RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy169
(280 letters)
>gnl|CDD|240019 cd04661, MRP_L46, Mitochondrial ribosomal protein L46 (MRP L46) is
a component of the large subunit (39S) of the mammalian
mitochondrial ribosome and a member of the Nudix
hydrolase superfamily. MRPs are thought to be involved
in the maintenance of the mitochondrial DNA. In general,
members of the Nudix superfamily require 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), which functions
as a metal binding and catalytic site. MRP L46 appears
to contain a modified nudix motif.
Length = 132
Score = 164 bits (418), Expect = 2e-51
Identities = 68/133 (51%), Positives = 97/133 (72%), Gaps = 3/133 (2%)
Query: 146 NNVKSMQRKLDKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIHAR 205
N+ KS+ RKLD LVLL+++K+G ++HWI+P GKR+EGET+RQTAER L E + A+
Sbjct: 1 NDRKSLDRKLDDTLVLLVQQKVGSQNHWILPQGKREEGETLRQTAERTLKELCGNNLKAK 60
Query: 206 FYGNAPCGFYKFKYPKSLQAESNVVGAKLFFFKAQYLEGDVKDK--KLEYTWAAREELPK 263
FYGNAP GFYK+KYPK+++ E VGAK+FFFKA+Y+ G + ++++ W A+EEL K
Sbjct: 61 FYGNAPVGFYKYKYPKAVRNEGI-VGAKVFFFKARYMSGQFELSQNQVDFKWLAKEELQK 119
Query: 264 LLLEDYNKNISLF 276
L Y +++ F
Sbjct: 120 YLNPPYLQSVKKF 132
>gnl|CDD|221223 pfam11788, MRP-L46, 39S mitochondrial ribosomal protein L46. This
is the L46 subunit of the mammalian mitochondrial
ribosome, conserved from plants and fungi.
Length = 121
Score = 54.1 bits (130), Expect = 2e-09
Identities = 23/121 (19%), Positives = 41/121 (33%), Gaps = 22/121 (18%)
Query: 45 WDLMSAVCLERKPLITRDFNEIEKKVQL----LMNELELENSMKSDHELRCIADQIRAEK 100
W + + V L R P++T + + EK L+ LE E S + +A+ ++
Sbjct: 1 WKIKAGVLLSRPPVVTPEPSPFEKAFYKYQKELLERLEWEFSRYFYFKKGTLAELPDFKE 60
Query: 101 MKDK---SLNVDMIDDALQQTGQDFVDMGLNELKKFT---------------PASRITKA 142
++ K Q+ E+ PA R+T+A
Sbjct: 61 LQKKPIEKDEGVAFPIGKPDAAQERERNDEQEIGLPKTSLEESEDDVSRKIKPAPRVTEA 120
Query: 143 D 143
D
Sbjct: 121 D 121
>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 = 49.4 bits (118), Expect = 1e-07
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 14/114 (12%)
Query: 160 VLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIHARFYGNAPCGFYKFKY 219
VLL++ W +P G + GET+ + A R + E+ G Y+ +
Sbjct: 14 VLLVRRADSPGGLWELPGGGVEPGETLEEAAIREVREE----TGLDVDVLRLLGVYEVES 69
Query: 220 PKSLQAESNVVGAKLFFFKAQYLEGDVK----DKKLEYTWAAREELPKLLLEDY 269
P A +F F A+ + G+ D+ E W +ELP L L
Sbjct: 70 PD------EGEHAVVFVFLARLVGGEPTLLPPDEISEVRWVTLDELPALALSPA 117
>gnl|CDD|215841 pfam00293, NUDIX, NUDIX domain.
Length = 133
Score = 39.4 bits (92), Expect = 3e-04
Identities = 30/127 (23%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 160 VLLIKEK--LGDKSHWIMPFGKRQEGETMRQTAERILAEKFN-KTIHARFYGNAPCGFYK 216
VLL++ W +P GK + GE+ + A R L E+ + + G Y
Sbjct: 16 VLLVRRSRPPVFPGLWELPGGKVEPGESPEEAAVRELEEETGLRVLLLLLLGV---LEYP 72
Query: 217 FKYPKSLQAESNVVGAKLFFFKAQYLEGDVK-----DKKLEYTWAAREELPKLLLEDYNK 271
G + F A+ L G+ + D+ E W EEL +LLL +
Sbjct: 73 APGRDG--------GEHVHVFLAELLGGEPEPQPNEDEVSEVRWVPLEELLELLLAGEIR 124
Query: 272 NISLFLM 278
+ L+
Sbjct: 125 EVIALLL 131
>gnl|CDD|223979 COG1051, COG1051, ADP-ribose pyrophosphatase [Nucleotide transport
and metabolism].
Length = 145
Score = 36.2 bits (84), Expect = 0.005
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 160 VLLIKEK-LGDKSHWIMPFGKRQEGETMRQTAERILAEK 197
+LL++ +W +P G + GET+ + A R L E+
Sbjct: 23 ILLVRRANEPGAGYWALPGGFVEIGETLEEAARRELKEE 61
>gnl|CDD|240041 cd04685, Nudix_Hydrolase_26, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily requires 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 = 133
Score = 36.2 bits (84), Expect = 0.005
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 160 VLLIKEKLGDKS---HWIMPFGKRQEGETMRQTAERILAE 196
VLL++ D W P G + GE+ Q A R L E
Sbjct: 14 VLLLRGDDPDSPGPDWWFTPGGGVEPGESPEQAARRELRE 53
>gnl|CDD|239642 cd03670, ADPRase_NUDT9, ADP-ribose pyrophosphatase (ADPRase)
catalyzes the hydrolysis of ADP-ribose to AMP and
ribose-5-P. Like other members of the Nudix hydrolase
superfamily of enzymes, it is thought to require a
divalent cation, such as Mg2+, for its activity. It also
contains a 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
(ADPRase-I, -II, and -Mn) and a single mitochondrial
enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It
can be distinugished from the cytosolic ADPRase by a
N-terminal target sequence unique to mitochondrial
ADPRase. NUDT9 functions as a monomer.
Length = 186
Score = 34.0 bits (78), Expect = 0.038
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 141 KADKENNVKSMQRKLDKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKF 198
K D + S+ K K ++ + K D W +P G GE + T +R E+
Sbjct: 31 KRDSSGD-GSIHPKSGKPILQFVAIKRPDSGEWAIPGGMVDPGEKISATLKREFGEEA 87
>gnl|CDD|240026 cd04669, Nudix_Hydrolase_11, 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 = 121
Score = 32.8 bits (75), Expect = 0.052
Identities = 22/111 (19%), Positives = 42/111 (37%), Gaps = 8/111 (7%)
Query: 156 DKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIHARFYGNAPCGFY 215
D+ +LLI+ K++++ P G +EGET + A+R E+ + F
Sbjct: 10 DQGEILLIRRIKPGKTYYVFPGGGIEEGETPEEAAKREALEELGLDVRVE------EIFL 63
Query: 216 KFKYPKSLQA--ESNVVGAKLFFFKAQYLEGDVKDKKLEYTWAAREELPKL 264
+ + V+ KL + E D + W ++L +
Sbjct: 64 IVNQNGRTEHYFLARVISGKLGLGVGEEFERQSDDNQYHPVWVDLDQLETI 114
>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 = 32.6 bits (75), Expect = 0.073
Identities = 26/127 (20%), Positives = 43/127 (33%), Gaps = 33/127 (25%)
Query: 156 DKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIH-------ARFYG 208
D L+L+ K + W +P G + GE+ + R + E+ T+ A Y
Sbjct: 10 DGKLLLIQKNGGPYEGRWDLPGGGIEPGESPEEALHREVLEETGLTVEIGRRLGSASRYF 69
Query: 209 NAP---------CGFYKFKYPKSLQAESNVVGAKLFFFKAQYLEGDVKDKKLEYTWAARE 259
+P C FY ++ VVG L + + W +
Sbjct: 70 YSPDGDYDAHHLCVFY----------DARVVGGAL-------PVQEPGEDSHGAAWLPLD 112
Query: 260 ELPKLLL 266
E + LL
Sbjct: 113 EAIERLL 119
>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 = 32.2 bits (74), Expect = 0.082
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 160 VLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
VLL++++ + +P GK + GET Q R L+E
Sbjct: 14 VLLVRKR--GTDVFYLPGGKIEAGETPLQALIRELSE 48
>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 = 31.9 bits (73), Expect = 0.11
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 160 VLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
VLL++ G W +P G + GET + A R L E
Sbjct: 14 VLLVRHTYGP--GWYLPGGGLERGETFAEAARRELLE 48
>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 = 32.1 bits (73), Expect = 0.12
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 156 DKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIHA 204
D L+L+ + + + HW +P GK E + R + E+ +IH+
Sbjct: 13 DGKLLLVKRLRAPEAGHWGIPGGKVDWMEAVEDAVVREIEEETGLSIHS 61
>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 = 31.5 bits (72), Expect = 0.14
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 160 VLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
VLL+++ S W +P GK + GET Q A R L E
Sbjct: 13 VLLVRK---SGSRWALPGGKIEPGETPLQAARRELQE 46
>gnl|CDD|223568 COG0494, MutT, NTP pyrophosphohydrolases including oxidative damage
repair enzymes [DNA replication, recombination, and
repair / General function prediction only].
Length = 161
Score = 31.7 bits (71), Expect = 0.19
Identities = 23/133 (17%), Positives = 42/133 (31%), Gaps = 16/133 (12%)
Query: 156 DKHLVLLIKEKLGDKSHWIMPFGKRQEGETM-RQTAER-------ILAEKFNKTIHARFY 207
VLL + + D W +P GK + GE + + A R + + + F
Sbjct: 22 GPGEVLLAQRR-DDGGLWELPGGKVEPGEELPEEAAARELEEETGLRVKDERLELLGEFP 80
Query: 208 GNAPCGFYKFKYPKSLQAESNVVGAKLFFFKAQYLEGDVKDKK--LEYTWAAREELPKLL 265
+ G + A++ A +EG + + W +EL L+
Sbjct: 81 PSPGDGSSVGG-----REHRVFFVAEVDDSLAVAIEGLSAPSEELEDLEWVPLDELAALV 135
Query: 266 LEDYNKNISLFLM 278
L +
Sbjct: 136 LAEDQVKRDAKKA 148
>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 = 31.5 bits (72), Expect = 0.20
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 160 VLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
VLLI GD W +P GK + GET + A R + E
Sbjct: 18 VLLIHRPRGDD--WSLPKGKLEPGETPPEAAVREVEE 52
>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 = 31.1 bits (71), Expect = 0.20
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 160 VLLIKEKLG-DKSHWIMPFGKRQEGETMRQTAERILAE 196
VLL++ D W P GK + GET+ Q A R L E
Sbjct: 13 VLLVRRANPPDAGLWSFPGGKVELGETLEQAALRELLE 50
>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 = 29.5 bits (67), Expect = 1.1
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 161 LLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
+ + ++ W P G EGE Q A R L E
Sbjct: 17 VFVGRRIDTPGAWQFPQGGIDEGEDPEQAALRELEE 52
>gnl|CDD|215492 PLN02907, PLN02907, glutamate-tRNA ligase.
Length = 722
Score = 30.1 bits (68), Expect = 1.4
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 242 LEGDVKDKKLEYTW-AAREELPKLLLEDYNKNIS 274
LEG VK KL+ TW EL L L +++ I+
Sbjct: 614 LEGSVKTTKLKLTWLPDTNELVPLSLVEFDYLIT 647
>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 = 28.7 bits (64), Expect = 1.9
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 160 VLLIKEKLGDKSH-WIMPFGKRQEGETMRQTAERILAE---------KFNKTIHARF 206
VLL++EK G K W +P G ++GE + A R E KF T RF
Sbjct: 27 VLLVQEKGGPKKGLWHIPSGAVEDGEFPQDAAVREACEETGLRVRPVKFLGTYLGRF 83
>gnl|CDD|240054 cd04699, Nudix_Hydrolase_39, 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 = 28.5 bits (64), Expect = 2.2
Identities = 34/137 (24%), Positives = 53/137 (38%), Gaps = 18/137 (13%)
Query: 147 NVKSMQRKLDKHLVLLIKEKLGDKSH----WIMPFGKRQEGETMRQTAERILAEKFNKTI 202
V ++ K + LI ++ D+ W +P GK +EGET + +R + E+ T+
Sbjct: 3 AVAALIVKDVGRI--LILKRSKDERTAPGKWELPGGKVEEGETFEEALKREVYEETGLTV 60
Query: 203 HARFYGNAPCGFYKFKYPKSLQAESNVVGAKLFFFKAQYLEGDVK--DKKLEYTWAAREE 260
F +S V F + L G VK D+ EY W EE
Sbjct: 61 -TPFLRYPSTVT---------HEDSGVYNVIYLVFVCEALSGAVKLSDEHEEYAWVTLEE 110
Query: 261 LPKLLLEDYNKNISLFL 277
L L + + +FL
Sbjct: 111 LAILKADILFEPSKIFL 127
>gnl|CDD|226143 COG3616, COG3616, Predicted amino acid aldolase or racemase [Amino
acid transport and metabolism].
Length = 368
Score = 29.3 bits (66), Expect = 2.2
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 133 FTPASRITKADKENNVKSMQRKLDKHLVLLIKEKLGDKSHWIMPFGKRQ--EGETM 186
TPA+ I + N+ MQ + D H V L + K+H + Q G
Sbjct: 17 DTPAALIDLDRLDGNIDRMQARADDHGVRL---RPHVKTHKCPELARIQLDAGAWG 69
>gnl|CDD|215353 PLN02654, PLN02654, acetate-CoA ligase.
Length = 666
Score = 29.5 bits (66), Expect = 2.3
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 154 KLDKHLVLLIKEKLG-----DKSHWIMPFGKRQEGETMRQTAERILAEKFNK 200
+L K L+L ++ ++G DK HW K + G+ MR+ +I + + ++
Sbjct: 593 ELRKSLILTVRNQIGAFAAPDKIHWAPGLPKTRSGKIMRRILRKIASRQLDE 644
>gnl|CDD|239948 cd04511, Nudix_Hydrolase_4, 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, 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 = 130
Score = 28.4 bits (64), Expect = 2.4
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 173 WIMPFGKRQEGETMRQTAER 192
W +P G + GET Q A R
Sbjct: 40 WTLPAGFMENGETTEQGALR 59
>gnl|CDD|233709 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily
of the penicillin binding proteins includes the member
from E. coli designated penicillin-binding protein 1C.
Members have both transglycosylase and transpeptidase
domains and are involved in forming cross-links in the
late stages of peptidoglycan biosynthesis. All members
of this subfamily are presumed to have the same basic
function [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 727
Score = 29.3 bits (66), Expect = 2.6
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 209 NAPCGFYKFKYPKSLQAESNVVGAKLFFFKAQYL--EGDVKDKKLEYTWAAREELPKL 264
AP + PK+ +A + + L Q V LE A E LP+L
Sbjct: 171 QAPSARRLDRLPKAAKAARDRL---LDRMVEQGPDDSEQVALAALEPLPALPEPLPQL 225
>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 = 28.0 bits (63), Expect = 2.9
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 152 QRKLDKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAE 196
+R ++ LL++ G HW P G + GE + A R E
Sbjct: 11 RRLNNEIEYLLLQASYG---HWDFPKGHVEPGEDDLEAALRETEE 52
>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 = 27.7 bits (62), Expect = 3.1
Identities = 21/75 (28%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 173 WIMPFGKRQEGETMRQTAERILAEKFNKTIHARFYGNAPCGFYKFKYPKSLQAESNVVGA 232
W P G + GET+ + A R + E+ A G+Y+ E+ V A
Sbjct: 23 WEFPGGHVEPGETIEEAARREVWEE----TGAELGSLTLVGYYQVD-LFESGFETLVYPA 77
Query: 233 K--LFFFKAQYLEGD 245
KA YLE D
Sbjct: 78 VSAQLEEKASYLETD 92
>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 = 27.9 bits (63), Expect = 3.4
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 159 LVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAER 192
++LL ++K W P GK + GET + A R
Sbjct: 14 VLLLNRKKGPGWGGWNGPGGKVEPGETPEECAIR 47
>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 = 27.1 bits (61), Expect = 6.1
Identities = 29/115 (25%), Positives = 38/115 (33%), Gaps = 25/115 (21%)
Query: 152 QRKLDKHLVLLIKEKLGDKSHWIMPFGKRQEGETMRQTAERILAEKFNKTIHARFYGNAP 211
QR KHL L W P GK + GET Q R L E+ +
Sbjct: 19 QRPAGKHLGGL----------WEFPGGKVEPGETPEQALVRELREELGIEVEVG----EL 64
Query: 212 CGFYKFKYP-KSLQAESNVVGAKLFFFKAQYLEGDVKDKK-LEYTWAAREELPKL 264
+ YP K + L F + G+ + + E W EEL L
Sbjct: 65 LATVEHDYPDKRV---------TLHVFLVELWSGEPQLLEHQELRWVPPEELDDL 110
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
0.318 0.133 0.378
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,001,030
Number of extensions: 1323104
Number of successful extensions: 1161
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1157
Number of HSP's successfully gapped: 51
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.2 bits)