RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11834
(230 letters)
>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 = 93.7 bits (234), Expect = 2e-24
Identities = 38/117 (32%), Positives = 55/117 (47%), Gaps = 5/117 (4%)
Query: 103 YPAELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQ 162
P G LE AG++D + E AR E+ EE GY+ LEK+ +F G + +R
Sbjct: 24 PPVG-GWLLELPAGLIDPGEDPEEAARRELEEETGYE--AGDLEKLGSFYPSPGFSDERI 80
Query: 163 TLFFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRSPSGFLFAMHWFL 219
LF E + G + E IEVV + L+EA E LA E+ + + + W
Sbjct: 81 HLFLAEDLSPGEE--GLLDEGEDIEVVLVPLDEALELLADGEIIDDATLIALLLWLA 135
>gnl|CDD|129162 TIGR00052, TIGR00052, nudix-type nucleoside diphosphatase,
YffH/AdpP family. Members of this family include
proteins of about 200 amino acids, including the
recently characterized nudix hydrolase YffH, shows to be
highly active as a GDP-mannose pyrophosphatase. It also
includes the C-terminal half of a 361-amino acid
protein, TrgB from Rhodobacter sphaeroides, shown
experimentally to help confer tellurite resistance. This
model also hits a region near the C-terminus of a
1092-amino acid protein of C. elegans [Unknown function,
Enzymes of unknown specificity].
Length = 185
Score = 87.2 bits (216), Expect = 2e-21
Identities = 51/196 (26%), Positives = 87/196 (44%), Gaps = 16/196 (8%)
Query: 27 QEALIKENQYCHPQFL---ITQHKDYYIVMNKITEAQIIETRSSQFIQPYSVKFVQVLLS 83
QE +IK+ Y L I H+ + + +I + ++ + Y K V+L
Sbjct: 3 QEIIIKDTLYSGFFSLLHNIFYHRLFKGGESIRVTREIYDRGNAAAVLLYDPKKDTVVLI 62
Query: 84 VYINSIPEEDRTGSIDVTKYPAELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVE 143
E+ R + + P L E AG+V+K +S ++AR E +EE GY V +
Sbjct: 63 -------EQFRIAAYVNGEEPWLL----ELSAGMVEKGESPEDVARREAIEEAGYQV--K 109
Query: 144 KLEKIQTFRSGVGSAGDRQTLFFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQD 203
L K+ +F G + LF EV D+ GGG DEE IEV+ + +A +++ +
Sbjct: 110 NLRKLLSFYMSPGGVTELIHLFIAEVDDNQAAGIGGGADEEEIEVLHLVFSQALQWIKEG 169
Query: 204 EVRSPSGFLFAMHWFL 219
++ + + L
Sbjct: 170 KIDNGKTVILLQWLQL 185
>gnl|CDD|215841 pfam00293, NUDIX, NUDIX domain.
Length = 133
Score = 59.8 bits (145), Expect = 1e-11
Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 8/118 (6%)
Query: 104 PAELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQT 163
P E G V+ +S E A E+ EE G V + L + + + G+
Sbjct: 24 PPVFPGLWELPGGKVEPGESPEEAAVRELEEETGLRVLLLLLLGVLEYPAPGRDGGEHVH 83
Query: 164 LFFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRSPSGFLFAMHWFLAA 221
+F E+ ++E+ EV + LEE E L E+R + LA
Sbjct: 84 VFLAELLGGEPEPQPN--EDEVSEVRWVPLEELLELLLAGEIR------EVIALLLAL 133
>gnl|CDD|184971 PRK15009, PRK15009, GDP-mannose pyrophosphatase NudK; Provisional.
Length = 191
Score = 58.7 bits (142), Expect = 9e-11
Identities = 37/102 (36%), Positives = 58/102 (56%), Gaps = 5/102 (4%)
Query: 106 ELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDV-PVEKLEKIQTFRSGVGSAGDRQTL 164
E G +E CAG++D ++ I R+E +EE GY+V V KL ++ GV +
Sbjct: 76 ESGQLIETCAGLLDNDEPEVCI-RKEAIEETGYEVGEVRKLFELYMSPGGVT---ELIHF 131
Query: 165 FFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVR 206
F E +D + N+GGGV++E IEV+E+ +A E + E+R
Sbjct: 132 FIAEYSDSQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIR 173
>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 = 41.7 bits (98), Expect = 4e-05
Identities = 26/115 (22%), Positives = 41/115 (35%), Gaps = 3/115 (2%)
Query: 92 EDRTGSIDVTKYPAELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTF 151
D G + + + G E G V+ ++L E A EV EE G DV V +L +
Sbjct: 8 LDEDGRVLLVRRADSPGGLWELPGGGVEPGETLEEAAIREVREETGLDVDVLRLLGVYEV 67
Query: 152 RSGVGSAGDRQTLFFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVR 206
S +F + +E+ EV + L+E +R
Sbjct: 68 ESPDEGEHAVVFVFLARLVGGEPTLL---PPDEISEVRWVTLDELPALALSPALR 119
>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 = 38.0 bits (89), Expect = 8e-04
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 9/96 (9%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDV-PVEKLEKIQTFRSGVGSAGDRQTLFFVEVTDDMK 174
G ++ ++ E A EV EE G + L I+ + S G + +++ M+
Sbjct: 34 GKLEPGETPPEAAVREVEEETGIRAEVGDPLGTIRYWFSSSGKRVHKTVHWWL-----MR 88
Query: 175 VNSGGGVDEELIEVVEMG---LEEAREYLAQDEVRS 207
G + EV E+ +EAR+ L+ R
Sbjct: 89 ALGGEFTPQPDEEVDEVRWLPPDEARDRLSYPNDRE 124
>gnl|CDD|223568 COG0494, MutT, NTP pyrophosphohydrolases including oxidative damage
repair enzymes [DNA replication, recombination, and
repair / General function prediction only].
Length = 161
Score = 35.6 bits (81), Expect = 0.008
Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 6/120 (5%)
Query: 89 IPEEDRTGSIDVTKYPAELGVTLEFCAGIVDKNKSLAEIA-REEVLEECGYDVPVEKLEK 147
+ D G + + + + G E G V+ + L E A E+ EE G V E+LE
Sbjct: 17 LVGRDGPGEVLLAQRRDDGG-LWELPGGKVEPGEELPEEAAARELEEETGLRVKDERLEL 75
Query: 148 IQTF----RSGVGSAGDRQTLFFVEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQD 203
+ F G G +FFV DD + G+ E+ ++ E A
Sbjct: 76 LGEFPPSPGDGSSVGGREHRVFFVAEVDDSLAVAIEGLSAPSEELEDLEWVPLDELAALV 135
>gnl|CDD|239647 cd03675, Nudix_Hydrolase_2, Contains a crystal structure of the
Nudix hydrolase from Nitrosomonas europaea, 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 = 134
Score = 35.2 bits (82), Expect = 0.008
Identities = 26/101 (25%), Positives = 42/101 (41%), Gaps = 5/101 (4%)
Query: 108 GVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQTLFFV 167
G+ AG ++ +SL E A E LEE G+ V L I + + D L F
Sbjct: 23 GLVFNQPAGHLEPGESLIEAAVRETLEETGWHVEPTALLGIYQWTA---PDSDTTYLRFA 79
Query: 168 EVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRSP 208
+ ++ +D ++ + LEE A+ +RSP
Sbjct: 80 FAAELLEHLPDQPLDSGIVRAHWLTLEEILALAAR--LRSP 118
>gnl|CDD|240029 cd04672, Nudix_Hydrolase_14, 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 = 34.1 bits (79), Expect = 0.014
Identities = 15/30 (50%), Positives = 16/30 (53%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKL 145
G D S AE +EV EE G DV V KL
Sbjct: 31 GWADVGLSPAENVVKEVKEETGLDVKVRKL 60
>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 = 31.2 bits (71), Expect = 0.17
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 113 FCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSG 154
F G +++ ++ E A+ E LEE G DV VE++ I
Sbjct: 29 FPGGGIEEGETPEEAAKREALEELGLDVRVEEIFLIVNQNGR 70
>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 = 31.3 bits (71), Expect = 0.18
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 115 AGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQ 149
AG ++ +++ E + EV EE G D L ++
Sbjct: 32 AGRMEPGETIEEAVKREVKEETGLDCEPTTLLSVE 66
>gnl|CDD|182682 PRK10729, nudF, ADP-ribose pyrophosphatase NudF; Provisional.
Length = 202
Score = 31.2 bits (71), Expect = 0.28
Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 91 EEDRTGSIDVTKYPAELGVTLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQT 150
E+ R + D ++ P LE AG++++ +S+ ++AR E +EE G + V + + + +
Sbjct: 68 EQIRIAAYDTSETPW----LLEMVAGMIEEGESVEDVARREAIEEAG--LIVGRTKPVLS 121
Query: 151 FRSGVGSAGDRQTLFFVEV 169
+ + G +R ++ EV
Sbjct: 122 YLASPGGTSERSSIMVGEV 140
>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 = 30.4 bits (69), Expect = 0.35
Identities = 17/40 (42%), Positives = 20/40 (50%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGV 155
G V+ +S A+ A EV EE G DV V L I T V
Sbjct: 32 GAVEPGESPADTAVREVREETGLDVEVTGLVGIYTGPVHV 71
>gnl|CDD|237772 PRK14631, PRK14631, hypothetical protein; Provisional.
Length = 174
Score = 29.9 bits (67), Expect = 0.76
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 81 LLSVYINSIPEEDRTGSIDVT-KYPAELGVTLEFCAGIVDKNKSLAE----IAREEVLE- 134
LL +YI+ + EE+ I+ + G+ +E C + + ++ + I+ E LE
Sbjct: 38 LLRIYIDRLVEENAEPVINEDGEVEQGRGIGVEDCVRVTQQVGAMLDVHDPISGEYALEV 97
Query: 135 -ECGYDVPVEKLEKIQTF 151
G+D P +LE++Q +
Sbjct: 98 SSPGWDRPFFQLEQLQGY 115
>gnl|CDD|236516 PRK09438, nudB, dihydroneopterin triphosphate pyrophosphatase;
Provisional.
Length = 148
Score = 29.1 bits (66), Expect = 1.2
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKLE 146
G +++ ++ A+ A EV EE G DV E+L
Sbjct: 38 GSLEEGETPAQTAIREVKEETGIDVLAEQLT 68
>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 = 28.9 bits (65), Expect = 1.3
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 101 TKYPAELGVTLEFC-AGIVDKNKSLAEIAREEVLEECGYDVP 141
P G F G V+ +S + AR E+ EE G V
Sbjct: 19 GDDPDSPGPDWWFTPGGGVEPGESPEQAARRELREETGITVA 60
>gnl|CDD|240033 cd04677, Nudix_Hydrolase_18, 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 = 132
Score = 28.3 bits (64), Expect = 1.5
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 115 AGIVDKNKSLAEIAREEVLEECGYDVPVEKL 145
G ++ +SL E AR E+ EE G +V +L
Sbjct: 36 GGAMELGESLEETARRELKEETGLEVEELEL 66
>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 = 28.1 bits (63), Expect = 1.9
Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 6/102 (5%)
Query: 110 TLEFCAGIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQTLFFVEV 169
E G V++ ++ E + EV EE G V G ++ V V
Sbjct: 30 KWELPGGKVEEGETFEEALKREVYEETGLTVTPFLRYPSTVTHEDSGVY---NVIYLVFV 86
Query: 170 TDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRSPSGF 211
+ ++ + +E E + LEE L D + PS
Sbjct: 87 CEA--LSGAVKLSDEHEEYAWVTLEELA-ILKADILFEPSKI 125
>gnl|CDD|218108 pfam04487, CITED, CITED. CITED, CBP/p300-interacting
transactivator with ED-rich tail, are characterized by a
conserved 32-amino acid sequence at the C-terminus.
CITED proteins do not bind DNA directly and are thought
to function as transcriptional co-activators.
Length = 206
Score = 28.7 bits (64), Expect = 2.0
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 6/30 (20%)
Query: 181 VDEELIE--VVEMGLEEARE----YLAQDE 204
+DEE++ V+E+GL+ E +L Q+E
Sbjct: 159 IDEEVLMSLVLELGLDRVNELPELWLGQNE 188
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 29.0 bits (66), Expect = 2.1
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 182 DEELIEVVEMGLEEAREYLAQ 202
DEEL+E+VEM E RE L++
Sbjct: 143 DEELLELVEM---EVRELLSK 160
>gnl|CDD|226468 COG3959, COG3959, Transketolase, N-terminal subunit [Carbohydrate
transport and metabolism].
Length = 243
Score = 28.8 bits (65), Expect = 2.2
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 132 VLEECGYDVPVEKLEKIQTFRSGVGSAGDRQTLFFVEVT 170
L E GY P E+LE + S + +R VEV+
Sbjct: 80 TLAEKGY-FPEEELETFRRIGSRLPGHPERNKTPGVEVS 117
>gnl|CDD|240037 cd04681, Nudix_Hydrolase_22, 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 = 130
Score = 28.1 bits (63), Expect = 2.2
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 110 TLEFCAGIVDKNKSLAEIAREEVLEECGYDVP 141
TL+ G VD +S E E+ EE G V
Sbjct: 28 TLDLPGGFVDPGESAEEALIREIREETGLKVT 59
>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 = 2.4
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKLEKI--QTFRSGVGSAGDRQTLFFVEVTDDM 173
G V+ + E A E EE G + +T V T F E+ D+
Sbjct: 34 GHVEPGEDDLEAALRETEEETGITAEQLFIVLGFKETLNYQVRGKLKTVTYFLAELRPDV 93
Query: 174 KVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRS 207
+V EE + + EEA + L +++++
Sbjct: 94 EVKLS----EEHQDYRWLPYEEALKLLTYEDLKA 123
>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 = 27.7 bits (62), Expect = 2.6
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVE 143
G +++ ++ AE AR E+LEE G + V
Sbjct: 30 GGLERGETFAEAARRELLEELGIRLAVV 57
>gnl|CDD|240022 cd04664, Nudix_Hydrolase_7, 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 = 27.7 bits (62), Expect = 3.1
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 115 AGIVDKNKSLAEIAREEVLEECGYDVP 141
G ++ +S AE AR EV EE G D
Sbjct: 34 TGGIEDGESPAEAARREVAEETGLDPE 60
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 28.3 bits (64), Expect = 4.1
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 182 DEELIEVVEMGLEEAREYLAQ 202
DEEL+E+VEM E RE L++
Sbjct: 143 DEELLELVEM---EVRELLSK 160
>gnl|CDD|223979 COG1051, COG1051, ADP-ribose pyrophosphatase [Nucleotide transport
and metabolism].
Length = 145
Score = 27.0 bits (60), Expect = 5.4
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKL 145
G V+ ++L E AR E+ EE G V V +L
Sbjct: 42 GFVEIGETLEEAARRELKEETGLRVRVLEL 71
>gnl|CDD|218797 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This
family consists of several Eukaryotic rRNA processing
protein EBP2 sequences. Ebp2p is required for the
maturation of 25S rRNA and 60S subunit assembly. Ebp2p
may be one of the target proteins of Rrs1p for executing
the signal to regulate ribosome biogenesis. This family
also plays a role in chromosome segregation.
Length = 270
Score = 27.7 bits (62), Expect = 5.5
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 143 EKLEKIQTFRSGVGSAGDRQTLFFVEVTDDMKVNSGG 179
+ LEKI+ + GD LF V D K S
Sbjct: 164 DMLEKIKKLKKKRKGGGDEGDLFDFLVDDAAKGGSKK 200
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 27.7 bits (62), Expect = 5.8
Identities = 12/40 (30%), Positives = 15/40 (37%)
Query: 167 VEVTDDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVR 206
+ MK+ VD L E V E RE L +E
Sbjct: 465 YSLLKLMKLKKRPDVDRHLAEEVRTLAEFVRELLKDEERV 504
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 27.2 bits (61), Expect = 5.9
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 182 DEELIEVVEMGLEEAREYLAQ 202
DEEL+E+VEM E RE L++
Sbjct: 133 DEELLELVEM---EVRELLSK 150
>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
of active transport proteins. Periplasmic
solute-binding domain of active transport proteins found
in bacteria and Archaea that is predicted to be involved
in the efflux of toxic compounds. Members of this
subgroup include proteins from Herminiimonas
arsenicoxydans, which is resistant to arsenic and
various heavy metals such as cadmium and zinc. Moreover,
they show significant sequence similarity to the cluster
of AmiC and active transport systems for short-chain
amides and urea (FmdDEF), and thus are likely to exhibit
a ligand-binding mode similar to that of the amide
sensor protein AmiC from Pseudomonas aeruginosa.
Length = 346
Score = 27.6 bits (62), Expect = 6.4
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 150 TFRSGVGSAGDRQTLFFVEVTDDMKVNSGGGVDEELIEVV--------EMGLEEAREYLA 201
TF SG + E+ + ++N+ GG+ IE+V + + EARE +
Sbjct: 6 TFLSGRAAIFGEPARNGAELAVE-EINAAGGIGGRKIELVVRDEAGKPDEAIREARELVE 64
Query: 202 QDEV 205
+ V
Sbjct: 65 NEGV 68
>gnl|CDD|178144 PLN02529, PLN02529, lysine-specific histone demethylase 1.
Length = 738
Score = 27.5 bits (61), Expect = 7.9
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 21/75 (28%)
Query: 45 QHKDYYIVMNKI------------TEAQIIETRSSQFIQPYSVKFVQVLLSVYIN----- 87
+ DY +V N I ++ QI ET SS++ S + +L + YIN
Sbjct: 89 EQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLLYNGYINFGVSP 148
Query: 88 ----SIPEEDRTGSI 98
IPEE GS+
Sbjct: 149 SFASPIPEEGTEGSV 163
>gnl|CDD|232870 TIGR00198, cat_per_HPI, catalase/peroxidase HPI. As catalase, this
enzyme catalyzes the dismutation of two molecules of
hydrogen peroxide to dioxygen and two molecules of
water. As a peroxidase, it uses hydrogen peroxide to
oxidize donor compounds and produce water. KatG from E.
coli is a homotetramer with two non-covalently
associated iron protoheme IX groups per tetramer, but
the ortholog from Synechococcus sp. is a homodimer with
one protoheme. Important sites (numbered according to E.
coli KatG) include heme ligands His-106 and His-267 and
active site Trp-318. Note that the translation
PID:g296476 from accession X71420 from Rhodobacter
capsulatus B10 contains extensive frameshift differences
from the rest of the orthologous family [Cellular
processes, Detoxification].
Length = 716
Score = 27.2 bits (60), Expect = 8.0
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 181 VDEELIEVVEMGLEEAREYLAQDEVRSPSGFL 212
D E +E + R YL +D +P L
Sbjct: 552 TDAESFTPLEPIADGFRNYLKRDYAVTPEELL 583
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 27.2 bits (61), Expect = 8.4
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 182 DEELIEVVEMGLEEAREYLAQ 202
DEEL+E+VEM E RE L++
Sbjct: 143 DEELLELVEM---EVRELLSE 160
>gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter
ATP-binding subunit. This model describes daunorubicin
resistance ABC transporter, ATP binding subunit in
bacteria and archaea. This model is restricted in its
scope to preferentially recognize the ATP binding
subunit associated with effux of the drug, daunorubicin.
This transport system belong to the larger ATP-Binding
Cassette (ABC) transporter superfamily. The
characteristic feature of these transporter is the
obligatory coupling of ATP hydrolysis to substrate
translocation. The minimal configuration of bacterial
ABC transport system: an ATPase or ATP binding subunit;
An integral membrane protein; a hydrophilic polypetpide,
which likely functions as substrate binding protein. In
eukaryotes proteins of similar function include p-gyco
proteins, multidrug resistance protein etc [Transport
and binding proteins, Other].
Length = 302
Score = 27.0 bits (60), Expect = 9.0
Identities = 22/99 (22%), Positives = 32/99 (32%), Gaps = 6/99 (6%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQT-----LFFVEVT 170
I+D + +AE EE+ G D + IQ+ + V L V V
Sbjct: 195 AIIDHGRIIAEGTPEELKRRLGKDTLESRPRDIQSLKVEVSMLIAELGETGLGLLAVTVD 254
Query: 171 DDMKVNSGGGVDEELIEVVEMGLEEAREYLAQDEVRSPS 209
D DE + E+VE + PS
Sbjct: 255 SDRIKILVPDGDETVPEIVEA-AIRNGIRIRSISTERPS 292
>gnl|CDD|239055 cd02140, Nitroreductase_4, Nitroreductase-like family 4. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 192
Score = 26.5 bits (59), Expect = 9.3
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 119 DKNKSLAEIAREEVLEECGYDVPVEKLEKIQTFRSGVGSAGDRQTLFFV--EVTDDMKVN 176
++++ L +I ++ + + EK+ F++G G+ LFF V ++
Sbjct: 53 EEHEKLWDIVKDTLRAIVPAEAFAATKEKLDGFKAGYGT-----VLFFEDQAVVKGLQEK 107
>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 = 26.1 bits (58), Expect = 9.8
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 116 GIVDKNKSLAEIAREEVLEECGYDVPVEKL 145
G V+ ++L + A E+LEE G + V +L
Sbjct: 32 GKVELGETLEQAALRELLEETGLEAEVGRL 61
>gnl|CDD|179567 PRK03355, PRK03355, glycerol-3-phosphate acyltransferase;
Validated.
Length = 783
Score = 27.0 bits (60), Expect = 9.8
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 179 GGVDEELIEVVEMGLEEAREYLAQDEVRSP---SGFLFA 214
+DE+ E+ + L R+Y+ Q VRS S LFA
Sbjct: 694 DTIDEK--ELTALALGLGRQYVLQGRVRSSESVSTLLFA 730
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 0.134 0.381
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,833,204
Number of extensions: 1140790
Number of successful extensions: 1139
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1130
Number of HSP's successfully gapped: 56
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
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: 57 (25.8 bits)