RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1172
(276 letters)
>gnl|CDD|239314 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 = 171 bits (436), Expect = 3e-53
Identities = 64/121 (52%), Positives = 83/121 (68%), Gaps = 9/121 (7%)
Query: 3 LQDIQSYSSCGEGDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAK 62
++DI+ Y ++P+PIIAD DR +A LGM+DP G LT RAVFIIDP K
Sbjct: 77 IEDIEEY-----TGVEIPFPIIADPDREVAKLLGMIDP----DAGSTLTVRAVFIIDPDK 127
Query: 63 KLRLSFLYPATTGRNFDEILRVLDSLQLTDTKKVATPVDWKVGMEIEVRPGLVSKDSEGK 122
K+RL YPATTGRNFDEILRV+D+LQLTD KVATP +WK G ++ V P + ++++ K
Sbjct: 128 KIRLILYYPATTGRNFDEILRVVDALQLTDKHKVATPANWKPGDDVIVPPSVSDEEAKKK 187
Query: 123 L 123
Sbjct: 188 F 188
Score = 106 bits (267), Expect = 4e-28
Identities = 34/52 (65%), Positives = 40/52 (76%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
WGILFSHP+DFTPVCTTEL +L EF++R K+I LS DSVESH WI+
Sbjct: 27 WGILFSHPADFTPVCTTELGAFAKLAPEFKKRNVKLIGLSVDSVESHIKWIE 78
>gnl|CDD|223527 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 108 bits (273), Expect = 4e-29
Identities = 38/92 (41%), Positives = 48/92 (52%), Gaps = 6/92 (6%)
Query: 14 EGDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPAT 73
G GK+ +P+IAD +A G+L P E L R FIIDP +R + P T
Sbjct: 92 GGIGKIKFPMIADPKGEIARAYGVLHPEEG------LALRGTFIIDPDGVIRHILVNPLT 145
Query: 74 TGRNFDEILRVLDSLQLTDTKKVATPVDWKVG 105
GRN DEILRV+D+LQ P +WK G
Sbjct: 146 IGRNVDEILRVIDALQFVAKHGEVCPANWKPG 177
Score = 79.6 bits (197), Expect = 4e-18
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKALVR 237
W +LF +P+DFT VC TE+ + +EF++R +VI +S DSV SH W +
Sbjct: 35 WVVLFFYPADFTFVCPTEIIAFAKRYEEFQKRGVEVIGVSTDSVFSHKAWKATIRE 90
>gnl|CDD|237297 PRK13189, PRK13189, peroxiredoxin; Provisional.
Length = 222
Score = 107 bits (270), Expect = 2e-28
Identities = 40/94 (42%), Positives = 56/94 (59%), Gaps = 5/94 (5%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRN 77
++ +PIIAD +A +LGM+ P + + T RAVFIIDP +R YP GRN
Sbjct: 97 EIEFPIIADDRGEIAKKLGMISPGKGTN-----TVRAVFIIDPKGIIRAILYYPQEVGRN 151
Query: 78 FDEILRVLDSLQLTDTKKVATPVDWKVGMEIEVR 111
DEILR++ +LQ +D K VATP +W I+ +
Sbjct: 152 MDEILRLVKALQTSDEKGVATPANWPPNDLIKDK 185
Score = 74.6 bits (184), Expect = 5e-16
Identities = 25/52 (48%), Positives = 33/52 (63%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
W +LFSHP+DFTPVCTTE + EF + ++I LS D V SH W++
Sbjct: 37 WFVLFSHPADFTPVCTTEFVAFQKRYDEFRELNTELIGLSIDQVFSHIKWVE 88
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 100 bits (251), Expect = 4e-24
Identities = 37/49 (75%), Positives = 44/49 (89%)
Query: 103 KVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLI 151
KVG EIE+RPG++SKDS G+ TC+PI +RIVSLFAE NELQ+AVPGGLI
Sbjct: 278 KVGDEIEIRPGIISKDSGGEFTCRPIRTRIVSLFAENNELQYAVPGGLI 326
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 89.1 bits (221), Expect = 1e-21
Identities = 43/103 (41%), Positives = 61/103 (59%), Gaps = 6/103 (5%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRN 77
K+P+P+IAD D+ LA + ++D E T R VFIIDP + +R YPA TGRN
Sbjct: 89 KIPFPVIADIDKELAREYNLID--ENSG----ATVRGVFIIDPNQIVRWMIYYPAETGRN 142
Query: 78 FDEILRVLDSLQLTDTKKVATPVDWKVGMEIEVRPGLVSKDSE 120
DEI+R+ +LQ+ +KVATP +W+ G E V ++E
Sbjct: 143 IDEIIRITKALQVNWKRKVATPANWQPGQEGIVPAPSTLDEAE 185
Score = 67.2 bits (164), Expect = 2e-13
Identities = 23/52 (44%), Positives = 36/52 (69%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
W +LFSHP+DFTPVCTTE + ++F++ +++ LS DS+ SH W++
Sbjct: 29 WVLLFSHPADFTPVCTTEFIAFSRRYEDFKKLGVELVGLSVDSIYSHIAWLR 80
>gnl|CDD|239659 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
the domain II of the gamma subunit of eukaryotic
translation initiation factor 2 (eIF2-gamma) found in
Eukaryota and Archaea. eIF2 is a G protein that delivers
the methionyl initiator tRNA to the small ribosomal
subunit and releases it upon GTP hydrolysis after the
recognition of the initiation codon. eIF2 is composed
three subunits, alpha, beta and gamma. Subunit gamma
shows strongest conservation, and it confers both tRNA
binding and GTP/GDP binding.
Length = 113
Score = 86.4 bits (215), Expect = 2e-21
Identities = 35/49 (71%), Positives = 42/49 (85%), Gaps = 1/49 (2%)
Query: 103 KVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLI 151
KVG EIE+RPG+V KD EGK+ C+PIF++IVSL AE N+LQ AVPGGLI
Sbjct: 41 KVGDEIEIRPGIVVKD-EGKIKCRPIFTKIVSLKAENNDLQEAVPGGLI 88
>gnl|CDD|183885 PRK13191, PRK13191, putative peroxiredoxin; Provisional.
Length = 215
Score = 83.4 bits (206), Expect = 3e-19
Identities = 41/110 (37%), Positives = 60/110 (54%), Gaps = 9/110 (8%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRN 77
++P+PIIAD ++A +LGM+ + T RAVFI+D +RL YP GRN
Sbjct: 95 EVPFPIIADPMGNVAKRLGMIHAESSTA-----TVRAVFIVDDKGTVRLILYYPMEIGRN 149
Query: 78 FDEILRVLDSLQLTDTKKVATPVDWK----VGMEIEVRPGLVSKDSEGKL 123
DEILR + +LQL D V TP +W +G ++ KD++ +L
Sbjct: 150 IDEILRAIRALQLVDKAGVVTPANWPNNELIGDKVINPAPRTIKDAKMRL 199
Score = 61.8 bits (150), Expect = 2e-11
Identities = 25/51 (49%), Positives = 34/51 (66%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWI 232
W +LFSHP DFTPVCTTE + +EF++ ++I LS DS SH +W+
Sbjct: 35 WFVLFSHPGDFTPVCTTEFYSFAKKYEEFKKLNTELIGLSVDSNISHIEWV 85
>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 = 80.7 bits (200), Expect = 5e-19
Identities = 24/54 (44%), Positives = 32/54 (59%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKAL 235
W +LF +P DFTPVCTTEL L +EF + +V+ +S DS SH W +
Sbjct: 24 WVVLFFYPKDFTPVCTTELCAFRDLAEEFAKGGAEVLGVSVDSPFSHKAWAEKE 77
Score = 73.4 bits (181), Expect = 3e-16
Identities = 27/66 (40%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 17 GKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGR 76
G L +P+++D D A G+L S G L RA FIIDP K+R + P TGR
Sbjct: 78 GGLNFPLLSDPDGEFAKAYGVLIE---KSAGGGLAARATFIIDPDGKIRYVEVEPLPTGR 134
Query: 77 NFDEIL 82
N +E+L
Sbjct: 135 NAEELL 140
>gnl|CDD|106544 PRK13599, PRK13599, putative peroxiredoxin; Provisional.
Length = 215
Score = 73.6 bits (180), Expect = 1e-15
Identities = 39/85 (45%), Positives = 48/85 (56%), Gaps = 5/85 (5%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRN 77
+P+P+IAD ++ QLGM+ P KG T RAVFI+D +RL YP GRN
Sbjct: 90 AIPFPVIADDLGKVSNQLGMIHP----GKGTN-TVRAVFIVDDKGTIRLIMYYPQEVGRN 144
Query: 78 FDEILRVLDSLQLTDTKKVATPVDW 102
DEILR L +LQ D VA P W
Sbjct: 145 VDEILRALKALQTADQYGVALPEKW 169
Score = 63.2 bits (153), Expect = 6e-12
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
W +LFSHP+DFTPVCTTE + +F++ ++I LS D V SH W++
Sbjct: 30 WFVLFSHPADFTPVCTTEFVEFARKANDFKELNTELIGLSVDQVFSHIKWVE 81
>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 = 70.3 bits (173), Expect = 2e-15
Identities = 25/54 (46%), Positives = 36/54 (66%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKAL 235
W +LF +P DFTPVCTTEL + L +EF++ +V+ +S DS ESH + + L
Sbjct: 27 WVVLFFYPKDFTPVCTTELPALADLYEEFKKLGVEVLGVSVDSPESHKKFAEKL 80
Score = 40.7 bits (96), Expect = 1e-04
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLR 65
LP+P+++D D +A G+L+ E L R F+IDP K+R
Sbjct: 81 GLPFPLLSDPDGEVAKAYGVLNEEE------GLALRTTFVIDPDGKIR 122
>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 = 70.6 bits (174), Expect = 6e-15
Identities = 34/91 (37%), Positives = 49/91 (53%), Gaps = 6/91 (6%)
Query: 15 GDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATT 74
G GK+ +P++AD + ++ G+LD E G+ L R FIIDP +R +
Sbjct: 89 GLGKINFPLLADPKKKISRDYGVLDEEE----GVAL--RGTFIIDPEGIIRHITVNDLPV 142
Query: 75 GRNFDEILRVLDSLQLTDTKKVATPVDWKVG 105
GR+ DE LRVLD+LQ + P +WK G
Sbjct: 143 GRSVDETLRVLDALQFVEEHGEVCPANWKPG 173
Score = 68.7 bits (169), Expect = 3e-14
Identities = 22/61 (36%), Positives = 33/61 (54%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKALVRDCIL 241
W +LF +P DFT VC TE+ +EF++ +V+ +S DS SH W ++ L
Sbjct: 31 WVVLFFYPLDFTFVCPTEIIAFSDRYEEFKKLNAEVLGVSTDSHFSHLAWRNTPRKEGGL 90
Query: 242 G 242
G
Sbjct: 91 G 91
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 69.7 bits (171), Expect = 1e-13
Identities = 23/49 (46%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 103 KVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLI 151
+VG EIE+RPG+V + GK +PI + IVSL A +++ A PGGL+
Sbjct: 247 RVGDEIEIRPGIVVEK-GGKTVWEPITTEIVSLQAGGEDVEEARPGGLV 294
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 56.5 bits (136), Expect = 1e-09
Identities = 30/91 (32%), Positives = 50/91 (54%), Gaps = 6/91 (6%)
Query: 15 GDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATT 74
G G + P++AD+ +S+A G+L ++ +G+ R +FIIDP LR +
Sbjct: 96 GLGTMAIPMLADKTKSIARSYGVL----EEEQGVAY--RGLFIIDPKGMLRQITVNDMPV 149
Query: 75 GRNFDEILRVLDSLQLTDTKKVATPVDWKVG 105
GRN +E+LR+L++ Q + P +WK G
Sbjct: 150 GRNVEEVLRLLEAFQFVEKHGEVCPANWKKG 180
Score = 50.3 bits (120), Expect = 2e-07
Identities = 21/50 (42%), Positives = 30/50 (60%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDW 231
W +LF +P DFT VC TE+ + +K F + C+V+A S DS +H W
Sbjct: 38 WVVLFFYPLDFTFVCPTEIIQFSDSVKRFNELNCEVLACSMDSEYAHLQW 87
>gnl|CDD|173427 PTZ00137, PTZ00137, 2-Cys peroxiredoxin; Provisional.
Length = 261
Score = 53.8 bits (129), Expect = 2e-08
Identities = 32/82 (39%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKALVRD-CI 240
+G+L +P DFT VC +EL + +KEFE+R KV+ +S DS SH W + VR +
Sbjct: 100 YGLLVFYPLDFTFVCPSELLGFSERLKEFEERGVKVLGVSVDSPFSHKAWKELDVRQGGV 159
Query: 241 LGLLINLSVDDFKEVEGRSRRF 262
L L D +EV S+ F
Sbjct: 160 SPLKFPLFSDISREV---SKSF 178
Score = 50.3 bits (120), Expect = 2e-07
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 7/87 (8%)
Query: 19 LPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRNF 78
L +P+ +D R ++ G+L +G + RA ++D A ++ +Y GR+
Sbjct: 162 LKFPLFSDISREVSKSFGLLR-----DEG--FSHRASVLVDKAGVVKHVAVYDLGLGRSV 214
Query: 79 DEILRVLDSLQLTDTKKVATPVDWKVG 105
DE LR+ D++Q + PV+WK G
Sbjct: 215 DETLRLFDAVQFAEKTGNVCPVNWKQG 241
>gnl|CDD|224146 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 51.9 bits (125), Expect = 2e-08
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 184 ILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKALVRDCILGL 243
+L+ +P DFTP CTTE L++EFE+ V+ +S DS +SH + + GL
Sbjct: 34 VLYFYPKDFTPGCTTEACDFRDLLEEFEKLGAVVLGISPDSPKSHKKFAEK------HGL 87
Query: 244 LINLSVDDFKEV 255
L D+ EV
Sbjct: 88 TFPLLSDEDGEV 99
Score = 38.8 bits (91), Expect = 8e-04
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 19 LPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGRNF 78
L +P+++D+D +A G+ + K R+ F+IDP K+R + G +
Sbjct: 87 LTFPLLSDEDGEVAEAYGVWGEKKMYGKEYMGIERSTFVIDPDGKIRYVWRKVKVKG-HA 145
Query: 79 DEILRVLDSLQ 89
DE+L L L
Sbjct: 146 DEVLAALKKLA 156
>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 = 51.0 bits (123), Expect = 3e-08
Identities = 20/52 (38%), Positives = 28/52 (53%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
+L+ +P D TP CT E L +EF+ VI +S DSVESH + +
Sbjct: 25 PVVLYFYPKDDTPGCTKEACDFRDLYEEFKALGAVVIGVSPDSVESHAKFAE 76
Score = 40.2 bits (95), Expect = 2e-04
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSF 68
LP+P+++D D LA G+ EK K M R+ F+IDP K+ +
Sbjct: 79 GLPFPLLSDPDGKLAKAYGV--WGEKKKKYM-GIERSTFLIDPDGKIVKVW 126
>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 = 51.1 bits (123), Expect = 4e-08
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 181 FWG----ILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIK 233
F G +L P FTPVCT EL + ++ FE +V+ +S DS S W +
Sbjct: 25 FRGRKPVVLVFFPLAFTPVCTKELCALRDSLELFEAAGAEVLGISVDSPFSLRAWAE 81
Score = 34.2 bits (79), Expect = 0.025
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 19 LPYPIIAD--QDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGR 76
L +P+++D +A G V + G+ RAVF+ID +R +++ R
Sbjct: 85 LTFPLLSDFWPHGEVAKAYG----VFDEDLGVAE--RAVFVIDRDGIIRYAWVSDDGEPR 138
Query: 77 NFDEILRVLD 86
+ + LD
Sbjct: 139 DLPDYDEALD 148
>gnl|CDD|184962 PRK15000, PRK15000, peroxidase; Provisional.
Length = 200
Score = 48.5 bits (115), Expect = 6e-07
Identities = 32/104 (30%), Positives = 50/104 (48%), Gaps = 7/104 (6%)
Query: 15 GDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATT 74
G G + Y ++AD R + G +E +G+ L R F+ID +R +
Sbjct: 94 GIGPVKYAMVADVKREIQKAYG----IEHPDEGVAL--RGSFLIDANGIVRHQVVNDLPL 147
Query: 75 GRNFDEILRVLDSLQLTDTKKVATPVDWKVGME-IEVRPGLVSK 117
GRN DE+LR++D+LQ + P W+ G E + P V+K
Sbjct: 148 GRNIDEMLRMVDALQFHEEHGDVCPAQWEKGKEGMNASPDGVAK 191
Score = 40.4 bits (94), Expect = 4e-04
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 184 ILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDW 231
+LF P DFT VC +EL + +EF++R +V+ +S DS H+ W
Sbjct: 38 VLFFWPMDFTFVCPSELIAFDKRYEEFQKRGVEVVGVSFDSEFVHNAW 85
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 49.5 bits (119), Expect = 7e-07
Identities = 23/49 (46%), Positives = 34/49 (69%), Gaps = 1/49 (2%)
Query: 103 KVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLI 151
KVG EIE+RPG+ ++ GK +PI ++IVSL A +++ A PGGL+
Sbjct: 246 KVGDEIEIRPGIKVEE-GGKTKWEPITTKIVSLRAGGEKVEEARPGGLV 293
>gnl|CDD|182423 PRK10382, PRK10382, alkyl hydroperoxide reductase subunit C;
Provisional.
Length = 187
Score = 46.5 bits (110), Expect = 3e-06
Identities = 19/59 (32%), Positives = 30/59 (50%)
Query: 173 ILECSIPAFWGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDW 231
+ E W + F +P+DFT VC TEL V +E ++ V ++S D+ +H W
Sbjct: 24 VTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAW 82
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 45.0 bits (107), Expect = 2e-05
Identities = 22/49 (44%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 103 KVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLI 151
KVG EIE+RPG + + GK +PI++ I SL A +++ A PGGL+
Sbjct: 241 KVGDEIEIRPG-IKVEKGGKTKWEPIYTEITSLRAGGYKVEEARPGGLV 288
>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 = 43.5 bits (103), Expect = 3e-05
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 182 WGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDW 231
W + F +P+DFT VC TEL + E ++ +V ++S D+ H W
Sbjct: 33 WSVFFFYPADFTFVCPTELEDLADNYAELKKLGVEVYSVSTDTHFVHKAW 82
Score = 42.4 bits (100), Expect = 6e-05
Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 21/113 (18%)
Query: 17 GKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLRLSFLYPATTGR 76
GK+ YP++ D L G+L G+ R F+IDP ++ ++ GR
Sbjct: 90 GKITYPMLGDPTGVLTRNFGVLIEEA----GLAD--RGTFVIDPEGVIQAVEIHDNGIGR 143
Query: 77 NFDEILRVLDSLQLTDTKKVAT------PVDWKVGMEIEVRPGLVSKDSEGKL 123
+ E+LR + + Q VA P WK G E ++P L D GK+
Sbjct: 144 DASELLRKIKAAQY-----VAAHPGEVCPAKWKEGAE-TLKPSL---DLVGKI 187
>gnl|CDD|220741 pfam10417, 1-cysPrx_C, C-terminal domain of 1-Cys peroxiredoxin.
This is the C-terminal domain of 1-Cys peroxiredoxin
(1-cysPrx), a member of the peroxiredoxin superfamily
which protect cells against membrane oxidation through
glutathione (GSH)-dependent reduction of phospholipid
hydroperoxides to corresponding alcohols. The C-terminal
domain is crucial for providing the extra cysteine
necessary for dimerisation of the whole molecule. Loss
of the enzyme's peroxidase activity is associated with
oxidation of the catalytic cysteine, upstream of this
domain; and glutathionylation, presumably through its
disruption of protein structure, facilitates access for
GSH, resulting in spontaneous reduction of the mixed
disulfide to the sulfhydryl and consequent activation of
the enzyme. The domain is associated with family
AhpC-TSA, pfam00578, which carries the catalytic
cysteine.
Length = 40
Score = 35.2 bits (82), Expect = 0.001
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 87 SLQLTDTKKVATPVDWKVGMEIEVRP 112
+LQ TD V TP +WK G ++ V P
Sbjct: 1 ALQFTDKHGVVTPANWKPGDKVIVPP 26
>gnl|CDD|239268 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 = 33.1 bits (76), Expect = 0.057
Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 17/70 (24%)
Query: 19 LPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCR-----------------AVFIIDPA 61
LP+P+ AD DR L LG++ + + L VF+I P
Sbjct: 80 LPFPVYADPDRKLYRALGLVRSLPWSNTPRALWKNAAIGFRGNDEGDGLQLPGVFVIGPD 139
Query: 62 KKLRLSFLYP 71
+ + +
Sbjct: 140 GTILFAHVDR 149
Score = 27.7 bits (62), Expect = 4.1
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 194 PVCTTELARVLQLIKEFEQRTCKVIALSCDSVE 226
P C L + +L+ E + +++A+ +S E
Sbjct: 37 PFCREYLRALSKLLPELDALGVELVAVGPESPE 69
>gnl|CDD|219888 pfam08534, Redoxin, Redoxin. This family of redoxins includes
peroxiredoxin, thioredoxin and glutaredoxin proteins.
Length = 142
Score = 30.4 bits (69), Expect = 0.43
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 15 GDGKLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLR 65
L YP++AD+D + G+ + L F+ID K+
Sbjct: 81 AKEGLKYPVLADRDGAFTKAYGLTED-------AGLRTPRYFLIDEDGKVV 124
Score = 30.0 bits (68), Expect = 0.75
Identities = 10/41 (24%), Positives = 21/41 (51%)
Query: 184 ILFSHPSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDS 224
+L P F P C+ E + +L K ++ + V+A++ +
Sbjct: 31 VLNFWPGAFCPTCSAEHPYLEKLSKLYKAKGVDVVAVNASN 71
>gnl|CDD|223750 COG0678, AHP1, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 165
Score = 30.0 bits (68), Expect = 0.69
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 184 ILFSHPSDFTPVCTT-ELARVLQLIKEFEQRTCKVIALSCDSV 225
+LFS P FTP C++ L L+L EF+ + I C SV
Sbjct: 41 VLFSLPGAFTPTCSSSHLPGYLELADEFKAKGVDEIY--CVSV 81
>gnl|CDD|235849 PRK06666, fliM, flagellar motor switch protein FliM; Validated.
Length = 337
Score = 29.4 bits (67), Expect = 2.1
Identities = 26/107 (24%), Positives = 36/107 (33%), Gaps = 34/107 (31%)
Query: 49 PLTCRAVFIIDPAKKLRLSFL-----------YPATTGRNFDEI-LRVLDSL--QLTDTK 94
PL A+ DP L F+ + GR F E R++D + +
Sbjct: 111 PLRGTALIEFDP----SLVFIMVDNLFGGDGRFHTKVGREFTETEQRIIDRILKLAFENL 166
Query: 95 KVATPVDWKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNE 141
K A W + IE V + P F+ IVS NE
Sbjct: 167 KEA----WSSVVPIEPE--YVRSEVN------PQFANIVS----PNE 197
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 29.3 bits (65), Expect = 2.2
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 70 YPATTGRNFDEILRVLDSLQLTDTKKVATPVDWKVGMEIEVRPGLVSKDSEGKLTCKPIF 129
+P G + +L S ++ T +D + G E+E P + G + P
Sbjct: 337 HPGQIGNGYAPVLDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTK 396
Query: 130 SRIVSLFAEQNEL-QFAV 146
+V F+E L +FAV
Sbjct: 397 PMVVETFSEYPPLGRFAV 414
>gnl|CDD|234312 TIGR03686, pupylate_PafA, proteasome accessory factor PafA.
Members of this family are PafA (proteasome accessory
factor A), a protein shown to regulate steady-state
levels of certain proteasome targets in Mycobacterium
tuberculosis. Iyer, et al (2008) suggest that PafA is
the ligase for Pup, a ubiquitin analog attached to an
epsilon-amino group of a Lys side-chain to direct the
target to the proteasome [Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 453
Score = 28.9 bits (65), Expect = 3.1
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 72 ATTGRNFDEILRVLDSLQLTDTKKVATPVDWKV 104
A R D R LD+++ D V T +DW +
Sbjct: 298 AEIERVLDLWGRTLDAIESGDFSAVDTEIDWAI 330
>gnl|CDD|217711 pfam03748, FliL, Flagellar basal body-associated protein FliL.
This FliL protein controls the rotational direction of
the flagella during chemotaxis. FliL is a cytoplasmic
membrane protein associated with the basal body.
Length = 99
Score = 26.7 bits (60), Expect = 4.7
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 233 KALVRDCILGLLINLSVDDFKEVEGRSR 260
L+RD IL LL + + +D EG+ +
Sbjct: 43 MPLIRDAILLLLSSKTAEDLSTPEGKEK 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 = 26.8 bits (60), Expect = 6.4
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 12/48 (25%)
Query: 18 KLPYPIIADQDRSLAVQLGMLDPVEKDSKGMPLTCRAVFIIDPAKKLR 65
+ +P++ D D LA G +G+P T F+ID ++R
Sbjct: 76 GITFPVLLDPDGELAKAYG--------VRGLPTT----FLIDRDGRIR 111
>gnl|CDD|224766 COG1853, COG1853, Conserved protein/domain typically associated
with flavoprotein oxygenases, DIM6/NTAB family [General
function prediction only].
Length = 176
Score = 27.3 bits (61), Expect = 7.4
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 144 FAVPGGLIDRFAAALLPGCSLLGC---QASLVILECSI 178
FA G D+FA A L +G +L LEC +
Sbjct: 86 FAGSGPGEDKFAGAGLTLVEKVGAPILAEALAWLECRV 123
>gnl|CDD|212674 cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of
Saccharmomyces cerevisiae Ssz1pp and similar proteins.
Saccharomyces cerevisiae Ssz1p (also known as
/Pdr13p/YHR064C) belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly and can direct incompetent "client"
proteins towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). Some
family members are not chaperones but rather, function
as NEFs for their Hsp70 partners, while other family
members function as both chaperones and NEFs. Ssz1 does
not function as a chaperone; it facilitates the
interaction between the HSP70 Ssb protein and its
partner J-domain protein Zuo1 (also known as zuotin) on
the ribosome. Ssz1 is found in a stable heterodimer
(called RAC, ribosome associated complex) with Zuo1.
Zuo1 can only stimulate the ATPase activity of Ssb, when
it is in complex with Ssz1. Ssz1 binds ATP but neither
nucleotide-binding, hydrolysis, or its SBD, is needed
for its in vivo function.
Length = 386
Score = 27.7 bits (62), Expect = 7.9
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 183 GILFSHPSDFTPVCTTELAR--------VLQLIKE 209
G + S P+ F+ T L + VLQLI E
Sbjct: 139 GAVLSVPTWFSDEQTEALVKAAEAAGLPVLQLIPE 173
>gnl|CDD|225859 COG3322, COG3322, Predicted periplasmic ligand-binding sensor
domain [Signal transduction mechanisms].
Length = 295
Score = 27.3 bits (61), Expect = 8.5
Identities = 26/134 (19%), Positives = 42/134 (31%), Gaps = 36/134 (26%)
Query: 55 VFIIDPAKKLRLSFLYPATTGRN---FDEIL-RVLDSLQLTDTKKVATPVDWKVG-MEIE 109
VF++DP+ KL S L T + +L + L ++V G + ++
Sbjct: 107 VFVVDPSGKLVYSKLVDQETATELPLPESLLEDIRRIGALLTRERVDEI---ISGLVLLD 163
Query: 110 VRPGLVS----KDSEGKLTCKP--IFSRIVSLFAEQNELQFAVPGGLIDRFAAALLPGCS 163
P ++S S + K IF R D +
Sbjct: 164 NGPAIISARPILTSTDEGPAKGTLIFGRKF-----------------DDSLLNSF----- 201
Query: 164 LLGCQASLVILECS 177
LLG Q + L
Sbjct: 202 LLGTQYDIENLRAP 215
>gnl|CDD|151399 pfam10952, DUF2753, Protein of unknown function (DUF2753). This
bacterial family of proteins has no known function.
Length = 140
Score = 26.6 bits (59), Expect = 9.6
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 157 ALLPGCSLLGCQASLVILECSIPAFWGILFSHPSDFTPVCTTELARVLQLIKEFEQRTCK 216
L+P C C++ + L C A L HP+ E+AR +Q I Q C+
Sbjct: 82 TLIPQCPNTECESFIDSLGCCQSALIDFLKRHPN-------PEIARQIQHIDTTSQ--CE 132
Query: 217 VIA 219
+IA
Sbjct: 133 LIA 135
>gnl|CDD|220906 pfam10926, DUF2800, Protein of unknown function (DUF2800). This is
a family of uncharacterized proteins found in bacteria
and viruses. Some members of this family are annotated
as being Phi APSE P51-like proteins.
Length = 363
Score = 27.3 bits (61), Expect = 9.6
Identities = 19/74 (25%), Positives = 25/74 (33%), Gaps = 23/74 (31%)
Query: 189 PSDFTPVCTTELARVLQLIKEFEQRTCKVIALSCDSVESHHDWIKALVRDCILGLLIN-L 247
D T ELA +L+ E+ VE++ L N
Sbjct: 243 TLDLTD---EELAELLEKADLLEKW--------AKDVEAY-----------ALDEARNGK 280
Query: 248 SVDDFKEVEGRSRR 261
V +K VEGRS R
Sbjct: 281 EVPGYKLVEGRSNR 294
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
0.323 0.140 0.423
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,114,158
Number of extensions: 1341576
Number of successful extensions: 1077
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1057
Number of HSP's successfully gapped: 65
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)