RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780212|ref|YP_003064625.1| bacterioferritin comigratory
protein [Candidatus Liberibacter asiaticus str. psy62]
(157 letters)
>gnl|CDD|31418 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 190 bits (483), Expect = 2e-49
Identities = 80/156 (51%), Positives = 104/156 (66%)
Query: 1 MTSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADF 60
M L VGDKAP F LP D + +SL L G +VLYFYPKD T GCT EA +F L +F
Sbjct: 1 MMMLKVGDKAPDFELPDQDGETVSLSDLRGKPVVLYFYPKDFTPGCTTEACDFRDLLEEF 60
Query: 61 DEESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVV 120
++ +++GISPDS SHKKF +KH L+ LL+DE EV ++Y VW EK M+GK+YMG+
Sbjct: 61 EKLGAVVLGISPDSPKSHKKFAEKHGLTFPLLSDEDGEVAEAYGVWGEKKMYGKEYMGIE 120
Query: 121 RTTFLIDEKGIIAQIWKPVTLKNHAQSVLKMVKSLK 156
R+TF+ID G I +W+ V +K HA VL +K L
Sbjct: 121 RSTFVIDPDGKIRYVWRKVKVKGHADEVLAALKKLA 156
>gnl|CDD|48566 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 = 178 bits (453), Expect = 6e-46
Identities = 71/143 (49%), Positives = 93/143 (65%), Gaps = 3/143 (2%)
Query: 8 DKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTIL 67
DKAP F LP D + +SL L G +VLYFYPKDDT GCT EA +F L +F ++
Sbjct: 1 DKAPDFTLPDQDGETVSLSDLRGKPVVLYFYPKDDTPGCTKEACDFRDLYEEFKALGAVV 60
Query: 68 IGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
IG+SPDS+ SH KF +K+ L LL+D ++ K+Y VW EK KKYMG+ R+TFLID
Sbjct: 61 IGVSPDSVESHAKFAEKYGLPFPLLSDPDGKLAKAYGVWGEKK---KKYMGIERSTFLID 117
Query: 128 EKGIIAQIWKPVTLKNHAQSVLK 150
G I ++W+ V K HA+ VL+
Sbjct: 118 PDGKIVKVWRKVKPKGHAEEVLE 140
>gnl|CDD|144244 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase (AhpC)
and thiol specific antioxidant (TSA).
Length = 124
Score = 143 bits (362), Expect = 3e-35
Identities = 56/130 (43%), Positives = 73/130 (56%), Gaps = 6/130 (4%)
Query: 6 VGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEEST 65
VGDKAP F LP D +E+SL G +VL+FYPKD T CT E + L +F +
Sbjct: 1 VGDKAPDFELPDLDGKEVSLSDYKGKWVVLFFYPKDFTPVCTTELPALADLYEEFKKLGV 60
Query: 66 ILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFL 125
++G+S DS SHKKF +K L LL+D EV ++Y V E + G +RTTF+
Sbjct: 61 EVLGVSVDSPESHKKFAEKLGLPFPLLSDPDGEVARAYGVLNE------EAGGALRTTFV 114
Query: 126 IDEKGIIAQI 135
ID G I I
Sbjct: 115 IDPDGKIRYI 124
>gnl|CDD|48520 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 = 140 bits (354), Expect = 2e-34
Identities = 52/143 (36%), Positives = 68/143 (47%), Gaps = 4/143 (2%)
Query: 9 KAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILI 68
KAP F LP+ D E+SL G +VL+FYPKD T CT E F L +F + ++
Sbjct: 1 KAPDFTLPATDGGEVSLSDFKGKWVVLFFYPKDFTPVCTTELCAFRDLAEEFAKGGAEVL 60
Query: 69 GISPDSIASHKKFHQKH-NLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
G+S DS SHK + +K L+ LL+D E K+Y V EKS R TF+ID
Sbjct: 61 GVSVDSPFSHKAWAEKEGGLNFPLLSDPDGEFAKAYGVLIEKSA---GGGLAARATFIID 117
Query: 128 EKGIIAQIWKPVTLKNHAQSVLK 150
G I + L
Sbjct: 118 PDGKIRYVEVEPLPTGRNAEELL 140
>gnl|CDD|48567 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 = 104 bits (261), Expect = 1e-23
Identities = 47/136 (34%), Positives = 65/136 (47%), Gaps = 9/136 (6%)
Query: 4 LSVGDKAPHFVLPSNDEQEISLL-ALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDE 62
L VGDKAP F LP + QE+ L G +VL F+P T CT E F+
Sbjct: 1 LEVGDKAPDFELPDQNGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALRDSLELFEA 60
Query: 63 ESTILIGISPDSIASHKKFHQKHNLSITLLAD--ESKEVLKSYDVWKEKSMFGKKYMGVV 120
++GIS DS S + + +++ L+ LL+D EV K+Y V+ E +
Sbjct: 61 AGAEVLGISVDSPFSLRAWAEENGLTFPLLSDFWPHGEVAKAYGVFDEDLGVAE------ 114
Query: 121 RTTFLIDEKGIIAQIW 136
R F+ID GII W
Sbjct: 115 RAVFVIDRDGIIRYAW 130
>gnl|CDD|48564 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 = 90.9 bits (226), Expect = 1e-19
Identities = 51/142 (35%), Positives = 73/142 (51%), Gaps = 19/142 (13%)
Query: 6 VGDKAPHF----VLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFD 61
VG KAP F V+P+ + +EISL G +VL+FYP D T C E I FS +F
Sbjct: 1 VGKKAPDFKATAVVPNGEFKEISLSDYKGKWVVLFFYPLDFTFVCPTEIIAFSDRYEEFK 60
Query: 62 EESTILIGISPDSIASHKKFHQKH-------NLSITLLADESKEVLKSYDVWKEKSMFGK 114
+ + ++G+S DS SH + ++ LLAD K++ + Y V E+
Sbjct: 61 KLNAEVLGVSTDSHFSHLAWRNTPRKEGGLGKINFPLLADPKKKISRDYGVLDEEE---- 116
Query: 115 KYMGV-VRTTFLIDEKGIIAQI 135
GV +R TF+ID +GII I
Sbjct: 117 ---GVALRGTFIIDPEGIIRHI 135
>gnl|CDD|30799 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 88.0 bits (218), Expect = 1e-18
Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 20/167 (11%)
Query: 3 SLSVGDKAPHFVLPS----NDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKA 58
+G KAP F + +EI+L G +VL+FYP D T C E I F+
Sbjct: 2 MSLIGKKAPDFTANAVLGGEIFEEITLSDYYGKWVVLFFYPADFTFVCPTEIIAFAKRYE 61
Query: 59 DFDEESTILIGISPDSIASHKKFHQK-------HNLSITLLADESKEVLKSYDVWKEKSM 111
+F + +IG+S DS+ SHK + + ++AD E+ ++Y V +
Sbjct: 62 EFQKRGVEVIGVSTDSVFSHKAWKATIREAGGIGKIKFPMIADPKGEIARAYGVLHPEE- 120
Query: 112 FGKKYMGV-VRTTFLIDEKGII-AQIWKPVTLKNHAQSVLKMVKSLK 156
G+ +R TF+ID G+I + P+T+ + +L+++ +L+
Sbjct: 121 ------GLALRGTFIIDPDGVIRHILVNPLTIGRNVDEILRVIDALQ 161
>gnl|CDD|36073 KOG0855, KOG0855, KOG0855, Alkyl hydroperoxide reductase, thiol
specific antioxidant and related enzymes
[Posttranslational modification, protein turnover,
chaperones].
Length = 211
Score = 82.9 bits (204), Expect = 4e-17
Identities = 47/136 (34%), Positives = 65/136 (47%), Gaps = 6/136 (4%)
Query: 3 SLSVGDKAPHFVLPSNDEQEISLLALGGSK-IVLYFYPKDDTSGCTAEAINFSSLKADFD 61
++ GD P F L D + ISL + G+K +VL+FYP T GCT +A F F
Sbjct: 62 KVNKGDAIPDFTLKDEDGKSISLKKITGNKPVVLFFYPAASTPGCTKQACGFRDNYEKFK 121
Query: 62 EESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVR 121
+ +IG+S D AS K F K NL LL+D EV+K K FG R
Sbjct: 122 KAGAEVIGLSGDDSASQKAFASKQNLPYHLLSDPKNEVIKDLGA--PKDPFGGL---PGR 176
Query: 122 TTFLIDEKGIIAQIWK 137
+ ++ D+ G+ I
Sbjct: 177 SHYIFDKGGVKQLIKN 192
>gnl|CDD|48565 cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily;
composed of PRXs containing only one conserved cysteine,
which serves as the peroxidatic cysteine. They are
homodimeric thiol-specific antioxidant (TSA) proteins
that confer a protective role in cells by reducing and
detoxifying hydrogen peroxide, peroxynitrite, and
organic hydroperoxides. As with all other PRXs, a
cysteine sulfenic acid intermediate is formed upon
reaction of 1-cys PRX with its substrates. Having no
resolving cysteine, the oxidized enzyme is resolved by
an external small-molecule or protein reductant such as
thioredoxin or glutaredoxin. Similar to typical 2-cys
PRX, 1-cys PRX forms a functional dimeric unit with a
B-type interface, as well as a decameric structure which
is stabilized in the reduced form of the enzyme. Other
oligomeric forms, tetramers and hexamers, have also been
reported. Mammalian 1-cys PRX is localized cellularly in
the cytosol and is expressed at high levels in brain,
eye, testes and lung. The seed-specific plant 1-cys PRXs
protect tissues from reactive oxygen species during
desiccation and are also called rehydrins..
Length = 203
Score = 76.3 bits (188), Expect = 3e-15
Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 13/159 (8%)
Query: 6 VGDKAPHFVLPSNDEQEISLLA-LGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEES 64
+GD AP+F + I LG S +L+ +P D T CT E F+ L +F + +
Sbjct: 1 LGDTAPNFEADT-THGPIKFHDYLGDSWGILFSHPADFTPVCTTELGAFAKLAPEFKKRN 59
Query: 65 TILIGISPDSIASHKKF------HQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMG 118
LIG+S DS+ SH K+ + + ++AD +EV K +
Sbjct: 60 VKLIGLSVDSVESHIKWIEDIEEYTGVEIPFPIIADPDREVAKLLGMIDP----DAGSTL 115
Query: 119 VVRTTFLIDEKGII-AQIWKPVTLKNHAQSVLKMVKSLK 156
VR F+ID I ++ P T + +L++V +L+
Sbjct: 116 TVRAVFIIDPDKKIRLILYYPATTGRNFDEILRVVDALQ 154
>gnl|CDD|36070 KOG0852, KOG0852, KOG0852, Alkyl hydroperoxide reductase, thiol
specific antioxidant and related enzymes
[Posttranslational modification, protein turnover,
chaperones].
Length = 196
Score = 68.8 bits (168), Expect = 6e-13
Identities = 45/122 (36%), Positives = 62/122 (50%), Gaps = 13/122 (10%)
Query: 21 QEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASH-- 78
+EI L G +VL+FYP D T C E I FS +F + +T ++GIS DS+ SH
Sbjct: 24 KEIKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSDRAPEFRKLNTEVLGISTDSVFSHLA 83
Query: 79 -----KKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLIDEKGIIA 133
+K L+I LL+D + E+ + Y V KE G R F+ID GI+
Sbjct: 84 WINTPRKQGGLGPLNIPLLSDLNHEISRDYGVLKEDE--GIAL----RGLFIIDPDGILR 137
Query: 134 QI 135
QI
Sbjct: 138 QI 139
>gnl|CDD|48563 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 = 60.6 bits (147), Expect = 2e-10
Identities = 41/138 (29%), Positives = 61/138 (44%), Gaps = 24/138 (17%)
Query: 5 SVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEES 64
VGDKAP F L ++D E+SL G V+ +P DT C + F+ A D
Sbjct: 1 KVGDKAPDFTLVTSDLSEVSLADFAGKVKVISVFPSIDTPVCATQTKRFNKEAAKLDN-- 58
Query: 65 TILIGISPDSIASHKKFHQKHNL-SITLLADESKEVLKSYDVWKEKSMFGKKYMGVV--- 120
T+++ IS D + K++ + ++T L+D FGK Y GV+
Sbjct: 59 TVVLTISADLPFAQKRWCGAEGVDNVTTLSDF------------RDHSFGKAY-GVLIKD 105
Query: 121 -----RTTFLIDEKGIIA 133
R F+IDE G +
Sbjct: 106 LGLLARAVFVIDENGKVI 123
>gnl|CDD|36072 KOG0854, KOG0854, KOG0854, Alkyl hydroperoxide reductase, thiol
specific antioxidant and related enzymes
[Posttranslational modification, protein turnover,
chaperones].
Length = 224
Score = 56.6 bits (136), Expect = 3e-09
Identities = 43/166 (25%), Positives = 75/166 (45%), Gaps = 10/166 (6%)
Query: 1 MTSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADF 60
L +GD P+F + + LG S VL+ +P D T CT E F+ L +F
Sbjct: 3 GPRLRLGDTVPNFEADTTVGKIKFHDYLGDSWGVLFSHPADFTPVCTTELGRFAKLAPEF 62
Query: 61 DEESTILIGISPDSIASHKKFHQ---------KHNLSITLLADESKEVLKSYDVWKEKSM 111
D+ + LI +S D + SHK + + H++ ++AD ++E+ ++ +
Sbjct: 63 DKRNVKLIALSVDDVESHKDWIKDIKSYAKVKNHSVPYPIIADPNRELAFLLNMLDPEEK 122
Query: 112 FGKKYMGVVRTTFLID-EKGIIAQIWKPVTLKNHAQSVLKMVKSLK 156
VR F+ID +K I P T + +L+++ SL+
Sbjct: 123 KNIGDGKTVRAVFVIDPDKKIRLSFLYPSTTGRNFDEILRVIDSLQ 168
>gnl|CDD|32260 COG2077, Tpx, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 158
Score = 54.9 bits (132), Expect = 9e-09
Identities = 37/135 (27%), Positives = 60/135 (44%), Gaps = 9/135 (6%)
Query: 2 TSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFD 61
VGDKAP F L D ++SL G K V+ +P DT C + F+ A
Sbjct: 16 NEPQVGDKAPDFTLVGKDLNDVSLADFAGKKKVISVFPSIDTPVCATQVRKFNEEAAKLG 75
Query: 62 EESTILIGISPDSIASHKKFHQKHNLS-ITLLAD-ESKEVLKSYDVW-KEKSMFGKKYMG 118
+T+++ IS D + K+F + + L+D + ++Y V E + G
Sbjct: 76 --NTVVLCISMDLPFAQKRFCGAEGIENVITLSDFRDRAFGENYGVLINEGPLAGL---- 129
Query: 119 VVRTTFLIDEKGIIA 133
+ R F++DE G +
Sbjct: 130 LARAVFVLDENGKVT 144
>gnl|CDD|48515 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 = 50.7 bits (121), Expect = 2e-07
Identities = 34/128 (26%), Positives = 58/128 (45%), Gaps = 21/128 (16%)
Query: 13 FVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCT---AEAINFSSLKADFDEESTILIG 69
F LP D + +SL L G +++ F+ S C AE +L ++ ++ ++G
Sbjct: 2 FSLPDLDGKPVSLSDLKGKVVLVNFW----ASWCPPCRAEMPELEALAKEYKDDGVEVVG 57
Query: 70 IS--PDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
++ D A+ K F +K+ ++ +L D E+ K+Y V + TTFLID
Sbjct: 58 VNVDDDDPAAVKAFLKKYGITFPVLLDPDGELAKAYGV------------RGLPTTFLID 105
Query: 128 EKGIIAQI 135
G I
Sbjct: 106 RDGRIRAR 113
>gnl|CDD|48519 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical
proteins that show sequence similarity to PRXs. Members
of this group contain a CXXC motif, similar to TRX. The
second cysteine in the motif corresponds to the
peroxidatic cysteine of PRX, however, these proteins do
not contain the other two 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. TRXs alter the
redox state of target proteins by catalyzing the
reduction of their disulfide bonds via the CXXC motif
using reducing equivalents derived from either NADPH or
ferredoxins..
Length = 149
Score = 50.0 bits (119), Expect = 3e-07
Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 13/135 (9%)
Query: 9 KAPHFVLPSNDEQEISLLAL-GGSKIVLYFY-----PKDDTSGCTAEAINFSSLKADFDE 62
AP F LP + ++L AL G +V+ FY P C S L + D
Sbjct: 1 TAPDFELPDAGGETVTLSALLGEGPVVVVFYRGFGCPF-----CREYLRALSKLLPELDA 55
Query: 63 ESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKE--KSMFGKKYMGVV 120
L+ + P+S + F + L + AD +++ ++ + + S +
Sbjct: 56 LGVELVAVGPESPEKLEAFDKGKFLPFPVYADPDRKLYRALGLVRSLPWSNTPRALWKNA 115
Query: 121 RTTFLIDEKGIIAQI 135
F +++G Q+
Sbjct: 116 AIGFRGNDEGDGLQL 130
>gnl|CDD|48518 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 = 42.9 bits (101), Expect = 4e-05
Identities = 29/137 (21%), Positives = 50/137 (36%), Gaps = 24/137 (17%)
Query: 7 GDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTI 66
G AP F LP D + SL K ++ + + A + L ++ +
Sbjct: 1 GSPAPDFSLPDTDGKTYSLADFADGKALVVMFICNHCPYVKAIEDRLNRLAKEYGAKGVA 60
Query: 67 LIGISPDSIASH--------KKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMG 118
++ I+ + I ++ K ++H L DE++EV K+Y G
Sbjct: 61 VVAINSNDIEAYPEDSPENMKAKAKEHGYPFPYLLDETQEVAKAY--------------G 106
Query: 119 VVRT--TFLIDEKGIIA 133
T FL D G +
Sbjct: 107 AACTPDFFLFDPDGKLV 123
>gnl|CDD|48560 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 = 34.8 bits (80), Expect = 0.010
Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 12/99 (12%)
Query: 11 PHFVLPSNDEQEISLLALGGSKIVLYFY----PKDDTSGCTAEAINFSSLKADFDEESTI 66
P F + D ++ L +L G +++YF+ P C + + L AD+ +
Sbjct: 1 PLFTATTLDGEQFDLESLSGKPVLVYFWATWCPV-----CRFTSPTVNQLAADY---PVV 52
Query: 67 LIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDV 105
+ + + +F QK ++ D + + V
Sbjct: 53 SVALRSGDDGAVARFMQKKGYGFPVINDPDGVISARWGV 91
>gnl|CDD|48517 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 = 33.7 bits (77), Expect = 0.023
Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 12/141 (8%)
Query: 10 APHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEEST---- 65
P F L D + ++L L G +++YF C N + +
Sbjct: 2 GPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQ 61
Query: 66 -ILIGISP--DSIASHKKFHQKHNLSITLL---ADESKEVLKSYDVWKEKSMFGKKYMGV 119
+ I + P D+ K + + L +E + + K++ V+ EK V
Sbjct: 62 VVFISVDPERDTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPEDDGDYLV 121
Query: 120 VRTT--FLIDEKGIIAQIWKP 138
+ +L+D G + + +
Sbjct: 122 DHSAAIYLVDPDGKLVRYYGG 142
>gnl|CDD|80347 cd02125, PA_VSR, PA_VSR: Protease-associated (PA) domain-containing
plant vacuolar sorting receptor (VSR). This group
includes various PA domain-containing VSRs such as
garden pea BP-80, pumpkin PV72, and various Arabidopsis
VSRs including AtVSR1. In contrast to most eukaryotes,
which only have one or two VSRs, plants have several.
This may in part be a reflection of having a more
complex vacuolar system with both lytic vacuoles and
storage vacuoles. The lytic vacuole is thought to be
equivalent to the mammalian lysosome and the yeast
vacuole. Pea BP-80 is a type 1 transmembrane protein,
involved in the targeting of proteins to the lytic
vacuole; it has been suggested that this protein also
mediates targeting to the storage vacuole. PV72 and
AtVSR1 may mediate transport of seed storage proteins to
protein storage vacuoles. The significance of the PA
domain to VSRs has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate..
Length = 127
Score = 28.4 bits (63), Expect = 0.82
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 29 GGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASHKKFH-QKHNL 87
GG+ + YPK++ +GC + F K++ IL+ + K ++ Q+
Sbjct: 8 GGTLTGVVVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGA 67
Query: 88 SITLLADESKEVLKSYD 104
+ L+AD E L + D
Sbjct: 68 AAVLVADNVDEPLLTMD 84
>gnl|CDD|144913 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 27.7 bits (62), Expect = 1.3
Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 21/114 (18%)
Query: 37 FYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASHKKFHQKHNLSITLLADES 96
Y +T G +E I+ + +E +L + SH + +L +
Sbjct: 210 LYDVPETEGERSELISK--VNKRIEELQRVL-----EQTESHLE---------KVLVKIA 253
Query: 97 KEVLKSYDVWKEKSMFGKKYMGVVRTTFLIDEKGIIAQIWKPVTLKNHAQSVLK 150
E+L W E+ + +K + F D K +IA+ W P ++ L+
Sbjct: 254 DELL----AWDEQ-VSKEKAVYETLNLFNYDTKTLIAEGWVPAKDLEKLKAALE 302
>gnl|CDD|173788 cd04056, Peptidases_S53, Peptidase domain in the S53 family.
Members of the peptidases S53 (sedolisin) family include
endopeptidases and exopeptidases sedolisin, kumamolysin,
and (PSCP) Pepstatin-insensitive Carboxyl Proteinase.
The S53 family contains a catalytic triad Glu/Asp/Ser
with an additional acidic residue Asp in the oxyanion
hole, similar to that of Asn in subtilisin. The
stability of these enzymes may be enhanced by calcium,
some members have been shown to bind up to 4 ions via
binding sites with different affinity. Some members of
this clan contain disulfide bonds. These enzymes can be
intra- and extracellular, some function at extreme
temperatures and pH values. Characterized sedolisins
include Kumamolisin, an extracellular calcium-dependent
thermostable endopeptidase from Bacillus. The enzyme is
synthesized with a 188 amino acid N-terminal preprotein
region which is cleaved after the extraction into the
extracellular space with low pH. One kumamolysin
paralog, kumamolisin-As, is believed to be a
collagenase. TPP1 is a serine protease that functions as
a tripeptidyl exopeptidase as well as an endopeptidase.
Less is known about PSCP from Pseudomonas which is
thought to be an aspartic proteinase.
Length = 361
Score = 26.1 bits (58), Expect = 4.5
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 2 TSLSVGDKAPHFVLPSNDEQEISL-----LALG-GSKIVLYFYPKDDTSG 45
+ V S E SL A+ G+ I LYF P T+G
Sbjct: 55 FIVVVIGGGNAPGTSSGWGGEASLDVEYAGAIAPGANITLYFAPGTVTNG 104
>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
mitochondrial malate dehydrogenases. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. Members of this subfamily are
localized to the glycosome and mitochondria. MDHs are
part of the NAD(P)-binding Rossmann fold superfamily,
which includes a wide variety of protein families
including the NAD(P)-binding domains of alcohol
dehydrogenases, tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 310
Score = 25.5 bits (57), Expect = 6.3
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 98 EVLKSYDVWKEKSMFGKKYMGVVRT-TFLIDEKGI 131
EVLK V+ K +FG + VVR TF+ + G+
Sbjct: 129 EVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGL 163
>gnl|CDD|36707 KOG1494, KOG1494, KOG1494, NAD-dependent malate dehydrogenase
[Energy production and conversion].
Length = 345
Score = 25.6 bits (56), Expect = 6.3
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 97 KEVLKSYDVWKEKSMFGKKYMGVVRT-TFLIDEKGI 131
EVLK V+ K +FG + VVR TF+ + +
Sbjct: 156 AEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEVLNL 191
>gnl|CDD|35558 KOG0337, KOG0337, KOG0337, ATP-dependent RNA helicase [RNA
processing and modification].
Length = 529
Score = 25.4 bits (55), Expect = 6.7
Identities = 22/111 (19%), Positives = 46/111 (41%), Gaps = 10/111 (9%)
Query: 51 INFSSLKADFDEESTILIGISPDSIASHK-KFHQK---HNLSITLLADESKEVLKSYDVW 106
+ F+ ++D + T +IG SP S+ S + + HQ N + +LA + + Y
Sbjct: 384 LIFAISHFEYDCDDTTVIGRSPQSLVSLESEGHQSILESNRELQVLARTADKAEMLY--- 440
Query: 107 KEKSMFGKKYMGVVRTTFLIDEKGIIAQIWKPVTLKNHAQSVLKMVKSLKQ 157
++ + R +I KG+ + +N + L ++ +K
Sbjct: 441 -TRTRPSPSPESLKRAKEMISSKGLHPR--FKSFGENEEKEKLDILYKIKN 488
>gnl|CDD|38634 KOG3424, KOG3424, KOG3424, 40S ribosomal protein S24 [Translation,
ribosomal structure and biogenesis].
Length = 132
Score = 25.3 bits (55), Expect = 8.0
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 3/83 (3%)
Query: 47 TAEAINFSSLKADFDEESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVW 106
T +A+ + F + + DS+ KKF K+ L LA++ K K
Sbjct: 51 TPDAVFVFGFRTHFGGGKSTGFALIYDSVEYAKKFEPKYRLVRLGLAEKIKTSRK---QR 107
Query: 107 KEKSMFGKKYMGVVRTTFLIDEK 129
KE+ KK G + +K
Sbjct: 108 KERKNRMKKIFGTGKRKAKKAKK 130
>gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182). This
family contains uncharacterized integral membrane
proteins.
Length = 771
Score = 25.2 bits (56), Expect = 9.0
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 12/48 (25%)
Query: 7 GDKAPHFVL-----PSNDEQEISLLALGGS------KIVLYFYPKDDT 43
G+K P F+L PS + I+ LA S K+VLY +PKD
Sbjct: 701 GEKKPEFILLLPFTPSGRDNLIAWLA-ARSDGENYGKLVLYEFPKDRL 747
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.315 0.131 0.370
Gapped
Lambda K H
0.267 0.0638 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,773,118
Number of extensions: 83295
Number of successful extensions: 218
Number of sequences better than 10.0: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 35
Length of query: 157
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,405,363
Effective search space: 312780773
Effective search space used: 312780773
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: 53 (24.4 bits)