RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy160
(346 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 = 1e-05
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 202 LETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYS 258
E +++ + + V F+ C C I LE++ +E + VK+ ++P+LA+ Y
Sbjct: 3 FEELIKSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYP--KVKFVKVDVDENPELAEEYG 60
Query: 259 IKTFPALVYFRNG 271
+++ P ++F+NG
Sbjct: 61 VRSIPTFLFFKNG 73
Score = 33.7 bits (78), Expect = 0.023
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 97 LDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFVKM---ADPRYARKWG 153
++L++ + V V F+ + LE++ + + FVK+ +P A ++G
Sbjct: 3 FEELIKSAKPVVVDFWAPWCGPCKAIAPVLEEL--AEEYPKVKFVKVDVDENPELAEEYG 60
Query: 154 VTKLPAVVYFR 164
V +P ++F+
Sbjct: 61 VRSIPTFLFFK 71
Score = 28.3 bits (64), Expect = 1.9
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 6 ENCPECDDILEELEHIDGDADQYGIDMVKI---SDTEAAAKYNIINLPSLVYFRK 57
C C I LE + + + + VK+ + E A +Y + ++P+ ++F+
Sbjct: 20 PWCGPCKAIAPVLEELAEEYPK--VKFVKVDVDENPELAEEYGVRSIPTFLFFKN 72
>gnl|CDD|222416 pfam13848, Thioredoxin_6, Thioredoxin-like domain.
Length = 183
Score = 40.0 bits (94), Expect = 5e-04
Identities = 30/161 (18%), Positives = 63/161 (39%), Gaps = 17/161 (10%)
Query: 35 ISDTEAAAKYNIINLPSLVYFRKQ--VPLLYDGDL-FDEEKILTWLTSQDVFEIKNEIEE 91
D E A KY I P+++ FRK + Y G+ + + ++ + E
Sbjct: 28 TFDKEVAKKYGI-KEPTILLFRKFDEKQVTYPGEDKTTFDDLKKFIQKN----SLPLVGE 82
Query: 92 VNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDG-ETDNMDITFVKMAD-PRYA 149
++L E + + + F + D +++ K+ R+E++ ++ V R
Sbjct: 83 FTPENAEELFESGKPL-LLFIKKDSEETEKLKNRVEEVAKKFKGKINFATVDGKSFGRVL 141
Query: 150 RKWGVT--KLPAVVY---FRHRFPSIYRGDLSEEEEVLQWL 185
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 = 36.4 bits (85), Expect = 0.003
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 197 ITRVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYG-IHMVKI---QDPQ 252
+T + +V++++ + V FY C C + EK+ E G + + K+ +
Sbjct: 3 LTDDNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTANND 62
Query: 253 LAKRYSIKTFPALVYFRNG--NPLIFEGE 279
L Y ++ +P + F NG P+ +EG
Sbjct: 63 LCSEYGVRGYPTIKLFPNGSKEPVKYEGP 91
Score = 28.3 bits (64), Expect = 2.2
Identities = 12/76 (15%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 8 CPECDDILEELEHIDGD-ADQYGIDMVKI---SDTEAAAKYNIINLPSLVYFRK--QVPL 61
C C + E E + + + + K+ ++ + ++Y + P++ F + P+
Sbjct: 27 CGHCKALAPEYEKLAKELKGDGKVVVAKVDCTANNDLCSEYGVRGYPTIKLFPNGSKEPV 86
Query: 62 LYDGDLFDEEKILTWL 77
Y+G E ++ ++
Sbjct: 87 KYEGPR-TLESLVEFI 101
>gnl|CDD|205373 pfam13192, Thioredoxin_3, Thioredoxin domain.
Length = 76
Score = 32.9 bits (76), Expect = 0.032
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 7 NCPECDDILEELEHIDGDADQYGID--MVKISDTEAAAKYNIINLPSLVYFRKQVPLLYD 64
C +C + E ++ + GID + K++D AKY +++ P+LV K V
Sbjct: 9 GCAKCPKLEEAVKEA---VAELGIDAEVEKVTDFPEIAKYGVMSTPALVINGKVV---SS 62
Query: 65 GDLFDEEKILTWLT 78
G + EE+I L
Sbjct: 63 GKVPSEEEIKELLK 76
Score = 26.3 bits (59), Expect = 6.9
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 219 LNCNICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKTFPALV 266
C C ++ E +++ E I + K+ D +Y + + PALV
Sbjct: 8 PGCAKCPKLEEAVKEAVAELGID-AEVEKVTDFPEIAKYGVMSTPALV 54
>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 = 0.19
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 107 VTVF--FYETDHKDSVKVLERLEKIDGETDNMDITFVKMADPRYARKWGVTKLPAVVYFR 164
V F K++ ++ L K + I DP R++ +T +PA V +
Sbjct: 26 PVVLRGFVNGSLKETAAAIQELVKKGDRDAGVQI------DPTLFRRYNITSVPAFVVVK 79
Score = 29.5 bits (67), Expect = 1.0
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 250 DPQLAKRYSIKTFPALVYFRNGNP 273
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 = 31.1 bits (71), Expect = 0.23
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 212 LAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYSIKTFPALVYF 268
L ++F+ C Q+ + E++ E + + I + P++++++ I P V+F
Sbjct: 17 LVLHFWAPWAEPCKQMNQVFEELAKEAFP-SVLFLSIEAEELPEISEKFEITAVPTFVFF 75
Query: 269 RNG 271
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 = 0.35
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 214 VYFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKIQDP-QLAKRYSIKTFPALVYFR 269
V FY C C +L L ++ + + + + KRY + P LV F
Sbjct: 2 VLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVFG 61
Query: 270 NGNPLIF 276
G + +
Sbjct: 62 PGIGVKY 68
>gnl|CDD|202542 pfam03119, DNA_ligase_ZBD, NAD-dependent DNA ligase C4 zinc
finger domain. DNA ligases catalyze the crucial step
of joining the breaks in duplex DNA during DNA
replication, repair and recombination, utilising either
ATP or NAD(+) as a cofactor. This family is a small
zinc binding motif that is presumably DNA binding. IT
is found only in NAD dependent DNA ligases.
Length = 27
Score = 28.6 bits (65), Expect = 0.37
Identities = 6/22 (27%), Positives = 9/22 (40%), Gaps = 3/22 (13%)
Query: 7 NCPECDDILEELEHIDGDADQY 28
+CP C L +G+ D
Sbjct: 1 HCPVCG---SPLVREEGEVDIR 19
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 31.5 bits (71), Expect = 0.41
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 214 VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKIQD----PQLAKRYSIKTFPALVYFR 269
V FY C+ C ++ E++ + G V D LAKR++IK +P L+ F
Sbjct: 57 VKFYAPWCSHCRKMAPAWERLAKA--LKGQVNVADLDATRALNLAKRFAIKGYPTLLLFD 114
Query: 270 NGNPLIFEG 278
G +EG
Sbjct: 115 KGKMYQYEG 123
>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 = 0.54
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 249 QDPQLAKRYSIKTFPALVYFRNGNPL 274
Q+ L R+ ++ FP+L++FR+G L
Sbjct: 70 QEEALGDRFGVRRFPSLLFFRDGRYL 95
Score = 29.6 bits (67), Expect = 0.81
Identities = 19/72 (26%), Positives = 27/72 (37%), Gaps = 12/72 (16%)
Query: 9 PECDD---ILEELEHIDGDADQYGIDMVKISDTEA-AAKYNIINLPSLVYFRKQVPLLYD 64
PE D +L EL + + V EA ++ + PSL++FR L
Sbjct: 41 PEVSDVAVVLPELLRAFPQRFRQAV--VAREQEEALGDRFGVRRFPSLLFFRDGRYL--- 95
Query: 65 GDLFDEEKILTW 76
G L I W
Sbjct: 96 GVL---AGIRDW 104
>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 = 0.61
Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 5/90 (5%)
Query: 195 ELIT--RVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECD-IYGIHMVKI-QD 250
E++T R + V + V FY C+ C + + E D + I V D
Sbjct: 2 EIVTLDRGDFDAAVNSGEIWFVNFYSPRCSHCHDLAPTWREFAKEMDGVIRIGAVNCGDD 61
Query: 251 PQLAKRYSIKTFPALVYFRNG-NPLIFEGE 279
L + + ++P+L F +G NP + G+
Sbjct: 62 RMLCRSQGVNSYPSLYVFPSGMNPEKYYGD 91
>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 = 0.62
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 243 IHMVKI---QDPQLAKRYSIKTFPALVYFRNGNPLIFE 277
I + K+ ++ LA++Y + +P L FRNG + +
Sbjct: 54 IKLAKVDATEEKDLAQKYGVSGYPTLKIFRNGEDSVSD 91
Score = 30.0 bits (68), Expect = 2.1
Identities = 30/173 (17%), Positives = 63/173 (36%), Gaps = 22/173 (12%)
Query: 30 IDMVKISDTEA---AAKYNIINLPSLVYFR--KQVPLLYDGDLFDEEKILTWLTSQD--- 81
I + K+ TE A KY + P+L FR + Y+G D + I+ ++ Q
Sbjct: 54 IKLAKVDATEEKDLAQKYGVSGYPTLKIFRNGEDSVSDYNGPR-DADGIVKYMKKQSGPA 112
Query: 82 VFEIKNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFV 141
V EI+ ++ ++ V V + D ++ + + + ++ F
Sbjct: 113 VKEIETV-ADLEA------FLADDDVVVIGFFKDLDS--ELNDTFLSVAEKLRDVYFFFA 163
Query: 142 KMADPRYARKWGVTKLPAVVYFR---HRFPSIYRGDLSEEEEVL-QWLITQKT 190
+D K G V++ S G++ + L +++ +
Sbjct: 164 HSSDVAAFAKLGAFPDSVVLFKPKDEDEKFSKVDGEMDTDVSDLEKFIRAESL 216
>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 = 31.2 bits (71), Expect = 0.65
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 23/71 (32%)
Query: 215 YFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKIQ--------------DPQLAKRY 257
+F+K +C C Q IL+ E D YGI ++ + D A++
Sbjct: 172 FFFKSDCPYCHQQAPILQAFE------DRYGIEVLPVSVDGGPLPGFPNARPDAGQAQQL 225
Query: 258 SIKTFPALVYF 268
I+T PA+
Sbjct: 226 KIRTVPAVFLA 236
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 31.6 bits (72), Expect = 0.69
Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 5/93 (5%)
Query: 191 EDRIELITRVMLETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYG--IHMVKI 248
+ + ++T + + E + + V FY C C ++ +K I + +
Sbjct: 31 SEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLASV 90
Query: 249 ---QDPQLAKRYSIKTFPALVYFRNGNPLIFEG 278
++ +LA+ + ++ +P + +F GNP+ + G
Sbjct: 91 DATEEMELAQEFGVRGYPTIKFFNKGNPVNYSG 123
Score = 31.3 bits (71), Expect = 0.88
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 36 SDTEAAAKYNIINLPSLVYFRKQVPLLYDGDLFDEEKILTW---LTSQDVFEIKNEIEEV 92
+ E A ++ + P++ +F K P+ Y G + I++W LT V E+++ E
Sbjct: 94 EEMELAQEFGVRGYPTIKFFNKGNPVNYSGGR-TADGIVSWIKKLTGPAVTEVESASE-- 150
Query: 93 NRRMLDKLLEENEFVTVFFYETDHKDS 119
KL+ + FV F+ E KDS
Sbjct: 151 -----IKLIAKKIFV-AFYGEYTSKDS 171
Score = 28.6 bits (64), Expect = 6.3
Identities = 26/117 (22%), Positives = 48/117 (41%), Gaps = 28/117 (23%)
Query: 85 IKNEIEEVNRRMLDKLLEENEFVTVFFY----------ETDHKDSVKVLE------RLEK 128
I + + DK + ENE V V FY ++K + K+L+ L
Sbjct: 30 ISEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKKSEIVLAS 89
Query: 129 IDGETDNMDITFVKMADPRYARKWGVTKLPAVVYFRHRFPSIYRGDLSEEEEVLQWL 185
+D T+ M++ A+++GV P + +F P Y G + + ++ W+
Sbjct: 90 VDA-TEEMEL----------AQEFGVRGYPTIKFFNKGNPVNYSGGRT-ADGIVSWI 134
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 30.3 bits (67), Expect = 0.71
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 214 VYFYKLNCNICDQILEGLEKVDDE----CDIYGIHMVKIQDPQLAKRY--SIKTFPALVY 267
V F+ C C LE++ +E ++ ++ V ++P LA + ++++ P L+
Sbjct: 37 VDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVN-VDDENPDLAAEFGVAVRSIPTLLL 95
Query: 268 FRNGNPLIFEGENKILKGTYI 288
F++G + K+L +
Sbjct: 96 FKDGKEVDRLVGGKVLPKEAL 116
>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 = 1.0
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 253 LAKRYSIKTFPALVYFRNGNPL 274
LA R+ + PAL++FR+G +
Sbjct: 75 LAARFGVLRTPALLFFRDGRYV 96
Score = 27.3 bits (61), Expect = 4.7
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 14/73 (19%)
Query: 9 PECDD---ILEELEHIDGDADQYGIDMVKISDTEAA--AKYNIINLPSLVYFRKQVPLLY 63
PE D +L EL + V E A A++ ++ P+L++FR +
Sbjct: 42 PEVLDVAVVLPELLKAFPGRFRAA---VVGRADEQALAARFGVLRTPALLFFRDGRYV-- 96
Query: 64 DGDLFDEEKILTW 76
G L I W
Sbjct: 97 -GVL---AGIRDW 105
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 29.7 bits (67), Expect = 1.2
Identities = 9/32 (28%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 243 IHMVKIQ---DPQLAKRYSIKTFPALVYFRNG 271
+ 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 = 1.2
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 207 EETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRYSIKTFP 263
E + + V + C C + L KV DE D +H V+I +D ++A+ I P
Sbjct: 11 ESDRLILVLYTSPTCGPCRTLKPILNKVIDEFD-GAVHFVEIDIDEDQEIAEAAGIMGTP 69
Query: 264 ALVYFRN 270
+ +F++
Sbjct: 70 TVQFFKD 76
>gnl|CDD|235583 PRK05731, PRK05731, thiamine monophosphate kinase; Provisional.
Length = 318
Score = 30.2 bits (69), Expect = 1.5
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 302 FCFSEKHPGAFQTELVLRSLKIKIIGKCEDG 332
F F ++ GA + + IIG+ +G
Sbjct: 268 FTFPPENRGALLAAAGHLGVGVTIIGRVTEG 298
>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 = 1.9
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 253 LAKRYSIKTFPALVYFRNGN-PLIFEGE 279
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 = 2.0
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 227 ILEGLEKVDDECDIYGIHMV 246
+L+ +VDD CD++G+H V
Sbjct: 323 MLKRWLRVDDPCDVFGVHGV 342
>gnl|CDD|222813 PHA00730, int, integrase.
Length = 337
Score = 29.8 bits (67), Expect = 2.3
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 42/141 (29%)
Query: 178 EEEVLQWLITQKTEDRIELITRVMLETMVEETQYLAV---------------YFYKLNCN 222
EE+ + L K + + L+ R++LE+ ++ L V Y LN
Sbjct: 182 LEEIKKTLQKVKEYENVYLLYRLLLESGSRLSEALKVLNEYNPENDICENGFCIYTLNWT 241
Query: 223 ICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKTFPALVYFRNGNPLIFEGENKI 282
G +KV Y H+ ++ ++ K Y K F +
Sbjct: 242 ------RGQKKV-----FYVFHITPLKKIKITKWYIDK---------------FVRRLDL 275
Query: 283 LKGTYIGTYISTKAFSL-IPF 302
+ YI +++TK L IP
Sbjct: 276 IPPKYIRKFVATKMLELGIPS 296
>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 = 2.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 251 PQLAKRYSIKTFPALVYFRNG 271
P LA Y ++ FP + +F+NG
Sbjct: 62 PDLASEYGVRGFPTIKFFKNG 82
>gnl|CDD|227757 COG5470, COG5470, Uncharacterized conserved protein [Function
unknown].
Length = 96
Score = 28.1 bits (63), Expect = 2.6
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 241 YGIHMVKIQDPQLAKRYSIKTFPALVYFRNGNPLIFEGENKILKGTYIGT 290
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 = 2.6
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 205 MVEETQYLAVYFYKLN---CNICDQILEGLEKVDDECDIYGIHMVKIQDPQLAKRYSIKT 261
+V+ ++ + +FY C I D+ LE L K E ++ K P L ++ +IK
Sbjct: 18 IVKSSERVVCHFYHPEFFRCKIMDKHLEILAKKHLETKFIKVNAEKA--PFLVEKLNIKV 75
Query: 262 FPALVYFRNGN 272
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 = 3.5
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 214 VYFYKLNCNICDQILEGLEKVDDECDIYG--IHMVKI---QDPQLAKRYSIKTFPALVYF 268
V F+ C C I LE++ E Y + VK+ ++P +A +Y I++ P L+ F
Sbjct: 19 VDFWAPWCGPCKMIAPILEELAKE---YEGKVKFVKLNVDENPDIAAKYGIRSIPTLLLF 75
Query: 269 RNGNP 273
+NG
Sbjct: 76 KNGKE 80
Score = 27.3 bits (61), Expect = 4.1
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 14 ILEEL-EHIDGDADQYGIDMVKISDTEAAAKYNIINLPSLVYFRK 57
ILEEL + +G +++ + D AAKY I ++P+L+ F+
Sbjct: 35 ILEELAKEYEGKVKFVKLNVDENPDI--AAKYGIRSIPTLLLFKN 77
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 27.7 bits (61), Expect = 3.5
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 192 DRIELITRVMLETMVEETQYLA-VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI-- 248
D+I +T +T V + V F+ C C I L+++ DE + + K+
Sbjct: 3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQ-GKLTVAKLNI 61
Query: 249 -QDPQLAKRYSIKTFPALVYFRNG 271
Q+P A +Y I+ P L+ F+NG
Sbjct: 62 DQNPGTAPKYGIRGIPTLLLFKNG 85
>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 = 4.1
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 55 FRKQVPLLYDGDLFDEEKILTWLTSQDVFEIKNEI 89
K + LYD D+ +EE IL W E K ++
Sbjct: 35 LPKILKSLYDADILEEEAILKWYEKAVSAEGKKKV 69
>gnl|CDD|110972 pfam02024, Leptin, Leptin.
Length = 146
Score = 28.0 bits (62), Expect = 4.5
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 71 EKILTWLTSQDVFEIKNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKID 130
++ILT L S++V +I N++E N R L LL F ++ LE LE +
Sbjct: 62 QQILTSLPSRNVIQISNDLE--NLRDLLHLLA--------FSKSCPLPQASGLETLESLG 111
Query: 131 G 131
G
Sbjct: 112 G 112
>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 = 4.7
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 78 TSQDVFEIKNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEK 128
+ QD E+ IEE++ D+LLE T + D V E L+
Sbjct: 82 SLQDALEVGVLIEELDIADYDRLLE----------RTQNPDIRDVFENLQA 122
>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 = 4.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 250 DPQLAKRYSIKTFPALVYFRNG 271
DPQ K++ I PA V ++G
Sbjct: 60 DPQWFKQFDITAVPAFVVVKDG 81
>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 = 27.3 bits (61), Expect = 5.0
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 198 TRVML-ETMVEETQYLAVYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQL 253
T V+ E M+E FY C C Q+ E+ D D GI++ K+ Q+P L
Sbjct: 12 TLVLEGEWMIE--------FYAPWCPACQQLQPEWEEFADWSDDLGINVAKVDVTQEPGL 63
Query: 254 AKRYSIKTFPALVYFRNG 271
+ R+ + P + + ++G
Sbjct: 64 SGRFFVTALPTIYHAKDG 81
>gnl|CDD|216334 pfam01153, Glypican, Glypican.
Length = 559
Score = 28.5 bits (64), Expect = 5.4
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 187 TQKTEDRIELITRVMLETMVEET 209
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 = 5.5
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 57 KQVPL----LYDGDLFDEEKILTW 76
K+VPL LYD D+ +EE IL W
Sbjct: 98 KKVPLILKALYDNDILEEEVILKW 121
>gnl|CDD|218740 pfam05768, DUF836, Glutaredoxin-like domain (DUF836). These
proteins are related to the pfam00462 family.
Length = 76
Score = 26.4 bits (59), Expect = 6.1
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 214 VYFYKLNCNICDQILEGLEKVDDECDIYGIHMVKI---QDPQLAKRY 257
+ K C++C+ E L ++ G + +I D +L RY
Sbjct: 3 TLYGKPGCHLCEGAKEVLAEL---EAALGFDLERIDIDDDEELFARY 46
>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 = 6.6
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 221 CNICDQILEGLEKVDDECDIYGIHMV 246
C + L+ K+DD D + +H V
Sbjct: 293 CYLAVSKLKKKLKIDDPLDAFAVHGV 318
>gnl|CDD|226715 COG4264, RhbC, Siderophore synthetase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 602
Score = 28.5 bits (64), Expect = 6.7
Identities = 23/134 (17%), Positives = 41/134 (30%), Gaps = 29/134 (21%)
Query: 86 KNEIEEVNRRMLDKLLEENEFVTVFFYETDHKDSVKVLERLEKIDGETDNMDITFVKMAD 145
K ++ +RR+L KLL E ET + + + I + D
Sbjct: 12 KELWQQADRRLLAKLLNE------LLRETILGPQKVIDIQ------DYHVYSIL-LIEED 58
Query: 146 PRYARKWGVTKLPAVVYFRHRF--PSIYRGDLSEE-----------EEVLQWLITQKTED 192
++ L A RH F P+ + + E + T +
Sbjct: 59 AAATYRFPARYLSAT--GRHLFVDPATLQVGADGDSPPLDALRFILEAAPELGATSEQLA 116
Query: 193 -RIELITRVMLETM 205
R+E + R +
Sbjct: 117 QRLEELLRTLASDA 130
>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 = 27.9 bits (63), Expect = 6.9
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 23/72 (31%)
Query: 214 VYFYKLNCNICDQ---ILEGLEKVDDECDIYGIHMVKI--------------QDPQLAKR 256
+FY+ +C C IL+ D YG ++ + D A+R
Sbjct: 125 FFFYRGDCPYCQAQAPILQAF------ADKYGFSVIPVSVDGGPLPGFPNNRVDTGQAQR 178
Query: 257 YSIKTFPALVYF 268
+KT PAL
Sbjct: 179 LGVKTTPALFLV 190
>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 = 26.0 bits (57), Expect = 7.2
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 55 FRKQVPLLYDGDLFDEEKILTWLTS--QDVFEIKNEIEEVNRRMLDKLLE 102
FR Q+ L D DEEK L L + +D F ++ ++ + D L E
Sbjct: 15 FRHQLMFLTKTDALDEEKWLNMLGNLLKDWFRYEDHFVHGHKSLFDILKE 64
>gnl|CDD|213571 TIGR00935, 2a45, arsenite/antimonite efflux pump membrane protein.
Members of this protein family are ArsB, a highly
hydrophobic integral membrane protein involved in
transport processes used to protect cells from arsenite
(or antimonite). Members of the seed alignment were
selected by adjacency to the ATPase subunit ArsA that
energizes the transport [Cellular processes,
Detoxification, Transport and binding proteins, Other].
Length = 426
Score = 28.2 bits (63), Expect = 7.9
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 31 DMVKISDTEAAAKYNIINLPSL--------VYFRKQVPLLYDGDLFDEEK 72
D I E AA N+ +L +YFRK +P YD E K
Sbjct: 165 DFFGIGFNEYAAVMIPPNIFALIASILVLYLYFRKDIPARYDVSQLREPK 214
>gnl|CDD|216526 pfam01487, DHquinase_I, Type I 3-dehydroquinase. Type I
3-dehydroquinase, (3-dehydroquinate dehydratase or
DHQase.) catalyzes the cis-dehydration of
3-dehydroquinate via a covalent imine intermediate
giving dehydroshikimate. Dehydroquinase functions in the
shikimate pathway which is involved in the biosynthesis
of aromatic amino acids. Type II 3-dehydroquinase
catalyzes the trans-dehydration of 3-dehydroshikimate
see pfam01220.
Length = 222
Score = 27.5 bits (62), Expect = 8.2
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 2 YINDENCPECDDILEELEHIDGDADQYGIDMVKI 35
Y + E P +D+L E + G D+VKI
Sbjct: 119 YHDFEGTPSWEDLLSLYEE----MQKLGADIVKI 148
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 0.141 0.414
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: 18,347,118
Number of extensions: 1835644
Number of successful extensions: 2051
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2042
Number of HSP's successfully gapped: 91
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
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: 59 (26.5 bits)