RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8729
(190 letters)
>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 = 167 bits (425), Expect = 8e-54
Identities = 63/118 (53%), Positives = 81/118 (68%), Gaps = 6/118 (5%)
Query: 47 VIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGM-PWP 105
+GLYFSA WCPPC+AFTP+L+E Y KLKE+G FEI+FVS DRSE S+ Y S M PW
Sbjct: 19 TVGLYFSASWCPPCRAFTPKLVEFYEKLKEEGKNFEIVFVSRDRSEESFNEYFSEMPPWL 78
Query: 106 AIPYA-SETRQSLASLYNVHGIPSLILLAVEAGGRLDVITTEARHELSEDPDGEFFPW 162
A+P+ E R+ L + V GIP+L++ ++ G DV+TT AR E+ EDP FPW
Sbjct: 79 AVPFEDEELRELLEKQFKVEGIPTLVV--LKPDG--DVVTTNARDEVEEDPGACAFPW 132
>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 = 165 bits (420), Expect = 5e-53
Identities = 58/116 (50%), Positives = 79/116 (68%), Gaps = 6/116 (5%)
Query: 48 IGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAI 107
+GLYFSA WCPPC+AFTP+L+E Y KLKE G FEI+F+S DR E S+ Y S MPW A+
Sbjct: 21 VGLYFSASWCPPCRAFTPKLVEFYEKLKESGKNFEIVFISWDRDEESFNDYFSKMPWLAV 80
Query: 108 PYA-SETRQSLASLYNVHGIPSLILLAVEAGGRLDVITTEARHELSEDPDGEFFPW 162
P++ E R L + + GIP+LI+L +A G +V+TT+AR + E + FP+
Sbjct: 81 PFSDRERRSRLNRTFKIEGIPTLIIL--DADG--EVVTTDARELVLE-YGADAFPF 131
>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 = 96.2 bits (240), Expect = 2e-26
Identities = 43/89 (48%), Positives = 58/89 (65%), Gaps = 4/89 (4%)
Query: 46 QVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMP-- 103
+V+ LYF A WCPPC+AFTP+L E Y KLK+ + EI++VS DR E ++ YL MP
Sbjct: 2 KVVLLYFWASWCPPCRAFTPELKELYEKLKKP--KVEIVYVSLDRDEEEWKKYLKKMPKD 59
Query: 104 WPAIPYASETRQSLASLYNVHGIPSLILL 132
W +P+ + R L LY V IP+L+LL
Sbjct: 60 WLNVPFGDKERNELLRLYGVKAIPTLVLL 88
>gnl|CDD|239306 cd03008, TryX_like_RdCVF, Tryparedoxin (TryX)-like family,
Rod-derived cone viability factor (RdCVF) subfamily;
RdCVF is a thioredoxin (TRX)-like protein specifically
expressed in photoreceptors. RdCVF was isolated and
identified as a factor that supports cone survival in
retinal cultures. Cone photoreceptor loss is responsible
for the visual handicap resulting from the inherited
disease, retinitis pigmentosa. RdCVF shows 33%
similarity to TRX but does not exhibit any detectable
thiol oxidoreductase activity.
Length = 146
Score = 62.9 bits (153), Expect = 5e-13
Identities = 33/113 (29%), Positives = 63/113 (55%), Gaps = 11/113 (9%)
Query: 46 QVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGY-----QFEIIFVSSDRSESSYQSYLS 100
+V+ L+F A P C+ F P+L + + +L ++ Y Q +++VS D+SE +S+L
Sbjct: 26 RVLLLFFGAVVSPQCQLFAPKLKDFFVRLTDEFYVDRSAQLALVYVSMDQSEQQQESFLK 85
Query: 101 GMP--WPAIPYASETRQSLASLYNVHGIPSLILLAVEAGGRLDVITTEARHEL 151
MP W +P+ E R+ L + ++V +P++++L + DV+ A E+
Sbjct: 86 DMPKKWLFLPFEDEFRRELEAQFSVEELPTVVVLKPDG----DVLAANAVDEI 134
>gnl|CDD|239264 cd02966, TlpA_like_family, TlpA-like family; composed of TlpA,
ResA, DsbE and similar proteins. TlpA, ResA and DsbE are
bacterial protein disulfide reductases with important
roles in cytochrome maturation. They are
membrane-anchored proteins with a soluble TRX domain
containing a CXXC motif located in the periplasm. The
TRX domains of this family contain an insert,
approximately 25 residues in length, which correspond to
an extra alpha helix and a beta strand when compared
with TRX. TlpA catalyzes an essential reaction in the
biogenesis of cytochrome aa3, while ResA and DsbE are
essential proteins in cytochrome c maturation. Also
included in this family are proteins containing a
TlpA-like TRX domain with domain architectures similar
to E. coli DipZ protein, and the N-terminal TRX domain
of PilB protein from Neisseria which acts as a disulfide
reductase that can recylce methionine sulfoxide
reductases.
Length = 116
Score = 58.8 bits (143), Expect = 1e-11
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSY-QSYLSGMPWPAIP 108
+ F A WCPPC+A P+L ++ K+DG E++ V+ D + + +++L P
Sbjct: 24 VNFWASWCPPCRAEMPELEALAKEYKDDG--VEVVGVNVDDDDPAAVKAFLKKYGIT-FP 80
Query: 109 YASETRQSLASLYNVHGIPSLILL 132
+ LA Y V G+P+ L+
Sbjct: 81 VLLDPDGELAKAYGVRGLPTTFLI 104
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 27/93 (29%)
Query: 40 SYIESCQVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYL 99
I+S + + + F A WC PCKA P L +L E+ + + + V D +
Sbjct: 5 ELIKSAKPVVVDFWAPWCGPCKAIAPVL----EELAEEYPKVKFVKVDVDEN-------- 52
Query: 100 SGMPWPAIPYASETRQSLASLYNVHGIPSLILL 132
LA Y V IP+ +
Sbjct: 53 ---------------PELAEEYGVRSIPTFLFF 70
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 47.0 bits (112), Expect = 2e-07
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 16/86 (18%)
Query: 50 LYFSAHWCPPCKAFTPQLI---ETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPA 106
+ F+ CP CK +L+ + LK++ F +I+V+ D S+
Sbjct: 10 VVFTDPDCPYCKKLHKELLKDPDVQEYLKDN---FVVIYVNVDDSK----------EVTD 56
Query: 107 IPYASETRQSLASLYNVHGIPSLILL 132
+ + + LA Y V G P+++ L
Sbjct: 57 FDGETLSEKELARKYGVRGTPTIVFL 82
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 23/83 (27%), Positives = 32/83 (38%), Gaps = 26/83 (31%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPY 109
+ F A WC PCKA P Y KL ++ Y+ ++ F D E+
Sbjct: 23 VDFYAPWCGPCKALAP----EYEKLAQE-YKDDVKFAKVDADEN---------------- 61
Query: 110 ASETRQSLASLYNVHGIPSLILL 132
LAS Y V G P++
Sbjct: 62 -----PDLASEYGVRGFPTIKFF 79
>gnl|CDD|216002 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase (AhpC)
and thiol specific antioxidant (TSA).
Length = 124
Score = 40.3 bits (95), Expect = 7e-05
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 46 QVIGLYF-SAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPW 104
+ + L+F + P C P L + Y + K+ G E++ VS D ES + + +
Sbjct: 26 KWVVLFFYPKDFTPVCTTELPALADLYEEFKKLGV--EVLGVSVDSPESH-KKFAEKLGL 82
Query: 105 PAIPYASETRQSLASLYNV 123
P P S+ +A Y V
Sbjct: 83 P-FPLLSDPDGEVAKAYGV 100
>gnl|CDD|179545 PRK03147, PRK03147, thiol-disulfide oxidoreductase; Provisional.
Length = 173
Score = 40.8 bits (96), Expect = 1e-04
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLS--GMPWPAI 107
L F WC PC+ P + E Y K KE G EII V+ D +E + +++++ G+
Sbjct: 66 LNFWGTWCKPCEKEMPYMNELYPKYKEKG--VEIIAVNVDETELAVKNFVNRYGL---TF 120
Query: 108 PYASETRQSLASLYNVHGIPSLILL 132
P A + + + Y V +P+ L+
Sbjct: 121 PVAIDKGRQVIDAYGVGPLPTTFLI 145
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 37.6 bits (86), Expect = 8e-04
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYL--SGMPWPAI 107
+ F A WCPPC+A P L E + D E++ V+ D + + P +
Sbjct: 37 VDFWAPWCPPCRAEAPLLEELAEEYGGD---VEVVAVNVDDENPDLAAEFGVAVRSIPTL 93
Query: 108 PYA 110
Sbjct: 94 LLF 96
>gnl|CDD|219888 pfam08534, Redoxin, Redoxin. This family of redoxins includes
peroxiredoxin, thioredoxin and glutaredoxin proteins.
Length = 142
Score = 37.3 bits (87), Expect = 0.001
Identities = 11/72 (15%), Positives = 27/72 (37%), Gaps = 3/72 (4%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPYAS 111
+ +CP C A P L + + K G +++ V++ ++ + P +
Sbjct: 35 WPGAFCPTCSAEHPYLEKLSKLYKAKG--VDVVAVNASNDPFFVMNFWAKEG-LKYPVLA 91
Query: 112 ETRQSLASLYNV 123
+ + Y +
Sbjct: 92 DRDGAFTKAYGL 103
>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 = 35.7 bits (83), Expect = 0.002
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDG 78
F A WC CKA P+ + ++LK DG
Sbjct: 22 FYAPWCGHCKALAPEYEKLAKELKGDG 48
>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
reductase A/B protein; Provisional.
Length = 521
Score = 36.8 bits (85), Expect = 0.004
Identities = 27/121 (22%), Positives = 54/121 (44%), Gaps = 20/121 (16%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQ-FEIIFVSS-----DRSESSYQSYLSGMPWP 105
F A WCP C + +L ET + ++ + +I V+S ++ + +Q + +G+ +P
Sbjct: 63 FWASWCPLCLS---ELGETEKWAQDAKFSSANLITVASPGFLHEKKDGDFQKWYAGLDYP 119
Query: 106 AIPYASETRQSLASLYNVHGIPSLILLAVEAGGRLDV-------ITTEARHELSEDPDGE 158
+P ++ +LA N+ PS ++ G DV I+ L +P+ +
Sbjct: 120 KLPVLTDNGGTLAQSLNISVYPSWAII----GKDGDVQRIVKGSISEAQALALIRNPNAD 175
Query: 159 F 159
Sbjct: 176 L 176
>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 = 33.8 bits (77), Expect = 0.006
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 2/58 (3%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAI 107
+ F A WCP C+A P L E L G +FE + V D + P +
Sbjct: 2 VLFYAPWCPFCQALRPVLAE--LALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTL 57
>gnl|CDD|239290 cd02992, PDI_a_QSOX, PDIa family, Quiescin-sulfhydryl oxidase
(QSOX) subfamily; QSOX is a eukaryotic protein
containing an N-terminal redox active TRX domain,
similar to that of PDI, and a small C-terminal flavin
adenine dinucleotide (FAD)-binding domain homologous to
the yeast ERV1p protein. QSOX oxidizes thiol groups to
disulfides like PDI, however, unlike PDI, this
oxidation is accompanied by the reduction of oxygen to
hydrogen peroxide. QSOX is localized in high
concentrations in cells with heavy secretory load and
prefers peptides and proteins as substrates, not
monothiols like glutathione. Inside the cell, QSOX is
found in the endoplasmic reticulum and Golgi. The flow
of reducing equivalents in a QSOX-catalyzed reaction
goes from the dithiol substrate -> dithiol of the QSOX
TRX domain -> dithiols of the QSOX ERV1p domain -> FAD
-> oxygen.
Length = 114
Score = 34.2 bits (79), Expect = 0.012
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKED 77
F A WC C+AF P T++KL D
Sbjct: 26 FYASWCGHCRAFAP----TWKKLARD 47
>gnl|CDD|239274 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small
monomeric protein with a conserved redox active CXXC
motif within a TRX fold, characterized by a glutaredoxin
(GRX)-like sequence and TRX-like activity profile. In
vitro, it displays protein disulfide reductase activity
that is dependent on TRX reductase, not glutathione
(GSH). It is part of the NrdHIEF operon, where NrdEF
codes for class Ib ribonucleotide reductase (RNR-Ib), an
efficient enzyme at low oxygen levels. Under these
conditions when GSH is mostly conjugated to spermidine,
NrdH can still function and act as a hydrogen donor for
RNR-Ib. It has been suggested that the NrdHEF system may
be the oldest RNR reducing system, capable of
functioning in a microaerophilic environment, where GSH
was not yet available. NrdH from Corynebacterium
ammoniagenes can form domain-swapped dimers, although it
is unknown if this happens in vivo. Domain-swapped
dimerization, which results in the blocking of the TRX
reductase binding site, could be a mechanism for
regulating the oxidation state of the protein.
Length = 73
Score = 33.0 bits (76), Expect = 0.013
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 51 YFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSG 101
++ CP CKA T R L E G FE + V D L+G
Sbjct: 4 VYTKPDCPYCKA-------TKRFLDERGIPFEEVDVDEDPEALEELKKLNG 47
>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 = 34.1 bits (79), Expect = 0.026
Identities = 31/115 (26%), Positives = 40/115 (34%), Gaps = 22/115 (19%)
Query: 18 SKGAKKTYNIGLAEGTVTTKVLSYIESCQVIGL-YFSAHWCPPCKAFTPQLIETYRKLKE 76
S A++TY L + Q GL +F CP C+A P L +
Sbjct: 96 SNAARQTYLA--QRKQKKDAALKSLA--QRYGLFFFYRGDCPYCQAQAPIL-----QAFA 146
Query: 77 DGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPYASETRQSLASLYNVHGIPSLIL 131
D Y F +I VS D G P P P + A V P+L L
Sbjct: 147 DKYGFSVIPVSVD-----------GGPLPGFPN-NRVDTGQAQRLGVKTTPALFL 189
>gnl|CDD|239302 cd03004, PDI_a_ERdj5_C, PDIa family, C-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 composed of
the three TRX domains located at the C-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.
Also included in the alignment is the single complete
TRX domain of an uncharacterized protein from Tetraodon
nigroviridis, which also contains a DnaJ domain at its
N-terminus.
Length = 104
Score = 32.3 bits (74), Expect = 0.035
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLK 75
F A WC PC+A P+L + R LK
Sbjct: 26 FYAPWCGPCQALLPELRKAARALK 49
>gnl|CDD|215931 pfam00462, Glutaredoxin, Glutaredoxin.
Length = 60
Score = 31.3 bits (72), Expect = 0.045
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 11/60 (18%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYL-SGMPWPAIP 108
+ F+ CP CK R L G +FE I V D + L WP +P
Sbjct: 2 VLFTKPTCPFCKR-------AKRLLDSLGVKFEEIDVDED---PEIREELKELSGWPTVP 51
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 32.2 bits (73), Expect = 0.048
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 40 SYIESCQVIGLYFSAHWCPPCKAFTPQ---LIETYRKLK 75
S + +++ + F A WC PCK P + Y K+
Sbjct: 13 STLSQNELVIVDFYAEWCGPCKRIAPFYEECSKEYTKMV 51
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 32.7 bits (75), Expect = 0.075
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 28/84 (33%)
Query: 51 YFSAHWCPPCKAFTPQLIETYRKL-KEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPY 109
F A WC PCK TP L KL E +F++ V+ D
Sbjct: 49 DFWAPWCGPCKQLTPTL----EKLAAEYKGKFKLAKVNCDAE------------------ 86
Query: 110 ASETRQSLASLYNVHGIPSLILLA 133
+A+ + V IP++
Sbjct: 87 -----PMVAAQFGVQSIPTVYAFK 105
>gnl|CDD|239309 cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for
copper sensitivity D protein (ScsD) and actinobacterial
DsbE homolog subfamily; composed of ScsD, the DsbE
homolog of Mycobacterium tuberculosis (MtbDsbE) and
similar proteins, all containing a redox-active CXXC
motif. The Salmonella typhimurium ScsD is a
thioredoxin-like protein which confers copper tolerance
to copper-sensitive mutants of E. coli. MtbDsbE has been
characterized as an oxidase in vitro, catalyzing the
disulfide bond formation of substrates like hirudin. The
reduced form of MtbDsbE is more stable than its oxidized
form, consistent with an oxidase function. This is in
contrast to the function of DsbE from gram-negative
bacteria which is a specific reductase of apocytochrome
c.
Length = 123
Score = 31.9 bits (73), Expect = 0.082
Identities = 24/102 (23%), Positives = 48/102 (47%), Gaps = 16/102 (15%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLS--GMPWPAI 107
+YF A WCP C+ +P T +L D Y + + S + + ++ G +P I
Sbjct: 25 VYFWATWCPVCRFTSP----TVNQLAAD-YPVVSVALRSG-DDGAVARFMQKKGYGFPVI 78
Query: 108 PYASETRQSLASLYNVHGIPSLILLAVEAGGRLDV---ITTE 146
+ +++ + V P++++ V+ GG + V +T+E
Sbjct: 79 N---DPDGVISARWGVSVTPAIVI--VDPGGIVFVTTGVTSE 115
>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 = 31.5 bits (72), Expect = 0.083
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 26/80 (32%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPYAS 111
F A WC PCK P L +L ++ Y+ ++ FV + E+
Sbjct: 21 FWAPWCGPCKMIAPIL----EELAKE-YEGKVKFVKLNVDEN------------------ 57
Query: 112 ETRQSLASLYNVHGIPSLIL 131
+A+ Y + IP+L+L
Sbjct: 58 ---PDIAAKYGIRSIPTLLL 74
>gnl|CDD|223767 COG0695, GrxC, Glutaredoxin and related proteins
[Posttranslational modification, protein turnover,
chaperones].
Length = 80
Score = 30.7 bits (70), Expect = 0.088
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 7/41 (17%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSE 92
++ CP CK R L G +E I V D E
Sbjct: 6 YTKPGCPYCKR-------AKRLLDRKGVDYEEIDVDDDEPE 39
>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 = 30.7 bits (70), Expect = 0.10
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 50 LYFSAHWCPPCKAFTPQLI--ETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMP 103
+ F A WCP C+A + + L E F ++ V + + G+P
Sbjct: 22 VDFGADWCPTCQALDRDFLSDPRVKALAEK---FVLLRVDVTTRDPNLLLDGQGVP 74
>gnl|CDD|133030 cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related
to eukaryotic DPM1. A family of bacterial enzymes
related to eukaryotic DPM1; Although the mechanism of
eukaryotic enzyme is well studied, the mechanism of the
bacterial enzymes is not well understood. The
eukaryotic DPM1 is the catalytic subunit of eukaryotic
Dolichol-phosphate mannose (DPM) synthase. DPM synthase
is required for synthesis of the
glycosylphosphatidylinositol (GPI) anchor, N-glycan
precursor, protein O-mannose, and C-mannose. The enzyme
has three subunits, DPM1, DPM2 and DPM3. DPM is
synthesized from dolichol phosphate and GDP-Man on the
cytosolic surface of the ER membrane by DPM synthase
and then is flipped onto the luminal side and used as a
donor substrate. This protein family belongs to
Glycosyltransferase 2 superfamily.
Length = 181
Score = 32.1 bits (74), Expect = 0.10
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 7/32 (21%)
Query: 67 LIETYRKLKE----DGYQFEIIFV---SSDRS 91
L E Y +LK GY +EIIFV S+DR+
Sbjct: 12 LPELYERLKAVLESLGYDYEIIFVDDGSTDRT 43
>gnl|CDD|224806 COG1894, NuoF, NADH:ubiquinone oxidoreductase, NADH-binding (51 kD)
subunit [Energy production and conversion].
Length = 424
Score = 32.2 bits (74), Expect = 0.13
Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 9/34 (26%)
Query: 43 ESCQVIGLYFSAHWCPPCKAFTPQLIETYRKLKE 76
ESC C PC+ T ++ +L
Sbjct: 347 ESC---------GKCTPCREGTGWMVRILERLVR 371
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 32.4 bits (74), Expect = 0.14
Identities = 19/80 (23%), Positives = 27/80 (33%), Gaps = 23/80 (28%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPYAS 111
F A WC CK P+ + + LKE EI+ S D +
Sbjct: 56 FYAPWCGHCKRLAPEYKKAAKMLKEKKS--EIVLASVD---------------------A 92
Query: 112 ETRQSLASLYNVHGIPSLIL 131
LA + V G P++
Sbjct: 93 TEEMELAQEFGVRGYPTIKF 112
>gnl|CDD|239254 cd02956, ybbN, ybbN protein family; ybbN is a hypothetical protein
containing a redox-inactive TRX-like domain. Its gene
has been sequenced from several gammaproteobacteria and
actinobacteria.
Length = 96
Score = 29.9 bits (68), Expect = 0.25
Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 27/93 (29%)
Query: 42 IESCQV-IGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLS 100
ES QV + + F A PP K P L +L E YQ + + +
Sbjct: 8 QESTQVPVVVDFWAPRSPPSKELLPLL----ERLAE-EYQGQFVLAKVN----------- 51
Query: 101 GMPWPAIPYASETRQSLASLYNVHGIPSLILLA 133
+ + +A + V +P++ L A
Sbjct: 52 ----------CDAQPQIAQQFGVQALPTVYLFA 74
>gnl|CDD|133022 cd04179, DPM_DPG-synthase_like, DPM_DPG-synthase_like is a member
of the Glycosyltransferase 2 superfamily. DPM1 is the
catalytic subunit of eukaryotic dolichol-phosphate
mannose (DPM) synthase. DPM synthase is required for
synthesis of the glycosylphosphatidylinositol (GPI)
anchor, N-glycan precursor, protein O-mannose, and
C-mannose. In higher eukaryotes,the enzyme has three
subunits, DPM1, DPM2 and DPM3. DPM is synthesized from
dolichol phosphate and GDP-Man on the cytosolic surface
of the ER membrane by DPM synthase and then is flipped
onto the luminal side and used as a donor substrate. In
lower eukaryotes, such as Saccharomyces cerevisiae and
Trypanosoma brucei, DPM synthase consists of a single
component (Dpm1p and TbDpm1, respectively) that
possesses one predicted transmembrane region near the C
terminus for anchoring to the ER membrane. In contrast,
the Dpm1 homologues of higher eukaryotes, namely
fission yeast, fungi, and animals, have no
transmembrane region, suggesting the existence of
adapter molecules for membrane anchoring. This family
also includes bacteria and archaea DPM1_like enzymes.
However, the enzyme structure and mechanism of function
are not well understood. The
UDP-glucose:dolichyl-phosphate glucosyltransferase
(DPG_synthase) is a transmembrane-bound enzyme of the
endoplasmic reticulum involved in protein N-linked
glycosylation. This enzyme catalyzes the transfer of
glucose from UDP-glucose to dolichyl phosphate. This
protein family belongs to Glycosyltransferase 2
superfamily.
Length = 185
Score = 30.6 bits (70), Expect = 0.27
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 65 PQLIETYRKLKEDGYQFEIIFV---SSDRS 91
P+L+E + E+GY +EII V S+D +
Sbjct: 13 PELVERLLAVLEEGYDYEIIVVDDGSTDGT 42
>gnl|CDD|239297 cd02999, PDI_a_ERp44_like, PDIa family, endoplasmic reticulum
protein 44 (ERp44)-like subfamily; composed of
uncharacterized PDI-like eukaryotic proteins containing
only one redox active TRX (a) domain with a CXXS motif,
similar to ERp44. CXXS is still a redox active motif;
however, the mixed disulfide formed with the substrate
is more stable than those formed by CXXC motif proteins.
PDI-related proteins are usually involved in the
oxidative protein folding in the ER by acting as
catalysts and folding assistants. ERp44 is involved in
thiol-mediated retention in the ER.
Length = 100
Score = 29.2 bits (66), Expect = 0.43
Identities = 22/92 (23%), Positives = 30/92 (32%), Gaps = 34/92 (36%)
Query: 45 CQVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPW 104
+ F A WCP +F P F LS M +
Sbjct: 18 EDYTAVLFYASWCPFSASFRPH--------------FNA---------------LSSM-F 47
Query: 105 PAIPY----ASETRQSLASLYNVHGIPSLILL 132
P I + S + SL S Y V G P+++L
Sbjct: 48 PQIRHLAIEESSIKPSLLSRYGVVGFPTILLF 79
>gnl|CDD|129481 TIGR00385, dsbE, periplasmic protein thiol:disulfide
oxidoreductases, DsbE subfamily. Involved in the
biogenesis of c-type cytochromes as well as in disulfide
bond formation in some periplasmic proteins [Protein
fate, Protein folding and stabilization].
Length = 173
Score = 30.1 bits (68), Expect = 0.44
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 8/95 (8%)
Query: 46 QVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWP 105
+ + L A WCPPC+A P L E L + G I+ V + +L + P
Sbjct: 64 KPVLLNVWASWCPPCRAEHPYLNE----LAKQG--LPIVGVDYKDDRQNAIKFLKELGNP 117
Query: 106 AIPYASETRQSLASLYNVHGIPSLILLAVEAGGRL 140
+ L V+G P L V+ G +
Sbjct: 118 YQLSLFDPDGMLGLDLGVYGAPETFL--VDGNGVI 150
>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 = 30.4 bits (69), Expect = 0.50
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 29/93 (31%)
Query: 40 SYIESCQVIGLYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYL 99
+I+S + + + F A WC CK+ P+ + +LK+ G
Sbjct: 13 DFIKSHEFVLVEFYAPWCGHCKSLAPEYEKAADELKKKG--------------------- 51
Query: 100 SGMPWPAIPYAS---ETRQSLASLYNVHGIPSL 129
P I A + LA Y V G P+L
Sbjct: 52 -----PPIKLAKVDATEEKDLAQKYGVSGYPTL 79
Score = 28.9 bits (65), Expect = 1.9
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 52 FSAHWCPPCKAFTP---QLIETYRKLKED 77
F A WC CK P +L E Y+ + D
Sbjct: 371 FYAPWCGHCKNLAPIYEELAEKYKDAESD 399
>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 = 29.2 bits (66), Expect = 0.51
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 46 QVIGLYFSAHWCPPCKAF 63
+++ L+F A W PCK
Sbjct: 15 KLLVLHFWAPWAEPCKQM 32
>gnl|CDD|217751 pfam03830, PTSIIB_sorb, PTS system sorbose subfamily IIB component.
Length = 151
Score = 29.7 bits (68), Expect = 0.51
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 62 AFTPQLIETYRKLKEDGYQFEIIFVSSDRSES 93
+ + IE +++LKE G + EI V SD+ E
Sbjct: 120 SLDEEDIEAFKELKEKGVEVEIQQVPSDKKED 151
>gnl|CDD|235450 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 30.1 bits (69), Expect = 0.58
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 61 KAFTPQLIETYRKLKEDGYQFEIIFVSSDRSE 92
+ F L E +L+E G ++F+ +
Sbjct: 67 RPFFDDLPEALDELRERGIDVRVLFLDASDEV 98
>gnl|CDD|239293 cd02995, PDI_a_PDI_a'_C, PDIa family, C-terminal TRX domain (a')
subfamily; composed of the C-terminal redox active a'
domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI,
ERp72 and ERp57 are endoplasmic reticulum (ER)-resident
eukaryotic proteins involved in oxidative protein
folding. They are 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. PDI and ERp57 have the abb'a'
domain structure (where a and a' are redox active TRX
domains while b and b' are redox inactive TRX-like
domains). PDI also contains an acidic region (c domain)
after the a' domain that is absent in ERp57. ERp72 has
an additional a domain at the N-terminus (a"abb'a'
domain structure). ERp57 interacts with the lectin
chaperones, calnexin and calreticulin, and specifically
promotes the oxidative folding of glycoproteins, while
PDI shows a wider substrate specificity. ERp72
associates with several ER chaperones and folding
factors to form complexes in the ER that bind nascent
proteins. EFP1 is a binding partner protein of thyroid
oxidase, which is responsible for the generation of
hydrogen peroxide, a crucial substrate of
thyroperoxidase, which functions to iodinate
thyroglobulin and synthesize thyroid hormones.
Length = 104
Score = 29.1 bits (66), Expect = 0.59
Identities = 13/28 (46%), Positives = 14/28 (50%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKED 77
+ F A WC CKA P E KLK D
Sbjct: 23 VEFYAPWCGHCKALAPIYEELAEKLKGD 50
>gnl|CDD|131251 TIGR02196, GlrX_YruB, Glutaredoxin-like protein, YruB-family. This
glutaredoxin-like protein family contains the conserved
CxxC motif and includes the Clostridium pasteurianum
protein YruB which has been cloned from a rubredoxin
operon. Somewhat related to NrdH, it is unknown whether
this protein actually interacts with
glutathione/glutathione reducatase, or, like NrdH, some
other reductant system.
Length = 74
Score = 28.5 bits (64), Expect = 0.61
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 7/50 (14%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSG 101
++ WCPPCK L G FE I V D + + G
Sbjct: 5 YTTPWCPPCKK-------AKEYLTSKGIAFEEIDVEKDSAAREEVLKVLG 47
>gnl|CDD|239265 cd02967, mauD, Methylamine utilization (mau) D family; mauD protein
is the translation product of the mauD gene found in
methylotrophic bacteria, which are able to use
methylamine as a sole carbon source and a nitrogen
source. mauD is an essential accessory protein for the
biosynthesis of methylamine dehydrogenase (MADH), the
enzyme that catalyzes the oxidation of methylamine and
other primary amines. MADH possesses an alpha2beta2
subunit structure; the alpha subunit is also referred to
as the large subunit. Each beta (small) subunit contains
a tryptophan tryptophylquinone (TTQ) prosthetic group.
Accessory proteins are essential for the proper
transport of MADH to the periplasm, TTQ synthesis and
the formation of several structural disulfide bonds.
Bacterial mutants containing an insertion on the mauD
gene were unable to grow on methylamine as a sole carbon
source, were found to lack the MADH small subunit and
had decreased amounts of the MADH large subunit.
Length = 114
Score = 28.9 bits (65), Expect = 0.64
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPY 109
L+F + CP CK P + R + +++ ++SD ++ +Q +L A PY
Sbjct: 26 LFFLSPTCPVCKKLLPVIRSIAR---AEADWLDVV-LASDGEKAEHQRFLKKHGLEAFPY 81
Query: 110 ASETRQSLASLYNVHGIPSLILL 132
+A Y V +P +LL
Sbjct: 82 VLSAELGMA--YQVSKLPYAVLL 102
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.5 bits (67), Expect = 0.73
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 67 LIETYRKLKEDGYQFEIIFVSSDRSESSYQS 97
+ RKLK GY+ E+ V+ E S+
Sbjct: 105 ARKLARKLKAAGYEVEVYVVAVPP-ELSWLG 134
>gnl|CDD|225976 COG3444, COG3444, Phosphotransferase system,
mannose/fructose/N-acetylgalactosamine-specific
component IIB [Carbohydrate transport and metabolism].
Length = 159
Score = 29.1 bits (66), Expect = 0.93
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 27 IGLAEGTVTTKVLSYIESCQVIGLYFSAHWCPPCKA--FTPQLIETYRKLKEDGYQFEII 84
+ L EG V I++ V G+ F KA + I ++KLK G + E+
Sbjct: 90 LRLVEGGVP------IKTINVGGMAFREGKKQITKAVSLDEKDIAAFKKLKAKGVEVEVR 143
Query: 85 FVSSDRSE 92
V +D
Sbjct: 144 KVPNDSKV 151
>gnl|CDD|184572 PRK14216, PRK14216, camphor resistance protein CrcB; Provisional.
Length = 132
Score = 28.7 bits (64), Expect = 1.2
Identities = 21/41 (51%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 131 LLAVEAGGRLDVITTEARHELSE--DPDGEFFPWPPKLVNV 169
L AV AGG L T AR LSE PD +PWP VNV
Sbjct: 9 LAAVFAGGALG---TLARAALSELAAPDPARWPWPTFTVNV 46
>gnl|CDD|239308 cd03010, TlpA_like_DsbE, TlpA-like family, DsbE (also known as
CcmG and CycY) subfamily; DsbE is a membrane-anchored,
periplasmic TRX-like reductase containing a CXXC motif
that specifically donates reducing equivalents to
apocytochrome c via CcmH, another cytochrome c
maturation (Ccm) factor with a redox active CXXC motif.
Assembly of cytochrome c requires the ligation of heme
to reduced thiols of the apocytochrome. In bacteria,
this assembly occurs in the periplasm. The reductase
activity of DsbE in the oxidizing environment of the
periplasm is crucial in the maturation of cytochrome c.
Length = 127
Score = 28.3 bits (64), Expect = 1.3
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 54 AHWCPPCKAFTPQLIETYRKLKEDGYQFEII 84
A WC PC+ P L+ L G + I
Sbjct: 34 ASWCAPCREEHPVLMA----LARQG-RVPIY 59
>gnl|CDD|224226 COG1307, DegV, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 282
Score = 29.1 bits (66), Expect = 1.4
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 66 QLIETYRKLKEDGYQFEI-IFVSSDRSESSYQS 97
+ E + KL + GY I I +SS S +YQS
Sbjct: 68 EFEELFEKLLQKGYDEVISIHISSGLS-GTYQS 99
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 29.1 bits (65), Expect = 1.4
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 66 QLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPY 109
Q+I + D Y I+ +S S + + YLSG P P I Y
Sbjct: 355 QMIGRAGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISY 398
>gnl|CDD|197996 smart00928, NADH_4Fe-4S, NADH-ubiquinone oxidoreductase-F
iron-sulfur binding region.
Length = 46
Score = 26.3 bits (59), Expect = 1.5
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 53 SAHWCPPCKAFTPQLIETYRKLKE 76
S C PC+ T L+E +++E
Sbjct: 15 SCGKCTPCREGTGWLLEILDRIEE 38
>gnl|CDD|213558 TIGR00762, DegV, EDD domain protein, DegV family. This family of
proteins is related to DegV of Bacillus subtilis and
includes paralogous sets in several species (B.
subtilis, Deinococcus radiodurans, Mycoplasma
pneumoniae) that are closer in percent identity to each
than to most homologs from other species. This suggests
both recent paralogy and diversity of function. DegV
itself is encoded immediately downstream of DegU, a
transcriptional regulator of degradation, but is itself
uncharacterized. Crystallography suggested a
lipid-binding site, while comparison of the crystal
structure to dihydroxyacetone kinase and to a mannose
transporter EIIA domain suggests a conserved domain,
EDD, with phosphotransferase activity [Unknown
function, General].
Length = 275
Score = 28.6 bits (65), Expect = 1.6
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 66 QLIETYRKLKEDGYQFEIIFVSSDRSESSYQS 97
+ +E Y KL E+G + I +SS S +YQS
Sbjct: 66 EFLELYEKLAEEGDEVLSIHLSSGLS-GTYQS 96
>gnl|CDD|225760 COG3219, COG3219, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 237
Score = 28.2 bits (63), Expect = 2.3
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 145 TEARHELSEDPDGEFFPWPPKLVNVLSP 172
T+ E++E PD + W + SP
Sbjct: 110 TQLLAEVAEAPDIDDIHWSNDSSMLASP 137
>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
thiotransferase enzyme MiaB. This model represents
homologs of the MiaB enzyme responsible for the
modification of the isopentenylated adenine-37 base of
most bacterial and eukaryotic tRNAs that read codons
beginning with uracil (all except tRNA(I,V) Ser).
Adenine-37 is next to the anticodon on the 3' side in
these tRNA's, and lack of modification at this site
leads to an increased spontaneous mutation frequency.
Isopentenylated A-37 is modified by methylthiolation at
position 2, either by MiaB alone or in concert with a
separate methylase yet to be discovered (MiaC?). MiaB
contains a 4Fe-4S cluster which is labile under
oxidizing conditions. Additionally, the sequence is
homologous (via PSI-BLAST searches) to the biotin
synthetase, BioB, which utilizes both an iron-sulfur
cluster and S-adenosym methionine (SAM) to generate a
radical which is responsible for initiating the
insertion of sulfur into the substrate. It is reasonable
to surmise that the methyl group of SAM becomes the
methyl group of the product, but this has not been
shown, and the possibility of a separate methylase
exists. This equivalog is a member of a subfamily
(TIGR00089) which contains several other hypothetical
equivalogs which are all probably enzymes with similar
function acting on different substrates. These enzymes
contain a TRAM domain (pfam01938) which is believed to
be responsible for binding to tRNAs. Hits to this model
span all major groups of bacteria and eukaryotes, but
not archaea, which are known to lack this particular
tRNA modification. The enzyme from Thermotoga maritima
has been cloned, expressed, spectroscopically
characterized and shown to complement the E. coli MiaB
enzyme [Protein synthesis, tRNA and rRNA base
modification].
Length = 438
Score = 28.2 bits (63), Expect = 2.5
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 10/46 (21%)
Query: 65 PQLIETYRKLKEDGYQFEIIFVSSD--------RSESSYQSYLSGM 102
PQ I+T K +I S+ R+E Y+S+++ M
Sbjct: 109 PQAIKTPLTQKF--MVVDIDSDESEVAGYFADFRNEGIYKSFINIM 152
>gnl|CDD|180247 PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
Length = 92
Score = 26.8 bits (60), Expect = 2.7
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 5/32 (15%)
Query: 56 WCPPCKAFTPQLIETYRK-----LKEDGYQFE 82
+CP CK T +E +K LK Q+
Sbjct: 10 YCPYCKTHTEHEVEKVKKGKRSELKWGQRQYR 41
>gnl|CDD|237957 PRK15401, PRK15401, alpha-ketoglutarate-dependent dioxygenase AlkB;
Provisional.
Length = 213
Score = 27.9 bits (63), Expect = 2.8
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 87 SSDRSESSYQSY--LSGMPWPAIP 108
+DR Y L+G PWPA+P
Sbjct: 71 VTDRRGYRYSPIDPLTGKPWPAMP 94
>gnl|CDD|143285 cd05877, Ig_LP_like, Immunoglobulin (Ig)-like domain of human
cartilage link protein (LP). Ig_LP_like:
immunoglobulin (Ig)-like domain similar to that that
found in human cartilage link protein (LP). In
cartilage, chondroitin-keratan sulfate proteoglycan
(CSPG), aggrecan, forms cartilage link protein
stabilized aggregates with hyaluronan (HA). These
aggregates contribute to the tissue's load bearing
properties. Aggregates having other CSPGs substituting
for aggrecan may contribute to the structural integrity
of many different tissues. Members of the vertebrate
HPLN (hyaluronan/HA and proteoglycan binding link)
protein family are physically linked adjacent to CSPG
genes.
Length = 106
Score = 26.9 bits (60), Expect = 3.4
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 7/47 (14%)
Query: 59 PCK-AFTPQLIETYR------KLKEDGYQFEIIFVSSDRSESSYQSY 98
PC+ + P+L + KL+ D + E + V+ SY SY
Sbjct: 8 PCRYHYEPELSAPRKIRVKWTKLESDYLKEEDVLVAIGTRHKSYGSY 54
>gnl|CDD|217911 pfam04123, DUF373, Domain of unknown function (DUF373). Archaeal
domain of unknown function. Predicted to be an integral
membrane protein with six transmembrane regions.
Length = 344
Score = 27.6 bits (62), Expect = 3.8
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 68 IETYRKLKEDGYQFEIIFVSSDR 90
++ Y +LK +G E+ VS
Sbjct: 54 VKIYDELKAEGEDVEVAVVSGSP 76
>gnl|CDD|237975 cd00001, PTS_IIB_man, PTS_IIB, PTS system, Mannose/sorbose specific
IIB subunit. The bacterial phosphoenolpyruvate: sugar
phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. This family is
one of four structurally and functionally distinct group
IIB PTS system cytoplasmic enzymes, necessary for the
uptake of carbohydrates across the cytoplasmic membrane
and their phosphorylation. The active site histidine
receives a phosphate group from the IIA subunit and
transfers it to the substrate.
Length = 151
Score = 27.2 bits (61), Expect = 3.8
Identities = 6/31 (19%), Positives = 16/31 (51%)
Query: 62 AFTPQLIETYRKLKEDGYQFEIIFVSSDRSE 92
+ + + +++L + G + EI V +D+
Sbjct: 119 SLDEEDVAAFKELAQKGVKVEIQMVPNDKKV 149
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 27.9 bits (63), Expect = 3.9
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 66 QLIETYRKLKEDGYQFE 82
+L YR+L E+GY +
Sbjct: 234 ELKAGYRELVEEGYHLD 250
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 27.0 bits (60), Expect = 4.1
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 31 EGTVTTKVLSYIESCQVIGLYFSAHWCPPCKAFTP 65
T T + ++ + + F A WC PC+ F P
Sbjct: 39 NATGET-LDKLLQDDLPVVIDFWAPWCGPCRNFAP 72
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 26.6 bits (58), Expect = 4.3
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 52 FSAHWCPPCKAFTPQLIE 69
F A WC PCK P L E
Sbjct: 28 FWAEWCGPCKMIAPILDE 45
>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 = 26.9 bits (60), Expect = 4.5
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 24/81 (29%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQSYLSGMPWPAIPYAS 111
F A WC C+ P + + +K + Q + ++ D + W +P
Sbjct: 27 FYADWCTVCQEMAPDVAKLKQKYGD---QVNFVMLNVDNPK-----------W--LPEID 70
Query: 112 ETRQSLASLYNVHGIPSLILL 132
Y V GIP + L
Sbjct: 71 R--------YRVDGIPHFVFL 83
>gnl|CDD|232970 TIGR00424, APS_reduc, 5'-adenylylsulfate reductase,
thioredoxin-independent. This enzyme, involved in the
assimilation of inorganic sulfate, is closely related to
the thioredoxin-dependent PAPS reductase of Bacteria
(CysH) and Saccharomyces cerevisiae. However, it has its
own C-terminal thioredoxin-like domain and is not
thioredoxin-dependent. Also, it has a substrate
preference for 5'-adenylylsulfate (APS) over
3'-phosphoadenylylsulfate (PAPS) so the pathway does not
require an APS kinase (CysC) to convert APS to PAPS.
Arabidopsis thaliana appears to have three isozymes, all
able to complement E. coli CysH mutants (even in
backgrounds lacking thioredoxin or APS kinase) but
likely localized to different compartments in
Arabidopsis [Central intermediary metabolism, Sulfur
metabolism].
Length = 463
Score = 27.7 bits (61), Expect = 4.8
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 12/82 (14%)
Query: 54 AHWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVSSDRSESSYQ-----SYLSGMPWP--- 105
A WCP C+A +E KL G + D+ E + Q S+ + + +P
Sbjct: 380 APWCPFCQAMEASYLELAEKLAGSGVKVAKFRADGDQKEFAKQELQLGSFPTILFFPKHS 439
Query: 106 --AIPYASETR--QSLASLYNV 123
I Y SE R SL S N+
Sbjct: 440 SRPIKYPSEKRDVDSLMSFVNL 461
>gnl|CDD|233866 TIGR02435, CobG, precorrin-3B synthase. An iron-sulfur protein. An
oxygen atom from dioxygen is incorporated into the
macrocycle at C-20. In the aerobic cobalamin biosythesis
pathway, four enzymes are involved in the conversion of
precorrin-3A to precorrin-6A. The first of the four
steps is carried out by EC 1.14.13.83, precorrin-3B
synthase (CobG), yielding precorrin-3B as the product.
This is followed by three methylation reactions, which
introduce a methyl group at C-17 (CobJ; EC 2.1.1.131),
C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152)
of the macrocycle, giving rise to precorrin-4,
precorrin-5 and precorrin-6A, respectively [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 390
Score = 27.5 bits (61), Expect = 4.8
Identities = 15/55 (27%), Positives = 25/55 (45%)
Query: 108 PYASETRQSLASLYNVHGIPSLILLAVEAGGRLDVITTEARHELSEDPDGEFFPW 162
P A+E R +L + + +P +A++ GGRL ++ A L G W
Sbjct: 109 PLAAELRAALENERALLELPPKFSVAIDGGGRLVLLGDTADVRLQALTTGAGVAW 163
>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 = 26.4 bits (59), Expect = 4.8
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 50 LYFSAHWCPPCKAF 63
+ F+A WC CK
Sbjct: 16 VDFTADWCVTCKVN 29
>gnl|CDD|239295 cd02997, PDI_a_PDIR, PDIa family, PDIR subfamily; composed of
proteins similar to human PDIR (for Protein Disulfide
Isomerase Related). PDIR is composed of three redox
active TRX (a) domains and an N-terminal redox inactive
TRX-like (b) domain. Similar to PDI, it is involved in
oxidative protein folding in the endoplasmic reticulum
(ER) through its isomerase and chaperone activities.
These activities are lower compared to PDI, probably
due to PDIR acting only on a subset of proteins. PDIR
is preferentially expressed in cells actively secreting
proteins and its expression is induced by stress.
Similar to PDI, the isomerase and chaperone activities
of PDIR are independent; CXXC mutants lacking isomerase
activity retain chaperone activity.
Length = 104
Score = 26.1 bits (58), Expect = 5.2
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKLKEDG 78
F A WC CK P+ + +LKEDG
Sbjct: 24 FYAPWCGHCKKMKPEFTKAATELKEDG 50
>gnl|CDD|239246 cd02948, TRX_NDPK, TRX domain, TRX and NDP-kinase (NDPK) fusion
protein family; most members of this group are fusion
proteins which contain one redox active TRX domain
containing a CXXC motif and three NDPK domains, and are
characterized as intermediate chains (ICs) of axonemal
outer arm dynein. Dyneins are molecular motors that
generate force against microtubules to produce cellular
movement, and are divided into two classes: axonemal
and cytoplasmic. They are supramolecular complexes
consisting of three protein groups classified according
to size: dynein heavy, intermediate and light chains.
Axonemal dyneins form two structures, the inner and
outer arms, which are attached to doublet microtubules
throughout the cilia and flagella. The human homolog is
the sperm-specific Sptrx-2, presumed to be a component
of the human sperm axoneme architecture. Included in
this group is another human protein, TRX-like protein
2, a smaller fusion protein containing one TRX and one
NDPK domain, which is also associated with microtubular
structures. The other members of this group are
hypothetical insect proteins containing a TRX domain
and outer arm dynein light chains (14 and 16kDa) of
Chlamydomonas reinhardtii. Using standard assays, the
fusion proteins have shown no TRX enzymatic activity.
Length = 102
Score = 26.1 bits (58), Expect = 5.6
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 46 QVIGLYFSAHWCPPCKAFTPQLIETYRKLKED 77
V+ +Y WC PCKA ++ ++K+K +
Sbjct: 20 TVVDVY--QEWCGPCKA----VVSLFKKIKNE 45
>gnl|CDD|239291 cd02993, PDI_a_APS_reductase, PDIa family, 5'-Adenylylsulfate
(APS) reductase subfamily; composed of plant-type APS
reductases containing a C-terminal redox active TRX
domain and an N-terminal reductase domain which is part
of a superfamily that includes N type ATP PPases. APS
reductase catalyzes the reduction of activated sulfate
to sulfite, a key step in the biosynthesis of
sulfur-containing metabolites. Sulfate is first
activated by ATP sulfurylase, forming APS, which can be
phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate
(PAPS). Depending on the organism, either APS or PAPS
can be used for sulfate reduction. Prokaryotes and
fungi use PAPS, whereas plants use both APS and PAPS.
Since plant-type APS reductase uses glutathione (GSH)
as its electron donor, the C-terminal domain may
function like glutaredoxin, a GSH-dependent member of
the TRX superfamily. The flow of reducing equivalents
goes from GSH -> C-terminal TRX domain -> N-terminal
reductase domain -> APS. Plant-type APS reductase shows
no homology to that of dissimilatory sulfate-reducing
bacteria, which is an iron-sulfur flavoenzyme. Also
included in the alignment is EYE2 from Chlamydomonas
reinhardtii, a protein required for eyespot assembly.
Length = 109
Score = 26.3 bits (58), Expect = 5.7
Identities = 11/29 (37%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 50 LYFSAHWCPPCKAFTPQLIETYRKLKEDG 78
LY A WCP C+A E KL
Sbjct: 28 LY--APWCPFCQAMEASYEELAEKLAGSN 54
>gnl|CDD|217709 pfam03744, BioW, 6-carboxyhexanoate--CoA ligase. This family
contains the enzyme 6-carboxyhexanoate--CoA ligase
EC:6.2.1.14. This enzyme is involved in the first step
of biotin synthesis, where it converts pimelate into
pimeloyl-CoA. The enzyme requires magnesium as a
cofactor and forms a homodimer.
Length = 232
Score = 26.8 bits (60), Expect = 5.8
Identities = 10/33 (30%), Positives = 11/33 (33%), Gaps = 2/33 (6%)
Query: 73 KLKEDGYQF--EIIFVSSDRSESSYQSYLSGMP 103
LKE G + FV SYL P
Sbjct: 196 NLKEAGDPSGGRVFFVDDSIDLEDLISYLENKP 228
>gnl|CDD|167205 PRK01295, PRK01295, phosphoglyceromutase; Provisional.
Length = 206
Score = 27.0 bits (60), Expect = 6.0
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 72 RKLKEDGYQFEIIFVSS-DRSESSYQSYLSGMPWPAIP 108
RKLK G +F+I F S+ R++ + Q L + P +
Sbjct: 42 RKLKAAGLKFDIAFTSALSRAQHTCQLILEELGQPGLE 79
>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 = 26.1 bits (58), Expect = 6.6
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 4/23 (17%)
Query: 52 FSAHWCPPCKAFTPQLIETYRKL 74
F A WC CK P Y KL
Sbjct: 20 FYAPWCGHCKNLAP----EYEKL 38
>gnl|CDD|218901 pfam06110, DUF953, Eukaryotic protein of unknown function (DUF953).
This family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 119
Score = 26.3 bits (58), Expect = 6.6
Identities = 20/105 (19%), Positives = 32/105 (30%), Gaps = 28/105 (26%)
Query: 35 TTKVLSYIESCQVIGLYFSA-------HWCPPCKAFTPQLIETYRKLKEDGYQFEIIFVS 87
V + I F+ WCP C P + E + ED F+
Sbjct: 9 NKAVKESENGSKPIFALFTGSKDTTGESWCPDCVRAEPVIREALKHAPED-----CHFIY 63
Query: 88 SDRSESSYQSYLSGMPW--PAIPYASETRQSLASLYNVHGIPSLI 130
D + Y W P P+ + + G+P+L+
Sbjct: 64 VDVGDRPY--------WKDPNNPFRKDPN------LKLTGVPTLL 94
>gnl|CDD|181605 PRK08993, PRK08993, 2-deoxy-D-gluconate 3-dehydrogenase; Validated.
Length = 253
Score = 26.8 bits (59), Expect = 7.3
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 118 ASLYNVHGIPSLILLAVEAGGRLDVITTEA 147
A L + GIP+L+ AV G +D++ A
Sbjct: 64 ADLRKIDGIPALLERAVAEFGHIDILVNNA 93
>gnl|CDD|132867 cd07229, Pat_TGL3_like, Triacylglycerol lipase 3. Triacylglycerol
lipase 3 (TGL3) are responsible for all the TAG lipase
activity of the lipid particle. Triacylglycerol (TAG)
lipases are also necessary for the mobilization of TAG
stored in lipid particles. TGL3 contains the consensus
sequence motif GXSXG, which is found in lipolytic
enzymes. This family includes Tgl3p from Saccharomyces
cerevisiae.
Length = 391
Score = 26.9 bits (60), Expect = 7.4
Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 1/69 (1%)
Query: 107 IPYASETRQSLASLYNVHGIPS-LILLAVEAGGRLDVITTEARHELSEDPDGEFFPWPPK 165
I A +L N P+ LI A A + L +D G PWPP
Sbjct: 215 ITVAPSAVSGSPNLLNYLTAPNVLIWSAALASNASSAALYRSVTLLCKDETGSIVPWPPV 274
Query: 166 LVNVLSPRH 174
V
Sbjct: 275 QVLFFRSWR 283
>gnl|CDD|214878 smart00878, Biotin_carb_C, Biotin carboxylase C-terminal domain.
Biotin carboxylase is a component of the acetyl-CoA
carboxylase multi-component enzyme which catalyses the
first committed step in fatty acid synthesis in animals,
plants and bacteria. Most of the active site residues
reported in reference are in this C-terminal domain.
Length = 107
Score = 25.8 bits (58), Expect = 8.1
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 153 EDPDGEFFPWPPKLVNVLSP 172
EDP F P P ++ P
Sbjct: 7 EDPANGFLPSPGRITRYRFP 26
>gnl|CDD|239222 cd02892, SQCY_1, Squalene cyclase (SQCY) domain subgroup 1; found
in class II terpene cyclases that have an alpha 6 -
alpha 6 barrel fold. Squalene cyclase (SQCY) and
2,3-oxidosqualene cyclase (OSQCY) are integral membrane
proteins that catalyze a cationic cyclization cascade
converting linear triterpenes to fused ring compounds.
This group contains bacterial SQCY which catalyzes the
convertion of squalene to hopene or diplopterol and
eukaryotic OSQCY which transforms the 2,3-epoxide of
squalene to compounds such as, lanosterol in mammals and
fungi or, cycloartenol in plants. Deletion of a single
glycine residue of Alicyclobacillus acidocaldarius SQCY
alters its substrate specificity into that of eukaryotic
OSQCY. Both enzymes have a second minor domain, which
forms an alpha-alpha barrel that is inserted into the
major domain.
Length = 634
Score = 26.8 bits (60), Expect = 9.6
Identities = 12/65 (18%), Positives = 19/65 (29%), Gaps = 8/65 (12%)
Query: 126 IPSLILLAVEAGGRLDVITTEARHELSEDPDGEFFPWPPKLVNVLSPRHCPKLYDSPALI 185
+P L + + R EL + P + +N R+ Y P
Sbjct: 162 VPMSYLYGKRPVAPITPLVLSLRDEL--------YVEPYEKINWYKHRNDLYDYRPPWQR 213
Query: 186 LFIVN 190
LF
Sbjct: 214 LFDAL 218
>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 = 25.4 bits (56), Expect = 9.8
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 52 FSAHWCPPCKAFTP 65
F A WCP C+ P
Sbjct: 23 FYAPWCPACQQLQP 36
>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 = 25.5 bits (56), Expect = 10.0
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 41 YIESCQVIGLYFSAHWCPPCKAFTPQL 67
Y ES ++I + +++ C PC+ P L
Sbjct: 9 YHESDRLILVLYTSPTCGPCRTLKPIL 35
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
0.317 0.136 0.417
Gapped
Lambda K H
0.267 0.0819 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,599,930
Number of extensions: 869504
Number of successful extensions: 984
Number of sequences better than 10.0: 1
Number of HSP's gapped: 969
Number of HSP's successfully gapped: 84
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.2 bits)