RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1180
(140 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 = 166 bits (424), Expect = 1e-53
Identities = 67/137 (48%), Positives = 92/137 (67%), Gaps = 13/137 (9%)
Query: 1 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKL 60
DI+ Y + PF II D +R++A L ++D + + L TVRAV+II PD+K++L
Sbjct: 79 DIEEYT---GVEIPFPIIADPDREVAKLLGMIDPDAGSTL----TVRAVFIIDPDKKIRL 131
Query: 61 SIVYPASTGRSVDEILRVLDSLQLFYKNNTVVTPANWKPGDKVMIHPAVKDDELPKLFPK 120
+ YPA+TGR+ DEILRV+D+LQL K+ V TPANWKPGD V++ P+V D+E K FPK
Sbjct: 132 ILYYPATTGRNFDEILRVVDALQLTDKHK-VATPANWKPGDDVIVPPSVSDEEAKKKFPK 190
Query: 121 GVDIVDMPSGVSYVRFT 137
G + VD Y+RFT
Sbjct: 191 GYETVDW-----YLRFT 202
>gnl|CDD|223527 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 108 bits (271), Expect = 2e-30
Identities = 38/106 (35%), Positives = 56/106 (52%), Gaps = 7/106 (6%)
Query: 11 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 70
G F +I D ++A +L E + +R +II PD ++ +V P + GR
Sbjct: 95 GKIKFPMIADPKGEIARAYGVLHPE------EGLALRGTFIIDPDGVIRHILVNPLTIGR 148
Query: 71 SVDEILRVLDSLQLFYKNNTVVTPANWKPGDKVMIHPAVKDDELPK 116
+VDEILRV+D+LQ K+ V PANWKPGDK + + L +
Sbjct: 149 NVDEILRVIDALQFVAKHG-EVCPANWKPGDKTIKPSPDLGEYLKE 193
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 88.4 bits (219), Expect = 9e-23
Identities = 40/102 (39%), Positives = 64/102 (62%), Gaps = 7/102 (6%)
Query: 12 DFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRS 71
PF +I D +++LA + +L+DE + TVR V+II P++ ++ I YPA TGR+
Sbjct: 89 KIPFPVIADIDKELAREYNLIDENSGA------TVRGVFIIDPNQIVRWMIYYPAETGRN 142
Query: 72 VDEILRVLDSLQLFYKNNTVVTPANWKPGDKVMIHPAVKDDE 113
+DEI+R+ +LQ+ +K V TPANW+PG + ++ DE
Sbjct: 143 IDEIIRITKALQVNWKRK-VATPANWQPGQEGIVPAPSTLDE 183
>gnl|CDD|237297 PRK13189, PRK13189, peroxiredoxin; Provisional.
Length = 222
Score = 88.5 bits (220), Expect = 1e-22
Identities = 39/101 (38%), Positives = 57/101 (56%), Gaps = 10/101 (9%)
Query: 12 DFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRS 71
+ F II D+ ++A KL ++ N TVRAV+II P ++ + YP GR+
Sbjct: 97 EIEFPIIADDRGEIAKKLGMISPGKGTN-----TVRAVFIIDPKGIIRAILYYPQEVGRN 151
Query: 72 VDEILRVLDSLQLFYKNNTVVTPANWKPG----DKVMIHPA 108
+DEILR++ +LQ + V TPANW P DKV++ PA
Sbjct: 152 MDEILRLVKALQTSDEKG-VATPANWPPNDLIKDKVIVPPA 191
>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 = 71.8 bits (177), Expect = 1e-16
Identities = 34/90 (37%), Positives = 47/90 (52%), Gaps = 7/90 (7%)
Query: 11 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 70
G F ++ D + ++ +LDEE L R +II P+ ++ V GR
Sbjct: 91 GKINFPLLADPKKKISRDYGVLDEEEGVAL------RGTFIIDPEGIIRHITVNDLPVGR 144
Query: 71 SVDEILRVLDSLQLFYKNNTVVTPANWKPG 100
SVDE LRVLD+LQ ++ V PANWKPG
Sbjct: 145 SVDETLRVLDALQFVEEHGEVC-PANWKPG 173
>gnl|CDD|183885 PRK13191, PRK13191, putative peroxiredoxin; Provisional.
Length = 215
Score = 70.3 bits (172), Expect = 9e-16
Identities = 44/114 (38%), Positives = 67/114 (58%), Gaps = 14/114 (12%)
Query: 8 DIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPAS 67
++K + PF II D ++A +L ++ E+ TVRAV+I+ ++L + YP
Sbjct: 91 NLKVEVPFPIIADPMGNVAKRLGMIHAESSTA-----TVRAVFIVDDKGTVRLILYYPME 145
Query: 68 TGRSVDEILRVLDSLQLFYKNNTVVTPANWKP----GDKVMIHPA---VKDDEL 114
GR++DEILR + +LQL K VVTPANW GDK +I+PA +KD ++
Sbjct: 146 IGRNIDEILRAIRALQLVDKAG-VVTPANWPNNELIGDK-VINPAPRTIKDAKM 197
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 58.8 bits (142), Expect = 1e-11
Identities = 30/94 (31%), Positives = 49/94 (52%), Gaps = 7/94 (7%)
Query: 11 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 70
G ++ D+ + +A +L+EE + R ++II P L+ V GR
Sbjct: 98 GTMAIPMLADKTKSIARSYGVLEEEQ------GVAYRGLFIIDPKGMLRQITVNDMPVGR 151
Query: 71 SVDEILRVLDSLQLFYKNNTVVTPANWKPGDKVM 104
+V+E+LR+L++ Q F + + V PANWK GD M
Sbjct: 152 NVEEVLRLLEAFQ-FVEKHGEVCPANWKKGDPTM 184
>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 = 54.1 bits (131), Expect = 3e-11
Identities = 20/41 (48%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 81 SLQLFYKNNTVVTPANWKPGDKVMIHPAVKDDELPKLFPKG 121
+LQ K+ VVTPANWKPGDKV++ P ++E K + +G
Sbjct: 1 ALQFTDKHG-VVTPANWKPGDKVIVPPPPTEEEAVKRYLEG 40
>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 = 54.1 bits (131), Expect = 4e-10
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 11 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 70
G F ++ D + + A +L E++ + RA +II PD K++ V P TGR
Sbjct: 78 GGLNFPLLSDPDGEFAKAYGVLIEKSAGGG---LAARATFIIDPDGKIRYVEVEPLPTGR 134
Query: 71 SVDEIL 76
+ +E+L
Sbjct: 135 NAEELL 140
>gnl|CDD|106544 PRK13599, PRK13599, putative peroxiredoxin; Provisional.
Length = 215
Score = 49.3 bits (117), Expect = 5e-08
Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 8/101 (7%)
Query: 14 PFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVD 73
PF +I D+ ++ +L ++ N TVRAV+I+ ++L + YP GR+VD
Sbjct: 92 PFPVIADDLGKVSNQLGMIHPGKGTN-----TVRAVFIVDDKGTIRLIMYYPQEVGRNVD 146
Query: 74 EILRVLDSLQLFYKNNTVVT---PANWKPGDKVMIHPAVKD 111
EILR L +LQ + + P N+ D V++ P+ +
Sbjct: 147 EILRALKALQTADQYGVALPEKWPNNYLIKDHVIVPPSTDE 187
>gnl|CDD|173427 PTZ00137, PTZ00137, 2-Cys peroxiredoxin; Provisional.
Length = 261
Score = 48.4 bits (115), Expect = 2e-07
Identities = 30/90 (33%), Positives = 45/90 (50%), Gaps = 8/90 (8%)
Query: 15 FAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVDE 74
F + D +R+++ LL +E + RA ++ +K VY GRSVDE
Sbjct: 164 FPLFSDISREVSKSFGLLRDE-------GFSHRASVLVDKAGVVKHVAVYDLGLGRSVDE 216
Query: 75 ILRVLDSLQLFYKNNTVVTPANWKPGDKVM 104
LR+ D++Q F + V P NWK GD+ M
Sbjct: 217 TLRLFDAVQ-FAEKTGNVCPVNWKQGDQAM 245
>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 = 45.9 bits (109), Expect = 6e-07
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 15 FAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVDE 74
+ ++GD L +L EE + R ++I P+ ++ ++ GR E
Sbjct: 94 YPMLGDPTGVLTRNFGVLIEE------AGLADRGTFVIDPEGVIQAVEIHDNGIGRDASE 147
Query: 75 ILRVLDSLQLFYKNNTVVTPANWKPGDK 102
+LR + + Q + V PA WK G +
Sbjct: 148 LLRKIKAAQYVAAHPGEVCPAKWKEGAE 175
>gnl|CDD|184962 PRK15000, PRK15000, peroxidase; Provisional.
Length = 200
Score = 42.7 bits (100), Expect = 1e-05
Identities = 23/94 (24%), Positives = 50/94 (53%), Gaps = 7/94 (7%)
Query: 11 GDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGR 70
G +A++ D R++ + + + + +R ++I + ++ +V GR
Sbjct: 96 GPVKYAMVADVKREIQKAYGI------EHPDEGVALRGSFLIDANGIVRHQVVNDLPLGR 149
Query: 71 SVDEILRVLDSLQLFYKNNTVVTPANWKPGDKVM 104
++DE+LR++D+LQ F++ + V PA W+ G + M
Sbjct: 150 NIDEMLRMVDALQ-FHEEHGDVCPAQWEKGKEGM 182
>gnl|CDD|182423 PRK10382, PRK10382, alkyl hydroperoxide reductase subunit C;
Provisional.
Length = 187
Score = 35.3 bits (81), Expect = 0.004
Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 8 DIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPAS 67
+ +A+IGD L D + E+ + RA +++ P ++ V
Sbjct: 87 ETIAKIKYAMIGDPTGALTRNFDNMREDE------GLADRATFVVDPQGIIQAIEVTAEG 140
Query: 68 TGRSVDEILRVLDSLQLFYKNNTVVTPANWKPGDKVM 104
GR ++LR + + Q + V PA WK G+ +
Sbjct: 141 IGRDASDLLRKIKAAQYVASHPGEVCPAKWKEGEATL 177
>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 = 33.7 bits (78), Expect = 0.012
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 10 KGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTG 69
K PF ++ D + LA + E+ K + R+ ++I PD K+
Sbjct: 77 KYGLPFPLLSDPDGKLAKAYGVWGEKKK---KYMGIERSTFLIDPDGKIVKVW-RKVKPK 132
Query: 70 RSVDEILR 77
+E+L
Sbjct: 133 GHAEEVLE 140
>gnl|CDD|224146 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 33.4 bits (77), Expect = 0.014
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 10 KGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTG 69
K F ++ DE+ ++A + E+ E R+ ++I PD K++ G
Sbjct: 84 KHGLTFPLLSDEDGEVAEAYGVWGEKKMYGKEYMGIERSTFVIDPDGKIRYVWRKVKVKG 143
Query: 70 RSVDEILRVLDSLQ 83
DE+L L L
Sbjct: 144 -HADEVLAALKKLA 156
>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 = 31.8 bits (73), Expect = 0.040
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 1 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYIIGPDRKLK 59
K + + FP ++ D + ++A +L+EE + +R ++I PD K++
Sbjct: 72 SHKKFAEKLGLPFP--LLSDPDGEVAKAYGVLNEE------EGLALRTTFVIDPDGKIR 122
>gnl|CDD|183050 PRK11241, gabD, succinate-semialdehyde dehydrogenase I;
Provisional.
Length = 482
Score = 28.7 bits (64), Expect = 0.90
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 1 DIKNYCLDIKGDFPFAIIGDENRDLAVKLDLLDEENKNNLETAITVRAVYI 51
DIK L++ G+ PF + D + D AV+ L + +N +T + +Y+
Sbjct: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGALA-SKFRNAGQTCVCANRLYV 297
>gnl|CDD|212118 cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins
from bacteria. This subfamily contains many
hypothetical proteins, and belongs to the YdjC-like
family of uncharacterized proteins from bacteria. The
YdjC-family is represented by an uncharacterised protein
YdjC (also known as ChbG) encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon in Escherichia coli, which encodes enzymes
involved in growth on an N,N'-diacetylchitobiose carbon
source. The molecular function of this subfamily is
unclear.
Length = 251
Score = 28.0 bits (63), Expect = 1.4
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 98 KPGDKVMIHPAVKDDELPKLFP 119
G +M HP + D+EL P
Sbjct: 215 GDGPLIMCHPGLPDEELSAADP 236
>gnl|CDD|176208 cd08246, crotonyl_coA_red, crotonyl-CoA reductase. Crotonyl-CoA
reductase, a member of the medium chain
dehydrogenase/reductase family, catalyzes the
NADPH-dependent conversion of crotonyl-CoA to
butyryl-CoA, a step in (2S)-methylmalonyl-CoA
production for straight-chain fatty acid biosynthesis.
Like enoyl reductase, another enzyme in fatty acid
synthesis, crotonyl-CoA reductase is a member of the
zinc-dependent alcohol dehydrogenase-like medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 393
Score = 28.2 bits (63), Expect = 1.5
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 96 NWKPGDKVMIHPAVKDDELP 115
NWK GD+V++H +V D P
Sbjct: 102 NWKVGDEVVVHCSVWDGNDP 121
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.2 bits (59), Expect = 6.3
Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 8/52 (15%)
Query: 28 KLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVDEILRVL 79
K+DLLDEE E +S A TG +DE+LR L
Sbjct: 280 KIDLLDEEE----EREKRAALELAALGGPVFLIS----AVTGEGLDELLRAL 323
>gnl|CDD|176212 cd08250, Mgc45594_like, Mgc45594 gene product and other MDR family
members. Includes Human Mgc45594 gene product of
undetermined function. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 26.1 bits (58), Expect = 7.2
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 111 DDELPKLFPKGVDIV 125
+ L K +PKGVD+V
Sbjct: 197 GEVLKKEYPKGVDVV 211
>gnl|CDD|223040 PHA03311, PHA03311, helicase-primase subunit BBLF4; Provisional.
Length = 782
Score = 26.4 bits (59), Expect = 7.4
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 53 GPDRKLKLSIVYPASTGRSVD-EILRV-LDSLQLFYKNNTVVTP 94
G + LKLS VY A + R L + L+ L+ Y+ +TV++
Sbjct: 725 GNHKNLKLSHVYVAMS-RVTSSNFLVMNLNPLREPYERDTVISE 767
>gnl|CDD|173333 PTZ00036, PTZ00036, glycogen synthase kinase; Provisional.
Length = 440
Score = 26.2 bits (57), Expect = 7.4
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 64 YPASTGRS-VDEILRVLDSLQLFYKNNTVVTPANWKPGDKVMIHPAVKDDELPKLFPKG 121
YP +G+S VD+++R++ L ++ N+ + P VK +L K+FPKG
Sbjct: 268 YPIFSGQSSVDQLVRIIQVLGTPTEDQLKEMNPNYAD----IKFPDVKPKDLKKVFPKG 322
>gnl|CDD|132286 TIGR03242, arg_catab_astE, succinylglutamate desuccinylase.
Members of this protein family are succinylglutamate
desuccinylase, the fifth and final enzyme of the
arginine succinyltransferase (AST) pathway for arginine
catabolism. This model excludes the related protein
aspartoacylase [Energy metabolism, Amino acids and
amines].
Length = 319
Score = 26.2 bits (58), Expect = 7.5
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 43 AITVRAVYIIGPDRKLKLSIVYPASTGRSVDEILRVLDSLQLFYKNNTV 91
AIT A+ + D + P R V I + DS +L ++T+
Sbjct: 226 AIT-SALRALISDEAIPARRTDPLRLFRVVSSITKHSDSFELHVASDTL 273
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 25.6 bits (57), Expect = 8.5
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 28 KLDLLDEENKNNLETAITVRAVYIIGPDRKLKLSIVYPASTGRSVDEILRVLDSLQ 83
K DL+DE+ +E I + + V + TG ++E+ LD L
Sbjct: 112 KADLVDEDRLELVEEEI--LELLAGTFLADAPIFPV-SSVTGEGIEELKNYLDELA 164
>gnl|CDD|188173 TIGR01852, lipid_A_lpxA,
acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine
O-acyltransferase. This model describes LpxA, an
enzyme for the biosynthesis of lipid A, a component
oflipopolysaccharide (LPS) in the outer membrane outer
leaflet of most Gram-negative bacteria. Some
differences are found between lipid A of different
species, but this protein represents the first step
(from UDP-N-acetyl-D-glucosamine) and appears to be
conserved in function. Proteins from this family
contain many copies of the bacterial transferase
hexapeptide repeat (pfam00132) [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 254
Score = 25.7 bits (57), Expect = 8.8
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 13 FPFAIIGDENRDLAVK 28
FP A+IG +DL K
Sbjct: 56 FPGAVIGGVPQDLKYK 71
>gnl|CDD|223973 COG1043, LpxA, Acyl-[acyl carrier protein].
Length = 260
Score = 25.6 bits (57), Expect = 9.4
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 13 FPFAIIGDENRDL 25
FPFA IG++ +DL
Sbjct: 61 FPFASIGEDPQDL 73
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 0.141 0.412
Gapped
Lambda K H
0.267 0.0800 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,355,897
Number of extensions: 668412
Number of successful extensions: 788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 770
Number of HSP's successfully gapped: 51
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.4 bits)