Score = 104 (41.7 bits), Expect = 1.5e-08, Sum P(2) = 1.5e-08
Identities = 24/65 (36%), Positives = 32/65 (49%)
Query: 50 RCTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFAGMEMNGKVDGLGRCNL 109
R A L LC GNRC+IIQL + ++P L++FL D F G + L R
Sbjct: 211 RSDPPANTLQLCVGNRCIIIQLFYCNRVPHVLRRFLGDRNHTFVGFWNSQDAGKLKRSRH 270
Query: 110 RCKTA 114
R + A
Sbjct: 271 RLEIA 275
Score = 95 (38.5 bits), Expect = 8.0e-05, P = 8.0e-05
Identities = 33/121 (27%), Positives = 54/121 (44%)
Query: 2 GKYELDIQGNNVKVTVVDHAALID-DNIXXXXXXXXRQRLVGIDVKFNHRCTKKAEMLIL 60
G+ + + N+ +T L + +N + +VG D ++ K +L L
Sbjct: 12 GRIRVTVARNDRDITSEVRTFLCNKENANKIIGLDTERSVVGGDSEYPPE--SKLVILEL 69
Query: 61 CAGNRCLIIQLCHL--GQIPESLKKFLADETICFAGMEMNGKVDGL-GRCNLRCKTAVEL 117
G CLII L ++ ++P SL FL F G+ +N + L C L CK AV++
Sbjct: 70 SDGQNCLIIPLPYVQGNKLPVSLTNFLNLPDFTFTGVGINKALKMLKSECGLTCKNAVDI 129
Query: 118 G 118
G
Sbjct: 130 G 130
Score = 100 (40.3 bits), Expect = 0.00073, P = 0.00073
Identities = 29/87 (33%), Positives = 43/87 (49%)
Query: 41 VGIDVK----FNHRCTKKAEMLILCAG-NRCLIIQLCHLGQIPESLKKFLADETICFAGM 95
VG D++ F TKK M+ LCA ++C + + + P LK FL DE I G+
Sbjct: 67 VGFDLEWPPSFTKGKTKKVAMVQLCASEDKCYLFHISSMSGFPPGLKMFLEDENIMKVGV 126
Query: 96 EMNG-KVDGLGRCNLRCKTAVELGHLA 121
+ G K L +++ K V+L LA
Sbjct: 127 GIEGDKWKLLSDYDIKLKNIVDLSDLA 153
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.326 0.142 0.432 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 123 115 0.00091 102 3 11 22 0.41 30
29 0.45 32
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 9
No. of states in DFA: 517 (55 KB)
Total size of DFA: 115 KB (2077 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 24
Search cpu time: 9.88u 0.15s 10.03t Elapsed: 00:00:00
Total cpu time: 9.88u 0.15s 10.03t Elapsed: 00:00:00
Start: Fri May 10 08:10:24 2013 End: Fri May 10 08:10:24 2013
GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA
Score = 69.5 bits (171), Expect = 4e-16
Identities = 35/111 (31%), Positives = 57/111 (51%), Gaps = 8/111 (7%)
Query: 18 VDHAALIDDNIAALKALLKRQRLVGIDVKFNHRCTKKAE----MLILCAGNRCLIIQLCH 73
D A ++ A+K LL ++++VG D ++ K +L L +RCL+ QL H
Sbjct: 1 TDSAQDAEE---AVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAH 57
Query: 74 LGQIPESLKKFLADETICFAGMEMNGKVDGLGR-CNLRCKTAVELGHLAAR 123
+ ++P SLK+ L D +I G+ + G L R + + V+L HLA R
Sbjct: 58 MDKLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKR 108
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
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.
>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.
>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-
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses 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) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
>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.
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.
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.
The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
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' exonucle
>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.
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
>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
Probab=97.23 E-value=0.00097 Score=48.27 Aligned_cols=78 Identities=22% Similarity=0.170 Sum_probs=54.7
Q ss_pred EEEEEee--ecCCCCCceEEEeeeCCeeEEEEccccCCChHHHHHhhcCCCceEEeeeechhhhhhccCCCccCce-eec
Q 037980 41 VGIDVKF--NHRCTKKAEMLILCAGNRCLIIQLCHLGQIPESLKKFLADETICFAGMEMNGKVDGLGRCNLRCKTA-VEL 117 (123)
Q Consensus 41 vG~D~Ew--~p~~~~~vallQl~~~~~cll~~l~~~~~~p~~L~~~L~d~~i~kvGv~i~~D~~kL~~~gl~~~~~-vDL 117 (123)
+.+|+|. ......++..+++|.+++++.+.+.+.......|+++|+|+++.|+|.+++.|.+.|.++|+...+. +|.
T Consensus 6 ~~~~~~~~~~~~~~~~l~~i~l~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt 85 (178)
T cd06140 6 VALYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDT 85 (178)
T ss_pred eEEEEEEcCCCcceeeEEEEEEEeCCcEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHHHHCCCcCCCcchhH
Confidence 3444444 3333457778999988777666543310022348999999999999999999998886699887654 665
Q ss_pred H
Q 037980 118 G 118 (123)
Q Consensus 118 ~ 118 (123)
.
T Consensus 86 ~ 86 (178)
T cd06140 86 M 86 (178)
T ss_pred H
Confidence 4
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.
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases
Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain 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. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which 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 patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases
The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
