ E + + I + P++++++ I P V+F
Sbjct: 17 LVLHFWAPWAEPCKQMNQVFEELAKEAFP-SVLFLSIEAEELPEISEKFEITAVPTFVFF 75
Query: 238 RNG 240
RNG
Sbjct: 76 RNG 78
>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 = 0.32
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 183 VYFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKIQDP-QLAKRYSIKTFPALVYFR 238
V FY C C +L L ++ + + + + KRY + P LV F
Sbjct: 2 VLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVFG 61
Query: 239 NGNPLIF 245
G + +
Sbjct: 62 PGIGVKY 68
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 31.1 bits (70), Expect = 0.46
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 183 VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKIQD----PQLAKRYSIKTFPALVYFR 238
V FY C+ C ++ E++ + G V D LAKR++IK +P L+ F
Sbjct: 57 VKFYAPWCSHCRKMAPAWERLAKA--LKGQVNVADLDATRALNLAKRFAIKGYPTLLLFD 114
Query: 239 NGNPLIFEG 247
G +EG
Sbjct: 115 KGKMYQYEG 123
>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 = 31.6 bits (72), Expect = 0.50
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 212 IHMVKI---QDPQLAKRYSIKTFPALVYFRNGNPLIFE 246
I + K+ ++ LA++Y + +P L FRNG + +
Sbjct: 54 IKLAKVDATEEKDLAQKYGVSGYPTLKIFRNGEDSVSD 91
Score = 29.6 bits (67), Expect = 2.1
Identities = 26/162 (16%), Positives = 58/162 (35%), Gaps = 19/162 (11%)
Query: 7 TEAAAKYNIINLPSLVYFR--KQVPLLYDGDLFDEEKILTWLTSQD---VFEIKNEIEEV 61
+ A KY + P+L FR + Y+G D + I+ ++ Q V EI+ ++
Sbjct: 65 KDLAQKYGVSGYPTLKIFRNGEDSVSDYNGPR-DADGIVKYMKKQSGPAVKEIETV-ADL 122
Query: 62 NRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFVKMADPRYARKW 121
++ V V + D ++ + + + ++ F +D K
Sbjct: 123 EA------FLADDDVVVIGFFKDLDS--ELNDTFLSVAEKLRDVYFFFAHSSDVAAFAKL 174
Query: 122 GVTKLPAVVYFR---HRFPSIYRGDLSEEEEVL-QWLITQKT 159
G V++ S G++ + L +++ +
Sbjct: 175 GAFPDSVVLFKPKDEDEKFSKVDGEMDTDVSDLEKFIRAESL 216
>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 = 30.0 bits (68), Expect = 0.52
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 218 QDPQLAKRYSIKTFPALVYFRNGNPL 243
Q+ L R+ ++ FP+L++FR+G L
Sbjct: 70 QEEALGDRFGVRRFPSLLFFRDGRYL 95
>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 = 29.8 bits (67), Expect = 0.54
Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 5/90 (5%)
Query: 164 ELIT--RVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECD-IYGIHMVKI-QD 219
E++T R + V + V FY C+ C + + E D + I V D
Sbjct: 2 EIVTLDRGDFDAAVNSGEIWFVNFYSPRCSHCHDLAPTWREFAKEMDGVIRIGAVNCGDD 61
Query: 220 PQLAKRYSIKTFPALVYFRNG-NPLIFEGE 248
L + + ++P+L F +G NP + G+
Sbjct: 62 RMLCRSQGVNSYPSLYVFPSGMNPEKYYGD 91
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 29.9 bits (66), Expect = 0.64
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 183 VYFYKLNCNICDQILEGLEKVDDE----CDIYGIHMVKIQDPQLAKRY--SIKTFPALVY 236
V F+ C C LE++ +E ++ ++ V ++P LA + ++++ P L+
Sbjct: 37 VDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVN-VDDENPDLAAEFGVAVRSIPTLLL 95
Query: 237 FRNGNPLIFEGENKILKGTYI 257
F++G + K+L +
Sbjct: 96 FKDGKEVDRLVGGKVLPKEAL 116
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 31.3 bits (71), Expect = 0.68
Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 5/93 (5%)
Query: 160 EDRIELITRVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYG--IHMVKI 217
+ + ++T + + E + + V FY C C ++ +K I + +
Sbjct: 31 SEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASV 90
Query: 218 ---QDPQLAKRYSIKTFPALVYFRNGNPLIFEG 247
++ +LA+ + ++ +P + +F GNP+ + G
Sbjct: 91 DATEEMELAQEFGVRGYPTIKFFNKGNPVNYSG 123
Score = 30.5 bits (69), Expect = 0.96
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 5 SDTEAAAKYNIINLPSLVYFRKQVPLLYDGDLFDEEKILTW---LTSQDVFEIKNEIEEV 61
+ E A ++ + P++ +F K P+ Y G + I++W LT V E+++ E
Sbjct: 94 EEMELAQEFGVRGYPTIKFFNKGNPVNYSGGR-TADGIVSWIKKLTGPAVTEVESASE-- 150
Query: 62 NRRMLDKLLEENEFVTVFFYETDHKDS 88
KL+ + FV F+ E KDS
Sbjct: 151 -----IKLIAKKIFV-AFYGEYTSKDS 171
Score = 27.8 bits (62), Expect = 7.4
Identities = 26/117 (22%), Positives = 48/117 (41%), Gaps = 28/117 (23%)
Query: 54 IKNEIEEVNRRMLDKLLEENEFVTVFFY----------ETDHKDSVKVLE------RLEK 97
I + + DK + ENE V V FY ++K + K+L+ L
Sbjct: 30 ISEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLAS 89
Query: 98 IDGETDNMDITFVKMADPRYARKWGVTKLPAVVYFRHRFPSIYRGDLSEEEEVLQWL 154
+D T+ M++ A+++GV P + +F P Y G + + ++ W+
Sbjct: 90 VDA-TEEMEL----------AQEFGVRGYPTIKFFNKGNPVNYSGGRT-ADGIVSWI 134
>gnl|CDD|233990 TIGR02740, TraF-like, TraF-like protein. This protein is related
to the F-type conjugation system pilus assembly proteins
TraF (TIGR02739)and TrbB (TIGR02738) both of which
exhibit a thioredoxin fold. The protein represented by
this model has the same length and architecture as TraF,
but lacks the CXXC-motif found in TrbB and believed to
be responsible for the disulfide isomerase activity of
that protein.
Length = 271
Score = 30.8 bits (70), Expect = 0.72
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 23/71 (32%)
Query: 184 YFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKIQ--------------DPQLAKRY 226
+F+K +C C Q IL+ E D YGI ++ + D A++
Sbjct: 172 FFFKSDCPYCHQQAPILQAFE------DRYGIEVLPVSVDGGPLPGFPNARPDAGQAQQL 225
Query: 227 SIKTFPALVYF 237
I+T PA+
Sbjct: 226 KIRTVPAVFLA 236
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 29.7 bits (67), Expect = 0.83
Identities = 9/32 (28%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 212 IHMVKIQ---DPQLAKRYSIKTFPALVYFRNG 240
+ VK+ + +L+ R+ I++ P ++ F+NG
Sbjct: 85 VRFVKVNTEAERELSARFRIRSIPTIMIFKNG 116
>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 = 29.0 bits (65), Expect = 0.92
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 176 EETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYSIKTFP 232
E + + V + C C + L KV DE D +H V+I +D ++A+ I P
Sbjct: 11 ESDRLILVLYTSPTCGPCRTLKPILNKVIDEFD-GAVHFVEIDIDEDQEIAEAAGIMGTP 69
Query: 233 ALVYFRN 239
+ +F++
Sbjct: 70 TVQFFKD 76
>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 = 29.2 bits (66), Expect = 0.98
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 222 LAKRYSIKTFPALVYFRNGNPL 243
LA R+ + PAL++FR+G +
Sbjct: 75 LAARFGVLRTPALLFFRDGRYV 96
>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 = 28.4 bits (64), Expect = 1.5
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 222 LAKRYSIKTFPALVYFRNGN-PLIFEGE 248
LA R+ + FP + +F G P+ +EG
Sbjct: 61 LASRFGVSGFPTIKFFPKGKKPVDYEGG 88
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 30.1 bits (68), Expect = 1.5
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 196 ILEGLEKVDDECDIYGIHMV 215
+L+ +VDD CD++G+H V
Sbjct: 323 MLKRWLRVDDPCDVFGVHGV 342
>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 = 28.0 bits (63), Expect = 1.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 220 PQLAKRYSIKTFPALVYFRNG 240
P LA Y ++ FP + +F+NG
Sbjct: 62 PDLASEYGVRGFPTIKFFKNG 82
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 28.1 bits (62), Expect = 2.0
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 161 DRIELITRVMLETMVEETQYLA-VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI-- 217
D+I +T +T V + V F+ C C I L+++ DE + + K+
Sbjct: 3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQ-GKLTVAKLNI 61
Query: 218 -QDPQLAKRYSIKTFPALVYFRNG 240
Q+P A +Y I+ P L+ F+NG
Sbjct: 62 DQNPGTAPKYGIRGIPTLLLFKNG 85
>gnl|CDD|227757 COG5470, COG5470, Uncharacterized conserved protein [Function
unknown].
Length = 96
Score = 27.7 bits (62), Expect = 2.1
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 210 YGIHMVKIQDPQLAKRYSIKTFPALVYFRNGNPLIFEGENKILKGTYIGT 259
Y I V ++DP+ K Y K PA+ F G L+ GE + L+G + T
Sbjct: 5 YWIADVDVRDPEQYKDYVSKAKPAIEKF-GGRYLVRGGEVETLEGEWRPT 53
>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 = 28.3 bits (64), Expect = 2.2
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 174 MVEETQYLAVYFYKLN---CNICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKT 230
+V+ ++ + +FY C I D+ LE L K E ++ K P L ++ +IK
Sbjct: 18 IVKSSERVVCHFYHPEFFRCKIMDKHLEILAKKHLETKFIKVNAEKA--PFLVEKLNIKV 75
Query: 231 FPALVYFRNGN 241
P ++ F+NG
Sbjct: 76 LPTVILFKNGK 86
>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 = 27.6 bits (62), Expect = 2.6
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 183 VYFYKLNCNICDQILEGLEKVDDECDIYG--IHMVKI---QDPQLAKRYSIKTFPALVYF 237
V F+ C C I LE++ E Y + VK+ ++P +A +Y I++ P L+ F
Sbjct: 19 VDFWAPWCGPCKMIAPILEELAKE---YEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLF 75
Query: 238 RNGNP 242
+NG
Sbjct: 76 KNGKE 80
>gnl|CDD|222813 PHA00730, int, integrase.
Length = 337
Score = 29.0 bits (65), Expect = 2.9
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 42/141 (29%)
Query: 147 EEEVLQWLITQKTEDRIELITRVMLETMVEETQYLAV---------------YFYKLNCN 191
EE+ + L K + + L+ R++LE+ ++ L V Y LN
Sbjct: 182 LEEIKKTLQKVKEYENVYLLYRLLLESGSRLSEALKVLNEYNPENDICENGFCIYTLNWT 241
Query: 192 ICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKTFPALVYFRNGNPLIFEGENKI 251
G +KV Y H+ ++ ++ K Y K F +
Sbjct: 242 ------RGQKKV-----FYVFHITPLKKIKITKWYIDK---------------FVRRLDL 275
Query: 252 LKGTYIGTYISTKAFSL-IPF 271
+ YI +++TK L IP
Sbjct: 276 IPPKYIRKFVATKMLELGIPS 296
>gnl|CDD|214705 smart00515, eIF5C, Domain at the C-termini of GCD6, eIF-2B
epsilon, eIF-4 gamma and eIF-5.
Length = 83
Score = 26.9 bits (60), Expect = 3.4
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 24 FRKQVPLLYDGDLFDEEKILTWLTSQDVFEIKNEI 58
K + LYD D+ +EE IL W E K ++
Sbjct: 35 LPKILKSLYDADILEEEAILKWYEKAVSAEGKKKV 69
>gnl|CDD|218740 pfam05768, DUF836, Glutaredoxin-like domain (DUF836). These
proteins are related to the pfam00462 family.
Length = 76
Score = 26.8 bits (60), Expect = 3.4
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 183 VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRY 226
+ K C++C+ E L ++ G + +I D +L RY
Sbjct: 3 TLYGKPGCHLCEGAKEVLAEL---EAALGFDLERIDIDDDEELFARY 46
>gnl|CDD|110972 pfam02024, Leptin, Leptin.
Length = 146
Score = 28.0 bits (62), Expect = 3.4
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 40 EKILTWLTSQDVFEIKNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKID 99
++ILT L S++V +I N++E N R L LL F ++ LE LE +
Sbjct: 62 QQILTSLPSRNVIQISNDLE--NLRDLLHLLA--------FSKSCPLPQASGLETLESLG 111
Query: 100 G 100
G
Sbjct: 112 G 112
>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 = 27.7 bits (62), Expect = 3.9
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 219 DPQLAKRYSIKTFPALVYFRNG 240
DPQ K++ I PA V ++G
Sbjct: 60 DPQWFKQFDITAVPAFVVVKDG 81
>gnl|CDD|153107 cd01048, Ferritin_like_AB2, Uncharacterized family of ferritin-like
proteins found in archaea and bacteria. Ferritin-like
domain found in archaea and bacteria, subgroup 2
(Ferritin_like_AB2). This uncharacterized domain is a
member of a broad superfamily of ferritin-like
diiron-carboxylate proteins whose function is unknown.
The conserved residues of a diiron center are present
within the putative active site.
Length = 135
Score = 27.6 bits (62), Expect = 3.9
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 47 TSQDVFEIKNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEK 97
+ QD E+ IEE++ D+LLE T + D V E L+
Sbjct: 82 SLQDALEVGVLIEELDIADYDRLLE----------RTQNPDIRDVFENLQA 122
>gnl|CDD|216334 pfam01153, Glypican, Glypican.
Length = 559
Score = 28.9 bits (65), Expect = 4.0
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 156 TQKTEDRIELITRVMLETMVEET 178
T + E+R+ L +RV E +++E+
Sbjct: 64 TSEMEERLSLQSRVDFEQLLQES 86
>gnl|CDD|211399 cd11561, W2_eIF5, C-terminal W2 domain of eukaryotic translation
initiation factor 5. eIF5 functions as a GTPase
acceleration protein (GAP), as well as a GDP
dissociation inhibitor (GDI) during translational
initiation in eukaryotes. The structure of this
C-terminal domain resembles that of a set of
concatenated HEAT repeats.
Length = 157
Score = 28.0 bits (63), Expect = 4.0
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 26 KQVPL----LYDGDLFDEEKILTW 45
K+VPL LYD D+ +EE IL W
Sbjct: 98 KKVPLILKALYDNDILEEEVILKW 121
>gnl|CDD|205373 pfam13192, Thioredoxin_3, Thioredoxin domain.
Length = 76
Score = 26.7 bits (60), Expect = 4.2
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 1 MVKISDTEAAAKYNIINLPSLVYFRKQVPLLYDGDLFDEEKILTWLT 47
+ K++D AKY +++ P+LV K V G + EE+I L
Sbjct: 33 VEKVTDFPEIAKYGVMSTPALVINGKVV---SSGKVPSEEEIKELLK 76
Score = 26.3 bits (59), Expect = 4.5
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 188 LNCNICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKTFPALV 235
C C ++ E +++ E I + K+ D +Y + + PALV
Sbjct: 8 PGCAKCPKLEEAVKEAVAELGID-AEVEKVTDFPEIAKYGVMSTPALV 54
>gnl|CDD|239292 cd02994, PDI_a_TMX, PDIa family, TMX subfamily; composed of
proteins similar to the TRX-related human transmembrane
protein, TMX. TMX is a type I integral membrane protein;
the N-terminal redox active TRX domain is present in the
endoplasmic reticulum (ER) lumen while the C-terminus is
oriented towards the cytoplasm. It is expressed in many
cell types and its active site motif (CPAC) is unique.
In vitro, TMX reduces interchain disulfides of insulin
and renatures inactive RNase containing incorrect
disulfide bonds. The C. elegans homolog, DPY-11, is
expressed only in the hypodermis and resides in the
cytoplasm. It is required for body and sensory organ
morphogeneis. Another uncharacterized TRX-related
transmembrane protein, human TMX4, is included in the
alignment. The active site sequence of TMX4 is CPSC.
Length = 101
Score = 27.0 bits (60), Expect = 4.7
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 167 TRVML-ETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQL 222
T V+ E M+E FY C C Q+ E+ D D GI++ K+ Q+P L
Sbjct: 12 TLVLEGEWMIE--------FYAPWCPACQQLQPEWEEFADWSDDLGINVAKVDVTQEPGL 63
Query: 223 AKRYSIKTFPALVYFRNG 240
+ R+ + P + + ++G
Sbjct: 64 SGRFFVTALPTIYHAKDG 81
>gnl|CDD|233145 TIGR00836, amt, ammonium transporter. The Ammonium Transporter
(Amt) Family (TC 2.A.49) All functionally characterized
members of the Amt family are ammonia or ammonium uptake
transporters. Some, but not others, also transport
methylammonium. The mechanism of energy coupling, if
any, to methyl-NH2 or NH3 uptake by the AmtB protein of
E. coli is not entirely clear. NH4+ uniport driven by
the pmf, energy independent NH3 facilitation, and
NH4+/K+ antiport have been proposed as possible
transport mechanisms. In Corynebacterium glutamicum and
Arabidopsis thaliana, uptake via the Amt1 homologues of
AmtB has been reported to be driven by the pmf
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 403
Score = 28.4 bits (64), Expect = 5.2
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 190 CNICDQILEGLEKVDDECDIYGIHMV 215
C + L+ K+DD D + +H V
Sbjct: 293 CYLAVSKLKKKLKIDDPLDAFAVHGV 318
>gnl|CDD|226685 COG4232, COG4232, Thiol:disulfide interchange protein
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 569
Score = 27.7 bits (62), Expect = 7.4
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 9/48 (18%)
Query: 6 DTEAAAKYNIINLPSLVYFRKQVPLLYDGDLFDEEKILTWLTSQDVFE 53
T + + +P+ ++F Q E +ILT + D F
Sbjct: 523 ITALLKRLGVFGVPTYLFFGPQGS---------EPEILTGFLTADAFL 561
>gnl|CDD|226715 COG4264, RhbC, Siderophore synthetase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 602
Score = 27.7 bits (62), Expect = 7.6
Identities = 23/134 (17%), Positives = 41/134 (30%), Gaps = 29/134 (21%)
Query: 55 KNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFVKMAD 114
K ++ +RR+L KLL E ET + + + I + D
Sbjct: 12 KELWQQADRRLLAKLLNE------LLRETILGPQKVIDIQ------DYHVYSIL-LIEED 58
Query: 115 PRYARKWGVTKLPAVVYFRHRF--PSIYRGDLSEE-----------EEVLQWLITQKTED 161
++ L A RH F P+ + + E + T +
Sbjct: 59 AAATYRFPARYLSAT--GRHLFVDPATLQVGADGDSPPLDALRFILEAAPELGATSEQLA 116
Query: 162 -RIELITRVMLETM 174
R+E + R +
Sbjct: 117 QRLEELLRTLASDA 130
>gnl|CDD|152460 pfam12025, Phage_C, Phage protein C. This family of phage
proteins is functionally uncharacterized. Proteins in
this family are typically between 68 to 86 amino acids
in length.
Length = 68
Score = 25.6 bits (56), Expect = 7.6
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 24 FRKQVPLLYDGDLFDEEKILTWLTS--QDVFEIKNEIEEVNRRMLDKLLE 71
FR Q+ L D DEEK L L + +D F ++ ++ + D L E
Sbjct: 15 FRHQLMFLTKTDALDEEKWLNMLGNLLKDWFRYEDHFVHGHKSLFDILKE 64
>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 = 26.4 bits (59), Expect = 8.0
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 222 LAKRYSIKTFPALVYFRNGN--PLIFEG 247
LAK+Y + FP L +F G+ P+ +EG
Sbjct: 67 LAKKYGVSGFPTLKFFPKGSTEPVKYEG 94
>gnl|CDD|222346 pfam13728, TraF, F plasmid transfer operon protein. TraF protein
undergoes proteolytic processing associated with export.
The 19 amino acids at the amino terminus of the
polypeptides appear to constitute a typical membrane
leader peptide - not included in this family, while the
remainder of the molecule is predicted to be primarily
hydrophilic in character. F plasmid TraF and TraH are
required for F pilus assembly and F plasmid transfer,
and they are both localised to the outer membrane in the
presence of the complete F transfer region, especially
TraV, the putative anchor.
Length = 215
Score = 27.2 bits (61), Expect = 8.4
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 23/72 (31%)
Query: 183 VYFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKI--------------QDPQLAKR 225
+FY+ +C C IL+ D YG ++ + D A+R
Sbjct: 125 FFFYRGDCPYCQAQAPILQAF------ADKYGFSVIPVSVDGGPLPGFPNNRVDTGQAQR 178
Query: 226 YSIKTFPALVYF 237
+KT PAL
Sbjct: 179 LGVKTTPALFLV 190
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 26.2 bits (58), Expect = 8.4
Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 19/87 (21%)
Query: 176 EETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIH----MVKIQDP----------- 220
+ + V F +C C ++ + L K D + + V + D
Sbjct: 3 GNGKPVLVVFTDPDCPYCKKLHKELLKDPDVQEYLKDNFVVIYVNVDDSKEVTDFDGETL 62
Query: 221 ---QLAKRYSIKTFPALVYF-RNGNPL 243
+LA++Y ++ P +V+ +G +
Sbjct: 63 SEKELARKYGVRGTPTIVFLDGDGKEV 89
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 26.8 bits (60), Expect = 8.9
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 17 NLPSLVYFRKQVPLLYDGDLFDEEKILTWLTSQD 50
+ F K + LYD D+ +EE IL W D
Sbjct: 107 SEEGGPLFAKLLHALYDLDILEEEAILEWWEEPD 140
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
0.321 0.140 0.409
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,053,115
Number of extensions: 1489899
Number of successful extensions: 1734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1727
Number of HSP's successfully gapped: 82
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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 (21.9 bits)
S2: 58 (26.1 bits)