RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780636|ref|YP_003065049.1| ribonuclease D [Candidatus
Liberibacter asiaticus str. psy62]
         (207 letters)



>gnl|CDD|30697 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and
           biogenesis].
          Length = 361

 Score =  218 bits (557), Expect = 7e-58
 Identities = 81/203 (39%), Positives = 112/203 (55%), Gaps = 7/203 (3%)

Query: 6   VHEGDIPAECAARY--VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA 63
           +  GD+ A   A      AIA+DTE + L     RLC++Q+S G+G   +I   AG  + 
Sbjct: 1   ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGA-SLIDPLAGILDL 59

Query: 64  PNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNL 123
           P LV +L D    KIFH  RFD+ VL   FG+   P+F T+IA++L    T  HGL D +
Sbjct: 60  PPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLV 118

Query: 124 KELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSC 183
           +ELLG+ + K++Q SDW A  LS+ QL+YAA+DV +L  L  + TE+L R GR + A   
Sbjct: 119 EELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDE 178

Query: 184 CNFLMDRA---ELDLLGWENVDI 203
              L  R     L    W  + I
Sbjct: 179 FRLLPTRRTYKVLPEDAWREIKI 201


>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 =  180 bits (459), Expect = 2e-46
 Identities = 64/171 (37%), Positives = 94/171 (54%), Gaps = 7/171 (4%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLSPGDGT--VDIIRIAAGQKNAPNLVGMLVDEKREKI 78
             IAVDTE + L     RLC++Q+S G     +D + I     +   L  +L D    K+
Sbjct: 13  GVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI----GDLSPLKELLADPNIVKV 68

Query: 79  FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138
           FH  R D+ +L   FG+  + +F T+IA+RL     +  GL   ++ELLG+ + K +Q S
Sbjct: 69  FHAAREDLELLKRDFGILPQNLFDTQIAARLLGLG-DSVGLAALVEELLGVELDKGEQRS 127

Query: 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMD 189
           DWS   L+DEQL+YAA DV +L  L  +  E+L+  GR + A   C  L+D
Sbjct: 128 DWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECELLLD 178


>gnl|CDD|144991 pfam01612, 3_5_exonuc, 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 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). 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 =  125 bits (315), Expect = 1e-29
 Identities = 53/155 (34%), Positives = 83/155 (53%), Gaps = 4/155 (2%)

Query: 20  VDAIAVDTET--LGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREK 77
              +AVDTET  L         C++Q+S G+G   II   A   +   L  +L D    K
Sbjct: 20  AKVVAVDTETTSLDTYSYTLVGCLIQISTGEGAY-IIDPLALGDDLEGLKRLLEDPNITK 78

Query: 78  IFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137
           + H  +FD+ VL   FG+++  +F T +A+ L   Y   H L D  ++ LG+ + K++Q 
Sbjct: 79  VGHNAKFDLEVLARDFGIKLENLFDTMLAAYL-LGYPRSHSLDDLAEKYLGVELDKSEQC 137

Query: 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172
           +DW A  LS+EQL+YAA D  +L  L  +  ++L+
Sbjct: 138 ADWRARPLSEEQLRYAAEDADYLLRLYDKLRKELE 172


>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. 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)..
          Length = 155

 Score =  105 bits (262), Expect = 1e-23
 Identities = 48/155 (30%), Positives = 69/155 (44%), Gaps = 4/155 (2%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80
             +A DTET GL   R +L  +Q++       I      +++   L  +L DE   K+ H
Sbjct: 1   KEVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGH 60

Query: 81  YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140
             +FD+ VL          +F T +A+ L       H L D  KE LGI + K +Q    
Sbjct: 61  DAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGK 120

Query: 141 S----ADDLSDEQLQYAASDVVHLHALRLQFTEKL 171
                A  LS+E L+YAA D   L  L  +  E+L
Sbjct: 121 GAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155


>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 = 67.9 bits (166), Expect = 2e-12
 Identities = 35/141 (24%), Positives = 61/141 (43%), Gaps = 9/141 (6%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLS---PGDGTVDIIRIAAGQKNAPNLVGMLVDEKR-E 76
           D IA D E          + ++QL          D + ++         + ML++     
Sbjct: 14  DVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVD----WQGLKMLLENPSIV 69

Query: 77  KIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ 136
           K  H    D+  L   FG +++ +F T IA+ L +    +  L   ++  LG  + K+  
Sbjct: 70  KALHGIEGDLWKLLRDFGEKLQRLFDTTIAANL-KGLPERWSLASLVEHFLGKTLDKSIS 128

Query: 137 SSDWSADDLSDEQLQYAASDV 157
            +DWS   L+++Q  YAA+DV
Sbjct: 129 CADWSYRPLTEDQKLYAAADV 149


>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 = 62.2 bits (152), Expect = 9e-11
 Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 3/123 (2%)

Query: 36  RDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95
           R+++ ++QL+  +    + ++A   K  P+L  +L D    K+    + D   L   FG+
Sbjct: 36  RNKVALLQLA-TESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGI 94

Query: 96  RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLG--INISKAQQSSDWSADDLSDEQLQYA 153
            VR V      ++          L   ++E+LG  ++  K  + S+W A  LS EQ+ YA
Sbjct: 95  EVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYA 154

Query: 154 ASD 156
           A+D
Sbjct: 155 ATD 157


>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 = 56.1 bits (135), Expect = 6e-09
 Identities = 38/153 (24%), Positives = 63/153 (41%), Gaps = 8/153 (5%)

Query: 22  AIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLV-DEKREKIFH 80
             A DTET  L      L ++QL+   G   +I + A    A  L+  L+ DEK  K+  
Sbjct: 1   VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPV-AHDYLALELLKPLLEDEKALKVGQ 59

Query: 81  YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINI--SKAQQSS 138
             ++D  +L   F       F T + + +  +   +  +   ++  LG  +   ++    
Sbjct: 60  NLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGK 119

Query: 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171
            W    L++EQ +YAA D        LQ   KL
Sbjct: 120 LWFNQPLTEEQGRYAAEDADVT----LQIHLKL 148


>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 = 54.6 bits (132), Expect = 2e-08
 Identities = 41/183 (22%), Positives = 78/183 (42%), Gaps = 26/183 (14%)

Query: 11  IPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGM- 69
             A    +    I +D E +  + R+ +LC+VQ++   G + +  I        ++V + 
Sbjct: 1   KEAIIHLKKQKVIGLDCEGVN-LGRKGKLCLVQIATRTGQIYLFDILKL----GSIVFIN 55

Query: 70  -----LVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIA-----SRLTRTYT--NQH 117
                L  +K  K+ H  R D   L++ +G+++  VF T++A      + T  +      
Sbjct: 56  GLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVI 115

Query: 118 GLKDNLKELLGINISK--------AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169
            L   L + L I+IS          +    W+   L+++ ++YAA DV+ L  L     +
Sbjct: 116 SLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLD 175

Query: 170 KLQ 172
            L 
Sbjct: 176 ALI 178


>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
           domains [DNA replication, recombination, and repair].
          Length = 593

 Score = 51.0 bits (122), Expect = 2e-07
 Identities = 41/167 (24%), Positives = 63/167 (37%), Gaps = 11/167 (6%)

Query: 16  AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN---LVGMLVD 72
                  IA DTET GL P    L  + ++  +     I +  G +       L  +L D
Sbjct: 18  KLNAAANIAFDTETDGLDPHGADLVGLSVASEEEAA-YIPLLHGPEQLNVLAALKPLLED 76

Query: 73  EKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGI--- 129
           E  +K+    ++D  VL    G+     F T +AS L       H L D  K  LG+   
Sbjct: 77  EGIKKVGQNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETI 135

Query: 130 ---NISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173
              +I+   +     AD   ++  +YAA D      L      +L +
Sbjct: 136 TFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182


>gnl|CDD|176651 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.
          Length = 193

 Score = 49.1 bits (118), Expect = 9e-07
 Identities = 38/154 (24%), Positives = 59/154 (38%), Gaps = 20/154 (12%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA--GQKNAPN------LVGMLVD 72
              A DTET  L P +  L  +  +   G    I +    G +  P       L  +L D
Sbjct: 6   KVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLED 65

Query: 73  EKREKIFHYGRFDIAVLFYTFGVRVRPVFC-TKIASRLTRTYTNQHGLKDNLKELLG--- 128
              +K+    +FD+ VL    G+ +R     T +AS L      +HGL D  +  LG   
Sbjct: 66  PSIKKVGQNLKFDLHVL-ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKT 124

Query: 129 INISK-----AQQSSDWSADDLSDEQLQYAASDV 157
           I+         +Q +        ++  +YAA D 
Sbjct: 125 ISFEDLVGKGKKQITF--DQVPLEKAAEYAAEDA 156


>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 = 45.3 bits (108), Expect = 1e-05
 Identities = 40/142 (28%), Positives = 63/142 (44%), Gaps = 19/142 (13%)

Query: 23  IAVDTET------LGLMPRRDRLCIVQLSP--GDGTVDIIRIAAGQKNAPNLVGMLVDEK 74
           IAVD E       LG        C++Q+S    D  VD +++   + +   L  +  D  
Sbjct: 27  IAVDLEHHSYRSYLGFT------CLMQISTREEDYIVDTLKL---RDDMHILNEVFTDPN 77

Query: 75  REKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134
             K+FH    DI  L   FG+ V  +F T  A+R+      +H L   L++   ++  K 
Sbjct: 78  ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNL--PRHSLAYLLQKYCNVDADKK 135

Query: 135 QQSSDWSADDLSDEQLQYAASD 156
            Q +DW    L +E ++YA  D
Sbjct: 136 YQLADWRIRPLPEEMIKYARED 157


>gnl|CDD|37417 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonuclease complex,
           subunit PM/SCL-100 (Rrp6) [Translation, ribosomal
           structure and biogenesis].
          Length = 687

 Score = 44.6 bits (105), Expect = 2e-05
 Identities = 45/171 (26%), Positives = 73/171 (42%), Gaps = 7/171 (4%)

Query: 20  VDAIAVDTETLGLMPRRDRLCIVQLS--PGDGTVDIIRIAAGQKNAPNLVGMLVDEKREK 77
           V   AVD E           C++Q+S    D  +D  ++   + +   L  +  D    K
Sbjct: 212 VIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKL---RDHIGILNEVFSDPGIVK 268

Query: 78  IFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137
           +FH    DI  L   FG+ V  +F T  ASRL      +  L   L+ + G+  +K  Q 
Sbjct: 269 VFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGL--PRPSLAYLLECVCGVLTNKKYQL 326

Query: 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLM 188
           +DW    L +E ++YA  D  +L  +     ++L+RL +    T   +  M
Sbjct: 327 ADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDM 377


>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 = 44.6 bits (106), Expect = 2e-05
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 117 HGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASD 156
            GL D ++E+LG  + K++Q S+W    L +EQ+ YAA D
Sbjct: 141 KGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALD 180


>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 = 40.3 bits (95), Expect = 4e-04
 Identities = 34/165 (20%), Positives = 62/165 (37%), Gaps = 10/165 (6%)

Query: 21  DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80
           D +A+  E LG       +  + L+ G G    I +     +   L   L DEK  K+ H
Sbjct: 4   DEVALYVELLGENYHTADIIGLALANGGGAY-YIPLELALLDLAALKEWLEDEKIPKVGH 62

Query: 81  YGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKA----- 134
             +    V     G+ +  V F T +A+ L     + + L D  K  LG  +        
Sbjct: 63  DAKRAY-VALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYG 121

Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179
           + +     D+  +   ++ A     +  L  +  E+L+   + +L
Sbjct: 122 KGAKFAVPDE--EVLAEHLARKAAAIARLAPKLEEELEENEQLEL 164


>gnl|CDD|39574 KOG4373, KOG4373, KOG4373, Predicted 3'-5' exonuclease [General
           function prediction only].
          Length = 319

 Score = 35.0 bits (80), Expect = 0.013
 Identities = 15/32 (46%), Positives = 18/32 (56%)

Query: 132 SKAQQSSDWSADDLSDEQLQYAASDVVHLHAL 163
            K  + SDWS   LSD+QL  A+ DV   H L
Sbjct: 249 DKEIRMSDWSVYPLSDDQLLQASIDVYVCHKL 280


>gnl|CDD|37418 KOG2207, KOG2207, KOG2207, Predicted 3'-5' exonuclease
           [Replication, recombination and repair].
          Length = 617

 Score = 33.4 bits (76), Expect = 0.039
 Identities = 17/41 (41%), Positives = 22/41 (53%)

Query: 118 GLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV 158
           GL D    LLG  ++K +Q S+W    L   Q+ YAA D V
Sbjct: 532 GLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAV 572


>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family.  DEDDh
           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. These proteins contain four
           invariant acidic residues in three conserved sequence
           motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
           are classified as such because of the presence of
           specific Hx(4)D conserved pattern at the ExoIII motif.
           The four conserved acidic residues are clustered around
           the active site and serve as ligands for the two metal
           ions required for catalysis. Most DEDDh exonucleases are
           the proofreading subunits (epsilon) or domains of
           bacterial DNA polymerase III, the main replicating
           enzyme in bacteria, which functions as the chromosomal
           replicase. Other members include other DNA and RNA
           exonucleases such as RNase T, Oligoribonuclease, and RNA
           exonuclease (REX), among others.
          Length = 159

 Score = 32.7 bits (75), Expect = 0.086
 Identities = 29/144 (20%), Positives = 45/144 (31%), Gaps = 32/144 (22%)

Query: 23  IAVDTETLGLMPRRDR---LCIVQLSPGDGTVD---------------IIRI----AAGQ 60
           +  DTET GL P++DR   +  V++  G   V+                  I        
Sbjct: 1   VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEML 60

Query: 61  KNAPNL---VGMLVDEKREKIF--HYGRFDIAVLFYTF-----GVRVRPVFCTKIASRLT 110
            +AP     +   ++    ++   H   FD+  L              P   T   +R  
Sbjct: 61  ADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRL 120

Query: 111 RTYTNQHGLKDNLKELLGINISKA 134
                 H L   L E  GI +  A
Sbjct: 121 LPGLRSHRLGLLLAERYGIPLEGA 144


>gnl|CDD|32998 COG3185, COG3185, 4-hydroxyphenylpyruvate dioxygenase and related
           hemolysins [Amino acid transport and metabolism /
           General function prediction only].
          Length = 363

 Score = 26.0 bits (57), Expect = 7.0
 Identities = 25/93 (26%), Positives = 31/93 (33%), Gaps = 8/93 (8%)

Query: 11  IPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGML 70
           I  E  A  VD  A+      L      L  V    G    D+     G + A   VG+ 
Sbjct: 113 IDTEIGAGEVDIPAIRGIGGSL------LYFVDRYGGRSIYDVEFEPNGAQGASGGVGLT 166

Query: 71  VDEKREKIFHYGRFDIAVLFYT--FGVRVRPVF 101
             +        G+ D  VLFY   FG R    F
Sbjct: 167 AIDHLTHNVKAGQMDTWVLFYESLFGFREIQYF 199


>gnl|CDD|30959 COG0614, FepB, ABC-type Fe3+-hydroxamate transport system,
           periplasmic component [Inorganic ion transport and
           metabolism].
          Length = 319

 Score = 26.0 bits (56), Expect = 7.2
 Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 2/59 (3%)

Query: 100 VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV 158
           V+  +       T      + D L+   G NI  A          +S EQ+  A  DV+
Sbjct: 195 VYVLRSPGGGLYTAGGNSFIGDILELAGGKNI--AADEEGPGGAQVSPEQILAADPDVI 251


>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
           3'-5' exonucleases [DNA replication, recombination, and
           repair].
          Length = 243

 Score = 25.9 bits (56), Expect = 8.7
 Identities = 29/147 (19%), Positives = 46/147 (31%), Gaps = 34/147 (23%)

Query: 23  IAVDTETLGLMPRRDRLC---IVQLSPGDG-------------------------TVDII 54
           + +D ET GL P++DR+     V L  G                           T +++
Sbjct: 16  VVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEML 75

Query: 55  RIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVL-----FYTFGVRVRPVFCTKIASRL 109
             A             +   R  + H   FD+  L          +   PV  T   +R 
Sbjct: 76  ADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARR 135

Query: 110 TRTYTNQHGLKDNLKELLGINISKAQQ 136
                ++  L D L E LGI+ +    
Sbjct: 136 HFPGFDRSSL-DALAERLGIDRNPFHP 161


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.137    0.408 

Gapped
Lambda     K      H
   0.267   0.0742    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,491,602
Number of extensions: 124608
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 24
Length of query: 207
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,340,536
Effective search space: 512183248
Effective search space used: 512183248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)