RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780127|ref|YP_003064540.1| putative DNA polymerase from
bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62]
         (675 letters)



>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to
           fill DNA gaps that arise during DNA repair,
           recombination and replication.  Family A polymerase
           (polymerase I) functions primarily to fill DNA gaps that
           arise during DNA repair, recombination and replication.
           DNA-dependent DNA polymerases can be classified in six
           main groups based upon phylogenetic relationships with
           E. coli polymerase I (classA), E. coli polymerase II
           (class B), E.coli polymerase III (class C),
           euryarchaaeota polymerase II (class D), human polymerase
            beta (class x), E. coli UmuC/DinB and eukaryotic RAP
           30/Xeroderma pigmentosum variant (class Y). Family A
           polymerase are found primarily in organisms related to
           prokaryotes and include prokaryotic DNA polymerase I
           ,mitochondrial polymerase delta, and several
           bacteriphage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
           have two functional domains located on the same
           polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
           Pol I uses its 5' nuclease activity to remove the
           ribonucleotide portion of newly synthesized Okazaki
           fragments and DNA polymerase activity to fill in the
           resulting gap. A combination of phylogenomic and
           signature sequence-based (or phonetic) approaches is
           used to understand the evolutionary relationships among
           bacteria. DNA polymerase I is one of the conserved
           proteins that is used to search for protein signatures.
           The structure of these polymerases resembles in overall
           morphology a cupped human right hand, with fingers
           (which bind an incoming nucleotide and interact with the
           single-stranded template), palm (which harbors the
           catalytic amino acid residues and also binds an incoming
           dNTP) and thumb (which binds double-stranded DNA)
           subdomains.
          Length = 378

 Score =  178 bits (455), Expect = 3e-45
 Identities = 73/195 (37%), Positives = 104/195 (53%), Gaps = 16/195 (8%)

Query: 268 SNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQP 327
                  K ++  R   S +++ K   +  AV SDGR+RG LQFYGA+RTGRW+G + Q 
Sbjct: 60  KTAPGDVKRVLELRQELSKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGRLVQV 119

Query: 328 QNLPRQERSEEILTQTIQALNRG---------ETIADPLGLASDCVRSCIIASNGKKLVV 378
           QNLPR    +  L    + +  G          ++ D L   S  +R+  I S G + +V
Sbjct: 120 QNLPRNYLKD--LDLARELVKSGDFDALELLYGSVPDVL---SQLIRTAFIPSEGHRFIV 174

Query: 379 ADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSK--EQRAIGKVME 436
           +D + IEARV+AW+AGE W++  FA    IY  + ++ F  P++K+ K    R  GKV E
Sbjct: 175 SDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAE 234

Query: 437 LALGYQGGAKVFKTM 451
           LALGY G     K M
Sbjct: 235 LALGYGGSVGALKAM 249



 Score =  114 bits (287), Expect = 1e-25
 Identities = 45/95 (47%), Positives = 59/95 (62%), Gaps = 4/95 (4%)

Query: 583 ATSQLMRERT---YGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDT 639
           A  + ++ER     GGKL ENIVQAI+RD L E M    K GYDIV+ VHDE+V E P+ 
Sbjct: 285 AAKKAVKERKTVKLGGKLVENIVQAIARDCLAEAMLRLEKAGYDIVMHVHDEVVIEVPEG 344

Query: 640 PYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYR 674
              S+  +  +M + P WA GLPL A+G+E+  Y 
Sbjct: 345 EG-SLEEVNEIMAQPPPWAPGLPLNADGFESPYYM 378


>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps
           that arise during DNA repair, recombination and
           replication.  DNA polymerase family A, 5'-3' polymerase
           domain. Family A polymerase functions primarily to fill
           DNA gaps that arise during DNA repair, recombination and
           replication. DNA-dependent DNA polymerases can be
           classified into six main groups based upon phylogenetic
           relationships with E. coli polymerase I (classA), E.
           coli polymerase II (class B), E.coli polymerase III
           (class C), euryarchaeota polymerase II (class D), human
           polymerase  beta (class X), E. coli UmuC/DinB and
           eukaryotic RAP 30/Xeroderma pigmentosum variant (class
           Y). Family A polymerases are found primarily in
           organisms related to prokaryotes and include prokaryotic
           DNA polymerase I, mitochondrial polymerase gamma, and
           several bacteriophage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic
           polymerase I (pol I) has two functional domains located
           on the same polypeptide; a 5'-3' polymerase and a 5'-3'
           exonuclease. Pol I uses its 5' nuclease activity to
           remove the ribonucleotide portion of newly synthesized
           Okazaki fragments and the DNA polymerase activity to
           fill in the resulting gap. The structure of these
           polymerases resembles in overall morphology a cupped
           human right hand, with fingers (which bind an incoming
           nucleotide and interact with the single-stranded
           template), palm (which harbors the catalytic amino acid
           residues and also binds an incoming dNTP) and thumb
           (which binds double-stranded DNA) subdomains.
          Length = 347

 Score = 80.2 bits (198), Expect = 2e-15
 Identities = 67/351 (19%), Positives = 103/351 (29%), Gaps = 97/351 (27%)

Query: 294 TLSEAVSSDGRLRGTLQFY-GASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGET 352
              +    DGR     ++  G + TGRW+      Q +PR++     L + I    R   
Sbjct: 48  PWLDQWVRDGRFHP--EYVPGGTVTGRWASRGGNAQQIPRRDP----LGRDI----RQAF 97

Query: 353 IADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTT 412
           +ADP                G  LVVAD + +E RVLA ++G++   +AF  G D+Y  T
Sbjct: 98  VADP----------------GWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTAT 141

Query: 413 YAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTF 472
            +  F  P+      +R   K+  L   Y                     S  + +    
Sbjct: 142 ASAMFGVPVG---GGERQHAKIANLGAMYGAT---------------SGISARLLAQLRR 183

Query: 473 EDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVV 532
              ++A +       ++P F         A E V+ A R   +G                
Sbjct: 184 ISTKEAAALIELFFSRFPAF-------PKAMEYVEDAARRGERG---------------G 221

Query: 533 QEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERT 592
                +  R      R                 RR                         
Sbjct: 222 YVRTLLGRRSPPPDIRWTEVVSDPAAASRARRVRR------------------------A 257

Query: 593 YGGKLTENIVQAISRDILCEGMKN------ATKNGYDIVLTVHDEIVSETP 637
            G      +VQ  + D     M               +V  VHDE+V   P
Sbjct: 258 AGRFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCP 308


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

 Score = 76.9 bits (189), Expect = 2e-14
 Identities = 81/303 (26%), Positives = 123/303 (40%), Gaps = 49/303 (16%)

Query: 159 FGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTIN-----------DRGYRIDLDLVL 207
             EY   D +AT  L   L P       L  L + I              G ++D+  + 
Sbjct: 158 ATEYAAEDADATLRLESILEPELLKTPVLLELYEEIEMPLVRVLARMERNGIKVDVQYLK 217

Query: 208 KLQELIAQERKKLDEDIVKL--TDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSIL 265
           +L + +  E  +L+E+I +L   +  I S +Q   L   LF   G+        T     
Sbjct: 218 ELSKELGCELAELEEEIYELAGEEFNINSPKQ---LGEILFEKLGLPPGLKKTKTGNYST 274

Query: 266 SHSNITQLAKD--LILNRLASSGSAILKLNTLSEAV-----SSDGRLRGTLQFYGASRTG 318
               + +LA D  L    L     A LK +T ++ +        GR+  +    G + TG
Sbjct: 275 DAEVLEKLADDHPLPKLILEYRQLAKLK-STYTDGLPKLINPDTGRIHTSFNQTGTA-TG 332

Query: 319 RWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVV 378
           R S      QN+P   RSEE           G  I           R   +A  G  L+ 
Sbjct: 333 RLSSSDPNLQNIPI--RSEE-----------GRKI-----------RKAFVAEKGYTLIS 368

Query: 379 ADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELA 438
           AD + IE R+LA ++ ++  ++AF  GEDI+  T A+ F  PI++V+ EQR   K +   
Sbjct: 369 ADYSQIELRILAHLSQDEGLLRAFTEGEDIHTATAAEVFGVPIEEVTSEQRRKAKAINFG 428

Query: 439 LGY 441
           L Y
Sbjct: 429 LIY 431


>gnl|CDD|176476 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol A is
           different from Escherichia coli  Pol A by three
           signature sequences.  Family A polymerase functions
           primarily to fill DNA gaps that arise during DNA repair,
           recombination and replication. DNA-dependent DNA
           polymerases can be classified in six main groups based
           upon phylogenetic relationships with E. coli polymerase
           I (classA), E. coli polymerase II (class B), E.coli
           polymerase III (class C), euryarchaaeota polymerase II
           (class D), human polymerase  beta (class x), E. coli
           UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum
           variant (class Y). Family A polymerase are found
           primarily in organisms related to prokaryotes and
           include prokaryotic DNA polymerase I ,mitochondrial
           polymerase delta, and several bacteriphage polymerases
           including those from odd-numbered phage (T3, T5, and
           T7). Prokaryotic Pol Is have two functional domains
           located on the same polypeptide; a 5'-3' polymerase and
           5'-3' exonuclease. Pol I uses its 5' nuclease activity
           to remove the ribonucleotide portion of newly
           synthesized Okazaki fragments and DNA polymerase
           activity to fill in the resulting gap. A combination of
           phylogenomic and signature sequence-based (or phonetic)
           approaches is used to understand the evolutionary
           relationships among bacteria. DNA polymerase I is one of
           the conserved proteins that is used for phylogenetic
           anaylsis of bacteria. Species of the phylum Aquificae
           grow in extreme thermophilic environments. The Aquificae
           are non-spore-forming, Gram-negative rods and strictly
           thermophilic. Phylum Aquificae Pol A is different from
           E. coli Pol I by three signature sequences consisting of
           a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa
           deletion. These signature sequences may provide a
           molecular marker for the family Aquificaceae and related
           species.
          Length = 324

 Score = 74.6 bits (184), Expect = 8e-14
 Identities = 52/200 (26%), Positives = 85/200 (42%), Gaps = 38/200 (19%)

Query: 263 SILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSG 322
            I  H  +  L +   LN+L S+    L  +         GR+  +    GA  +GR S 
Sbjct: 25  YIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPV----TGRIHPSFNQIGA-ASGRMS- 78

Query: 323 CVFQP--QNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVAD 380
           C   P  Q +PR+                               R C +A  G KL++AD
Sbjct: 79  C-SNPNLQQIPREREF----------------------------RRCFVAPEGNKLIIAD 109

Query: 381 LAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALG 440
            + IE R+ A I+G++  I A+  GED++  T +     PI++++KE+R + K +   L 
Sbjct: 110 YSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLI 169

Query: 441 YQGGAKVFKTMASHC-GLDL 459
           Y   AK  +  A    G+++
Sbjct: 170 YGMSAKGLREYARTNYGVEM 189



 Score = 28.4 bits (64), Expect = 6.7
 Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 4/40 (10%)

Query: 602 VQAISRDILCEGM----KNATKNGYDIVLTVHDEIVSETP 637
           +Q    DIL   +             IVL VHDEIV E P
Sbjct: 246 IQGTGADILKLALALLVDRLKDLDAKIVLCVHDEIVLEVP 285


>gnl|CDD|176474 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to
           fill DNA gaps that arise during DNA repair,
           recombination and replication.  Family A polymerase
           (polymerase I) functions primarily to fill DNA gaps that
           arise during DNA repair, recombination and replication.
           DNA-dependent DNA polymerases can be classified in six
           main groups based upon phylogenetic relationships with
           E. coli polymerase I (classA), E. coli polymerase II
           (class B), E.coli polymerase III (class C),
           euryarchaaeota polymerase II (class D), human polymerase
            beta (class x), E. coli UmuC/DinB and eukaryotic RAP
           30/Xeroderma pigmentosum variant (class Y). Family A
           polymerase are found primarily in organisms related to
           prokaryotes and include prokaryotic DNA polymerase I
           (pol I) ,mitochondrial polymerase delta, and several
           bacteriphage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
           have two functional domains located on the same
           polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
           Pol I uses its 5' nuclease activity to remove the
           ribonucleotide portion of newly synthesized Okazaki
           fragments and DNA polymerase activity to fill in the
           resulting gap. A combination of phylogenomic and
           signature sequence-based (or phonetic) approaches is
           used to understand the evolutionary relationships among
           bacteria. DNA polymerase I is one of the conserved
           proteins that is used to search for protein signatures.
           The structure of these polymerases resembles in overall
           morphology a cupped human right hand, with fingers
           (which bind an incoming nucleotide and interact with the
           single-stranded template), palm (which harbors the
           catalytic amino acid residues and also binds an incoming
           dNTP) and thumb (which binds double-stranded DNA)
           subdomains.
          Length = 377

 Score = 74.4 bits (184), Expect = 1e-13
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 364 VRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDK 423
           +R   +A  G  L+ AD + IE R+LA ++G++  I+AF NGEDI+  T A+ F  P ++
Sbjct: 141 IRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEE 200

Query: 424 VSKEQRAIGKV 434
           V+ E R I K 
Sbjct: 201 VTPEMRRIAKA 211


>gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A. 
          Length = 383

 Score = 65.8 bits (161), Expect = 4e-11
 Identities = 43/148 (29%), Positives = 60/148 (40%), Gaps = 25/148 (16%)

Query: 299 VSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLG 358
              DGR+  +    G   TGR S              S +   Q I        I +  G
Sbjct: 105 DPDDGRIHTSYNQAGT-ATGRLS--------------STDPNLQNI-------PIRNEYG 142

Query: 359 LASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFN 418
                +R+  IA  G  LV AD + IE R+LA ++G++  I+AF  G DI+  T A  F 
Sbjct: 143 RE---IRAAFIAEPGYVLVAADYSQIELRILAHLSGDENLIEAFRTGADIHTLTAADIFG 199

Query: 419 TPIDKVSKEQRAIGKVMELALGYQGGAK 446
             + +V+  QR   K       Y   AK
Sbjct: 200 VDLHEVTGNQRRNAKTFNFGRIYGASAK 227


>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity
           family A enzyme implicated in translesion synthesis and
           in somatic hypermutation.  DNA polymerase theta is a
           low-fidelity family A enzyme implicated in translesion
           synthesis (TLS) and in somatic hypermutation (SHM).
           DNA-dependent DNA polymerases can be classified in six
           main groups based upon phylogenetic relationships with
           E. coli polymerase I (classA), E. coli polymerase II
           (class B), E.coli polymerase III (class C),
           euryarchaaeota polymerase II (class D), human polymerase
            beta (class x), E. coli UmuC/DinB and eukaryotic RAP
           30/Xeroderma pigmentosum variant (class Y). Family A
           polymerase functions primarily to fill DNA gaps that
           arise during DNA repair, recombination and replication.
           Pol theta is an exception among family A polymerases and
           generates processive single base substitutions. Family A
           polymerase are found primarily in organisms related to
           prokaryotes and include prokaryotic DNA polymerase I
           (pol I) ,mitochondrial polymerase delta, and several
           bacteriphage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
           have two functional domains located on the same
           polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
           Pol I uses its 5' nuclease activity to remove the
           ribonucleotide portion of newly synthesized Okazaki
           fragments and DNA polymerase activity to fill in the
           resulting gap. Polymerase theta mostly has
           amino-terminal helicase domain, a carboxy-terminal
           polymerase domain and an intervening space region.
          Length = 373

 Score = 58.4 bits (142), Expect = 7e-09
 Identities = 46/196 (23%), Positives = 89/196 (45%), Gaps = 20/196 (10%)

Query: 279 LNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQP--QNLPRQERS 336
           L++L ++    L L     +     R+  T    G + TGR S    +P  QN+P+    
Sbjct: 55  LSKLLTTYVEPLLLLCKLSSSLQMYRIHPTWNQTGTA-TGRLS-SS-EPNLQNVPKDFEI 111

Query: 337 EEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGED 396
           ++  +    +     TI+         +R   I   G+ L+ AD + +E R+LA ++G+ 
Sbjct: 112 KDAPSPPAGSEGDIPTIS---------LRHAFIPPPGRVLLSADYSQLELRILAHLSGDP 162

Query: 397 WKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCG 456
             I+   +G D++    A+    P+++V+ E+R   K +   + Y  GA   K++A   G
Sbjct: 163 ALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGA---KSLAEQLG 219

Query: 457 LDL---QQFSQNVKST 469
           +     +QF ++ K+ 
Sbjct: 220 VSEEEAKQFIESFKNA 235


>gnl|CDD|176477 cd08640, DNA_pol_A_plastid_like, DNA polymerase A type from
           plastids of higher plants possibly involve in DNA
           replication or in the repair of errors occurring during
           replication.  DNA polymerase A type from plastids of
           higher plants possibly involve in DNA replication or in
           the repair of errors occurring during replication.
           Family A polymerase functions primarily to fill DNA gaps
           that arise during DNA repair, recombination and
           replication. DNA-dependent DNA polymerases can be
           classified in six main groups based upon phylogenetic
           relationships with E. coli polymerase I (classA), E.
           coli polymerase II (class B), E.coli polymerase III
           (class C), euryarchaaeota polymerase II (class D), human
           polymerase  beta (class x), E. coli UmuC/DinB and
           eukaryotic RAP 30/Xeroderma pigmentosum variant (class
           Y). Family A polymerase are found primarily in organisms
           related to prokaryotes and include prokaryotic DNA
           polymerase I ,mitochondrial polymerase delta, and
           several bacteriphage polymerases including those from
           odd-numbered phage (T3, T5, and T7).   The
           three-dimensional structure of plastid DNA polymerase
           has substantial similarity to Pol I. The structure of
           Pol I resembles in overall morphology a cupped human
           right hand, with fingers (which bind an incoming
           nucleotide and interact with the single-stranded
           template), palm (which harbors the catalytic amino acid
           residues and also binds an incoming dNTP) and thumb
           (which binds double-stranded DNA) subdomains.
          Length = 371

 Score = 50.9 bits (122), Expect = 1e-06
 Identities = 39/156 (25%), Positives = 59/156 (37%), Gaps = 36/156 (23%)

Query: 279 LNRLASSGSA----ILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQP--QNLPR 332
           L  + S  +     I+ L  L     S GR+  +L     + TGR S     P  QN P 
Sbjct: 48  LKEIKSISTLLSTFIIPLQELLN--DSTGRIHCSLNIN--TETGRLSS--RNPNLQNQPA 101

Query: 333 QERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWI 392
            E+                   D        +R   IAS G  L+VAD + +E R+LA +
Sbjct: 102 LEK-------------------DRYK-----IRKAFIASPGNTLIVADYSQLELRLLAHM 137

Query: 393 AGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQ 428
                 I+AF  G D +  T +  +    + V+  +
Sbjct: 138 TRCKSMIEAFNAGGDFHSRTASGMYPHVAEAVANGE 173



 Score = 28.5 bits (64), Expect = 6.5
 Identities = 7/18 (38%), Positives = 14/18 (77%)

Query: 621 GYDIVLTVHDEIVSETPD 638
           G+ ++L +HDE++ E P+
Sbjct: 316 GWKLLLQIHDEVILEGPE 333


>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
           subgroup of the DEDDh 3'-5' exonuclease domain family
           with similarity to the epsilon subunit of DNA polymerase
           III.  This subfamily is composed of uncharacterized
           bacterial proteins with similarity to the epsilon
           subunit of DNA polymerase III (Pol III), a multisubunit
           polymerase which is the main DNA replicating enzyme in
           bacteria, functioning as the chromosomal replicase. The
           Pol III holoenzyme is a complex of ten different
           subunits, three of which (alpha, epsilon, and theta)
           compose the catalytic core. The Pol III epsilon subunit,
           encoded by the dnaQ gene, is a DEDDh-type 3'-5'
           exonuclease which is responsible for the proofreading
           activity of the polymerase, increasing the fidelity of
           DNA synthesis. It contains three conserved sequence
           motifs termed ExoI, ExoII and ExoIII, with a specific
           Hx(4)D conserved 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 epsilon
           subunit of Pol III also functions as a stabilizer of the
           holoenzyme complex.
          Length = 156

 Score = 39.4 bits (93), Expect = 0.004
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 57  LLQYLRDETVMCVAHNSLFERILFKKTL---GIDIPSKRWICTSVLART--NGLPS-SLK 110
           +  +L    V  VAHN+ F+R + +  L   G+  P  +++CT  LAR     LP+  L 
Sbjct: 71  IKPFLGGSLV--VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLN 128

Query: 111 NACLALNFSEH 121
                L    +
Sbjct: 129 TVAEHLGIELN 139


>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 = 38.1 bits (89), Expect = 0.008
 Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 7/68 (10%)

Query: 56  DLLQYLRDETVMCVAHNSLFERILFKKTL---GIDIPSKRWICTSVLART--NGLPSSLK 110
           + L++L    +  VAHN+ F+     + L   G       WI T  LAR    GL S   
Sbjct: 72  EFLEFLGGRVL--VAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRL 129

Query: 111 NACLALNF 118
              LA  +
Sbjct: 130 GLLLAERY 137


>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 = 34.6 bits (80), Expect = 0.10
 Identities = 32/174 (18%), Positives = 52/174 (29%), Gaps = 33/174 (18%)

Query: 6   IDIETRSPQPLPKVGVWAYAEQAVITLC--AYAWDDEPVKLWDRTEQSAMPSDLLQYLRD 63
           +D ET S                +I +     A+  +P+ L D  E           L D
Sbjct: 25  VDTETTSLDT-----YSYTLVGCLIQISTGEGAYIIDPLALGDDLEGLKRL------LED 73

Query: 64  ETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLT 123
             +  V HN+ F+  +  +  GI +       T + A   G P S     LA  +   L 
Sbjct: 74  PNITKVGHNAKFDLEVLARDFGIKLE--NLFDTMLAAYLLGYPRSHSLDDLAEKY---LG 128

Query: 124 KMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRL 177
              +     A +       P  +               Y   D +    L+ +L
Sbjct: 129 VELDKSEQCADWRA----RPLSEEQ-----------LRYAAEDADYLLRLYDKL 167


>gnl|CDD|153319 cd07635, BAR_GRAF2, The Bin/Amphiphysin/Rvs (BAR) domain of GTPase
           Regulator Associated with Focal adhesion 2.  BAR domains
           are dimerization, lipid binding and curvature sensing
           modules found in many different proteins with diverse
           functions. GTPase Regulator Associated with Focal
           adhesion kinase 2 (GRAF2), also called Rho GTPase
           activating protein 10 (ARHGAP10) or PS-GAP, is a GAP
           with activity towards Cdc42 and RhoA which regulates
           caspase-activated p21-activated protein kinase-2
           (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to
           its stabilization and decrease of cell death. It is
           highly expressed in skeletal muscle and also interacts
           with PKNbeta, which is a target of Rho. GRAF2 contains
           an N-terminal BAR domain, followed by a Pleckstrin
           homology (PH) domain, a Rho GAP domain, and a C-terminal
           SH3 domain. BAR domains form dimers that bind to
           membranes, induce membrane bending and curvature, and
           may also be involved in protein-protein interactions.
           The BAR domain of the related protein GRAF directly
           interacts with its Rho GAP domain and inhibits its
           activity. Autoinhibited GRAF is capable of binding
           membranes and tubulating liposomes, showing that the
           membrane-tubulation and GAP-inhibitory functions of the
           BAR domain can occur simultaneously.
          Length = 207

 Score = 32.7 bits (74), Expect = 0.37
 Identities = 31/131 (23%), Positives = 58/131 (44%), Gaps = 10/131 (7%)

Query: 118 FSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRL 177
           FS  L  +EE + ++A     ++   P +  R   + A +   +   ++ E    L ++ 
Sbjct: 72  FSNFLKNLEEQREIMALNVTETL-IKPLERFRKEQLGAVKEEKKKFDKETEKNYSLLEKH 130

Query: 178 IPLSDGERDLWLLDQTIN-----DRGYRIDLDLVLKLQELIAQERKKLD--EDIVKLTDG 230
           + LS  +++  L +  +         Y + L+ V KLQE+  QERKK +  E ++    G
Sbjct: 131 LNLSAKKKEPQLQEADVQVEQNRQHFYELSLEYVCKLQEI--QERKKFECVEPMLSFFQG 188

Query: 231 IIRSSRQTYAL 241
           +     Q Y L
Sbjct: 189 VFTFYHQGYEL 199


>gnl|CDD|38861 KOG3657, KOG3657, KOG3657, Mitochondrial DNA polymerase gamma,
           catalytic subunit [Replication, recombination and
           repair].
          Length = 1075

 Score = 31.5 bits (71), Expect = 0.76
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 154 QAWQLFGEYCKRDVEATRELFKRLIPL 180
           + +Q    YC RDV AT ++F RL PL
Sbjct: 356 ENFQPLMNYCARDVIATHQVFFRLFPL 382


>gnl|CDD|34607 COG5002, VicK, Signal transduction histidine kinase [Signal
           transduction mechanisms].
          Length = 459

 Score = 31.1 bits (70), Expect = 0.96
 Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 202 DLDLVLKL-QELIAQERKKLDEDIVKLTDGIIRSSR 236
           DL   ++  Q    QER+KLD  +  +TDG+I + R
Sbjct: 94  DLTKRVQEAQANTEQERRKLDSVLAYMTDGVIATDR 129


>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 = 30.9 bits (70), Expect = 1.1
 Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 5/96 (5%)

Query: 24  YAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKT 83
           Y E A+I LC     +E   L+D    S     L   L + +++   H    +     + 
Sbjct: 29  YGEVALIQLCV---SEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRD 85

Query: 84  LGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFS 119
            G     +R   T++ A   GLP     A L  +F 
Sbjct: 86  FGE--KLQRLFDTTIAANLKGLPERWSLASLVEHFL 119


>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
           fill DNA gaps that arise during DNA repair,
           recombination and replication.  Family A polymerase
           functions primarily to fill DNA gaps that arise during
           DNA repair, recombination and replication. DNA-dependent
           DNA polymerases can be classified in six main groups
           based upon phylogenetic relationships with E. coli
           polymerase I (classA), E. coli polymerase II (class B),
           E.coli polymerase III (class C), euryarchaaeota
           polymerase II (class D), human polymerase  beta (class
           x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma
           pigmentosum variant (class Y). Family A polymerase are
           found primarily in organisms related to prokaryotes and
           include prokaryotic DNA polymerase I ,mitochondrial
           polymerase delta, and several bacteriphage polymerases
           including those from odd-numbered phage (T3, T5, and
           T7). Prokaryotic Pol Is have two functional domains
           located on the same polypeptide; a 5'-3' polymerase and
           5'-3' exonuclease. Pol I uses its 5' nuclease activity
           to remove the ribonucleotide portion of newly
           synthesized Okazaki fragments and DNA polymerase
           activity to fill in the resulting gap. A combination of
           phylogenomic and signature sequence-based (or phonetic)
           approaches is used to understand the evolutionary
           relationships among bacteria. DNA polymerase I is one of
           the conserved proteins that is used to search for
           protein signatures. The structure of these polymerases
           resembles in overall morphology a cupped human right
           hand, with fingers (which bind an incoming nucleotide
           and interact with the single-stranded template), palm
           (which harbors the catalytic amino acid residues and
           also binds an incoming dNTP) and thumb (which binds
           double-stranded DNA) subdomains.
          Length = 429

 Score = 30.9 bits (70), Expect = 1.1
 Identities = 11/26 (42%), Positives = 13/26 (50%)

Query: 365 RSCIIASNGKKLVVADLAGIEARVLA 390
           R       G  LV AD +G+E R LA
Sbjct: 178 RELFGVPPGWSLVGADASGLELRCLA 203


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

 Score = 30.6 bits (68), Expect = 1.6
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 56  DLLQYLRDETVMCVAHNSLFERILFKKT---LGIDIPSKRWICTSVLAR 101
           + L ++    ++ VAHN+ F+    +     LGI+IP    + T  LAR
Sbjct: 87  EFLDFIGGLRLL-VAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALAR 134


>gnl|CDD|73156 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
           retrotransposon and non-LTR retrovirus reverse
           transcriptase (RT). This subfamily contains both non-LTR
           retrotransposons and non-LTR retrovirus RTs. RTs
           catalyze the conversion of single-stranded RNA into
           double-stranded DNA for integration into host
           chromosomes. RT is a multifunctional enzyme with
           RNA-directed DNA polymerase, DNA directed DNA polymerase
           and ribonuclease hybrid (RNase H) activities..
          Length = 220

 Score = 29.9 bits (67), Expect = 2.2
 Identities = 30/122 (24%), Positives = 43/122 (35%), Gaps = 15/122 (12%)

Query: 197 RGYRIDLDLVLKLQELIAQERKKLDE------DIVKLTDGIIRSS-------RQTYALRM 243
           R  R   D +L L+E+I + ++K         D  K  D +           RQ   L  
Sbjct: 56  RPGRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKALGVRQGDPLSP 115

Query: 244 YLFLITGIDLVDMSEGTLKSILSHSNITQL--AKDLILNRLASSGSAILKLNTLSEAVSS 301
            LF +   DL+ +     +  L    IT L  A D++L     S      L  L E    
Sbjct: 116 LLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEWSKE 175

Query: 302 DG 303
            G
Sbjct: 176 SG 177


>gnl|CDD|107374 cd06379, PBP1_iGluR_NMDA_NR1, N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the NR1, an essential channel-forming subunit
           of the NMDA receptor.  N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the NR1, an essential channel-forming subunit
           of the NMDA receptor. The ionotropic N-methyl-d-asparate
           (NMDA) subtype of glutamate receptor serves critical
           functions in neuronal development, functioning, and
           degeneration in the mammalian central nervous system.
           The functional NMDA receptor is a heterotetramer
           ccomposed of two NR1 and two NR2 (A, B, C, and D) or of
           NR3 (A and B) subunits.  The receptor controls a cation
           channel that is highly permeable to monovalent ions and
           calcium and exhibits voltage-dependent inhibition by
           magnesium. Dual agonists, glutamate and glycine, are
           required for efficient activation of the NMDA receptor. 
           When co-expressed with NR1, the NR3 subunits form
           receptors that are activated by glycine alone and
           therefore can be classified as excitatory glycine
           receptors. NR1/NR3 receptors are calcium-impermeable and
           unaffected by ligands acting at the NR2
           glutamate-binding site.
          Length = 377

 Score = 30.1 bits (68), Expect = 2.2
 Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 339 ILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKL 376
           +L   IQ L   E I +P     +CV + +I   G   
Sbjct: 282 VLASAIQELFEKENITEP---PRECVGNTVIWETGPLF 316


>gnl|CDD|99825 cd05782, DNA_polB_like1_exo, Uncharacterized bacterial subgroup of
           the DEDDy 3'-5' exonuclease domain of family-B DNA
           polymerases.  A subfamily of the 3'-5' exonuclease
           domain of family-B DNA polymerases. This subfamily is
           composed of uncharacterized bacterial family-B DNA
           polymerases. Family-B DNA polymerases contain an
           N-terminal DEDDy DnaQ-like exonuclease domain in the
           same polypeptide chain as the polymerase domain, similar
           to family-A DNA polymerases. This exonuclease domain
           contains three sequence motifs termed ExoI, ExoII and
           ExoIII, with a specific YX(3)D pattern at ExoIII. These
           motifs are involved in metal binding and catalysis. The
           exonuclease domain of family-B DNA polymerases has a
           fundamental role in proofreading activity. It contains a
           beta hairpin structure that plays an important role in
           active site switching in the event of a nucleotide
           misincorporation. Family-B DNA polymerases are
           predominantly involved in DNA replication and DNA
           repair.
          Length = 208

 Score = 29.5 bits (67), Expect = 3.1
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 161 EYCKRDVEATRELFKR 176
           EYC+ DV  T  L+ R
Sbjct: 193 EYCETDVLNTYLLYLR 208


>gnl|CDD|31416 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
           function prediction only].
          Length = 368

 Score = 28.8 bits (64), Expect = 5.8
 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 6/49 (12%)

Query: 128 GKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKR 176
           GK ++A+        P         V+A +L GE+         EL++R
Sbjct: 163 GKTMMAKALANEAKVPLL------LVKATELIGEHVGDGARRIHELYER 205


>gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182).  This
           family contains uncharacterized integral membrane
           proteins.
          Length = 771

 Score = 28.3 bits (64), Expect = 7.6
 Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 8/36 (22%)

Query: 35  YAWDDE-PV-KLWDR------TEQSAMPSDLLQYLR 62
           Y  D E P+ K W +         SAMP DL  +LR
Sbjct: 610 YVVDPEDPILKTWQKIFPGLFKPLSAMPDDLRSHLR 645


>gnl|CDD|100005 cd02198, YjgH_like, YjgH belongs to a large family of
           YjgF/YER057c/UK114-like proteins present in bacteria,
           archaea, and eukaryotes with no definitive function. The
           conserved domain is similar in structure to chorismate
           mutase but there is no sequence similarity and no
           functional connection. Members of this family have been
           implicated in isoleucine (Yeo7, Ibm1, aldR) and purine
           (YjgF) biosynthesis, as well as threonine anaerobic
           degradation (tdcF) and mitochondrial DNA maintenance
           (Ibm1). This domain homotrimerizes forming a distinct
           intersubunit cavity that may serve as a small molecule
           binding site..
          Length = 111

 Score = 28.0 bits (63), Expect = 9.0
 Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 470 STFEDWEQAESHHLWMQDQYPEF-AVKDKLIG 500
            +F+D  +  + H+ M    P F AVKD+   
Sbjct: 51  CSFDDVVELTTFHVDMAAHLPAFAAVKDEYFK 82


  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
   0.319    0.134    0.400 

Gapped
Lambda     K      H
   0.267   0.0670    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,055,194
Number of extensions: 421157
Number of successful extensions: 942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 935
Number of HSP's successfully gapped: 33
Length of query: 675
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 575
Effective length of database: 4,102,837
Effective search space: 2359131275
Effective search space used: 2359131275
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: 61 (27.4 bits)