RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5651
(843 letters)
>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila
Egalitarian (Egl) and similar proteins. The Egalitarian
(Egl) protein subfamily is composed of Drosophila Egl
and similar proteins. Egl is a component of an
mRNA-binding complex which is required for oocyte
specification. Egl 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. 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. The conservation of this
subfamily throughout eukaryotes suggests that its
members may be part of ancient RNA processing complexes
that are likely to participate in the regulated
processing of specific mRNAs. Some members of this
subfamily do not have a completely conserved YX(3)D
pattern at the ExoIII motif.
Length = 197
Score = 153 bits (388), Expect = 2e-42
Identities = 68/181 (37%), Positives = 99/181 (54%), Gaps = 5/181 (2%)
Query: 37 NESKVGLDLEGMDLGVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILK 96
+ +GLD EG++LG GK+ LV +A + G+I++FD+ I+F L ++LES +ILK
Sbjct: 9 KQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILK 68
Query: 97 VIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPH-TIGLNDLLKFY 155
VIH D+ L + I+L NV+DTQ A LQ + P I L LL Y
Sbjct: 69 VIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQ----EQETGGFNPDRVISLVQLLDKY 124
Query: 156 KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRL 215
+ K++++ L RE+P W RPLT DM+ YAA DV LL L++ M K +
Sbjct: 125 LYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKFLKA 184
Query: 216 L 216
+
Sbjct: 185 V 185
>gnl|CDD|218289 pfam04845, PurA, PurA ssDNA and RNA-binding protein. This family
represents most of the length of the protein.
Length = 218
Score = 138 bits (350), Expect = 3e-37
Identities = 71/203 (34%), Positives = 109/203 (53%), Gaps = 18/203 (8%)
Query: 311 TKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALLTAH- 369
+K NK+FY D+KQ+ +FIKI+EV +++I +SMSV RD+L+ + +
Sbjct: 6 SKRLDIQNKRFYLDVKQNARGRFIKIAEVGAGGRKSRITLSMSVAAEFRDYLSKFIEHYA 65
Query: 370 ----QNTPRHRYRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVG--GKLSSI 423
QN +KSE L++D R+Y+LDLK+N R RF+ I+Q + G G+ I
Sbjct: 66 QLGPQNGEHLPEDGRSALKSEFLVRDNRKYYLDLKENQRGRFLRIAQTVMRGGSGQRQQI 125
Query: 424 AFPAQDLGPIIGLISDLQQEHS---CPEDEDGAPEGNYMRCNNKRFFFNVSKNGKGTFMR 480
A PAQ + ++DL +++ ++ PEG + +NKRF+F+V N +G FMR
Sbjct: 126 ALPAQGMIEFRDALTDLIEDYGEGDEEDEPAELPEGTSLTVDNKRFYFDVGSNKRGVFMR 185
Query: 481 ISE--------ISTPSKVLTNIG 495
ISE I+ P K T
Sbjct: 186 ISEVKPNYRNSITVPEKAWTRFR 208
Score = 42.1 bits (99), Expect = 5e-04
Identities = 38/196 (19%), Positives = 83/196 (42%), Gaps = 16/196 (8%)
Query: 244 QLRRWRKDLMSSKRP-YPYIEEVNSNEYIWRNDYNVPLANAKLLNNPINRMFH------- 295
Q +R+ D+ + R + I EV + ++ + ++ A + +++
Sbjct: 12 QNKRFYLDVKQNARGRFIKIAEVGAGGR--KSRITLSMSVAAEFRDYLSKFIEHYAQLGP 69
Query: 296 KEKESANEERIEVIDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMD---QTRNQIHISM 352
+ E E+ + ++ N+K+Y D+K+++ +F++I++ M R QI +
Sbjct: 70 QNGEHLPEDGRSALKSEFLVRDNRKYYLDLKENQRGRFLRIAQTVMRGGSGQRQQIALPA 129
Query: 353 SVVGHLRDHLNALLTAHQNTPRHRYRDTHTIKSEVLIKDTRRYFLDLKDNGRARFVTISQ 412
+ RD L L+ + + L D +R++ D+ N R F+ IS+
Sbjct: 130 QGMIEFRDALTDLIEDYGEGDEEDEPAELP-EGTSLTVDNKRFYFDVGSNKRGVFMRISE 188
Query: 413 LLPVGGKLSSIAFPAQ 428
+ P +SI P +
Sbjct: 189 VKP--NYRNSITVPEK 202
Score = 37.5 bits (87), Expect = 0.016
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 302 NEERIEVIDTKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDH 361
+E E+ + NK+FYFD+ +K F++ISEV RN I + RD
Sbjct: 152 EDEPAELPEGTSLTVDNKRFYFDVGSNKRGVFMRISEVK-PNYRNSITVPEKAWTRFRDI 210
Query: 362 LN 363
Sbjct: 211 FC 212
Score = 33.6 bits (77), Expect = 0.27
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 793 VPPSYRASITIPERSWDRFIETFHQTCD 820
V P+YR SIT+PE++W RF + F + +
Sbjct: 189 VKPNYRNSITVPEKAWTRFRDIFCKYSE 216
>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 = 91.4 bits (228), Expect = 3e-21
Identities = 50/187 (26%), Positives = 84/187 (44%), Gaps = 31/187 (16%)
Query: 33 ATILNESKVGLDLEGMDLGV-DGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLES 91
+ + + +D E M L ++ L+ ++ G++++ D + + L E+L
Sbjct: 7 ERLASAGVIAVDTEFMRLNTYYPRLCLIQIS-TGGEVYLIDPLAIGDL---SPLKELLAD 62
Query: 92 DRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDL 151
I+KV H A D L +F I +N++DTQ A L L D +GL L
Sbjct: 63 PNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDS-----------VGLAAL 111
Query: 152 LKFY---KISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEY 208
++ ++ K Q R + W RPLT + L YAA DV LL L+ ++ +E
Sbjct: 112 VEELLGVELD-----KGEQ---RSD---WSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160
Query: 209 ALKQNRL 215
++ RL
Sbjct: 161 E-EEGRL 166
>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 = 89.3 bits (222), Expect = 2e-20
Identities = 50/193 (25%), Positives = 79/193 (40%), Gaps = 23/193 (11%)
Query: 19 TNLITDVQEAQSAMATILNESK-VGLDLEGMDLG-VDGKVSLVSLALQNGKIFIFDVYSC 76
++TD + + + + V LD E L GK+ L+ +++ FI D +
Sbjct: 1 VIVVTDSETLEELLEKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGAFIIDPLAL 60
Query: 77 PLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRL 136
+ L ++LE + I KV H A D L F I L+N++DT A L L P
Sbjct: 61 G-DDLEI-LKDLLEDETITKVGHNAKFDLHVLA-RFGIELENIFDTMLA-AYLLLGGPSK 116
Query: 137 LSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVES 196
+ +L K + S W RPL+ + L YAA D ++
Sbjct: 117 HGLATLLLGYLGVELDKEEQKS-----------------DWGARPLSEEQLEYAAEDADA 159
Query: 197 LLALFHRMTKEYA 209
LL L+ ++ KE
Sbjct: 160 LLRLYEKLEKELE 172
>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 = 87.7 bits (218), Expect = 6e-20
Identities = 49/189 (25%), Positives = 79/189 (41%), Gaps = 25/189 (13%)
Query: 22 ITDVQEAQSAMATILNESKVGLDLEGMDL---GVDGKVSLVSLALQNGKIFIFDVYSCPL 78
+T E + + +LN V +D E L L+ ++ G +I D +
Sbjct: 4 VTTEDELEDLIEELLNAKVVAVDTETTSLDTYSYTLVGCLIQISTGEG-AYIIDPLALGD 62
Query: 79 IMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLS 138
+ L +LE I KV H A D L +F I+L+N++DT A L
Sbjct: 63 DL--EGLKRLLEDPNITKVGHNAKFDLEVLARDFGIKLENLFDTMLAAYLLGY------- 113
Query: 139 QDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLL 198
P + L+DL + Y + + + W+ RPL+ + L YAA D + LL
Sbjct: 114 ----PRSHSLDDLAEKY----LGVELDKSEQ-CAD---WRARPLSEEQLRYAAEDADYLL 161
Query: 199 ALFHRMTKE 207
L+ ++ KE
Sbjct: 162 RLYDKLRKE 170
>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 = 76.8 bits (190), Expect = 3e-16
Identities = 52/188 (27%), Positives = 83/188 (44%), Gaps = 25/188 (13%)
Query: 22 ITDVQEAQSAMATILNESKV-GLDLEGM---DLGVDGKVSLVSLALQNGKIFIFDVYSCP 77
Q+A+ A+ +L + KV G D E G KV+L+ LA ++ + +F +
Sbjct: 1 TDSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATES-RCLLFQLAHMD 59
Query: 78 LIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLL 137
+ L ++LE ILKV G GDA L +F I ++ V D +L+
Sbjct: 60 KLP--PSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLA-KRVGPRRKLV 116
Query: 138 S-QDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVES 196
S LV +G L K K ++ N W+ RPL+ + +LYAA D +
Sbjct: 117 SLARLVEEVLG----LPLSK------PKKVR---CSN---WEARPLSKEQILYAATDAYA 160
Query: 197 LLALFHRM 204
L L+ ++
Sbjct: 161 SLELYRKL 168
>gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D,
WRN, and similar proteins. The RNase D-like group is
composed of RNase D, WRN, and similar proteins. They
contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease
domain that contains 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. RNase D is involved in the 3'-end
processing of tRNA precursors. RNase D-like proteins in
eukaryotes include yeast Rrp6p, human PM/Scl-100 and
Drosophila melanogaster egalitarian (Egl) protein. WRN
is a unique DNA helicase possessing exonuclease
activity. Mutation in the WRN gene is implicated in
Werner syndrome, a disease associated with premature
aging and increased predisposition to cancer. Yeast
Rrp6p and the human Polymyositis/scleroderma autoantigen
100kDa (PM/Scl-100) are exosome-associated proteins
involved in the degradation and processing of precursors
to stable RNAs. Egl is a component of an mRNA-binding
complex which is required for oocyte specification. The
Egl subfamily does not possess a completely conserved
YX(3)D pattern at the ExoIII motif.
Length = 161
Score = 73.7 bits (181), Expect = 3e-15
Identities = 47/167 (28%), Positives = 76/167 (45%), Gaps = 26/167 (15%)
Query: 41 VGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIH 99
+ D+E G+V+L+ L + K ++FD S L + L +LE+ I+K +H
Sbjct: 16 IAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLS--LSVDWQGLKMLLENPSIVKALH 73
Query: 100 GAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISP 159
G GD LL +F +L+ ++DT A +P L L++ +
Sbjct: 74 GIEGDLWKLLRDFGEKLQRLFDTTIAANLK-----------GLPERWSLASLVEHFL--- 119
Query: 160 NNFK--KNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
K+I + W RPLT D LYAAADV +LL ++ ++
Sbjct: 120 -GKTLDKSIS---CAD---WSYRPLTEDQKLYAAADVYALLIIYTKL 159
>gnl|CDD|223426 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and
biogenesis].
Length = 361
Score = 75.8 bits (187), Expect = 1e-14
Identities = 59/241 (24%), Positives = 98/241 (40%), Gaps = 38/241 (15%)
Query: 22 ITDVQEAQSAMATILNESKVGLDLEGMDLGV-DGKVSLVSLALQNGKIFIFDVYSCPLIM 80
IT +A A + + +D E M L ++ L+ ++ G + D + ++
Sbjct: 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEG-ASLIDPLA-GILD 58
Query: 81 FDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQD 140
L +L ++K+ H A D LL+ F + ++DTQ A
Sbjct: 59 LP-PLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGF--------- 108
Query: 141 LVPHTIGLNDLLKFYKISPNNFK--KNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLL 198
+ GL DL++ + K+ Q R + W RPL+ L YAAADVE LL
Sbjct: 109 --GTSHGLADLVEELL----GVELDKSEQ---RSD---WLARPLSEAQLEYAAADVEYLL 156
Query: 199 ALFHRMTKEYALKQNRLLLDNLIYETLFNHVVPLNIRKRRQFRQNQLRRWRK-DLMSSKR 257
L+ ++T+E A ++ RL E F + RR ++ WR+ + S
Sbjct: 157 PLYDKLTEELA-REGRLEW----AEDEFRLLP-----TRRTYKVLPEDAWREIKIAHSLD 206
Query: 258 P 258
P
Sbjct: 207 P 207
>gnl|CDD|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain
of family-A DNA polymerases, RNase D, WRN, and similar
proteins. DEDDy exonucleases, part of the DnaQ-like (or
DEDD) exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. They contain four invariant acidic
residues in three conserved sequence motifs termed ExoI,
ExoII and ExoIII. DEDDy exonucleases are classified as
such because of the presence of a specific YX(3)D
pattern at ExoIII. The four conserved acidic residues
serve as ligands for the two metal ions required for
catalysis. This family of DEDDy exonucleases includes
the proofreading domains of family A DNA polymerases, as
well as RNases such as RNase D and yeast Rrp6p. The
Egalitarian (Egl) and Bacillus-like DNA Polymerase I
subfamilies do not possess a completely conserved YX(3)D
pattern at the ExoIII motif. In addition, the
Bacillus-like DNA polymerase I subfamily has inactive
3'-5' exonuclease domains which do not possess the
metal-binding residues necessary for activity.
Length = 150
Score = 58.8 bits (142), Expect = 3e-10
Identities = 39/165 (23%), Positives = 60/165 (36%), Gaps = 19/165 (11%)
Query: 41 VGLDLEGMDL-GVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIH 99
D E L + + L+ LA++ G + V + L +LE ++ LKV
Sbjct: 2 FAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAH--DYLALELLKPLLEDEKALKVGQ 59
Query: 100 GAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGLNDLLKFYKISP 159
D G LL+ F +DT L R LV +G L+KF I+
Sbjct: 60 NLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK-LIKFESIAG 118
Query: 160 NNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRM 204
W +PLT + YAA D + L + ++
Sbjct: 119 KL---------------WFNQPLTEEQGRYAAEDADVTLQIHLKL 148
>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 = 57.6 bits (140), Expect = 2e-09
Identities = 47/156 (30%), Positives = 67/156 (42%), Gaps = 29/156 (18%)
Query: 69 FIFDVYSCPLIMFD--GKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLKNVYDTQCAF 126
+I D L + D L+EV ILKV HGA D L +F + + N++DT A
Sbjct: 55 YIVD----TLKLRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAA 110
Query: 127 TALQLSDPRLLSQDLVPHTIGLNDLLKFY-KISPNNFKKNIQNLYRENPHIWKTRPLTSD 185
L L PR L LL+ Y + + K Q W+ RPL +
Sbjct: 111 RVLNL--PRH----------SLAYLLQKYCNVDAD---KKYQL------ADWRIRPLPEE 149
Query: 186 MLLYAAADVESLLALFHRMTKEYALKQNRLLLDNLI 221
M+ YA D LL ++ R+ E L++ L NL+
Sbjct: 150 MIKYAREDTHYLLYIYDRLRNE-LLERANALAPNLL 184
>gnl|CDD|197840 smart00712, PUR, DNA/RNA-binding repeats in PUR-alpha/beta/gamma
and in hypothetical proteins from spirochetes and the
Bacteroides-Cytophaga-Flexibacter bacteria.
Length = 63
Score = 50.7 bits (122), Expect = 3e-08
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 311 TKMYQCFNKKFYFDIKQSKSTKFIKISEVNMDQTRNQIHISMSVVGHLRDHLNALL 366
+K NK+FYFD+K+++ +F++ISEV + R+ I + RD L L+
Sbjct: 4 SKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGRSSITVPEQGAAEFRDALTKLI 59
Score = 45.3 bits (108), Expect = 2e-06
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 383 IKSEVLIKDTRRYFLDLKDNGRARFVTISQLLPVGGKLSSIAFPAQDLGPIIGLISDL 440
+ S+ L + +R++ D+K+N R RF+ IS++ GG+ SSI P Q ++ L
Sbjct: 2 LASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGR-SSITVPEQGAAEFRDALTKL 58
Score = 38.4 bits (90), Expect = 7e-04
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 459 MRCNNKRFFFNVSKNGKGTFMRISEIST 486
+ NKRF+F+V +N +G F+RISE+
Sbjct: 7 LTVENKRFYFDVKENRRGRFLRISEVKN 34
>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 = 50.8 bits (122), Expect = 4e-07
Identities = 49/173 (28%), Positives = 77/173 (44%), Gaps = 21/173 (12%)
Query: 41 VGLDLE---GMDLGVDGKVSLVSLALQNGKIFIFDV---YSCPLIMFDGKLHEVLESDRI 94
VG+D E D +V+++ LA + ++F+ D+ + +D L + E +
Sbjct: 25 VGIDSEWKPSFLGDSDPRVAILQLATE-DEVFLLDLLALENLESEDWDRLLKRLFEDPDV 83
Query: 95 LKVIHGAFGD------AGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLSQDLVPHTIGL 148
LK+ G D + L R++NV D Q LQ SD L +L T GL
Sbjct: 84 LKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGL 143
Query: 149 NDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALF 201
DL++ ++ K+ Q N W+ RPL + +LYAA D LL +F
Sbjct: 144 ADLVQ--EVLGKPLDKSEQC---SN---WERRPLREEQILYAALDAYCLLEVF 188
>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D. This model describes ribonuclease
D, a 3'-exonuclease shown to act on tRNA both in vitro
and when overexpressed in vivo. Trusted members of this
family are restricted to the Proteobacteria; Aquifex,
Mycobacterial, and eukaryotic homologs are not
full-length homologs. Ribonuclease D is not essential in
E. coli and is deleterious when overexpressed. Its
precise biological role is still unknown [Transcription,
RNA processing].
Length = 367
Score = 46.7 bits (111), Expect = 3e-05
Identities = 61/261 (23%), Positives = 97/261 (37%), Gaps = 73/261 (27%)
Query: 21 LITDVQEAQSAMATILNESKVGLDLEGM-------DLGVDGKVSLVSLALQNGKIFIFDV 73
IT E + + V LD E + LG L+ +A ++ + D
Sbjct: 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLG------LIQVA-DGEQLALID- 52
Query: 74 YSCPLIMFD-GKLHEVLESDRILKVIHGA------FGDAGGLLSNFNIRLKNVYDTQCAF 126
PL++ D L E+L + ++KV+H A F + G L + ++DTQ A
Sbjct: 53 ---PLVIIDWSPLKELLRDESVVKVLHAASEDLEVFLNLFGELP------QPLFDTQIAA 103
Query: 127 TALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYRENPHIWKTRPLTSDM 186
++G L++ ++ K+ E+ W RPLT
Sbjct: 104 AFCGF-----------GMSMGYAKLVQ--EVLGVELDKS------ESRTDWLARPLTDAQ 144
Query: 187 LLYAAADVESLLALFHRMTKE--------YALKQNRLLLDNLIYETLFNHVVP----LNI 234
L YAAADV LL L+ ++ + + ++ LL D Y V P +I
Sbjct: 145 LEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYV-----VNPEDAWRDI 199
Query: 235 RKRRQFRQNQLR------RWR 249
+ Q R QL WR
Sbjct: 200 KNAWQLRPQQLAVLQALAAWR 220
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 39.3 bits (93), Expect = 0.010
Identities = 41/221 (18%), Positives = 75/221 (33%), Gaps = 36/221 (16%)
Query: 12 LRTLMNRTNLITDVQEAQSAMATILNESK-------------VGLDLEGMDLG-VDGKVS 57
++L+ R + TIL+E + D E L + ++
Sbjct: 276 FKSLLRRAAAAEAAPLDEEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELV 335
Query: 58 LVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGLLSNFNIRLK 117
+S A++ G+ + + L +LE I KV D +L+ + I L+
Sbjct: 336 GLSFAVEPGEAAYIPLDQLDREVLA-ALKPLLEDPAIKKVGQNLKYDL-HVLARYGIELR 393
Query: 118 NVYDTQCAFTALQLSDPRLLSQDLVPH-TIGLNDLLKFY-KISPNNFKKNIQNLYRENPH 175
+ D L S L P GL+ L + Y +F++
Sbjct: 394 GIAF-----------DTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQ------ 436
Query: 176 IWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNRLL 216
+ + + YAA D + L L + + L++ LL
Sbjct: 437 LTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK-LLEEPGLL 476
>gnl|CDD|237876 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
Provisional.
Length = 553
Score = 37.3 bits (87), Expect = 0.032
Identities = 28/121 (23%), Positives = 42/121 (34%), Gaps = 26/121 (21%)
Query: 97 VIHGAFGDAGGLLSNFNIRLKNVYDTQCAFTALQLSDPRLLS--QDLVPHTIGLNDLLKF 154
V LL+ +R++ +D A L S+ R S +G L K
Sbjct: 51 VWASTAALYPRLLA-AGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALG-EGLDKP 108
Query: 155 YKISPNNFKKNIQNLYRENPHIWKTRPLTSDMLLYAAADVESLLALFHRMTKEYALKQNR 214
+ S + P + LLYAAAD + LL L+ A + NR
Sbjct: 109 PQTSA------------------LSDPPDEEQLLYAAADADVLLELYA----VLADQLNR 146
Query: 215 L 215
+
Sbjct: 147 I 147
>gnl|CDD|236771 PRK10829, PRK10829, ribonuclease D; Provisional.
Length = 373
Score = 35.0 bits (81), Expect = 0.14
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 177 WKTRPLTSDMLLYAAADVESLLALFHRMTKE 207
W RPL+ YAAADV LL + ++ E
Sbjct: 139 WLARPLSERQCEYAAADVFYLLPIAAKLMAE 169
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 34.4 bits (80), Expect = 0.28
Identities = 43/281 (15%), Positives = 95/281 (33%), Gaps = 31/281 (11%)
Query: 518 NIIIKMKRRINIITTMKRSNIIKMKRRTNIITKMKMSNIKMKINTIKMKMKTNNITKAKM 577
NI ++ +++ + K ++ K K K+K + A +
Sbjct: 15 NIPDDLQSEALESAEIEKVVVDKKSKKWEFHLKFPNILPIEDFKLFKEKLKQSFSHIADI 74
Query: 578 KTSIKMKIN-------IITKMKMEIIAKMKMNNTKMKISVTTKMESV--KMVNIFTRMEM 628
K + +++ ++ EII K K N+ K + + V + I E+
Sbjct: 75 KVTFSIEVENITFTEELLLDYWNEIIEKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEI 134
Query: 629 KTNIIARVKRMTNVKMKINIIIKIMMAKTSIKMTTNIIIKMKISMIMKAKIHINKVKVNI 688
+ + + K + +IK + + I + K + + +
Sbjct: 135 ERDHL--------KKKHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEKL 186
Query: 689 TKMIMTKIITKVKMKTSIKMKINTFKVKMKISI-ITKMNITNIKMKINVITKMNMETNNI 747
K + + K + + ++I I K IT +K ++N E +
Sbjct: 187 AKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEEITPMK-------EINEEERRV 239
Query: 748 TIK-MIRMTDIKMKINTITKIKVANIIIKVTKKTNNIITKM 787
++ + K++I K + K+T T++II K
Sbjct: 240 VVEGYV----FKVEIKE-LKSGRHILTFKITDYTSSIIVKK 275
>gnl|CDD|162730 TIGR02148, Fibro_Slime, fibro-slime domain. This model
represents a conserved region of about 90 amino acids,
shared in at least 4 distinct large putative proteins
from the slime mold Dictyostelium discoideum and 10
proteins from the rumen bacterium Fibrobacter
succinogenes, and in no other species so far. We
propose here the name fibro-slime domain.
Length = 90
Score = 29.6 bits (67), Expect = 1.6
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 40 KVGLDLEGMDLGVDGKVSLVSLALQNGKIFIFDVYSC 76
K+ +D+ G V G V L +L L+ GK + FD++ C
Sbjct: 37 KLVVDIGGQHPAVPGAVDLDTLGLKEGKTYPFDIFYC 73
>gnl|CDD|117056 pfam08479, POTRA_2, POTRA domain, ShlB-type. The POTRA domain (for
polypeptide-transport-associated domain) is found
towards the N-terminus of ShlB family proteins
(pfam03865). ShlB is important in the secretion and
activation of the haemolysin ShlA. It has been
postulated that the POTRA domain has a chaperone-like
function over ShlA; it may fold back into the C-terminal
beta-barrel channel.
Length = 76
Score = 28.7 bits (65), Expect = 2.2
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 127 TALQLSDPRLLSQDLVPHTIGLNDLLKFYKISPNNFKKNIQNLYREN 173
T L +D L Q + +GL DL N K + N Y E
Sbjct: 12 TLLPPADLAALLQPYLGRCLGLADL--------NQLAKALTNAYIER 50
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
exonuclease domain of Bacillus stearothermophilus DNA
polymerase I and similar family-A DNA polymerases.
Bacillus stearothermophilus-like Polymerase I (Pol I), a
subgroup of the family-A DNA polymerases, contains an
inactive DnaQ-like 3'-5' exonuclease domain in the same
polypeptide chain as the polymerase region. The
exonuclease-like domain of these proteins possess the
same fold as the Klenow fragment (KF) of Escherichia
coli Pol I, but does not contain the four critical
metal-binding residues necessary for activity. The
function of this domain is unknown. It might act as a
spacer between the polymerase and the 5'-3' exonuclease
domains. Some members of this subgroup, such as those
from Bacillus sphaericus and Thermus aquaticus, are
thermostable DNA polymerases.
Length = 178
Score = 30.3 bits (69), Expect = 2.6
Identities = 25/90 (27%), Positives = 36/90 (40%), Gaps = 10/90 (11%)
Query: 40 KVGLDLEGMDLGVDGKVSLVSLALQNGKIFIFDVYSCPLIMFDGKLHEVLESDRILKVIH 99
+V L +E + ++ LAL NG + ++ L E LE ++I KV H
Sbjct: 5 EVALYVELLG-ENYHTADIIGLALANGGGAYYIPLEL-ALLDLAALKEWLEDEKIPKVGH 62
Query: 100 GAFGDAGG---LLSNFNIRLKNV-YDTQCA 125
DA L I L V +DT A
Sbjct: 63 ----DAKRAYVALKRHGIELAGVAFDTMLA 88
>gnl|CDD|238141 cd00229, SGNH_hydrolase, SGNH_hydrolase, or GDSL_hydrolase, is a
diverse family of lipases and esterases. The tertiary
fold of the enzyme is substantially different from that
of the alpha/beta hydrolase family and unique among all
known hydrolases; its active site closely resembles the
typical Ser-His-Asp(Glu) triad from other serine
hydrolases, but may lack the carboxlic acid.
Length = 187
Score = 30.5 bits (68), Expect = 2.7
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 140 DLVPHTIGLNDLLKFYKISPNNFKKNIQNLYR 171
DLV +G NDL + S + FK N++ L
Sbjct: 67 DLVIIELGTNDLGRGGDTSIDEFKANLEELLD 98
>gnl|CDD|131393 TIGR02340, chap_CCT_alpha, T-complex protein 1, alpha subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
alpha chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 536
Score = 31.2 bits (71), Expect = 2.8
Identities = 32/161 (19%), Positives = 60/161 (37%), Gaps = 30/161 (18%)
Query: 463 NKRFFFNVSKNGKGTFMRISEISTPSKVLTNIGIKS----NIKTDTNIRTNNINVKMKTN 518
+ +V GK + +++ S SK+ IG+ S NI D + N +
Sbjct: 129 KENLSVSVDTLGKEALINVAKTSMSSKI---IGLDSDFFSNIVVDAVLAVKTTNENGEIK 185
Query: 519 IIIKMKRRINIIT----TMKRSNIIK------------MKRRTNIITKMKMSNIKMKINT 562
IK +NI+ + + S ++K M +R I K K++ + +
Sbjct: 186 YPIK---AVNILKAHGKSARESYLVKGYALNCTRASQQMPKR---IKKAKIACLDFNLQK 239
Query: 563 IKMKMKTN-NITKAKMKTSIKMKINIITKMKMEIIAKMKMN 602
KM + + I+ + ITK +++ I N
Sbjct: 240 AKMALGVQIVVDDPAKLEQIRQREADITKERIKKILDAGAN 280
>gnl|CDD|218271 pfam04796, RepA_C, Plasmid encoded RepA protein. Family of plasmid
encoded proteins involved in plasmid replication. The
role of RepA in the replication process is not clearly
understood.
Length = 161
Score = 30.0 bits (68), Expect = 3.3
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 209 ALKQNRLLLDNLIYETLFNHVVPLNIRKRRQFRQNQL 245
L ++ + L +E+L +H VPL++R R + L
Sbjct: 100 GLWESTVTLSEEFFESLVDHPVPLDLRALRALNGSPL 136
>gnl|CDD|137602 PRK09945, PRK09945, hypothetical protein; Provisional.
Length = 418
Score = 30.8 bits (69), Expect = 3.6
Identities = 24/63 (38%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 54 GKVSLVSLALQNGK----IFIFDV-YSCPLIMFDGKLHEVLESDRILKVIHGAFGDAGGL 108
G +SL +LA NG+ F D Y+C L++ +G VLE R K+I GGL
Sbjct: 88 GAISLSTLATVNGRHPEGEFSVDQGYACGLLLENGGNLRVLEGHRAEKII---LDQEGGL 144
Query: 109 LSN 111
L N
Sbjct: 145 LVN 147
>gnl|CDD|106256 PRK13296, PRK13296, tRNA CCA-pyrophosphorylase; Provisional.
Length = 360
Score = 29.6 bits (66), Expect = 7.6
Identities = 37/195 (18%), Positives = 87/195 (44%), Gaps = 19/195 (9%)
Query: 568 KTNNITKAKMKTSIKMKINIITKMKMEIIAKMKMNNTKMKISVTTKMESVKMVNIFTRME 627
+ + K +KT ++N +T+ ++ I +NN K+ + ++E++K+ IF +
Sbjct: 155 EMLALIKELVKTG---ELNHLTRERLHIEFVKALNNPKIFFTTLKELEALKI--IFPNIS 209
Query: 628 MKTNIIA-------RVKRMTNVKMKINIIIKIMMAKTSIKMTTNIIIKMKISMIMKAKIH 680
+I + + +N+ KI + + + + + +++ K ++KA I
Sbjct: 210 CILPLIPNKSFFENPIYKGSNINEKITLCLLKIPQQQLDDIRKELLLTNKHYKLLKASIA 269
Query: 681 INKV--KVNITKMIMTKIITKVKM---KTSIKMKINTFKVKMKI--SIITKMNITNIKMK 733
I+K+ +IT + ++I + K +N +K +KI +I N ++
Sbjct: 270 ISKILEDRSITAEEIFQLIKNANIIRDKNLFAESLNLYKKYLKICDTITPHRNYQLLQTT 329
Query: 734 INVITKMNMETNNIT 748
IN I ++++ I
Sbjct: 330 INTIKNASIDSLTIK 344
>gnl|CDD|165307 PHA03006, PHA03006, hypothetical protein; Provisional.
Length = 323
Score = 29.2 bits (65), Expect = 9.7
Identities = 56/279 (20%), Positives = 107/279 (38%), Gaps = 47/279 (16%)
Query: 488 SKVLTNIGIKSNIKTDTNIRTNNINVKMKTNIIIKMKRRINIITTMKRSNIIKMKRRTNI 547
+K NI D N + + ++ + II K++ + NI + + T
Sbjct: 76 NKDEEEECFDENILIDDNNDNDEDKINIEDHNIIPKKKKSSFSDIKPEINIFE-ENNTKE 134
Query: 548 ITKMKMSNIKMKINTIKMKMKTNNITKAKMKTSIKMKINIITKMKMEIIAKMKMNNTKMK 607
K ++ + K + IK KT EII K+K N ++K
Sbjct: 135 KLKNVINQFEKKQDPIKDLSKT------------------------EIIKKLKDENKELK 170
Query: 608 ISVTTKMESVKMVNIFTRMEMKTN-IIARVKRMTNVKMKINIIIKI----MMAKTSIKMT 662
+S + + ++ +I + K + N +K++I + I ++ + I+
Sbjct: 171 KKQKKMEKSENLNELIKKLNGCCEELINKKKEIINFAIKLDISLPIDDFEILDEDEIEEI 230
Query: 663 TNIIIKMKISMIMKAKIHINKVKVNITKMIMTKIITKVKMKTSIKMKINTFKVKMKISII 722
+II I I+K +I+ +I+ I + ++ K ++TFK+ I I
Sbjct: 231 YDII----------ENIKIHKNSFDISMIIIKLIFSCIE-----KCLVDTFKLNEFIDIS 275
Query: 723 TKMNITNIKMKINVITKMNMETNNITIKMIRMTDIKMKI 761
++ I K N NNI+ I DI ++I
Sbjct: 276 KEITDDFIDNKCK--ATKNFINNNISTPEIPFIDIGIQI 312
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 0.133 0.370
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,524,767
Number of extensions: 4031494
Number of successful extensions: 3824
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3704
Number of HSP's successfully gapped: 145
Length of query: 843
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 738
Effective length of database: 6,280,432
Effective search space: 4634958816
Effective search space used: 4634958816
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 (21.9 bits)
S2: 63 (28.2 bits)