RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17592
(183 letters)
>gnl|CDD|239266 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II.
Length = 142
Score = 166 bits (423), Expect = 2e-53
Identities = 53/122 (43%), Positives = 74/122 (60%), Gaps = 1/122 (0%)
Query: 62 IGGKFELVDCNNKPVKSEDFLGKWALIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPN 121
IG F L D + +PV D GK L+YFG+THCPD+CP L +A + ++ +
Sbjct: 1 IGPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGG-DD 59
Query: 122 ITPIFISVDPERDTPELVGKYVKEFSPKFIGLTGTVEQVAAACKAYRVYFSAGPKDKDSD 181
+ +FISVDPERDTPE++ Y K F P +IGLTGT E++ A KA+ VY+ P+D
Sbjct: 60 VQVVFISVDPERDTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPEDDGDY 119
Query: 182 YI 183
+
Sbjct: 120 LV 121
>gnl|CDD|224910 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved
in biogenesis of respiratory and photosynthetic systems
[General function prediction only].
Length = 207
Score = 147 bits (374), Expect = 3e-45
Identities = 60/157 (38%), Positives = 89/157 (56%), Gaps = 4/157 (2%)
Query: 28 AVTGGGILFYMWNLKKAKQNALEKERRRNLGKVAIGGKFELVDCNNKPVKSEDFLGKWAL 87
+ L + +A V IGG FEL D + KP +D GK +L
Sbjct: 14 LLLALLFLLLVGLAAEASDKGDRFNLD--AAAVYIGGDFELTDQDGKPFTLKDLKGKPSL 71
Query: 88 IYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNITPIFISVDPERDTPELVGKYVKE-F 146
++FG+THCPD+CP L ++ A++ K+ G+ ++ +FI+VDPERDTPE++ KY + F
Sbjct: 72 VFFGYTHCPDVCPTTLAELKALLKKL-GEGEGDDVQVVFITVDPERDTPEVLKKYAELNF 130
Query: 147 SPKFIGLTGTVEQVAAACKAYRVYFSAGPKDKDSDYI 183
P++IGLTGT EQ+ KAY V++S P D +Y
Sbjct: 131 DPRWIGLTGTPEQIEEVAKAYGVFYSKVPLDDSQNYT 167
>gnl|CDD|202321 pfam02630, SCO1-SenC, SCO1/SenC. This family is involved in
biogenesis of respiratory and photosynthetic systems.
SCO1 is required for a post-translational step in the
accumulation of subunits COXI and COXII of cytochrome c
oxidase. SenC is required for optimal cytochrome c
oxidase activity and maximal induction of genes encoding
the light-harvesting and reaction centre complexes of R.
capsulatus.
Length = 152
Score = 144 bits (366), Expect = 9e-45
Identities = 59/128 (46%), Positives = 88/128 (68%), Gaps = 3/128 (2%)
Query: 56 NLGKVAIGGKFELVDCNNKPVKSEDFLGKWALIYFGFTHCPDICPDELEKMAAVVNKIDG 115
N K ++GG F L+D N K SE+ GK +LIYFGFT+CPDICP L+++ ++ K+
Sbjct: 3 NRPKNSLGGPFTLIDQNGKNFTSENLKGKLSLIYFGFTNCPDICPPALDRLTDIIKKLK- 61
Query: 116 QPNVPNITPIFISVDPERDTPELVGKYVKEFSPKFIGLTGTVEQVAAACKAYRVYFSAGP 175
N+ ++ P+FISVDPERDTP+++ +Y+K F P FIGLTGT +++ + K ++V++S
Sbjct: 62 AENI-DVQPVFISVDPERDTPKVLKEYLKNFHPSFIGLTGTTDEIKSVAKKFKVFYSKVI 120
Query: 176 KDKDS-DY 182
DK DY
Sbjct: 121 VDKPEQDY 128
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYF-GFTHCPDICPDELEKMAAVVNKIDGQPNVPNITP 124
FEL D + K V D+ GKW +++F P +C EL +A + + +
Sbjct: 8 FELPDLDGKEVSLSDYKGKWVVLFFYPKDFTP-VCTTELPALADLYEEFKKL----GVEV 62
Query: 125 IFISVDPE 132
+ +SVD
Sbjct: 63 LGVSVDSP 70
>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 = 39.9 bits (94), Expect = 7e-05
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNITPI 125
F L D + KPV D GK L+ F + CP C E+ ++ A+ + + +
Sbjct: 2 FSLPDLDGKPVSLSDLKGKVVLVNFWASWCP-PCRAEMPELEALAKEYKDD----GVEVV 56
Query: 126 FISVDPERDTPELVGKYVKEFSPKF 150
++VD D P V ++K++ F
Sbjct: 57 GVNVD--DDDPAAVKAFLKKYGITF 79
>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 = 36.9 bits (86), Expect = 8e-04
Identities = 15/69 (21%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 83 GKWALIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNITPIFISVDPERDTPELVGKY 142
GK L+YF + CP C ++ + K+ P + +++S+D + + + KY
Sbjct: 1 GKVVLLYFWASWCPP-CRAFTPELKELYEKL----KKPKVEIVYVSLDRDEEEWK---KY 52
Query: 143 VKEFSPKFI 151
+K+ ++
Sbjct: 53 LKKMPKDWL 61
>gnl|CDD|211789 TIGR03137, AhpC, peroxiredoxin. This peroxiredoxin (AhpC,
alkylhydroperoxide reductase subunit C) is one subunit
of a two-subunit complex with subunit F(TIGR03140).
Usually these are found as an apparent operon. The gene
has been characterized in Bacteroides fragilis where it
is important in oxidative stress defense. This gene
contains two invariant cysteine residues, one near the
N-terminus and one near the C-terminus, each followed
immediately by a proline residue [Cellular processes,
Detoxification, Cellular processes, Adaptations to
atypical conditions].
Length = 187
Score = 35.1 bits (81), Expect = 0.009
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 13/48 (27%)
Query: 63 GGKFELVDCNNKPVKSEDFLGKWALIYF---GFTHCPDICPDELEKMA 107
G+F V ED GKW++ +F FT +CP ELE +A
Sbjct: 18 NGEF-------VEVTDEDVKGKWSVFFFYPADFTF---VCPTELEDLA 55
>gnl|CDD|181857 PRK09437, bcp, thioredoxin-dependent thiol peroxidase; Reviewed.
Length = 154
Score = 34.9 bits (81), Expect = 0.009
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 65 KFELVDCNNKPVKSEDFLGKWALIYF 90
KF L D + + V DF G+ L+YF
Sbjct: 12 KFSLPDQDGEQVSLTDFQGQRVLVYF 37
>gnl|CDD|239269 cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the
different classes of PRXs including many proteins
originally known as bacterioferritin comigratory
proteins (BCP), based on their electrophoretic mobility
before their function was identified. PRXs are
thiol-specific antioxidant (TSA) proteins also known as
TRX peroxidases and alkyl hydroperoxide reductase C22
(AhpC) proteins. They confer a protective antioxidant
role in cells through their peroxidase activity in
which hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using
reducing equivalents derived from either TRX,
glutathione, trypanothione and AhpF. They are distinct
from other peroxidases in that they have no cofactors
such as metals or prosthetic groups. The first step of
catalysis, common to all PRXs, is the nucleophilic
attack by the catalytic cysteine (also known as the
peroxidatic cysteine) on the peroxide leading to
cleavage of the oxygen-oxygen bond and the formation of
a cysteine sulfenic acid intermediate. The second step
of the reaction, the resolution of the intermediate,
distinguishes the different types of PRXs. The presence
or absence of a second cysteine (the resolving
cysteine) classifies PRXs as either belonging to the
2-cys or 1-cys type. The resolving cysteine of 2-cys
PRXs is either on the same chain (atypical) or on the
second chain (typical) of a functional homodimer.
Structural and motif analysis of this growing family
supports the need for a new classification system. The
peroxidase activity of PRXs is regulated in vivo by
irreversible cysteine over-oxidation into a sulfinic
acid, phosphorylation and limited proteolysis.
Length = 140
Score = 33.3 bits (77), Expect = 0.028
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYF 90
F L + V DF GKW +++F
Sbjct: 5 FTLPATDGGEVSLSDFKGKWVVLFF 29
>gnl|CDD|223527 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 33.0 bits (76), Expect = 0.051
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 17/76 (22%)
Query: 60 VAIGGKFELVDCNNKPVKSEDFLGKWALIYF---GFTHCPDICPDELEKMAAVVNKIDGQ 116
V G FE + D+ GKW +++F FT +CP E+ A + +
Sbjct: 17 VLGGEIFE-------EITLSDYYGKWVVLFFYPADFT---FVCPTEIIAFAKRYEEFQKR 66
Query: 117 PNVPNITPIFISVDPE 132
+ I +S D
Sbjct: 67 ----GVEVIGVSTDSV 78
>gnl|CDD|239315 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
comigratory protein (BCP) subfamily; composed of
thioredoxin-dependent thiol peroxidases, widely
expressed in pathogenic bacteria, that protect cells
against toxicity from reactive oxygen species by
reducing and detoxifying hydroperoxides. The protein
was named BCP based on its electrophoretic mobility
before its function was known. BCP shows substrate
selectivity toward fatty acid hydroperoxides rather
than hydrogen peroxide or alkyl hydroperoxides. BCP
contains the peroxidatic cysteine but appears not to
possess a resolving cysteine (some sequences, not all,
contain a second cysteine but its role is still
unknown). Unlike other PRXs, BCP exists as a monomer.
The plant homolog of BCP is PRX Q, which is expressed
only in leaves and is cellularly localized in the
chloroplasts and the guard cells of stomata. Also
included in this subfamily is the fungal nuclear
protein, Dot5p (for disrupter of telomere silencing
protein 5), which functions as an alkyl-hydroperoxide
reductase during post-diauxic growth.
Length = 140
Score = 32.1 bits (74), Expect = 0.073
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYF 90
F L D + + V D GK ++YF
Sbjct: 6 FTLPDQDGETVSLSDLRGKPVVLYF 30
>gnl|CDD|224146 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 31.8 bits (73), Expect = 0.082
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYF 90
FEL D + + V D GK ++YF
Sbjct: 13 FELPDQDGETVSLSDLRGKPVVLYF 37
>gnl|CDD|239267 cd02969, PRX_like1, Peroxiredoxin (PRX)-like 1 family;
hypothetical proteins that show sequence similarity to
PRXs. Members of this group contain a conserved
cysteine that aligns to the first cysteine in the CXXC
motif of TRX. This does not correspond to the
peroxidatic cysteine found in PRXs, which aligns to the
second cysteine in the CXXC motif of TRX. In addition,
these proteins do not contain the other two conserved
residues of the catalytic triad of PRX. PRXs confer a
protective antioxidant role in cells through their
peroxidase activity in which hydrogen peroxide,
peroxynitrate, and organic hydroperoxides are reduced
and detoxified using reducing equivalents derived from
either thioredoxin, glutathione, trypanothione and
AhpF.
Length = 171
Score = 31.1 bits (71), Expect = 0.18
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 66 FELVDCNNKPVKSEDFL-GKWALIYFGFTHCP 96
F L D + K DF GK ++ F HCP
Sbjct: 7 FSLPDTDGKTYSLADFADGKALVVMFICNHCP 38
>gnl|CDD|233291 TIGR01143, murF,
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine
ligase. This family consists of the strictly bacterial
MurF gene of peptidoglycan biosynthesis. This enzyme is
almost always
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,
6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a
few species, MurE adds lysine rather than
diaminopimelate. This enzyme acts on the product from
MurE activity, and so is also subfamily rather than
equivalog. Staphylococcus aureus is an example of
species in this MurF protein would differ [Cell
envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 417
Score = 31.5 bits (72), Expect = 0.24
Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 10/86 (11%)
Query: 97 DICPDELEKMA-AVVNKIDGQPNVPNITPIFISVDPERDTPELVGKYVKEFSPKFIGLTG 155
D L A AVV +D + N P + D L +FS K IG+TG
Sbjct: 24 DFVEQALAAGAVAVV--VDREVGPDNGLPQILVDDTLEALQALASAKRAKFSGKVIGITG 81
Query: 156 -----TVEQVAAAC--KAYRVYFSAG 174
T +++ AA Y+V + G
Sbjct: 82 SSGKTTTKEMLAAILSHKYKVVATPG 107
>gnl|CDD|239313 cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys PRX
subfamily; PRXs are thiol-specific antioxidant (TSA)
proteins, which confer a protective role in cells
through its peroxidase activity by reducing hydrogen
peroxide, peroxynitrite, and organic hydroperoxides. The
functional unit of typical 2-cys PRX is a homodimer. A
unique intermolecular redox-active disulfide center is
utilized for its activity. Upon reaction with peroxides,
its peroxidatic cysteine is oxidized into a sulfenic
acid intermediate which is resolved by bonding with the
resolving cysteine from the other subunit of the
homodimer. This intermolecular disulfide bond is then
reduced by thioredoxin, tryparedoxin or AhpF. Typical
2-cys PRXs, like 1-cys PRXs, form decamers which are
stabilized by reduction of the active site cysteine.
Typical 2-cys PRX interacts through beta strands at one
edge of the monomer (B-type interface) to form the
functional homodimer, and uses an A-type interface
(similar to the dimeric interface in atypical 2-cys PRX
and PRX5) at the opposite end of the monomer to form the
stable decameric (pentamer of dimers) structure.
Length = 173
Score = 30.6 bits (70), Expect = 0.27
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 74 KPVKSEDFLGKWALIYF---GFTHCPDICPDELEKMA 107
K + D+ GKW +++F FT +CP E+ +
Sbjct: 20 KEISLSDYKGKWVVLFFYPLDFTF---VCPTEIIAFS 53
>gnl|CDD|237614 PRK14113, PRK14113, urease accessory protein UreE; Provisional.
Length = 152
Score = 30.3 bits (68), Expect = 0.30
Identities = 16/37 (43%), Positives = 19/37 (51%)
Query: 127 ISVDPERDTPELVGKYVKEFSPKFIGLTGTVEQVAAA 163
I V ER P LVG+ +K K I + G E VA A
Sbjct: 41 IGVFLERGHPLLVGEILKTECGKIIQVKGKAEDVATA 77
>gnl|CDD|239316 cd03018, PRX_AhpE_like, Peroxiredoxin (PRX) family, AhpE-like
subfamily; composed of proteins similar to Mycobacterium
tuberculosis AhpE. AhpE is described as a 1-cys PRX
because of the absence of a resolving cysteine. The
structure and sequence of AhpE, however, show greater
similarity to 2-cys PRXs than 1-cys PRXs. PRXs are
thiol-specific antioxidant (TSA) proteins that confer a
protective role in cells through their peroxidase
activity in which hydrogen peroxide, peroxynitrate, and
organic hydroperoxides are reduced and detoxified using
reducing equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF. The first step of
catalysis is the nucleophilic attack by the peroxidatic
cysteine on the peroxide leading to the formation of a
cysteine sulfenic acid intermediate. The absence of a
resolving cysteine suggests that functional AhpE is
regenerated by an external reductant. The solution
behavior and crystal structure of AhpE show that it
forms dimers and octamers.
Length = 149
Score = 29.5 bits (67), Expect = 0.51
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 66 FELVDCNNKPVKSEDFLGKWA--LIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNIT 123
FEL D N + V+ +F G+ L++F P +C E + A+ + ++
Sbjct: 10 FELPDQNGQEVRLSEFRGRKPVVLVFFPLAFTP-VCTKE---LCALRDSLE-LFEAAGAE 64
Query: 124 PIFISVDP 131
+ ISVD
Sbjct: 65 VLGISVDS 72
>gnl|CDD|182438 PRK10413, PRK10413, hydrogenase 2 accessory protein HypG;
Provisional.
Length = 82
Score = 28.2 bits (63), Expect = 0.69
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 71 CNNKPVKSEDFLGKWALIYFGF 92
C P D LG+W L++ GF
Sbjct: 37 CEGNP---ADLLGQWVLVHVGF 55
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 28.5 bits (64), Expect = 0.84
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 12/79 (15%)
Query: 83 GKWALIYFGFTHCPDIC---PDELEKMAAVVNKIDGQPNVPNITPIFISVDPERDTPELV 139
GK L+ F CP C EL K V + N I+++VD ++ +
Sbjct: 5 GKPVLVVFTDPDCPY-CKKLHKELLKDPDVQEYLKD-----NFVVIYVNVDDSKEVTDFD 58
Query: 140 GK--YVKEFSPKFIGLTGT 156
G+ KE + K+ G+ GT
Sbjct: 59 GETLSEKELARKY-GVRGT 76
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 29.8 bits (67), Expect = 0.99
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 13 KTDKFPITWKSVAVTAVT-GGGILFYMWNLKKAKQNALE--KERRRNLGKVAIGGKFELV 69
K ++FP +W+S+ AV G G L ++ + A++ ALE K+ +R L K + EL
Sbjct: 219 KIERFPNSWESLVYDAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELA 278
Query: 70 D 70
D
Sbjct: 279 D 279
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 28.3 bits (62), Expect = 1.4
Identities = 16/86 (18%), Positives = 27/86 (31%), Gaps = 6/86 (6%)
Query: 66 FELVDCNNKPVKSEDFLGKWALIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNITPI 125
+ + P+ + GK L+ F CP C E + + + G V +
Sbjct: 15 ASFEELDGAPLSLSELKGKPVLVDFWAPWCPP-CRAEAPLLEELAEEYGGDVEVVAV--- 70
Query: 126 FISVDPERDTPELVGKYVKEFSPKFI 151
D D G V+ P +
Sbjct: 71 -NVDDENPDLAAEFGVAVRSI-PTLL 94
>gnl|CDD|178015 PLN02392, PLN02392, probable steroid reductase DET2.
Length = 260
Score = 28.2 bits (63), Expect = 2.3
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 32 GGILFYMWNLK--KAKQNALEKERRRNLG-KVAIGGKFELVDCNNKPVKSEDFLG----K 84
GG++ ++W ++ L +R G KV GG FELV C N + ++LG
Sbjct: 154 GGLVVFLWGMRINVWSDRVLVGLKREGGGYKVPRGGWFELVSCPNYFGEIVEWLGWAVMT 213
Query: 85 WALIYFGF 92
W+ FGF
Sbjct: 214 WSWAGFGF 221
>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 = 27.6 bits (62), Expect = 2.4
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 3/64 (4%)
Query: 67 ELVDCNNKPVKSEDFLGKWALIYFGFTHCPDICPDELEKMAAVVNKIDGQPNVPNITPIF 126
L+ + V GK +YF + CP C K+ K+ N +F
Sbjct: 2 FLLRNDGGKVPVSSLEGKTVGLYFSASWCPP-CRAFTPKLVEFYEKLKESGK--NFEIVF 58
Query: 127 ISVD 130
IS D
Sbjct: 59 ISWD 62
>gnl|CDD|185066 PRK15111, PRK15111, antimicrobial peptide ABC transporter permease
SapC; Provisional.
Length = 296
Score = 28.1 bits (63), Expect = 2.7
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 101 DELEKMAAVVNKIDGQPN--------VPNITPIFIS 128
DELEK + ++DG +PNIT ++
Sbjct: 183 DELEKEYVIAARLDGASTLNILWYAVLPNITAGLVT 218
>gnl|CDD|211425 cd11583, Orc6_mid, Middle domain of the origin recognition complex
subunit 6. Orc6 is a subunit of the origin recognition
complex in eukaryotes, and it may be involved in binding
to DNA. This model describes the central or middle
domain of Orc6, whose structure resembles that of TFIIB,
a DNA-binding transcription factor. Orc6 appears to form
distinct complexes with DNA, and a putative DNA-binding
site has been identified.
Length = 94
Score = 26.5 bits (59), Expect = 3.2
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 152 GLTGTVEQVAAACKAYRVYFSAGPKDKDSDYI 183
G +E+ Y++ F A + + +D+
Sbjct: 13 GCKEAIEEAEKLLNRYKLPFLASEQRRVADFS 44
>gnl|CDD|223841 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 27.7 bits (62), Expect = 3.5
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 15/89 (16%)
Query: 97 DICPDELEKMAAVVNKIDGQPNVPNITPIFISVDPERDTPELVGK----YVKEFSPKFIG 152
D L AA V + P I + + V DT E +GK Y ++F+ K I
Sbjct: 52 DFIEQALAAGAAAV-LVARPVLPPAIPLVVLLVL---DTLEALGKLAKAYRQKFNAKVIA 107
Query: 153 LTG------TVEQVAAACK-AYRVYFSAG 174
+TG T E +AA +V+ + G
Sbjct: 108 ITGSNGKTTTKEMLAAILSTKGKVHATPG 136
>gnl|CDD|225392 COG2836, COG2836, Uncharacterized conserved protein [Function
unknown].
Length = 232
Score = 27.7 bits (62), Expect = 3.5
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 80 DFLGKWALIYFGFTHCPDIC 99
FLG + L G HC +C
Sbjct: 5 SFLGIFLLGLLGGGHCLGMC 24
>gnl|CDD|239112 cd02621, Peptidase_C1A_CathepsinC, Cathepsin C; also known as
Dipeptidyl Peptidase I (DPPI), an atypical papain-like
cysteine peptidase with chloride dependency and
dipeptidyl aminopeptidase activity, resulting from its
tetrameric structure which limits substrate access. Each
subunit of the tetramer is composed of three peptides:
the heavy and light chains, which together adopts the
papain fold and forms the catalytic domain; and the
residual propeptide region, which forms a beta barrel
and points towards the substrate's N-terminus. The
subunit composition is the result of the unique
characteristic of procathepsin C maturation involving
the cleavage of the catalytic domain and the
non-autocatalytic excision of an activation peptide
within its propeptide region. By removing N-terminal
dipeptide extensions, cathepsin C activates granule
serine peptidases (granzymes) involved in cell-mediated
apoptosis, inflammation and tissue remodelling.
Loss-of-function mutations in cathepsin C are associated
with Papillon-Lefevre and Haim-Munk syndromes, rare
diseases characterized by hyperkeratosis and early-onset
periodontitis. Cathepsin C is widely expressed in many
tissues with high levels in lung, kidney and placenta.
It is also highly expressed in cytotoxic lymphocytes and
mature myeloid cells.
Length = 243
Score = 27.3 bits (61), Expect = 4.1
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 135 TPELVGKYVKEF---SPKFIGLTGTVEQ--VAAACKAYRVYFSAG 174
P LVGK+ ++F + + T ++ A+ + R YFS
Sbjct: 77 FPFLVGKFAEDFGIVTEDYFPYTADDDRPCKASPSECRRYYFSDY 121
>gnl|CDD|221519 pfam12302, DUF3629, Protein of unknown function (DUF3629). This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 256 and 292 amino
acids in length.
Length = 253
Score = 26.9 bits (59), Expect = 5.4
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 9 PVRNKTDKFPITWKSVAVTAVTG 31
PVRN+ P +W S V A TG
Sbjct: 149 PVRNREKCKPNSWVSATVLAATG 171
>gnl|CDD|177990 PLN02361, PLN02361, alpha-amylase.
Length = 401
Score = 27.1 bits (60), Expect = 6.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 12 NKTDKFPITWKSVAVTAVTGG 32
N+ D P+ W AVT+ TGG
Sbjct: 113 NRYDGIPLPWDEHAVTSCTGG 133
>gnl|CDD|182423 PRK10382, PRK10382, alkyl hydroperoxide reductase subunit C;
Provisional.
Length = 187
Score = 26.5 bits (58), Expect = 7.0
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 76 VKSEDFLGKWALIYFGFTHCPDICPDELEKMA 107
V +D G+W++ +F +CP EL +A
Sbjct: 24 VTEKDTEGRWSVFFFYPADFTFVCPTELGDVA 55
>gnl|CDD|150464 pfam09799, Transmemb_17, Predicted membrane protein. This is a
100 amino acid region of a family of proteins conserved
from nematodes to humans. It is predicted to be a
transmembrane region but its function is not known.
Length = 109
Score = 25.7 bits (57), Expect = 7.5
Identities = 5/28 (17%), Positives = 12/28 (42%)
Query: 12 NKTDKFPITWKSVAVTAVTGGGILFYMW 39
N +K P V +T +++++
Sbjct: 60 NLAEKVPALAGFVLLTLPIQLPLIYFLL 87
>gnl|CDD|227902 COG5615, COG5615, Predicted integral membrane protein [Function
unknown].
Length = 161
Score = 26.3 bits (58), Expect = 7.5
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 17 FPITWKSVAVTAVTGGGILFYM 38
W +VA+ V+G + +
Sbjct: 57 GWWVWATVAILPVSGVYLGYEY 78
>gnl|CDD|239312 cd03014, PRX_Atyp2cys, Peroxiredoxin (PRX) family, Atypical 2-cys
PRX subfamily; composed of PRXs containing peroxidatic
and resolving cysteines, similar to the homodimeric
thiol specific antioxidant (TSA) protein also known as
TRX-dependent thiol peroxidase (Tpx). Tpx is a
bacterial periplasmic peroxidase which differs from
other PRXs in that it shows substrate specificity
toward alkyl hydroperoxides over hydrogen peroxide. As
with all other PRXs, the peroxidatic cysteine
(N-terminal) of Tpx is oxidized into a sulfenic acid
intermediate upon reaction with peroxides. Tpx is able
to resolve this intermediate by forming an
intramolecular disulfide bond with a conserved
C-terminal cysteine (the resolving cysteine), which can
then be reduced by thioredoxin. This differs from the
typical 2-cys PRX which resolves the oxidized cysteine
by forming an intermolecular disulfide bond with the
resolving cysteine from the other subunit of the
homodimer. Atypical 2-cys PRX homodimers have a
loop-based interface (A-type for alternate), in
contrast with the B-type interface of typical 2-cys and
1-cys PRXs.
Length = 143
Score = 26.0 bits (58), Expect = 8.3
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 65 KFELVDCNNKPVKSEDFLGKWALI 88
F LV + V DF GK +I
Sbjct: 8 DFTLVTSDLSEVSLADFAGKVKVI 31
>gnl|CDD|172588 PRK14098, PRK14098, glycogen synthase; Provisional.
Length = 489
Score = 26.6 bits (59), Expect = 8.6
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 1 MRLYSSELPVRNKTDKFPITWKSVAVTAVTGGGI-LFYMWNLKKAKQNAL 49
+RL E+P++ KTD V VTA+ I ++++N K K+N L
Sbjct: 63 LRLSDIEVPLKEKTDLL-----HVKVTALPSSKIQTYFLYNEKYFKRNGL 107
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 26.1 bits (58), Expect = 9.6
Identities = 13/22 (59%), Positives = 17/22 (77%), Gaps = 2/22 (9%)
Query: 40 NLKKAKQ--NALEKERRRNLGK 59
LKK+KQ ALEK+R++N GK
Sbjct: 144 ELKKSKQLDKALEKKRKKNAGK 165
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.423
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,670,645
Number of extensions: 912151
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 851
Number of HSP's successfully gapped: 49
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.7 bits)
S2: 56 (25.4 bits)