RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13064
(192 letters)
>gnl|CDD|191168 pfam05026, DCP2, Dcp2, box A domain. This domain is always found
to the amino terminal side of pfam00293. This domain is
specific to mRNA decapping protein 2 and this region
has been termed Box A. Removal of the cap structure is
catalyzed by the Dcp1-Dcp2 complex.
Length = 85
Score = 112 bits (282), Expect = 8e-33
Identities = 38/85 (44%), Positives = 52/85 (61%)
Query: 13 KDILDDLSSRFVINIPHEERGDVIRICFQMELAYWFYLDFYCTQDESLFKAGLKEFFFQM 72
DILDDL RF+IN+P EE V R+CFQ+E A+WFY DFY + SL L++F Q+
Sbjct: 1 DDILDDLCVRFIINLPEEELSSVERVCFQIEEAHWFYEDFYRPLNPSLPSLSLRDFAQQI 60
Query: 73 FHHIPSLTHFARKIDTVLDDWRHYK 97
F H P L + + L+ ++ YK
Sbjct: 61 FEHCPLLWKWKEDHEEALEKFKRYK 85
>gnl|CDD|239644 cd03672, Dcp2p, mRNA decapping enzyme 2 (Dcp2p), the catalytic
subunit, and Dcp1p are the two components of the
decapping enzyme complex. Decapping is a key step in
both general and nonsense-mediated 5'->3' mRNA-decay
pathways. Dcp2p contains an all-alpha helical N-terminal
domain and a C-terminal domain which has the Nudix fold.
While decapping is not dependent on the N-terminus of
Dcp2p, it does affect its efficiency. Dcp1p binds the
N-terminal domain of Dcp2p stimulating the decapping
activity of Dcp2p. Decapping permits the degradation of
the transcript and is a site of numerous control inputs.
It is responsible for nonsense-mediated decay as well as
AU-rich element (ARE)-mediated decay. In addition, it
may also play a role in the levels of mRNA. Enzymes
belonging to the Nudix superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity and are
recognized by a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V).
Length = 145
Score = 83.1 bits (206), Expect = 1e-20
Identities = 25/50 (50%), Positives = 38/50 (76%), Gaps = 1/50 (2%)
Query: 136 VPTFGAILIDKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
+P +GAI++++ L +VLLV+ + ++ SW FPKGK+N+DE CAIREV
Sbjct: 1 IPVYGAIILNEDLDKVLLVKGWKSK-SWSFPKGKINKDEDDHDCAIREVY 49
>gnl|CDD|239217 cd02883, Nudix_Hydrolase, Nudix hydrolase is a superfamily of
enzymes found in all three kingdoms of life, and it
catalyzes the hydrolysis of NUcleoside DIphosphates
linked to other moieties, X. Enzymes belonging to this
superfamily require a divalent cation, such as Mg2+ or
Mn2+ for their activity. Members of this family are
recognized by a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which forms a
structural motif that functions as a metal binding and
catalytic site. Substrates of nudix hydrolase include
intact and oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
and "house-cleaning" enzymes. Substrate specificity is
used to define child families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required. This
superfamily consists of at least nine families: IPP
(isopentenyl diphosphate) isomerase, ADP ribose
pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A
pyrophosphatase,
MTH1-7,8-dihydro-8-oxoguanine-triphosphatase,
diadenosine tetraphosphate hydrolase, NADH
pyrophosphatase, GDP-mannose hydrolase and the
c-terminal portion of the mutY adenine glycosylase.
Length = 123
Score = 44.8 bits (106), Expect = 2e-06
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 140 GAILIDKSLTQVLLVQ-SFFARASWGFPKGKVNQDEPPMTCAIREVK 185
GA+++D +VLLV+ + W P G V E AIREV+
Sbjct: 4 GAVILD-EDGRVLLVRRADSPGGLWELPGGGVEPGETLEEAAIREVR 49
>gnl|CDD|215841 pfam00293, NUDIX, NUDIX domain.
Length = 133
Score = 44.0 bits (104), Expect = 4e-06
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 137 PTFGAILIDKSLTQVLLVQ---SFFARASWGFPKGKVNQDEPPMTCAIREVK 185
G +L+++ +VLLV+ W P GKV E P A+RE++
Sbjct: 3 RAVGVVLLNED-GEVLLVRRSRPPVFPGLWELPGGKVEPGESPEEAAVRELE 53
>gnl|CDD|239520 cd03428, Ap4A_hydrolase_human_like, Diadenosine tetraphosphate
(Ap4A) hydrolase is a member of the Nudix hydrolase
superfamily. Ap4A hydrolases are well represented in a
variety of prokaryotic and eukaryotic organisms.
Phylogenetic analysis reveals two distinct subgroups
where plant enzymes fall into one subfamily and
fungi/animals/archaea enzymes, represented by this
subfamily, fall into another. Bacterial enzymes are
found in both subfamilies. Ap4A is a potential
by-product of aminoacyl tRNA synthesis, and accumulation
of Ap4A has been implicated in a range of biological
events, such as DNA replication, cellular
differentiation, heat shock, metabolic stress, and
apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically
into ATP and AMP. It is important in the invasive
properties of bacteria and thus presents a potential
target for inhibition of such invasive bacteria. Besides
the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U
is Ile, Leu, or Val) that functions as a metal binding
and catalytic site, and a required divalent cation, Ap4A
hydrolase is structurally similar to the other members
of the nudix superfamily with some degree of variation.
Several regions in the sequences are poorly defined and
substrate and metal binding sites are only predicted
based on kinetic studies.
Length = 130
Score = 43.0 bits (102), Expect = 1e-05
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 139 FGAILI--DKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
GAI+ + + LL+Q+ + W FPKG V E + A+RE +
Sbjct: 5 AGAIIYRRLNNEIEYLLLQA--SYGHWDFPKGHVEPGEDDLEAALRETE 51
>gnl|CDD|223568 COG0494, MutT, NTP pyrophosphohydrolases including oxidative damage
repair enzymes [DNA replication, recombination, and
repair / General function prediction only].
Length = 161
Score = 43.3 bits (101), Expect = 1e-05
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 141 AILIDKSLTQVLLVQSFFARASWGFPKGKVNQDE-PPMTCAIREVK 185
++ +VLL Q W P GKV E P A RE++
Sbjct: 16 VLVGRDGPGEVLLAQRRDDGGLWELPGGKVEPGEELPEEAAARELE 61
>gnl|CDD|239645 cd03673, Ap6A_hydrolase, Diadenosine hexaphosphate (Ap6A) hydrolase
is a member of the Nudix hydrolase superfamily. Ap6A
hydrolase specifically hydrolyzes diadenosine
polyphosphates, but not ATP or diadenosine triphosphate,
and it generates ATP as the product. Ap6A, the most
preferred substrate, hydrolyzes to produce two ATP
molecules, which is a novel hydrolysis mode for Ap6A.
These results indicate that Ap6A hydrolase is a
diadenosine polyphosphate hydrolase. It requires the
presence of a divalent cation, such as Mn2+, Mg2+, Zn2+,
and Co2+, for activity. Members of the Nudix superfamily
are recognized by a highly conserved 23-residue nudix
motif (GX5EX7REUXEEXGU, where U = I, L or V), which
forms a structural motif that functions as a metal
binding and catalytic site.
Length = 131
Score = 39.9 bits (94), Expect = 1e-04
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 140 GAILIDKSLTQ--VLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
G ++ S VLL+ W PKGK+ E P A+REV+
Sbjct: 5 GGVVFRGSDGGIEVLLI-HRPRGDDWSLPKGKLEPGETPPEAAVREVE 51
>gnl|CDD|240030 cd04673, Nudix_Hydrolase_15, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 122
Score = 39.5 bits (93), Expect = 1e-04
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 140 GAILIDKSLTQVLLVQSFFARA------SWGFPKGKVNQDEPPMTCAIREVK 185
GA++ +VLLV+ RA W FP GKV E A+RE+
Sbjct: 4 GAVVFRGG--RVLLVR----RANPPDAGLWSFPGGKVELGETLEQAALRELL 49
>gnl|CDD|239516 cd03424, ADPRase_NUDT5, ADP-ribose pyrophosphatase (ADPRase)
catalyzes the hydrolysis of ADP-ribose and a variety of
additional ADP-sugar conjugates to AMP and
ribose-5-phosphate. Like other members of the Nudix
hydrolase superfamily, it requires a divalent cation,
such as Mg2+, for its activity. It also contains a
highly conserved 23-residue Nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V) which functions
as a metal binding site/catalytic site. In addition to
the Nudix motif, there are additional conserved amino
acid residues, distal from the signature sequence, that
correlate with substrate specificity. In humans, there
are four distinct ADPRase activities, three putative
cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single
mitochondrial enzyme (ADPRase-m). Human ADPRase-II is
also referred to as NUDT5. It lacks the N-terminal
target sequence unique to mitochondrial ADPRase. The
different cytosolic types are distinguished by their
specificities for substrate and specific requirement for
metal ions. NUDT5 forms a homodimer.
Length = 137
Score = 39.8 bits (94), Expect = 2e-04
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 140 GAILIDKSLTQVLLVQSF---FARASWGFPKGKVNQDEPPMTCAIREVK 185
+ D +V+LV+ + P G ++ E P A RE++
Sbjct: 6 AVLPYDDD-GKVVLVRQYRPPVGGWLLELPAGLIDPGEDPEEAARRELE 53
>gnl|CDD|239519 cd03427, MTH1, MutT homolog-1 (MTH1) is a member of the Nudix
hydrolase superfamily. MTH1, the mammalian counterpart
of MutT, hydrolyzes oxidized purine nucleoside
triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to
monophosphates, thereby preventing the incorporation of
such oxygen radicals during replication. This is an
important step in the repair mechanism in genomic and
mitochondrial DNA. Like other members of the Nudix
family, it requires a divalent cation, such as Mg2+ or
Mn2+, for activity, and contain the Nudix motif, a
highly conserved 23-residue block (GX5EX7REUXEEXGU,
where U = I, L or V), that functions as a metal binding
and catalytic site. MTH1 is predominantly localized in
the cytoplasm and mitochondria. Structurally, this
enzyme adopts a similar fold to MutT despite low
sequence similarity outside the conserved nudix motif.
The most distinctive structural difference between MutT
and MTH1 is the presence of a beta-hairpin, which is
absent in MutT. This results in a much deeper and
narrower substrate binding pocket. Mechanistically, MTH1
contains dual specificity for nucleotides that contain
2-OH-adenine bases and those that contain 8-oxo-guanine
bases.
Length = 137
Score = 38.7 bits (91), Expect = 4e-04
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 142 ILIDKSLTQVLLV--QSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
+ K +VLL+ + W P GKV E P CAIRE+K
Sbjct: 5 LCFIKDPDKVLLLNRKKGPGWGGWNGPGGKVEPGETPEECAIRELK 50
>gnl|CDD|223979 COG1051, COG1051, ADP-ribose pyrophosphatase [Nucleotide transport
and metabolism].
Length = 145
Score = 38.5 bits (90), Expect = 5e-04
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 12/61 (19%)
Query: 131 HYKQSVPTFGAILIDKSLTQVLLVQSFFARAS------WGFPKGKVNQDEPPMTCAIREV 184
Y+ + GA+++ ++LLV+ RA+ W P G V E A RE+
Sbjct: 5 GYRTPLVAVGALIVRN--GRILLVR----RANEPGAGYWALPGGFVEIGETLEEAARREL 58
Query: 185 K 185
K
Sbjct: 59 K 59
>gnl|CDD|163260 TIGR03432, yjhG_yagF, putative dehydratase, YjhG/YagF family. This
homolog of dihydroxy-acid dehydratases has an odd,
sparse distribution. Members are found in two
Acidobacteria, two Planctomycetes, Bacillus clausii
KSM-K16, and (in two copies each) in strains K12-MG1655
and W3110 of Escherichia coli. The local context is not
well conserved, but a few members are adjacent to
homologs of the gluconate:H+ symporter (see TIGR00791)
[Unknown function, Enzymes of unknown specificity].
Length = 640
Score = 34.8 bits (80), Expect = 0.025
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 75 HIPSLTHFA-RKIDTVLDDWRHYKQSVPTF 103
HIP++ H A + TV DDW + VP
Sbjct: 309 HIPAIAHAAGCRRPTV-DDWTRINRKVPRL 337
>gnl|CDD|240024 cd04666, Nudix_Hydrolase_9, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 122
Score = 33.0 bits (76), Expect = 0.028
Identities = 19/50 (38%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 139 FGAI--LIDKSLTQVLLVQSFFARAS--WGFPKGKVNQDEPPMTCAIREV 184
GAI +VLLV S R + W PKG +DE P A RE
Sbjct: 3 AGAIPYRETGGEVEVLLVTS---RRTGRWIVPKGGPEKDESPAEAAAREA 49
>gnl|CDD|239643 cd03671, Ap4A_hydrolase_plant_like, Diadenosine tetraphosphate
(Ap4A) hydrolase is a member of the Nudix hydrolase
superfamily. Members of this family are well represented
in a variety of prokaryotic and eukaryotic organisms.
Phylogenetic analysis reveals two distinct subgroups
where plant enzymes fall into one group (represented by
this subfamily) and fungi/animals/archaea enzymes fall
into another. Bacterial enzymes are found in both
subfamilies. Ap4A is a potential by-product of aminoacyl
tRNA synthesis, and accumulation of Ap4A has been
implicated in a range of biological events, such as DNA
replication, cellular differentiation, heat shock,
metabolic stress, and apoptosis. Ap4A hydrolase cleaves
Ap4A asymmetrically into ATP and AMP. It is important in
the invasive properties of bacteria and thus presents a
potential target for the inhibition of such invasive
bacteria. Besides the signature nudix motif
(G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A
hydrolase is structurally similar to the other members
of the nudix superfamily with some degree of variations.
Several regions in the sequences are poorly defined and
substrate and metal binding sites are only predicted
based on kinetic studies.
Length = 147
Score = 32.9 bits (76), Expect = 0.035
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 132 YKQSVPTFGAILIDKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
Y+ +V G +L ++ +V + + +W FP+G +++ E P A+RE++
Sbjct: 2 YRPNV---GVVLFNEDG-KVFVGRRIDTPGAWQFPQGGIDEGEDPEQAALRELE 51
>gnl|CDD|240032 cd04676, Nudix_Hydrolase_17, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 129
Score = 32.7 bits (75), Expect = 0.038
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 136 VPTFGAILIDKSLTQVLLVQSFFARAS---WGFPKGKVNQDEPPMTCAIREVK 185
+P A++ D +VLL++ R+ W P G V E P A+REV+
Sbjct: 2 LPGVTAVVRD-DEGRVLLIR----RSDNGLWALPGGAVEPGESPADTAVREVR 49
>gnl|CDD|240046 cd04690, Nudix_Hydrolase_31, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 118
Score = 31.9 bits (73), Expect = 0.069
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 141 AILIDKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
A+++ + +VLLV+ + P GK+ E P+ IRE+
Sbjct: 5 ALILVRD-GRVLLVRKR-GTDVFYLPGGKIEAGETPLQALIRELS 47
>gnl|CDD|240052 cd04696, Nudix_Hydrolase_37, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 125
Score = 32.0 bits (73), Expect = 0.073
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 136 VPTFGAILIDKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
+ T GA LI ++LLV++ R WG P GKV E RE +
Sbjct: 2 LVTVGA-LIYAPDGRILLVRTTKWRGLWGVPGGKVEWGETLEEALKREFR 50
>gnl|CDD|226604 COG4119, COG4119, Predicted NTP pyrophosphohydrolase [DNA
replication, recombination, and repair / General
function prediction only].
Length = 161
Score = 31.8 bits (72), Expect = 0.13
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 151 VLLVQS---FFAR---ASWGFPKGKVNQDEPPMTCAIRE 183
VLLV F+A +W PKG+ E P A RE
Sbjct: 20 VLLVHPGGPFWAGKDDGAWSIPKGEYTGGEDPWLAARRE 58
>gnl|CDD|240036 cd04680, Nudix_Hydrolase_21, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 120
Score = 30.7 bits (70), Expect = 0.18
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 150 QVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREV 184
+VLLV+ + W P G + + E A RE+
Sbjct: 13 RVLLVRHTYG-PGWYLPGGGLERGETFAEAARREL 46
>gnl|CDD|236189 PRK08211, PRK08211, putative dehydratase; Provisional.
Length = 655
Score = 32.0 bits (73), Expect = 0.19
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 75 HIPSLTHFA-RKIDTVLDDWRHYKQSVPTFGAIL 107
HIP++ H A + TV DDW + VP ++L
Sbjct: 315 HIPAIAHAAGCRRPTV-DDWTRINRRVPRLVSVL 347
>gnl|CDD|240035 cd04679, Nudix_Hydrolase_20, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 125
Score = 30.5 bits (69), Expect = 0.23
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 140 GAILIDKSLTQVLLVQSFFA--RASWGFPKGKVNQDEPPMTCAIREVK 185
GA ++ ++LLV+ A WG P GKV+ E +RE++
Sbjct: 6 GAAILRDD-GKLLLVKRLRAPEAGHWGIPGGKVDWMEAVEDAVVREIE 52
>gnl|CDD|234044 TIGR02872, spore_ytvI, sporulation integral membrane protein YtvI.
Three lines of evidence show this protein to be involved
in sporulation. First, it is under control of a
sporulation-specific sigma factor, sigma-E. Second,
mutation leads to a sporulation defect. Third, it if
found in exactly those genomes whose bacteria are
capable of sporulation, except for being absent in
Clostridium acetobutylicum ATCC824. This protein has
extensive hydrophobic regions and is likely an integral
membrane protein [Cellular processes, Sporulation and
germination].
Length = 341
Score = 31.5 bits (72), Expect = 0.23
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 17/88 (19%)
Query: 79 LTHFARKIDTVLDDWRHYKQSVPTFGAILI--------DKSLTQVLLFLRQGLTVLDDWR 130
L + I ++DD Y S+P I +K L V+ F ++
Sbjct: 92 LNNINDHILPLIDDLESYYGSLPPGQQYTIVNNIQTLLEKLLNYVVSFAT---NLITSIP 148
Query: 131 HYKQSVPTFGAILIDKSLTQVLLVQSFF 158
+ S+P F +L+ L+ +FF
Sbjct: 149 SFIASIPNFLIVLL------FTLIATFF 170
>gnl|CDD|235436 PRK05379, PRK05379, bifunctional nicotinamide mononucleotide
adenylyltransferase/ADP-ribose pyrophosphatase;
Provisional.
Length = 340
Score = 31.1 bits (71), Expect = 0.31
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 130 RHYKQSV------PTFGAILIDKSLTQ---VLLVQ--SFFARASWGFPKGKVNQDEPPMT 178
Y+++ PTF + +D + Q VLLV+ + + W P G + QDE +
Sbjct: 188 EQYRKAWAAAPYPPTF--VTVDAVVVQSGHVLLVRRRAEPGKGLWALPGGFLEQDETLLD 245
Query: 179 CAIREVK 185
+RE++
Sbjct: 246 ACLRELR 252
>gnl|CDD|239517 cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase
is a prototypical Nudix hydrolase that catalyzes the
hydrolysis of nucleoside and deoxynucleoside
triphosphates (NTPs and dNTPs) by substitution at a
beta-phosphorus to yield a nucleotide monophosphate
(NMP) and inorganic pyrophosphate (PPi). This enzyme
requires two divalent cations for activity; one
coordinates the phosphoryl groups of the NTP/dNTP
substrate, and the other coordinates to the enzyme. It
also contains the Nudix motif, a highly conserved
23-residue block (GX5EX7REUXEEXGU, where U = I, L or V),
that functions as metal binding and catalytic site. MutT
pyrophosphohydrolase is important in preventing errors
in DNA replication by hydrolyzing mutagenic nucleotides
such as 8-oxo-dGTP (a product of oxidative damage),
which can mispair with template adenine during DNA
replication, to guanine nucleotides.
Length = 124
Score = 29.8 bits (68), Expect = 0.35
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 12/53 (22%)
Query: 140 GAILIDKSLTQVLLVQSFFARAS-------WGFPKGKVNQDEPPMTCAIREVK 185
AI+ID ++L+ Q R + W FP GKV E P +RE++
Sbjct: 5 AAIIIDDD-GRILIAQ----RPAGKHLGGLWEFPGGKVEPGETPEQALVRELR 52
>gnl|CDD|240020 cd04662, Nudix_Hydrolase_5, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 126
Score = 29.8 bits (67), Expect = 0.47
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 150 QVLLVQS---FFAR---ASWGFPKGKVNQDEPPMTCAIRE 183
+VLLV F+A +W PKG+ + E P+ A RE
Sbjct: 16 EVLLVHPGGPFWANKDLGAWSIPKGEYTEGEDPLLAAKRE 55
>gnl|CDD|183303 PRK11762, nudE, adenosine nucleotide hydrolase NudE; Provisional.
Length = 185
Score = 29.8 bits (68), Expect = 0.55
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 164 GFPKGKVNQDEPPMTCAIREVK 185
GFPKG ++ E P+ A RE+K
Sbjct: 77 GFPKGLIDPGETPLEAANRELK 98
>gnl|CDD|214789 smart00724, TLC, TRAM, LAG1 and CLN8 homology domains. Protein
domain with at least 5 transmembrane alpha-helices.
Lag1p and Lac1p are essential for acyl-CoA-dependent
ceramide synthesis, TRAM is a subunit of the translocon
and the CLN8 gene is mutated in Northern epilepsy
syndrome. The family may possess multiple functions
such as lipid trafficking, metabolism, or sensing. Trh
homologues possess additional homeobox domains.
Length = 205
Score = 30.0 bits (68), Expect = 0.56
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 40 FQMELAYWFYLDFYCTQDESLFKAGLKEFFFQMFHHIPSLTHFA 83
+ L Y+ + + L + K+F + HHI +L +
Sbjct: 50 YLFSLGYFIHDLVALLLFQDLKR---KDFKEMLVHHIATLLLIS 90
>gnl|CDD|240027 cd04670, Nudix_Hydrolase_12, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 127
Score = 28.4 bits (64), Expect = 1.1
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 140 GAILIDKSLTQVLLVQSFFARA-SWGFPKGKVNQDEPPMTCAIREVK 185
G +++++ +VL+VQ W P G V+ E A+REV
Sbjct: 6 GGLVLNEK-NEVLVVQERNKTPNGWKLPGGLVDPGEDIFDGAVREVL 51
>gnl|CDD|240055 cd04700, DR1025_like, DR1025 from Deinococcus radiodurans, a member
of the Nudix hydrolase superfamily, show nucleoside
triphosphatase and dinucleoside polyphosphate
pyrophosphatase activities. Like other enzymes belonging
to this superfamily, it requires a divalent cation, in
this case Mg2+, for its activity. It also contains a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. In general,
substrates of nudix hydrolases include intact and
oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
& "house-cleaning" enzymes. Substrate specificity is
used to define families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 142
Score = 28.3 bits (63), Expect = 1.3
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 131 HYKQSVPTFGAILIDKSLTQVLLVQSFFA--RASWGFPKGKVNQDEPPMTCAIREV 184
H + GA+++++ VLLVQ + W P G V E P A+RE
Sbjct: 8 HVEVEARAAGAVILNER-NDVLLVQEKGGPKKGLWHIPSGAVEDGEFPQDAAVREA 62
>gnl|CDD|234820 PRK00714, PRK00714, RNA pyrophosphohydrolase; Reviewed.
Length = 156
Score = 28.2 bits (64), Expect = 1.7
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 140 GAILIDKSLTQVLLVQSFFARASWGFPKGKVNQDEPPMTCAIRE 183
G IL+++ QV + SW FP+G ++ E P RE
Sbjct: 12 GIILLNRQ-GQVFWGRRIGQGHSWQFPQGGIDPGETPEQAMYRE 54
>gnl|CDD|240038 cd04682, Nudix_Hydrolase_23, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 122
Score = 28.1 bits (63), Expect = 1.7
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 163 WGFPKGKVNQDEPPMTCAIREV 184
W P G E P+ C +RE+
Sbjct: 31 WDLPGGHREGGETPLECVLREL 52
>gnl|CDD|240025 cd04667, Nudix_Hydrolase_10, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 112
Score = 27.7 bits (62), Expect = 2.2
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 150 QVLLVQSFFARASWGFPKGKVNQDEPPMTCAIREVK 185
+VLLV+ +R W P GK+ E P+ A RE++
Sbjct: 12 RVLLVRKSGSR--WALPGGKIEPGETPLQAARRELQ 45
>gnl|CDD|182721 PRK10776, PRK10776, nucleoside triphosphate pyrophosphohydrolase;
Provisional.
Length = 129
Score = 27.6 bits (62), Expect = 2.2
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 163 WGFPKGKVNQDEPPMTCAIREVK 185
W FP GK+ E P IRE++
Sbjct: 33 WEFPGGKIEAGETPEQALIRELQ 55
>gnl|CDD|236516 PRK09438, nudB, dihydroneopterin triphosphate pyrophosphatase;
Provisional.
Length = 148
Score = 27.6 bits (62), Expect = 2.8
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 8/41 (19%)
Query: 149 TQVLLVQSFFARAS----WGFPKGKVNQDEPPMTCAIREVK 185
VL++Q RA W G + + E P AIREVK
Sbjct: 19 LGVLMLQ----RADDPDFWQSVTGSLEEGETPAQTAIREVK 55
>gnl|CDD|215059 PLN00111, PLN00111, accumulation of photosystem one; Provisional.
Length = 399
Score = 28.1 bits (63), Expect = 2.9
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 19 LSSRFVINIPHEERGDVIRICFQMEL 44
L RF I H+ER DV RI +EL
Sbjct: 172 LYDRFGKRIKHDERFDVPRIPAIVEL 197
>gnl|CDD|240023 cd04665, Nudix_Hydrolase_8, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 118
Score = 27.3 bits (61), Expect = 3.1
Identities = 10/23 (43%), Positives = 10/23 (43%)
Query: 163 WGFPKGKVNQDEPPMTCAIREVK 185
W FP G V E A REV
Sbjct: 23 WEFPGGHVEPGETIEEAARREVW 45
>gnl|CDD|240042 cd04686, Nudix_Hydrolase_27, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 131
Score = 26.9 bits (60), Expect = 3.8
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 141 AILIDKSLTQVLLVQSFFARASWG---FPKGKVNQDEPPMTCAIREV 184
AI++ ++LL+ + +G FP G V + E + IRE+
Sbjct: 5 AIILQGD--KILLLYT----KRYGDYKFPGGGVEKGEDHIEGLIREL 45
>gnl|CDD|240028 cd04671, Nudix_Hydrolase_13, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 123
Score = 27.0 bits (60), Expect = 3.8
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 140 GAILIDKSLTQVLLVQSF--FARASWGFPKGKVNQDEPPMTCAIREVK 185
A++++ + +VLL+Q R W P G++ E REVK
Sbjct: 4 AAVILN-NQGEVLLIQEAKRSCRGKWYLPAGRMEPGETIEEAVKREVK 50
>gnl|CDD|188537 TIGR04022, sulfur_SfnB, sulfur acquisition oxidoreductase, SfnB
family. Members of this protein family belong to the
greater family of acyl-CoA dehydrogenases. This family
includes the sulfate starvation induced protein SfnB of
Pseudomonas putida strain DS1, which is both encoded
nearby to and phylogenetically closely correlated with
the dimethyl sulphone monooxygenase SfnG. This family
shows considerable sequence similarity to the
Rhodococcus dibenzothiophene desulfurization enzyme
DszC, although that enzyme falls outside of the scope of
this family [Central intermediary metabolism, Sulfur
metabolism].
Length = 391
Score = 27.6 bits (62), Expect = 4.6
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 100 VPTFGAILIDKSLTQVLLFLRQ---GLTVLDDWRHYKQSVPTFGAILID 145
+P +D VL F+ + GLTV+DDW + Q G +L+D
Sbjct: 160 IPVLA---LDDDGRPVLAFVPRDAPGLTVIDDWSGFGQRTTASGTVLLD 205
>gnl|CDD|217978 pfam04231, Endonuclease_1, Endonuclease I. Bacterial periplasmic
or secreted endonuclease I (EC:3.1.21.1) E. coli
endonuclease I (EndoI) is a sequence independent
endonuclease located in the periplasm. It is inhibited
by different RNA species. It is thought to normally
generate double strand breaks in DNA, except in the
presence of high salt concentrations and RNA, when it
generates single strand breaks in DNA. Its biological
role is unknown. Other family members are known to be
extracellular. This family also includes a non-specific,
Mg2+ activated ribonuclease precursor.
Length = 207
Score = 27.3 bits (61), Expect = 4.8
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 28 PHEERGDVIRICFQMELAYWFYLDFYCTQDESLFKA 63
P E +GD+ R F M + Y Q L A
Sbjct: 141 PDEVKGDIARAYFYMAVRYEGLRLSK--QQRQLLLA 174
>gnl|CDD|232918 TIGR00321, dhys, deoxyhypusine synthase. Deoxyhypusine synthase is
responsible for the first step in creating hypusine.
Hypusine is a modified amino acid found in eukaryotes
and in archaea in their respective forms of initiation
factor 5A. Its presence is confirmed in archaeal genera
Pyrococcus (PMID:12761201), Sulfolobus, Halobacterium,
and Haloferax (PMID:10648545), but in an older report
was not detected in Methanococcus voltae (J Biol Chem
1987 Dec 5;262(34):16585-9). This family of apparent
orthologs has an unusual UPGMA difference tree, in which
the members from the archaea M. jannaschii and P.
horikoshii cluster with the known eukaryotic
deoxyhypusine synthases. Separated by a fairly deep
branch, although still strongly related, is a small
cluster of proteins from Methanobacterium
thermoautotrophicum and Archeoglobus fulgidus, the
latter of which has two [Protein fate, Protein
modification and repair].
Length = 301
Score = 27.4 bits (61), Expect = 5.6
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 9/80 (11%)
Query: 51 DFYCTQDE-SLFKAGLKEFFFQMFHHIPSLT--HFARKIDTVLDDWR------HYKQSVP 101
D + + +F+ L E F +M P +T F +I ++D R YK+ +P
Sbjct: 117 DVFVPNENFEVFEEWLVEIFSEMLGEQPIITPSEFIDEIGKRINDKRSSIRYAAYKRKIP 176
Query: 102 TFGAILIDKSLTQVLLFLRQ 121
F L D S+ +L F +
Sbjct: 177 IFCPALTDSSIGLMLFFYTK 196
>gnl|CDD|225958 COG3424, BcsA, Predicted naringenin-chalcone synthase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 356
Score = 27.0 bits (60), Expect = 6.0
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 8/52 (15%)
Query: 58 ESLFKAGLKEFFFQM-FHHIPSLTHFARKIDT----VLDDWRHYKQSVPTFG 104
+S E FQ IP + H +I+ + DW Y++ FG
Sbjct: 18 QSEITDSFAELPFQEGREDIPRVLHANAQINRRHLVLPLDW--YREP-HGFG 66
>gnl|CDD|131752 TIGR02705, nudix_YtkD, nucleoside triphosphatase YtkD. The
functional assignment to the proteins of this family is
contentious. Reference challenges the findings of
reference , both in interpretation and in enzyme assay
results. This protein belongs to the nudix family and
shares some sequence identity with E. coli MutT but
appears not to be functionally interchangeable with it
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 156
Score = 26.6 bits (59), Expect = 6.4
Identities = 11/21 (52%), Positives = 11/21 (52%)
Query: 165 FPKGKVNQDEPPMTCAIREVK 185
FP GKV E AIREV
Sbjct: 49 FPGGKVEPGETSKEAAIREVM 69
>gnl|CDD|200031 TIGR00586, mutt, mutator mutT protein. All proteins in this family
for which functions are known are involved in repairing
oxidative damage to dGTP (they are 8-oxo-dGTPases). This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University). Lowering the
threshold picks up members of MutT superfamily well [DNA
metabolism, DNA replication, recombination, and repair].
Length = 128
Score = 26.4 bits (58), Expect = 6.4
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 162 SWGFPKGKVNQDEPPMTCAIREVK--IIFCQH 191
FP GK E P +RE++ I QH
Sbjct: 32 LLEFPGGKEEGGETPEQAVVRELEEEIGIPQH 63
>gnl|CDD|224766 COG1853, COG1853, Conserved protein/domain typically associated
with flavoprotein oxygenases, DIM6/NTAB family [General
function prediction only].
Length = 176
Score = 26.5 bits (59), Expect = 7.9
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 20 SSRFVINIPHEERGDVIRICF 40
+ FV+N+ E+ + + F
Sbjct: 66 TGEFVVNVLSEDLQEAVAKTF 86
>gnl|CDD|193544 cd05668, M20_Acy1_like3, M20 Peptidase Aminoacylase 1 subfamily.
Peptidase M20 family, Uncharacterized subfamily of
bacterial uncharacterized proteins predicted as putative
amidohydrolases. These are a class of zinc binding
homodimeric enzymes involved in hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 374
Score = 26.8 bits (60), Expect = 8.0
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 164 GFPKGKVNQDEPPMTCAIREVKIIF 188
G P G+V E P CA R ++I
Sbjct: 157 GLPLGEVVLKEGPFNCASRGMRIRL 181
>gnl|CDD|153177 cd04905, ACT_CM-PDT, C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT)
enzyme and the prephenate dehydratase (PDT) enzyme.
The C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT)
enzyme and the prephenate dehydratase (PDT) enzyme,
found in plants, fungi, bacteria, and archaea. The
P-protein of E. coli (CM-PDT, PheA) catalyzes the
conversion of chorismate to prephenate and then the
decarboxylation and dehydration to form phenylpyruvate.
These are the first two steps in the biosynthesis of
L-Phe and L-Tyr via the shikimate pathway in
microorganisms and plants. The E. coli P-protein
(CM-PDT) has three domains with an N-terminal domain
with chorismate mutase activity, a middle domain with
prephenate dehydratase activity, and an ACT regulatory
C-terminal domain. The prephenate dehydratase enzyme
has a PDT and ACT domain. The ACT domain is essential
to bring about the negative allosteric regulation by
L-Phe binding. L-Phe binds with positive cooperativity;
with this binding, there is a shift in the protein to
less active tetrameric and higher oligomeric forms from
a more active dimeric form. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 80
Score = 25.2 bits (56), Expect = 8.3
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 46 YWFYLDFYCTQDESLFKAGLKE 67
Y F++DF ++ L+E
Sbjct: 44 YVFFIDFEGHIEDPNVAEALEE 65
>gnl|CDD|188651 cd09819, An_peroxidase_bacterial_1, Uncharacterized bacterial
family of heme peroxidases. Animal heme peroxidases are
diverse family of enzymes which are not restricted to
metazoans; members are also found in fungi, and plants,
and in bacteria - like this family of uncharacterized
proteins.
Length = 465
Score = 26.9 bits (60), Expect = 8.8
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 70 FQMFHHI--PSLTHFARKIDTVL 90
++ F I + FARKIDT L
Sbjct: 295 WRRFFDIDGSAPPQFARKIDTKL 317
>gnl|CDD|216687 pfam01763, Herpes_UL6, Herpesvirus UL6 like. This family consists
of various proteins from the herpesviridae that are
similar to herpes simplex virus type I UL6 virion
protein. UL6 is essential for cleavage and packaging of
the viral genome.
Length = 556
Score = 26.8 bits (60), Expect = 9.2
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 68 FFFQMFHHIPSLTHFARKIDTVLDDWRHYKQSVPT 102
F Q+F+ + A D VL DWR ++ ++
Sbjct: 29 FIRQLFYTLLKTALNACTYDDVLSDWRKHEAAIAK 63
>gnl|CDD|240040 cd04684, Nudix_Hydrolase_25, Contains a crystal structure of the
Nudix hydrolase from Enterococcus faecalis, which has an
unknown function. In general, members of the Nudix
hydrolase superfamily catalyze the hydrolysis of
NUcleoside DIphosphates linked to other moieties, X.
Enzymes belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity. They
also contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which forms a
structural motif that functions as a metal binding and
catalytic site. Substrates of nudix hydrolases include
intact and oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
& "house-cleaning" enzymes. Substrate specificity is
used to define families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 128
Score = 25.7 bits (57), Expect = 9.5
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 4/47 (8%)
Query: 141 AILIDKSLTQVLLVQ--SFFARASWGFPKGKVNQDEPPMTCAIREVK 185
A++ ++LL+Q W P G + E P REV
Sbjct: 5 AVIPRDG--KLLLIQKNGGPYEGRWDLPGGGIEPGESPEEALHREVL 49
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
0.328 0.142 0.450
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,101,185
Number of extensions: 945301
Number of successful extensions: 1033
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1029
Number of HSP's successfully gapped: 61
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.3 bits)