RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781193|ref|YP_003065606.1| 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 = 180 bits (458), Expect = 2e-45 Identities = 87/264 (32%), Positives = 129/264 (48%), Gaps = 30/264 (11%) Query: 203 LAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRV 262 L + D + +L +E + LT GL + +LK WL + G L + V Sbjct: 1 LVNAAIACDDQYKEELLEEAKELT-GL-DNPNSPAQLKDWLNEQGGEVDSLLKKDV---V 55 Query: 263 LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGC 322 K +V R S+++V K + A+ SDGR+RG LQF GA+RTGRW+G Sbjct: 56 ALLLKTAPGDVKRVLELRQELSKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGR 115 Query: 323 VFPPQNLPR-------------PSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVI 369 + QNLPR S + L+ + +P ++S +R+ I Sbjct: 116 LVQVQNLPRNYLKDLDLARELVKSGDFDALELLYGSVP----------DVLSQLIRTAFI 165 Query: 370 ASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQ- 428 SEG + +V+D + IEARV+AW+AGEQW+L F T +Y + ++ F V ++ K+ Sbjct: 166 PSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKIGKNSH 225 Query: 429 -RAIGKVMELALGYQGGAKAFQKM 451 R GKV ELALGY G A + M Sbjct: 226 LRQKGKVAELALGYGGSVGALKAM 249 Score = 111 bits (280), Expect = 6e-25 Identities = 44/83 (53%), Positives = 54/83 (65%), Gaps = 1/83 (1%) Query: 592 TYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLM 651 GGKL ENIVQA++RD LAE M+ KAGYDIV+ VHDE+V E P E + + +M Sbjct: 297 KLGGKLVENIVQAIARDCLAEAMLRLEKAGYDIVMHVHDEVVIEVP-EGEGSLEEVNEIM 355 Query: 652 TSNPSWAKGLPLKAEGYESKRYR 674 P WA GLPL A+G+ES Y Sbjct: 356 AQPPPWAPGLPLNADGFESPYYM 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 = 91.3 bits (227), Expect = 7e-19 Identities = 74/387 (19%), Positives = 121/387 (31%), Gaps = 100/387 (25%) Query: 297 AMNSDGRLRGTLQFL-GASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPD 355 DGR +++ G + TGRW+ Q +PR ++ Sbjct: 52 QWVRDGRFHP--EYVPGGTVTGRWASRGGNAQQIPRRDPLGRDI---------------- 93 Query: 356 PLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYAR 415 R +A G LVVAD + +E RVLA ++G++ +AF G DLY T + Sbjct: 94 ---------RQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATASA 144 Query: 416 SFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEW 475 F V V +R K+ L Y GA T+G++ A L + ++ Sbjct: 145 MFGVP---VGGGERQHAKIANLGAMY--GA--------TSGISARLLAQLRRISTKEAA- 190 Query: 476 EDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENG 535 E F A E V+ A R+ + +T Sbjct: 191 ALIELFFSRFPAF-----------PKAMEYVEDAARRGERGG----------YVRT---- 225 Query: 536 KAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGG 595 ++ R+ P R S +R G Sbjct: 226 --LLGRRSP-----------------PPDIRW------TEVVSDPAAASRARRVRRAAGR 260 Query: 596 KLTENIVQAVSRDILAEGMMN------ATKAGYDIVLTVHDEIVCETP-DTDEFNASMLY 648 +VQ + D M+ +V VHDE+V P + E A+++ Sbjct: 261 FARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVR 320 Query: 649 HLM-TSNPSWAKGLPLKAEGYESKRYR 674 + +P++ +R Sbjct: 321 EAAEQAVRLLFGSVPVRFPVKIGVVWR 347 >gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A. Length = 383 Score = 79.7 bits (197), Expect = 3e-15 Identities = 101/448 (22%), Positives = 157/448 (35%), Gaps = 132/448 (29%) Query: 239 LKTWLFLETGLHLEDLTETTCQRVLSSN--KKLTPQA------IQVFNNRMRASRSAVLK 290 L LF E GL T+ T R +++ + L A I + + + V K Sbjct: 40 LGVLLFEELGLPKTKKTDKTGARSTNADVLESLREDAHEIIKIILEYRQLSKLQSTYVDK 99 Query: 291 LNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSI 350 L +++ DGR+ + G TGR S QN+P + E+ Sbjct: 100 LPLMID--PDDGRIHTSYNQAGT-ATGRLSSTDPNLQNIPIRNEYGREI----------- 145 Query: 351 TSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYV 410 R+ IA G LV AD + IE R+LA ++G++ ++AF TG D++ Sbjct: 146 --------------RAAFIAEPGYVLVAADYSQIELRILAHLSGDENLIEAFRTGADIHT 191 Query: 411 TTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNS 470 T A F V +VT +QR K Y AK ++ L ++ Sbjct: 192 LTAADIFGVDLHEVTGNQRRNAKTFNFGRIYGASAKGLSQL-----LGISR--------- 237 Query: 471 APEEWEDAENFCRWMQENHP--EHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAF 528 E+A+ F E P + E K+A + + Sbjct: 238 -----EEAKEFIEKYFERFPGVKRYREKTR--------KEAKK--------------GGY 270 Query: 529 EQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLT 588 +T+ +RR +P + R+ R+ R+ LNT Sbjct: 271 VETLFG-------RRRYLPDI--------------DSRNRSLRE-AAERAALNT------ 302 Query: 589 REYTYGGKLTENIVQAVSRDILAEGMMNATKAGYD------IVLTVHDEIVCETPDTD-E 641 +Q + DIL M+ +A + + L VHDEIV E P + E Sbjct: 303 ------------PIQGSAADILKLAMIKLDEALVEKGLDARMCLQVHDEIVFEVPKEEAE 350 Query: 642 FNASMLYHLMTSNPSWAKGL--PLKAEG 667 A+ + LM A L PL E Sbjct: 351 AVAAQIKELME----RAMFLDVPLLVEV 374 >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 = 78.9 bits (195), Expect = 4e-15 Identities = 42/155 (27%), Positives = 69/155 (44%), Gaps = 32/155 (20%) Query: 301 DGRLRGTLQFLGASRTGRWSGCVFPP-QNLPRPSRSHEELDQIITHLPTSITSDPDPLQI 359 GR+ + +GA +GR S C P Q +PR Sbjct: 60 TGRIHPSFNQIGA-ASGRMS-CSNPNLQQIPREREF------------------------ 93 Query: 360 ISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNV 419 R C +A EG KL++AD + IE R+ A ++G++ + A++ GEDL+ T + Sbjct: 94 -----RRCFVAPEGNKLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGK 148 Query: 420 APAQVTKDQRAIGKVMELALGYQGGAKAFQKMAST 454 ++TK++R + K + L Y AK ++ A T Sbjct: 149 PIEEITKEERQLAKAVNFGLIYGMSAKGLREYART 183 Score = 29.6 bits (67), Expect = 2.8 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 4/40 (10%) Query: 602 VQAVSRDILAEGM--MNATKAGYD--IVLTVHDEIVCETP 637 +Q DIL + + D IVL VHDEIV E P Sbjct: 246 IQGTGADILKLALALLVDRLKDLDAKIVLCVHDEIVLEVP 285 >gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]. Length = 593 Score = 74.2 bits (182), Expect = 1e-13 Identities = 43/130 (33%), Positives = 62/130 (47%), Gaps = 9/130 (6%) Query: 325 PPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIIS------DCVRSCVIASEGKKLVV 378 P P R H +Q T +SDP+ LQ I +R +A +G L+ Sbjct: 310 PKLINPDTGRIHTSFNQTGTATGRLSSSDPN-LQNIPIRSEEGRKIRKAFVAEKGYTLIS 368 Query: 379 ADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELA 438 AD + IE R+LA ++ ++ L+AF GED++ T A F V +VT +QR K + Sbjct: 369 ADYSQIELRILAHLSQDEGLLRAFTEGEDIHTATAAEVFGVPIEEVTSEQRRKAKAINFG 428 Query: 439 LGYQGGAKAF 448 L Y G AF Sbjct: 429 LIY--GMSAF 436 >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 = 69.8 bits (172), Expect = 2e-12 Identities = 28/71 (39%), Positives = 44/71 (61%) Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423 +R +A EG L+ AD + IE R+LA ++G++ ++AF+ GED++ T A F V P + Sbjct: 141 IRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEE 200 Query: 424 VTKDQRAIGKV 434 VT + R I K Sbjct: 201 VTPEMRRIAKA 211 Score = 28.9 bits (66), Expect = 4.7 Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 3/44 (6%) Query: 624 IVLTVHDEIVCETPDTD-EFNASMLYHLMTSNPSWAKGLPLKAE 666 ++L VHDE+V E P+ + E A+++ M + + +PLK + Sbjct: 328 MLLQVHDELVFEVPEEELEEVAALVKEEMENAVELS--VPLKVD 369 >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 = 59.9 bits (146), Expect = 2e-09 Identities = 38/149 (25%), Positives = 64/149 (42%), Gaps = 15/149 (10%) Query: 301 DGRLRGT-LQFLGASRTGRWSGCVFPP-QNLPRPSRSHEELDQIITHLPTSITSDPDPLQ 358 R+ T Q A TGR S P QN+P+ I P+ + Sbjct: 78 MYRIHPTWNQTGTA--TGRLS-SSEPNLQNVPKDF--------EIKDAPSPPAGSEGDIP 126 Query: 359 IISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFN 418 IS +R I G+ L+ AD + +E R+LA ++G+ ++ +G D++ A+ Sbjct: 127 TIS--LRHAFIPPPGRVLLSADYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLG 184 Query: 419 VAPAQVTKDQRAIGKVMELALGYQGGAKA 447 +VT ++R K + + Y GAK+ Sbjct: 185 KPVEEVTDEERQQAKQLVYGILYGMGAKS 213 Score = 29.9 bits (68), Expect = 2.4 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 14/66 (21%) Query: 601 IVQAVSRDILAEGMMN-----------ATKAGYDIVLTVHDEIVCETPDT--DEFNASML 647 ++Q + DI+ M+N +VL +HDE++ E P++ DE A ++ Sbjct: 288 VIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHDELLFEVPESDVDEV-ARII 346 Query: 648 YHLMTS 653 M + Sbjct: 347 KRSMEN 352 >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 = 55.5 bits (134), Expect = 5e-08 Identities = 48/222 (21%), Positives = 74/222 (33%), Gaps = 60/222 (27%) Query: 259 CQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAM-----NSDGRLRGTLQFLGA 313 C S + +A + + L L+T + + +S GR+ +L Sbjct: 27 CYENGVSGGEEGKEACEAIEALKEIKSISTL-LSTFIIPLQELLNDSTGRIHCSLNIN-- 83 Query: 314 SRTGRWSGCVFPP--QNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIAS 371 + TGR S P QN P + D +I R IAS Sbjct: 84 TETGRLSS--RNPNLQNQPAL--------------------EKDRYKI-----RKAFIAS 116 Query: 372 EGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTT------------------- 412 G L+VAD + +E R+LA M + ++AF G D + T Sbjct: 117 PGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGGDFHSRTASGMYPHVAEAVANGEVLL 176 Query: 413 --YARSFNVAP--AQVTKDQRAIGKVMELALGYQGGAKAFQK 450 + AP K +R KV+ ++ Y A K Sbjct: 177 EWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAYGKTAHGLAK 218 Score = 31.6 bits (72), Expect = 0.76 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 5/50 (10%) Query: 621 GYDIVLTVHDEIVCETP-DTDEFNASMLYHLMTSNPSWAKGL--PLKAEG 667 G+ ++L +HDE++ E P + + ++ M NP + L PL+ +G Sbjct: 316 GWKLLLQIHDEVILEGPEEKADEALKIVKDCM-ENP-FFGPLDVPLEVDG 363 >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 = 52.1 bits (126), Expect = 5e-07 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 7/76 (9%) Query: 51 PVMPQVLKEALEN-TDVTIVAHNSYFERTVLKAC---FNLDIPIHRWICTLVLARS--NG 104 P P+V E +VAHN+ F+R+VL+A + L P ++++CT+ LAR Sbjct: 62 PTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL 121 Query: 105 LPS-ALKAVGEALKLS 119 LP+ L V E L + Sbjct: 122 LPNHKLNTVAEHLGIE 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 = 43.8 bits (104), Expect = 2e-04 Identities = 29/152 (19%), Positives = 50/152 (32%), Gaps = 25/152 (16%) Query: 30 VILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIP 89 L + + D + + LK LE+ ++T V HN+ F+ VL F I Sbjct: 41 GCLIQISTGEGAYII-DPLALGDDLEGLKRLLEDPNITKVGHNAKFDLEVLARDF--GIK 97 Query: 90 IHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGET---HECLYDRN 146 + T++ A G P + L +L ++ E +C R Sbjct: 98 LENLFDTMLAAYLLGYP-------RSHSL--------DDLAEKYLGVELDKSEQCADWRA 142 Query: 147 KPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178 +P E Y D ++ +L Sbjct: 143 RPLSEEQ----LRYAAEDADYLLRLYDKLRKE 170 >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 = 42.7 bits (101), Expect = 3e-04 Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%) Query: 51 PVMPQVLKEALE-NTDVTIVAHNSYFERTVLKACF---NLDIPIHRWICTLVLAR 101 P +VL E LE +VAHN+ F+ L + WI TL LAR Sbjct: 64 PPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLAR 118 >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 = 40.0 bits (93), Expect = 0.002 Identities = 24/153 (15%), Positives = 45/153 (29%), Gaps = 21/153 (13%) Query: 30 VILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIP 89 ++ + D + + LKE LE+ D+T V H++ F+ VL Sbjct: 19 LVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPG 78 Query: 90 IHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEG-KELIARFCKGET---HECLYDR 145 T++ A L+ + +L + E + Sbjct: 79 NI--FDTMLAAY---------------LLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKG 121 Query: 146 NKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178 K R EY D ++++L Sbjct: 122 AKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 >gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]. Length = 243 Score = 39.0 bits (90), Expect = 0.004 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%) Query: 40 HPVELWDCVHDPVMPQVLKEALE--NTDVTIVAHNSYFERTVLKACF---NLDIPIHRWI 94 H + P +VL E L+ +VAHN+ F+ L+ ++IP + Sbjct: 68 HGITDEMLADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVL 127 Query: 95 CTLVLAR 101 TL LAR Sbjct: 128 DTLALAR 134 >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 = 38.7 bits (91), Expect = 0.005 Identities = 29/142 (20%), Positives = 49/142 (34%), Gaps = 19/142 (13%) Query: 55 QVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWIC-TLVLAR---SNGLPSALK 110 LK LE+ + V N F+ VL N I + T++ + L Sbjct: 57 AALKPLLEDPSIKKVGQNLKFDLHVLA---NHGIELRGPAFDTMLASYLLNPGRRRHGLD 113 Query: 111 AVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTRE 170 + A + K ++L+ KG+ E EY D +T Sbjct: 114 DL--AERYLGHKTISFEDLVG---KGKKQITFDQV----PLEKA---AEYAAEDADITLR 161 Query: 171 IFKRLEPLSSKEQELWYLDQTI 192 +++ L+P +E L L + I Sbjct: 162 LYELLKPKLKEEPGLLELYEEI 183 >gnl|CDD|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme 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 = 167 Score = 32.5 bits (75), Expect = 0.39 Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 6/43 (13%) Query: 65 DVTIVAHNSYFERTVLKACFNLD------IPIHRWICTLVLAR 101 +V HN+ F+ L A +L I R I TL LAR Sbjct: 81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALAR 123 >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 = 32.0 bits (73), Expect = 0.51 Identities = 11/26 (42%), Positives = 13/26 (50%) Query: 365 RSCVIASEGKKLVVADLAGIEARVLA 390 R G LV AD +G+E R LA Sbjct: 178 RELFGVPPGWSLVGADASGLELRCLA 203 >gnl|CDD|39364 KOG4162, KOG4162, KOG4162, Predicted calmodulin-binding protein [Signal transduction mechanisms]. Length = 799 Score = 31.5 bits (71), Expect = 0.68 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 9/90 (10%) Query: 161 CKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQ 220 G V E F++ P S E E WY A + + + E K + Sbjct: 335 RCGQFEVLAEQFEQALPFSFGEHERWYQ------LALSYSAAGSDSKAVNLLRESLKKSE 388 Query: 221 ELESLTYGLVSSSRCLEKLKTWLFLETGLH 250 + ++ L++S C+E+LK +E GL Sbjct: 389 QPSDISVLLMASKLCIERLKL---VEEGLD 415 >gnl|CDD|32445 COG2264, PrmA, Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]. Length = 300 Score = 30.3 bits (68), Expect = 1.8 Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 5/56 (8%) Query: 457 LNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQ 512 L FAH+++ E+WE W + HP E I + + + Sbjct: 80 ALLELFAHVIEQEEDEEDWERE-----WKKYFHPVRIGERFVIVPSWREYPEPSDE 130 >gnl|CDD|145226 pfam01937, DUF89, Protein of unknown function DUF89. This family has no known function. Length = 314 Score = 29.2 bits (66), Expect = 3.7 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 6/50 (12%) Query: 19 CGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTI 68 G+ + D +I F ++ W+ M L E L D+ I Sbjct: 227 AGLDELLADGKLIDSGSDFWTPGLDYWE------MSPELYEELSKADLVI 270 >gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention. Length = 343 Score = 28.9 bits (65), Expect = 5.4 Identities = 33/133 (24%), Positives = 44/133 (33%), Gaps = 19/133 (14%) Query: 203 LAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRV 262 A +N I D+ D L G VS R + G+ E L+ ++ Sbjct: 190 EAVGINPIGDLLAASPDALLALW--GGVSGER-------LWYALRGIDDEPLSPPRPRKS 240 Query: 263 LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGC 322 S + L N A L L L + DGR L+ + GRWSG Sbjct: 241 FSHERVLPRD----SRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTVDGRWSGH 296 Query: 323 VFPPQNLPRPSRS 335 PSRS Sbjct: 297 ------ADIPSRS 303 >gnl|CDD|111839 pfam02993, MCPVI, Minor capsid protein VI. This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation. Length = 238 Score = 28.6 bits (64), Expect = 6.1 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%) Query: 188 LDQTINDRGYCVDVA--LAHTLNQIVDVERTKLDQELESL 225 L Q + D G V ++ +VD+ R K++++LE L Sbjct: 66 LRQGLKDSGLQRKVVEGAGQGIHGLVDIGRQKVEKDLEKL 105 >gnl|CDD|35829 KOG0609, KOG0609, KOG0609, Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]. Length = 542 Score = 28.0 bits (62), Expect = 7.9 Identities = 26/114 (22%), Positives = 46/114 (40%), Gaps = 24/114 (21%) Query: 215 RTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTET---TCQRVLSSNK---- 267 R E++ + Y VS ++ FLE G + +L T + + V++S K Sbjct: 377 RPPRSDEVDGVEYHFVSKEEMEADIRAGKFLEYGEYEGNLYGTSLDSVRNVIASGKICVL 436 Query: 268 KLTPQAIQVFNN----------------RMRASRSAVLKLNTLVEAMNSDGRLR 305 + PQA++V +RA R V ++T+V +D L+ Sbjct: 437 DVEPQALKVLRTAEFKPYVIFIAPPSLEELRALR-KVAVMSTIVAKQFTDEDLQ 489 >gnl|CDD|38861 KOG3657, KOG3657, KOG3657, Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]. Length = 1075 Score = 28.1 bits (62), Expect = 8.8 Identities = 12/28 (42%), Positives = 16/28 (57%) Query: 151 REAWRLFGEYCKGDVTVTREIFKRLEPL 178 RE ++ YC DV T ++F RL PL Sbjct: 355 RENFQPLMNYCARDVIATHQVFFRLFPL 382 >gnl|CDD|144091 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain. Length = 245 Score = 28.0 bits (63), Expect = 9.6 Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 19/71 (26%) Query: 421 PAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAEN 480 PA + D R V L GGA ++ TG + L K Sbjct: 94 PAILWNDTRTAEIVENLK--ELGGADKLYEI---TGNTIWPGFTLSKL------------ 136 Query: 481 FCRWMQENHPE 491 RW++E+ PE Sbjct: 137 --RWLKEHEPE 145 >gnl|CDD|147383 pfam05170, AsmA, AsmA family. The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant. AsmA may have a role in LPS biogenesis. Length = 537 Score = 27.8 bits (62), Expect = 9.8 Identities = 6/32 (18%), Positives = 11/32 (34%) Query: 509 AWRQKHSRVSELWNELHQAFEQTIENGKAIIA 540 W+ + R+S L + NG + Sbjct: 270 RWQTGNVRLSGNLKSLTANLDDLSFNGLKWVG 301 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 0.133 0.403 Gapped Lambda K H 0.267 0.0672 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,115,569 Number of extensions: 424426 Number of successful extensions: 1080 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1070 Number of HSP's successfully gapped: 37 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)