RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12566
(220 letters)
>gnl|CDD|176655 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of
Caenorhabditis elegans mut-7 and similar proteins. The
mut-7 subfamily is composed of Caenorhabditis elegans
mut-7 and similar proteins found in plants and
metazoans. Mut-7 is implicated in posttranscriptional
gene silencing. It contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain possessing three conserved sequence
motifs, termed ExoI, ExoII and ExoIII, with a specific
YX(3)D pattern at ExoIII. These motifs are clustered
around the active site and contain four conserved acidic
residues that serve as ligands for the two metal ions
required for catalysis.
Length = 193
Score = 83.1 bits (206), Expect = 6e-20
Identities = 42/129 (32%), Positives = 69/129 (53%), Gaps = 3/129 (2%)
Query: 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDI 142
I +VD+ ++ + L + L+ +G+D+EWKP+ G S P +A+LQ+AT D V++LD+
Sbjct: 1 IHIVDSEEELEALLLALS-LEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDL 59
Query: 143 ITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDL 202
+ L L L +F + D+LK+GF D+ + S P +C + LDL
Sbjct: 60 LALENL-ESEDWDR-LLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDL 117
Query: 203 QLLWSKLVA 211
Q L +L
Sbjct: 118 QNLAKELQK 126
>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar
proteins. WRN is a unique RecQ DNA helicase exhibiting
an exonuclease activity. It contains a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. These motifs
are clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. Mutations in the
WRN gene cause Werner syndrome, an autosomal recessive
disorder associated with premature aging and increased
susceptibility to cancer and type II diabetes. WRN
interacts with key proteins involved in DNA replication,
recombination, and repair. It is believed to maintain
genomic stability and life span by participating in DNA
processes. WRN is stimulated by Ku70/80, an important
regulator of genomic stability.
Length = 170
Score = 60.3 bits (147), Expect = 1e-11
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 11/94 (11%)
Query: 86 VDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITL 145
D+A A+++ L +G DTEW+P+ G +ALLQ+AT R + + +
Sbjct: 1 TDSAQDAEEAVKEL--LGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHM 58
Query: 146 SKLPC-YAQLCHDLELIVFANDDLLKIGFNLMPD 178
KLP QL + +LK+G + D
Sbjct: 59 DKLPPSLKQLL--------EDPSILKVGVGIKGD 84
>gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease
D and similar proteins. Ribonuclease (RNase) D is a
bacterial enzyme involved in the maturation of small
stable RNAs and the 3' maturation of tRNA. It contains a
DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing
three conserved sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and contain
four conserved acidic residues that serve as ligands for
the two metal ions required for catalysis. In vivo,
RNase D only becomes essential upon removal of other
ribonucleases. Eukaryotic RNase D homologs include yeast
Rrp6p, human PM/Scl-100, and the Drosophila melanogaster
egalitarian protein.
Length = 178
Score = 38.3 bits (90), Expect = 0.001
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 17/81 (20%)
Query: 95 ALQDF-ARLDHNSHLGLDTE---WKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPC 150
L+D RL + +DTE P L L+QI+T VY++D + + L
Sbjct: 1 ELEDLCERLASAGVIAVDTEFMRLNTYY-----PRLCLIQISTGGEVYLIDPLAIGDLSP 55
Query: 151 YAQLCHDLELIVFANDDLLKI 171
+L A+ +++K+
Sbjct: 56 LKEL--------LADPNIVKV 68
>gnl|CDD|216604 pfam01612, DNA_pol_A_exo1, 3'-5' exonuclease. This domain is
responsible for the 3'-5' exonuclease proofreading
activity of E. coli DNA polymerase I (polI) and other
enzymes, it catalyzes the hydrolysis of unpaired or
mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
polI it is also found in the Werner syndrome helicase
(WRN), focus forming activity 1 protein (FFA-1) and
ribonuclease D (RNase D). Werner syndrome is a human
genetic disorder causing premature aging; the WRN
protein has helicase activity in the 3'-5' direction.
The FFA-1 protein is required for formation of a
replication foci and also has helicase activity; it is a
homologue of the WRN protein. RNase D is a 3'-5'
exonuclease involved in tRNA processing. Also found in
this family is the autoantigen PM/Scl thought to be
involved in polymyositis-scleroderma overlap syndrome.
Length = 172
Score = 30.3 bits (69), Expect = 0.41
Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 14/104 (13%)
Query: 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDI 142
+V T D+ L + + +DTE + L+QI+T + YI+D
Sbjct: 1 YRIVTTEDELEDL---IEELLNAKVVAVDTETTSLDTYSYTLVGCLIQISTGEGAYIID- 56
Query: 143 ITLSKLPCYAQLCHDLELI--VFANDDLLKIGFNLMPDVSIIKT 184
L+ DLE + + + ++ K+G N D+ ++
Sbjct: 57 -PLALGD-------DLEGLKRLLEDPNITKVGHNAKFDLEVLAR 92
>gnl|CDD|143638 cd07557, trimeric_dUTPase, Trimeric dUTP diphosphatases.
Trimeric dUTP diphosphatases, or dUTPases, are the most
common family of dUTPase, found in bacteria,
eukaryotes, and archaea. They catalyze the hydrolysis
of the dUTP-Mg complex (dUTP-Mg) into dUMP and
pyrophosphate. This reaction is crucial for the
preservation of chromosomal integrity as it removes
dUTP and therefore reduces the cellular dUTP/dTTP
ratio, and prevents dUTP from being incorporated into
DNA. It also provides dUMP as the precursor for dTTP
synthesis via the thymidylate synthase pathway.
dUTPases are homotrimeric, except some monomeric viral
dUTPases, which have been shown to mimic a trimer.
Active sites are located at the subunit interface.
Length = 92
Score = 28.2 bits (64), Expect = 1.1
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 62 NGWDVCKPAEEYYSLTLPPNSIILVDTADKFA 93
G+D+ E++ + LPP +LV T +
Sbjct: 1 AGYDLR-LGEDFEGIVLPPGETVLVPTGEAIE 31
>gnl|CDD|214681 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 28.9 bits (65), Expect = 1.4
Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 12/102 (11%)
Query: 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIA-TRDRVYILD 141
+I+V ++ L+ + LDTE S L L+QI+ T + +I
Sbjct: 1 VIVVTDSETLEELLEKLR--AAGGEVALDTETTGLDSYSGK--LVLIQISVTGEGAFI-- 54
Query: 142 IITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIK 183
I L ++ DL ++ + K+G N D+ ++
Sbjct: 55 -IDPLALGDDLEILKDL----LEDETITKVGHNAKFDLHVLA 91
>gnl|CDD|184865 PRK14863, PRK14863, bifunctional regulator KidO; Provisional.
Length = 292
Score = 28.3 bits (63), Expect = 3.1
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 109 GLDTEWKPNLSGGSPPTLA--LLQIATRDRVYILDI 142
GLD G +P A +L IA R + +LD
Sbjct: 16 GLDPGSSSAPRGRTPEAEARDILNIAARAGLSVLDA 51
>gnl|CDD|163706 cd08150, catalase_like, Catalase-like heme-binding proteins and
protein domains. Catalase is a ubiquitous enzyme found
in both prokaryotes and eukaryotes involved in the
protection of cells from the toxic effects of peroxides.
It catalyses the conversion of hydrogen peroxide to
water and molecular oxygen. Several other related
protein families share the catalase fold and bind to
heme, but do not necessarily have catalase activity.
Length = 283
Score = 27.5 bits (61), Expect = 5.1
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 43 VGFDLRDKIAEEESEQDVDNG---WDVCKPAEEYYSLTLPPN 81
V +D R ++ ++ +DN W P E +T+PP
Sbjct: 197 VVYDFRIQLNDDTDATTIDNPTILWPTEHPVEAVAKITIPPP 238
>gnl|CDD|214454 MTH00198, ND2, NADH dehydrogenase subunit 2; Provisional.
Length = 607
Score = 27.9 bits (62), Expect = 5.1
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 114 WKPNLSGGSP-PTLALLQIATRDRVYIL--DIITLSKL 148
W P++ G+P PT AL+ I + VYIL ++ SKL
Sbjct: 321 WTPDVYEGAPTPTTALIAIIPKFTVYILLTSLVITSKL 358
>gnl|CDD|233446 TIGR01513, NAPRTase_put, putative nicotinate
phosphoribosyltransferase. A deep split separates two
related families of proteins, one of which includes
experimentally characterized examples of nicotinate
phosphoribosyltransferase, an the first enzyme of NAD
salvage biosynthesis. This model represents the other
family. Members have a different (longer) spacing of
several key motifs and have an additional C-terminal
domain of up to 100 residues. One argument suggesting
that this family represents the same enzyme is that no
species has a member of both families. Another is that
the gene encoding this protein is located near other NAD
salvage biosynthesis genes in Nostoc and in at least
four different Gram-positive bacteria. NAD and NADP are
ubiquitous in life. Most members of this family are
Gram-positive bacteria. An additional set of mutually
closely related archaeal sequences score between the
trusted and noise cutoffs [Biosynthesis of cofactors,
prosthetic groups, and carriers, Pyridine nucleotides].
Length = 443
Score = 27.3 bits (61), Expect = 6.2
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 70 AEEYYSLTLPPNSIILVDTADKFASALQDFARL 102
A Y+ P +++LVDT D S L + +
Sbjct: 207 AFRAYAKLYPKATVLLVDTYDTLRSGLPNAIAV 239
>gnl|CDD|143467 cd07149, ALDH_y4uC, Uncharacterized ALDH (y4uC) with similarity to
Tortula ruralis aldehyde dehydrogenase ALDH21A1.
Uncharacterized aldehyde dehydrogenase (ORF name y4uC)
with sequence similarity to the moss Tortula ruralis
aldehyde dehydrogenase ALDH21A1 (RNP123) believed to
play an important role in the detoxification of
aldehydes generated in response to desiccation- and
salinity-stress, and similar sequences are included in
this CD.
Length = 453
Score = 27.2 bits (61), Expect = 7.7
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 56 SEQDVDNGWDVCKPA-EEYYSLTLPPNSIILVDTADKFASALQDFARL 102
SE+DV+ K +E SL + IL A ++FAR
Sbjct: 19 SEEDVEKAIAAAKEGAKEMKSLPAYERAEILERAAQLLEERREEFART 66
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast
Rrp6p, human polymyositis/scleroderma autoantigen
100kDa, and similar proteins. Yeast Rrp6p and its human
homolog, the polymyositis/scleroderma autoantigen 100kDa
(PM/Scl-100), are exosome-associated proteins involved
in the degradation and processing of precursors to
stable RNAs. Both proteins contain a DEDDy-type
DnaQ-like 3'-5' exonuclease domain possessing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. The motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. PM/Scl-100, an
autoantigen present in the nucleolar compartment of the
cell, reacts with autoantibodies produced by about 50%
of patients with polymyositis-scleroderma overlap
syndrome.
Length = 192
Score = 26.8 bits (60), Expect = 8.0
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 36/100 (36%)
Query: 84 ILVDTADKFASAL------QDFA-RLDHN---SHLGLDTEWKPNLSGGSPPTLALLQIAT 133
VDT +K + ++ A L+H+ S+LG L+QI+T
Sbjct: 6 TFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGF---------------TCLMQIST 50
Query: 134 RDRVYILDIITLSKLPCYAQLCHDLELI--VFANDDLLKI 171
R+ YI+D + L D+ ++ VF + ++LK+
Sbjct: 51 REEDYIVDTLKLR---------DDMHILNEVFTDPNILKV 81
>gnl|CDD|222366 pfam13764, E3_UbLigase_R4, E3 ubiquitin-protein ligase UBR4. This
is a family of E## ubiquitin ligase enzymes.
Length = 794
Score = 27.3 bits (61), Expect = 8.2
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 155 CHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSE 190
C DLEL+ DD G L+ + II L +
Sbjct: 25 CRDLELVALLEDDN---GMELLVNNKIISLDLSVKD 57
>gnl|CDD|238804 cd01570, NAPRTase_A, Nicotinate phosphoribosyltransferase
(NAPRTase), subgroup A. Nicotinate
phosphoribosyltransferase catalyses the formation of
NAMN and PPi from 5-phosphoribosy -1-pyrophosphate
(PRPP) and nicotinic acid, this is the first, and also
rate limiting, reaction in the NAD salvage synthesis.
This salvage pathway serves to recycle NAD degradation
products. This subgroup is present in bacteria and
eukaryota (except funghi).
Length = 327
Score = 26.8 bits (60), Expect = 9.5
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 74 YSLTLPPNSIILVDTADKFASALQDFARL 102
++ P N +LVDT D S L + +
Sbjct: 211 FAEAYPDNFTLLVDTYDTLRSGLPNAIAV 239
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
0.320 0.137 0.423
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,166,872
Number of extensions: 1039721
Number of successful extensions: 867
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 20
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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: 57 (25.8 bits)