RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13065
(114 letters)
>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 = 106 bits (268), Expect = 5e-31
Identities = 39/96 (40%), Positives = 55/96 (57%), Gaps = 6/96 (6%)
Query: 13 AKQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIPGVPIDFKFAPQTRGEIKACQWFP 72
++V EETGFD S I +D Y+E Q +LY++PGVP D F P+TR EI +WF
Sbjct: 45 IREVYEETGFDISKYIDKDDYIELIIRGQNVKLYIVPGVPEDTPFEPKTRKEISKIEWFD 104
Query: 73 IGDLPSSRKEIKTVLINGTPVGTNAFFMIMPFINSI 108
I DLP+ + + +N FFM++PFI +
Sbjct: 105 IKDLPTKKN------KKIPGLNSNKFFMVIPFIKPL 134
>gnl|CDD|215841 pfam00293, NUDIX, NUDIX domain.
Length = 133
Score = 34.8 bits (80), Expect = 0.002
Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 2/64 (3%)
Query: 16 VLEETGFDSS--HLIAEDSYLETTYNDQLTRLYLIPGVPIDFKFAPQTRGEIKACQWFPI 73
+ EETG L+ Y + + + E+ +W P+
Sbjct: 52 LEEETGLRVLLLLLLGVLEYPAPGRDGGEHVHVFLAELLGGEPEPQPNEDEVSEVRWVPL 111
Query: 74 GDLP 77
+L
Sbjct: 112 EELL 115
>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 = 31.9 bits (73), Expect = 0.020
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 13 AKQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYL-IPGVPIDFKFAPQTRGEIKACQWF 71
+++ EETG L YL + TR ++ + VP + P+ EI C+W
Sbjct: 41 RRELQEETGLQGLDL----LYL-FHVDGGSTRHHVFVASVPPSAQ--PKPSNEIADCRWL 93
Query: 72 PIGDLPSSRKEIKTVLI 88
+ L T LI
Sbjct: 94 SLDALGDLNASAATRLI 110
>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 = 32.1 bits (73), Expect = 0.024
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 1/64 (1%)
Query: 16 VLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIP-GVPIDFKFAPQTRGEIKACQWFPIG 74
V EETG D L Y + ++ + + + + EI +W +
Sbjct: 48 VREETGLDVDVLRLLGVYEVESPDEGEHAVVFVFLARLVGGEPTLLPPDEISEVRWVTLD 107
Query: 75 DLPS 78
+LP+
Sbjct: 108 ELPA 111
>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 = 30.4 bits (69), Expect = 0.083
Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 15/72 (20%)
Query: 13 AKQVLEETGFDSS---HLIAEDSYLETTYNDQL----TRLYLIPGVPIDFKFAPQTRGEI 65
+++LEE G + L+ + + D + R P + EI
Sbjct: 43 RRELLEELGIRLAVVAELLGVYYHSASGSWDHVIVFRARADTQPVIRPS--------HEI 94
Query: 66 KACQWFPIGDLP 77
++FP LP
Sbjct: 95 SEARFFPPDALP 106
>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 = 29.9 bits (68), Expect = 0.14
Identities = 22/81 (27%), Positives = 30/81 (37%), Gaps = 7/81 (8%)
Query: 14 KQVLEETGFDSSH--LIAEDSYLETTYNDQLTRLY--LIPGVPIDFKFAPQTRGEIKACQ 69
K+V EETG D L A D + Q ++Y + +F P E
Sbjct: 45 KEVKEETGLDVKVRKLAAVDDRNKHHPPPQPYQVYKLFFLCEILGGEFKPNI--ETSEVG 102
Query: 70 WFPIGDLPS-SRKEIKTVLIN 89
+F + DLP S K I
Sbjct: 103 FFALDDLPPLSEKRNTEEQIE 123
>gnl|CDD|234393 TIGR03914, UDG_fam_dom, uracil-DNA glycosylase family domain. This
model represents a clade within the uracil-DNA
glycosylase superfamily. Among characterized proteins,
it most closely resembles the Thermus thermophilus
uracil-DNA glycosylase TTUDGA, which acts uracil
(deamidated cytosine) in both single-stranded DNA and
U/G pairs of double-stranded DNA. This domain may occur
either as a stand-alone protein or as the C-terminal
domain of a fusion with another domain that always pairs
with a particular radical-SAM family protein.
Length = 230
Score = 28.4 bits (64), Expect = 0.65
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 9/25 (36%)
Query: 55 FKFAPQ---------TRGEIKACQW 70
FKF P+ GE+ AC+W
Sbjct: 126 FKFEPRGKRRLHQKPNAGEVDACRW 150
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 26.9 bits (60), Expect = 1.8
Identities = 10/45 (22%), Positives = 21/45 (46%)
Query: 12 EAKQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIPGVPIDFK 56
E K+++E+ S + + +E D + L+ G P+ F+
Sbjct: 13 EVKKLVEKLEEYSGEELPGKAEVEVAKCDDKFEIILVDGEPLLFQ 57
>gnl|CDD|212112 cd10801, LamB_YcsF_like_1, uncharacterized proteins similar to the
Aspergillus nidulans lactam utilization protein LamB.
This mainly bacterial subfamily of the LamB/YbgL family,
contains many well conserved uncharacterized proteins.
Although their molecular function remains unknown, those
proteins show high sequence similarity to the
Aspergillus nidulans lactam utilization protein LamB,
which might be required for conversion of exogenous
2-pyrrolidinone to endogenous GABA.
Length = 233
Score = 26.4 bits (59), Expect = 3.1
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 101 IMPFINSINIA 111
+MP I+S NIA
Sbjct: 17 LMPLISSCNIA 27
>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 = 26.1 bits (58), Expect = 3.2
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 3 EEIMMNIISEAKQVLEETGFDSSHL--IAEDSYLETTYNDQLTR--LYLIPGV-PIDFKF 57
E+I + E VLEETG D+ + + + + LY I + P+ F
Sbjct: 40 EDIFDGAVRE---VLEETGIDTEFVSVVG----FRHAHPGAFGKSDLYFICRLKPLSFDI 92
Query: 58 APQTRGEIKACQWFPIGDL 76
T EI A +W P+ +
Sbjct: 93 NFDTS-EIAAAKWMPLEEY 110
>gnl|CDD|198378 cd10427, FGGY_GK_1, Uncharacterized subgroup; belongs to the
glycerol kinases subfamily of the FGGY family of
carbohydrate kinases. This subgroup contains
uncharacterized bacterial proteins belonging to the
glycerol kinase subfamily of the FGGY family of
carbohydrate kinases. The glycerol kinase subfamily
includes glycerol kinases (GK; EC 2.7.1.30), and
glycerol kinase-like proteins from all three kingdoms
of living organisms. Glycerol is an important
intermediate of energy metabolism and it plays
fundamental roles in several vital physiological
processes. GKs are involved in the entry of external
glycerol into cellular metabolism. They catalyze the
rate-limiting step in glycerol metabolism by
transferring a phosphate from ATP to glycerol thus
producing glycerol 3-phosphate (G3P) in the cytoplasm.
Under different conditions, GKs from different species
may exist in different oligomeric states. The monomer
of GKs is composed of two large domains separated by a
deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 487
Score = 26.5 bits (59), Expect = 3.6
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 3 EEIMMNIISEAKQVLEETGFDSS 25
EEI N + K +LEE G D +
Sbjct: 46 EEIYENTLQAVKDLLEEFGIDPA 68
>gnl|CDD|179214 PRK01060, PRK01060, endonuclease IV; Provisional.
Length = 281
Score = 26.3 bits (59), Expect = 3.7
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 10 ISEAKQVLEETGFDSSHLIAEDSYL 34
I K E+ G ++ YL
Sbjct: 49 IEAFKAACEKYGISPEDILVHAPYL 73
>gnl|CDD|235312 PRK04792, tolB, translocation protein TolB; Provisional.
Length = 448
Score = 26.5 bits (59), Expect = 3.7
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 7 MNIISEAKQVLEETGFDSSHLIAEDSYL---ETTYNDQLTRLYLIPGVPIDFKFA---PQ 60
++ + A QVL T D S +A + + TTY + ++ V ID +F P
Sbjct: 379 QDLETGAMQVLTSTRLDESPSVAPNGTMVIYSTTYQGK----QVLAAVSIDGRFKARLPA 434
Query: 61 TRGEIKACQWFP 72
+GE+K+ W P
Sbjct: 435 GQGEVKSPAWSP 446
>gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional.
Length = 348
Score = 25.8 bits (57), Expect = 6.4
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 2 MEEIMMNIISEAKQVLEETG 21
+E++++NI+ A Q L G
Sbjct: 238 IEQVLLNIVRNALQALGPEG 257
>gnl|CDD|178769 PLN03230, PLN03230, acetyl-coenzyme A carboxylase carboxyl
transferase; Provisional.
Length = 431
Score = 25.7 bits (56), Expect = 7.4
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 8 NIISEAKQVLEETGFDSSHLIAEDSYLETTYNDQLTR 44
N I E +++ +TG D S IAE LE Y DQ+ R
Sbjct: 87 NRIDEVRELANKTGVDFSAQIAE---LEERY-DQVRR 119
>gnl|CDD|236143 PRK08055, PRK08055, chorismate mutase; Provisional.
Length = 181
Score = 25.4 bits (56), Expect = 7.8
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 66 KACQWFPIGDLPSSRKEIKTVLINGTPVGTNAFFMIMPFINSINIAGK 113
KA PI DL +K + G + I PFI + A K
Sbjct: 48 KAEHHLPIEDLTQEQKVLAEAEEEAASNGLDP-ESIKPFIVAQMDAAK 94
>gnl|CDD|213509 TIGR00134, gatE_arch, glutamyl-tRNA(Gln) amidotransferase, subunit
E. This peptide is found only in the Archaea. It is
paralogous to the gatB-encoded subunit of Glu-tRNA(Gln)
amidotransferase. The GatABC system operates in many
bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln).
However, the homologous system in archaea instead
converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln)
is converted to Gln-tRNA(Gln) by a heterodimeric
amidotransferase of GatE (this protein) and GatD. The
Archaea have an Asp-tRNA(Asn) amidotransferase instead
of an Asp--tRNA ligase, but the genes have not been
identified. It is likely that this protein replaces gatB
in Asp-tRNA(Asn) amidotransferase but that both enzymes
share gatA [Protein synthesis, tRNA aminoacylation].
Length = 620
Score = 25.6 bits (56), Expect = 8.1
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 7 MNIISEA----KQVLE---ETGFDSSHLIAEDSYLET 36
M ++ E K V++ GF + L+A D +LET
Sbjct: 108 MRVVDEFHTMRKIVIDGSNTGGFQRTGLVATDGHLET 144
>gnl|CDD|212099 cd10787, LamB_YcsF_like, LamB/YcsF family of lactam utilization
protein. The LamB/YbgL family includes the Aspergillus
nidulans protein LamB, and its homologs from all three
kingdoms of life. The lamb gene locates at the lam locus
of Aspergillus nidulans, consisting of two divergently
transcribed genes, lamA and lamB, needed for the
utilization of lactams such as 2-pyrrolidinone. Both
genes are under the control of the positive regulatory
gene amdR and are subject to carbon and nitrogen
metabolite repression. Although the exact molecular
function of LamB is unknown, it might be required for
conversion of exogenous 2-pyrrolidinone to endogenous
GABA.
Length = 238
Score = 25.1 bits (56), Expect = 8.5
Identities = 5/11 (45%), Positives = 8/11 (72%)
Query: 101 IMPFINSINIA 111
++P + S NIA
Sbjct: 22 LLPLVTSANIA 32
>gnl|CDD|177873 PLN02228, PLN02228, Phosphoinositide phospholipase C.
Length = 567
Score = 25.4 bits (55), Expect = 8.6
Identities = 12/26 (46%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 48 IPGVPIDFKFAPQTRGEIKACQWFPI 73
I GVP D R E QWFPI
Sbjct: 466 IAGVPRD---TVSYRTETAVDQWFPI 488
>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
Length = 815
Score = 25.6 bits (56), Expect = 8.9
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 7 MNIISEAKQVLEETGFDSSHLIAEDS 32
+ I + + LE G D LI E++
Sbjct: 92 LGIYDDVQGALEAMGLDLEELIDEEN 117
>gnl|CDD|221064 pfam11294, DUF3095, Protein of unknown function (DUF3095). Some
members in this bacterial family of proteins are
annotated as adenylyl cyclase however this cannot be
confirmed. Currently no function is known.
Length = 373
Score = 25.3 bits (56), Expect = 8.9
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 68 CQWFPIGDLPSSRKEIKTVLINGTPVGTNAFFM 100
C+W I PS EI ++L+ A F
Sbjct: 177 CRWDEI---PSRNGEILSLLVVPGSSTDPADFR 206
>gnl|CDD|212668 cd10225, MreB_like, MreB and similar proteins. MreB is a bacterial
protein which assembles into filaments resembling those
of eukaryotic F-actin. It is involved in determining the
shape of rod-like bacterial cells, by assembling into
large fibrous spirals beneath the cell membrane. MreB
has also been implicated in chromosome segregation;
specifically MreB is thought to bind to and segregate
the replication origin of bacterial chromosomes.
Length = 320
Score = 25.1 bits (56), Expect = 9.5
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 2 MEEIMMNIISEAKQVLEET 20
++E + I+ K VLE+T
Sbjct: 243 LKEPLDEIVEAIKSVLEKT 261
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
0.321 0.138 0.402
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,858,392
Number of extensions: 498676
Number of successful extensions: 562
Number of sequences better than 10.0: 1
Number of HSP's gapped: 559
Number of HSP's successfully gapped: 36
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)