RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus Liberibacter asiaticus str. psy62] (976 letters) >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 = 602 bits (1555), Expect = e-172 Identities = 205/382 (53%), Positives = 277/382 (72%), Gaps = 6/382 (1%) Query: 591 DQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQW 650 D + L+++S E+ K L LEE IY+L+GE+FN++SPKQLG++LF KL P G KTKTG Sbjct: 1 DTEYLEELSEELEKELAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTGYS 60 Query: 651 KTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMT 710 T A+ LE++ ++PI++ ILE+R+L+K+KSTY D+LP IN +T R+HT ++ T T Sbjct: 61 -TDAEVLEKL-ADEHPIVELILEYRELTKLKSTYVDALPKLINPKTGRIHTSFNQTVTAT 118 Query: 711 GRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQV 770 GRL+S +PNLQNIPI+T+ G++IR+AF++ L+SADYSQIELRILAH++ L + Sbjct: 119 GRLSSSDPNLQNIPIRTEEGREIRKAFVAEEGWVLLSADYSQIELRILAHLSGDEALIEA 178 Query: 771 FENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAAD 830 F+N DIH AAE+FGV E+V+P+MRR AK +NF IIYGIS F L+ QL I R EA + Sbjct: 179 FKNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQLGISRKEAKE 238 Query: 831 YIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINA 890 YI RYF R+PG+ EY+E+T R+ GYVET+FGRR + EINS ++R ER AIN Sbjct: 239 YIDRYFARYPGVKEYMEETVEEAREKGYVETLFGRRRYIPEINSKNRNVRAFAERIAINT 298 Query: 891 PIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEK 950 PIQG+AADI + AMI VHK+L++ L +MLLQ+HDELVFEVPEEE+ + ++ ME Sbjct: 299 PIQGTAADIIKLAMIRVHKALKEEGLKARMLLQVHDELVFEVPEEELEEVAALVKEEMEN 358 Query: 951 ACLPKINLRVPLKVNIKVSNNW 972 A + L VPLKV++ V NW Sbjct: 359 A----VELSVPLKVDVGVGKNW 376 >gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]. Length = 593 Score = 596 bits (1538), Expect = e-171 Identities = 266/612 (43%), Positives = 386/612 (63%), Gaps = 28/612 (4%) Query: 368 YTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETI 427 Y I + + W+ KL + +F TD +D + + ++++ + E Sbjct: 3 YGTITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVA---------SEEEAA 53 Query: 428 FIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFE 487 +I L Q +L+ LK E+E K+G N+KYD VL GI Sbjct: 54 YIPLLHGPEQ---------LNVLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAF 104 Query: 488 DIMLMSYVLDSGRSSHDIASIAQKWLSYT---RKEILKSRKSSIPIDKISDSQVQEHAIE 544 D ML SY+L+ G +H++ +A+++L ++I K + + + E+A E Sbjct: 105 DTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAE 164 Query: 545 NSNVILQLWLLLRPKLI-VEKLLHVYERLDKPMIDVVSQMEITGIQIDQDLLKQVSAEIS 603 +++ L+L +L P+L+ LL +YE ++ P++ V+++ME GI++D LK++S E+ Sbjct: 165 DADATLRLESILEPELLKTPVLLELYEEIEMPLVRVLARMERNGIKVDVQYLKELSKELG 224 Query: 604 KNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGA-KTKTGQWKTTAQDLEQINC 662 L LEE IY+L+GE+FN++SPKQLG+ILF KL P G KTKTG + T A+ LE++ Sbjct: 225 CELAELEEEIYELAGEEFNINSPKQLGEILFEKLGLPPGLKKTKTGNYSTDAEVLEKLA- 283 Query: 663 GDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQN 722 D+P+ K ILE+RQL+K+KSTY D LP IN T R+HT ++ T TGRL+S +PNLQN Sbjct: 284 DDHPLPKLILEYRQLAKLKSTYTDGLPKLINPDTGRIHTSFNQTGTATGRLSSSDPNLQN 343 Query: 723 IPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVA 782 IPI+++ G+KIR+AF++ LISADYSQIELRILAH+++ L + F DIH A Sbjct: 344 IPIRSEEGRKIRKAFVAEKGYTLISADYSQIELRILAHLSQDEGLLRAFTEGEDIHTATA 403 Query: 783 AEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGI 842 AE+FGV IE+V+ + RR AK INF +IYG+S F LA QL IPR EA +YI RYF R+PG+ Sbjct: 404 AEVFGVPIEEVTSEQRRKAKAINFGLIYGMSAFGLAQQLGIPRKEAKEYIDRYFERYPGV 463 Query: 843 HEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRR 902 EY+E+TK R++GYVET+FGRR + +INS +R ERAAINAPIQG+AADI + Sbjct: 464 KEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRAAAERAAINAPIQGTAADIIKL 523 Query: 903 AMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEKACLPKINLRVPL 962 AMI V K+L++ KL ++LLQ+HDELVFEVP+EE+ +++ ME A +NL VPL Sbjct: 524 AMIKVDKALKEEKLKARLLLQVHDELVFEVPKEELEEVKKLLKAIMENA----VNLSVPL 579 Query: 963 KVNIKVSNNWQE 974 +V++ + NW E Sbjct: 580 EVDVGIGKNWDE 591 >gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A. Length = 383 Score = 397 bits (1021), Expect = e-110 Identities = 187/384 (48%), Positives = 253/384 (65%), Gaps = 5/384 (1%) Query: 590 IDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKT-KTG 648 +D + L+++S E+ L LE I +L+GE+FNL SPKQLG +LF +L P KT KTG Sbjct: 1 VDVEYLEELSNELGAQLADLEFKIPELAGEEFNLGSPKQLGVLLFEELGLPKTKKTDKTG 60 Query: 649 QWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLAST 708 T A LE + + IIK ILE+RQLSK++STY D LP I+ R+HT Y+ A T Sbjct: 61 ARSTNADVLESLREDAHEIIKIILEYRQLSKLQSTYVDKLPLMIDPDDGRIHTSYNQAGT 120 Query: 709 MTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLY 768 TGRL+S +PNLQNIPI+ + G++IR AFI+ P L++ADYSQIELRILAH++ L Sbjct: 121 ATGRLSSTDPNLQNIPIRNEYGREIRAAFIAEPGYVLVAADYSQIELRILAHLSGDENLI 180 Query: 769 QVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEA 828 + F DIH + AA+IFGV++ +V+ RR+AKT NF IYG S L+ L I R EA Sbjct: 181 EAFRTGADIHTLTAADIFGVDLHEVTGNQRRNAKTFNFGRIYGASAKGLSQLLGISREEA 240 Query: 829 ADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAI 888 ++I++YF RFPG+ Y EKT+ ++ GYVET+FGRR + +I+S S+R ERAA+ Sbjct: 241 KEFIEKYFERFPGVKRYREKTRKEAKKGGYVETLFGRRRYLPDIDSRNRSLREAAERAAL 300 Query: 889 NAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSM 948 N PIQGSAADI + AMI + ++L + L +M LQ+HDE+VFEVP+EE + I M Sbjct: 301 NTPIQGSAADILKLAMIKLDEALVEKGLDARMCLQVHDEIVFEVPKEEAEAVAAQIKELM 360 Query: 949 EKACLPKINLRVPLKVNIKVSNNW 972 E+A + L VPL V + NW Sbjct: 361 ERA----MFLDVPLLVEVGQGRNW 380 >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 = 328 bits (842), Expect = 6e-90 Identities = 136/346 (39%), Positives = 202/346 (58%), Gaps = 29/346 (8%) Query: 651 KTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHI--NKRTQ--RVHTFYSLA 706 T+ + LEQ+ +P+ K ILE+R+LSK+ +TY + L + Q R+H ++ Sbjct: 30 STSKEVLEQLK-RLHPLPKLILEYRKLSKLLTTYVEPLLLLCKLSSSLQMYRIHPTWNQT 88 Query: 707 STMTGRLASLEPNLQNIP----IKTDLGQK-----------IRRAFISPPTKKLISADYS 751 T TGRL+S EPNLQN+P IK +R AFI PP + L+SADYS Sbjct: 89 GTATGRLSSSEPNLQNVPKDFEIKDAPSPPAGSEGDIPTISLRHAFIPPPGRVLLSADYS 148 Query: 752 QIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYG 811 Q+ELRILAH++ L ++ + D+ +M+AA+ G +E+V+ + R+ AK + + I+YG Sbjct: 149 QLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYG 208 Query: 812 ISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDE 871 + LA QL + EA +I+ + + +PG+ +I +T R+NG+VET+ GRR + E Sbjct: 209 MGAKSLAEQLGVSEEEAKQFIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPE 268 Query: 872 INSPKSSIRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATK-----MLLQIHD 926 INS SS R ER A+N IQGSAADI + AMI++H+ L ++LQIHD Sbjct: 269 INSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEKLHSLLPNLPAGRARLVLQIHD 328 Query: 927 ELVFEVPEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNW 972 EL+FEVPE ++ ++II SME A L VPL V + + +W Sbjct: 329 ELLFEVPESDVDEVARIIKRSMENAA----KLSVPLPVKVSIGKSW 370 >gnl|CDD|28892 cd00008, 53EXOc, 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.. Length = 240 Score = 278 bits (712), Expect = 6e-75 Identities = 122/245 (49%), Positives = 166/245 (67%), Gaps = 5/245 (2%) Query: 5 NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64 L L+DGSS YRA++A P L GLP NA+ GF NML KL+ KE ++ AV+ Sbjct: 1 KRLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLI----KEYKPTYVAVV 56 Query: 65 FDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATY 124 FD TFR+E+YP+YKANR K+PE L Q+PL++ +A GIP +EI+G+EADD+I T Sbjct: 57 FDAGGKTFRHELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTL 116 Query: 125 TYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQA 184 AE EG+ V I+S DKDL+QLVS + +K++ + E+VI+K+G+ P +++ +A Sbjct: 117 AKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPMKKKLVTEENVIEKYGVTPAQIIDYKA 176 Query: 185 LTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSR 244 L GDS DNIPG+PGIG KTAA LL+EYG+LE IL N +IK K RE + E E A LS+ Sbjct: 177 LMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKG-KLREKLEEGKEMAFLSK 235 Query: 245 KLVML 249 +L + Sbjct: 236 RLATI 240 >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 = 262 bits (672), Expect = 3e-70 Identities = 103/327 (31%), Positives = 161/327 (49%), Gaps = 23/327 (7%) Query: 664 DNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNI 723 +P + +LE+++L+K+ S R R H Y T+TGR AS N Q I Sbjct: 25 AHPAVPLLLEYKKLAKLWSANGWPWL-DQWVRDGRFHPEYVPGGTVTGRWASRGGNAQQI 83 Query: 724 PIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAA 783 P + LG+ IR+AF++ P L+ AD SQ+ELR+LA ++ L + F D++ A+ Sbjct: 84 PRRDPLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATAS 143 Query: 784 EIFGVNIEKVSPQMRRHAKTINFSIIYG----ISPFRLATQLRIPRSEAADYIKRYFHRF 839 +FGV V R+HAK N +YG IS LA RI EAA I+ +F RF Sbjct: 144 AMFGV---PVGGGERQHAKIANLGAMYGATSGISARLLAQLRRISTKEAAALIELFFSRF 200 Query: 840 PGIHEYIEKTKNFVRQ---NGYVETIFGRRIH-----------YDEINSPKSSIRNINER 885 P + +E ++ R+ GYV T+ GRR S +R R Sbjct: 201 PAFPKAMEYVEDAARRGERGGYVRTLLGRRSPPPDIRWTEVVSDPAAASRARRVRRAAGR 260 Query: 886 AAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIV 945 A N +QG+AAD + AM+++ + LE+ L +++ +HDE+V P+EE + I+ Sbjct: 261 FARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVR 320 Query: 946 HSMEKACLPKINLRVPLKVNIKVSNNW 972 + E + + VP++ +K+ W Sbjct: 321 EAAE-QAVRLLFGSVPVRFPVKIGVVW 346 >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 = 256 bits (656), Expect = 2e-68 Identities = 119/330 (36%), Positives = 173/330 (52%), Gaps = 26/330 (7%) Query: 668 IKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNIPIKT 727 I+ + E + +S + ST+ L +N T R+H ++ +T TGRL+S PNLQN P Sbjct: 45 IEALKEIKSISTLLSTFIIPLQELLNDSTGRIHCSLNI-NTETGRLSSRNPNLQNQPALE 103 Query: 728 DLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFG 787 KIR+AFI+ P LI ADYSQ+ELR+LAH+ + + + F D H A+ ++ Sbjct: 104 KDRYKIRKAFIASPGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGGDFHSRTASGMYP 163 Query: 788 VNIEKVSPQM-----------------------RRHAKTINFSIIYGISPFRLATQLRIP 824 E V+ RR AK +NFSI YG + LA ++ Sbjct: 164 HVAEAVANGEVLLEWKSEGKPPAPLLKDKFKSERRKAKVLNFSIAYGKTAHGLAKDWKVK 223 Query: 825 RSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINE 884 EA + ++ P + ++ +KTK R+ GY T+ GR + +I S R E Sbjct: 224 LKEAERTVDAWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGHAE 283 Query: 885 RAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQII 944 RAAIN PIQGSAADI +AM+ ++++L +L K+LLQIHDE++ E PEE+ A +I+ Sbjct: 284 RAAINTPIQGSAADIAMKAMLRIYRNLRLKRLGWKLLLQIHDEVILEGPEEKADEALKIV 343 Query: 945 VHSMEKACLPKINLRVPLKVNIKVSNNWQE 974 ME L VPL+V+ V NW E Sbjct: 344 KDCMENP--FFGPLDVPLEVDGSVGYNWYE 371 >gnl|CDD|30607 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]. Length = 310 Score = 242 bits (619), Expect = 3e-64 Identities = 126/299 (42%), Positives = 179/299 (59%), Gaps = 13/299 (4%) Query: 1 MQKENHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASH 60 M K L L+DGSS +YRA +A P G P A++GF ML++L++ +H Sbjct: 7 MNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLE----PTH 62 Query: 61 FAVIFDYPAVTFRNEIYPDYKANRPKI-PEMLLPQLPLVRLATQAFGIPAIEIQGFEADD 119 V+FD TFR+E+ +YKANR K P+ L PQ+P++ A GIP +E+ G EADD Sbjct: 63 PVVVFDGKPPTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADD 122 Query: 120 IIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVK---EEKIDIEHVIKKW-GIP 175 I T A K+G V IIS DKDL+QLVSP + + K E+ +D+E V +K+ G+ Sbjct: 123 PIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKFKGLT 182 Query: 176 PEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILE 235 PE+++ L+AL GDS DNIPG+ GIG KTA LLQEYG+LE + N IK KK RE +LE Sbjct: 183 PEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIK-KKTREKLLE 241 Query: 236 YAETARLSRKLVMLRTDVPITIPLEHLI---LEDCNGPRLISFLKALEFTKLINRVATT 291 E A LS+ L ++TDVP+ LE ++ + + + +L+ L F +L+ + + Sbjct: 242 DKEKAFLSKPLATIKTDVPLEFDLEDILELLVPEHDFSKLLEERVELGFKRLLKAIGSV 300 >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 = 237 bits (607), Expect = 1e-62 Identities = 112/340 (32%), Positives = 190/340 (55%), Gaps = 37/340 (10%) Query: 649 QWKTTAQDLEQ--------INCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVH 700 +WK ++LE+ + ++P ++ +LE+R+L+K+ ST+ + LP HI+ T R+H Sbjct: 5 RWKELEKELERERQEAAKELYIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPVTGRIH 64 Query: 701 TFYSLASTMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAH 760 ++ +GR++ PNLQ IP + + RR F++P KLI ADYSQIELRI A Sbjct: 65 PSFNQIGAASGRMSCSNPNLQQIPREREF----RRCFVAPEGNKLIIADYSQIELRIAAE 120 Query: 761 IAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQ 820 I+ + ++ D+HR+ A+ I G IE+++ + R+ AK +NF +IYG+S L Sbjct: 121 ISGDERMISAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREY 180 Query: 821 LR----IPRS--EAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVE--TIFGRRIHYDEI 872 R + S EA + + +F + GI + + ++ G +E T+ GRR ++ Sbjct: 181 ARTNYGVEMSLEEAEKFRESFFFFYKGIL----RWHHRLKAKGPIEVRTLLGRRRVFEYF 236 Query: 873 NSPKSSIRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEV 932 + A+N PIQG+ ADI + A+ + L+D L K++L +HDE+V EV Sbjct: 237 TFTE----------ALNYPIQGTGADILKLALALLVDRLKD--LDAKIVLCVHDEIVLEV 284 Query: 933 PEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNW 972 PE+E A +I+ SME+A + +VP++V + +S++W Sbjct: 285 PEDEAEEAKKILESSMEEAGKRILK-KVPVEVEVSISDSW 323 >gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal resolvase-like domain. Length = 169 Score = 196 bits (500), Expect = 3e-50 Identities = 75/173 (43%), Positives = 102/173 (58%), Gaps = 9/173 (5%) Query: 5 NHLFLVDGSSFIYRAFYATPLLS-RKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63 L L+DGSS +RAF+A P + G P NA+ GF ML KLL+ + + AV Sbjct: 1 KKLLLIDGSSLAFRAFFALPKVPLTNSKGEPTNAVYGFLRMLLKLLKEEKPT----YVAV 56 Query: 64 IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123 +FD A TFR+E+Y +YKANR K P+ L PQ+PL++ A GIP +E+ G+EADD+I T Sbjct: 57 VFDAGAPTFRHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLEVPGYEADDVIGT 116 Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTT----CLYDTVKEEKIDIEHVIKKW 172 AEKEG+ V I+S DKDL+QLVS + E V++K+ Sbjct: 117 LAKKAEKEGYDVRIVSGDKDLLQLVSDKVNVAVLNPGRTEFTLYTPEEVVEKY 169 >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 = 120 bits (303), Expect = 2e-27 Identities = 55/189 (29%), Positives = 104/189 (55%), Gaps = 17/189 (8%) Query: 396 TDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKK 455 T ++D ++ + I+ + + ++ +I L H D G+ +E+L+ LK Sbjct: 14 TTSLDPMQAELVGISFAV---EPGEAY-----YIPLG-H---DYGGEQLPREEVLAALKP 61 Query: 456 FFENEHFLKIGHNIKYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLS 514 E+ K+G N+K+D VL +GI +RG D ML SY+L+ GR H + +A+++L Sbjct: 62 LLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLG 121 Query: 515 Y---TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLI-VEKLLHVYE 570 + + ++++ K I D++ + E+A E++++ L+L+ LL+PKL LL +YE Sbjct: 122 HKTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKEEPGLLELYE 181 Query: 571 RLDKPMIDV 579 ++ P+I V Sbjct: 182 EIEMPLIPV 190 >gnl|CDD|110372 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold. Length = 100 Score = 109 bits (275), Expect = 4e-24 Identities = 49/89 (55%), Positives = 64/89 (71%), Gaps = 1/89 (1%) Query: 174 IPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENI 233 + PE+++ +AL GDS DNIPG+PGIG KTAA LL+EYG+LENI N ++K K RE + Sbjct: 1 LTPEQIIDYKALVGDSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK-GKLREKL 59 Query: 234 LEYAETARLSRKLVMLRTDVPITIPLEHL 262 L E A LSRKL ++TDVP+ + LE L Sbjct: 60 LNGKEDAFLSRKLATIKTDVPLELTLEDL 88 >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 = 102 bits (256), Expect = 5e-22 Identities = 84/386 (21%), Positives = 147/386 (38%), Gaps = 55/386 (14%) Query: 621 FNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQLSKI 680 FN SS K + L K + T++G+ K L ++ D P K + E+ + K Sbjct: 65 FNPSSRKHIAKRLKAKYGWEPQEFTESGEPKVDEDVLSKL---DYPEAKLLAEYLLVQKR 121 Query: 681 KSTYADSLPN---HINKRTQRVHTFYSLASTMTGRLASLEPNLQNIP-IKTDLGQKIRRA 736 AD N + R+H + +TGR PN+ +P + + G++ R Sbjct: 122 LGQLADG-NNAWLKLVHEDGRIHGAVNTNGAVTGRATHFSPNMAQVPAVGSPYGKECREL 180 Query: 737 FISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQ 796 F PP L+ AD S +ELR LAH ++ +++ +I N + + Sbjct: 181 FGVPPGWSLVGADASGLELRCLAH------YLARYDGGAYTRKVLGGDIHWANAQAMGLL 234 Query: 797 MRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYI------------------------ 832 R AKT ++ +YG +L + A + Sbjct: 235 SRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVR 294 Query: 833 KRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPI 892 + P + + I+K K ++ G++ + GRRI +R + AA+N + Sbjct: 295 ANFLKGLPALGKLIKKVKEAAKKRGHLVGLDGRRIR----------VR--SAHAALNTLL 342 Query: 893 QGSAADITRRAMISVHKSLEDHKLAT----KMLLQIHDELVFEVPEEEITTASQIIVHSM 948 Q + A + ++ ++ + L + +HDE+ E + +I V + Sbjct: 343 QSAGAILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAA 402 Query: 949 EKACLPKINLRVPLKVNIKVSNNWQE 974 EKA N R PL + NW E Sbjct: 403 EKAGE-HFNFRCPLAGEFDIGRNWAE 427 >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 = 95.4 bits (238), Expect = 8e-20 Identities = 40/140 (28%), Positives = 71/140 (50%), Gaps = 7/140 (5%) Query: 444 TLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFE-DIMLMSYVLDSGRSS 502 L L+ LK++ E+E K+GH+ K + L R+GI + G D ML +Y+LD RSS Sbjct: 39 ELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSS 98 Query: 503 HDIASIAQKWLSY---TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPK 559 +D+A +A+++L + +E+ D + + EH + I +L L + Sbjct: 99 YDLADLAKRYLGRELPSDEEVYGKGAKFAVPD---EEVLAEHLARKAAAIARLAPKLEEE 155 Query: 560 LIVEKLLHVYERLDKPMIDV 579 L + L +Y ++ P+ +V Sbjct: 156 LEENEQLELYYEVELPLAEV 175 >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 = 80.0 bits (197), Expect = 3e-15 Identities = 42/167 (25%), Positives = 77/167 (46%), Gaps = 22/167 (13%) Query: 396 TDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKK 455 T ++ K + I I+T + +I + E L LK+ Sbjct: 9 TTGLNYHRGKLVGIQIATAGEA---------AYIPDELELE-----------EDLEALKE 48 Query: 456 FFENEHFLKIGHNIKYDKLVLHRYGISMRGF-EDIMLMSYVLDSGRSSHDIASIAQKWLS 514 E+E K+GH+ K+D +VL R GI + G D ML +Y+L+ G SH + +A+++L Sbjct: 49 LLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLG 108 Query: 515 Y-TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKL 560 K+ K + + ++ E+A E+++ +L+L+ L +L Sbjct: 109 IELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155 >gnl|CDD|28961 cd00080, HhH2_motif, Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.. Length = 75 Score = 78.4 bits (193), Expect = 8e-15 Identities = 41/78 (52%), Positives = 54/78 (69%), Gaps = 3/78 (3%) Query: 170 KKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKR 229 +K G+ PE+ + L L GD DNIPG+PGIG KTA LL+EYG+LEN+L N +IK Sbjct: 1 EKLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKIKL--- 57 Query: 230 RENILEYAETARLSRKLV 247 RE +LE+ E A+LS+ L Sbjct: 58 REKLLEHKELAKLSKLLA 75 >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 = 67.7 bits (166), Expect = 2e-11 Identities = 36/114 (31%), Positives = 62/114 (54%), Gaps = 7/114 (6%) Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHR-YGISMRGFEDIMLMSYVLDSGRSSHDIASI 508 L LK+ E+ + K+GHN K+D VL R +GI + D ML +Y+L R SH + + Sbjct: 64 LEGLKRLLEDPNITKVGHNAKFDLEVLARDFGIKLENLFDTMLAAYLLGYPR-SHSLDDL 122 Query: 509 AQKWLSY-TRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLI 561 A+K+L K + +S+ Q++ +A E+++ +L+L+ LR +L Sbjct: 123 AEKYLGVELDKSEQCADWR---ARPLSEEQLR-YAAEDADYLLRLYDKLRKELE 172 >gnl|CDD|176649 cd06128, DNA_polA_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Pol I resemble the fold of the 3'-5' exonuclease domain of KF without the proofreading activity of KF. The four critical metal-binding residues are not conserved in BF Pol I and Taq Pol I, and they are unable to bind metals necessary for exonuclease activity. Length = 151 Score = 65.1 bits (158), Expect = 8e-11 Identities = 40/110 (36%), Positives = 63/110 (57%), Gaps = 1/110 (0%) Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGF-EDIMLMSYVLDSGRSSHDIASI 508 L LK E+E LK+G N+KYD+++L YGI +RG D ML +Y+LD HD+ S+ Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSL 101 Query: 509 AQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRP 558 A++WL + + ++I+ + E+A E++ V LQL L + P Sbjct: 102 AERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMWP 151 >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 = 63.0 bits (154), Expect = 4e-10 Identities = 90/360 (25%), Positives = 143/360 (39%), Gaps = 83/360 (23%) Query: 622 NLSSPKQLGDILFTK-LKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQ-LSK 679 N +SP QL D L + + S K K L + GD +K +LE RQ LSK Sbjct: 28 NPNSPAQLKDWLNEQGGEVDSLLK------KDVVALLLKTAPGD---VKRVLELRQELSK 78 Query: 680 IKSTYADSLPNHINKRTQRVH---TFYSLASTMTGRLASLEPNLQNIP------------ 724 +++ + RV FY A+ TGR A +QN+P Sbjct: 79 TSVKKYEAMERAVCS-DGRVRGLLQFYG-ANR-TGRWAGRLVQVQNLPRNYLKDLDLARE 135 Query: 725 ----------------IKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLY 768 + L Q IR AFI + I +D+S IE R++A +A Sbjct: 136 LVKSGDFDALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRL 195 Query: 769 QVFENSLDIHRMVAAEIFGVNIEKVSP--QMRRHAKTINFSIIYGISPFRL----ATQLR 822 VF I+ A+++FGV +EK+ +R+ K ++ YG S L A ++ Sbjct: 196 DVFATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAELALGYGGSVGALKAMGALEMG 255 Query: 823 IPRSEAADYIKRYFHRFPGIHEY---IEKT-KNFVRQNGYVETIFGRRIHYDEINSPKSS 878 + E + + + P I + ++K K V++ V+ K Sbjct: 256 LTEDELPGIVDAWRNANPNIVKLWWDVDKAAKKAVKERKTVKL------------GGK-L 302 Query: 879 IRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEIT 938 + NI +Q A D AM+ + K+ D +++ +HDE+V EVPE E + Sbjct: 303 VENI---------VQAIARDCLAEAMLRLEKAGYD------IVMHVHDEVVIEVPEGEGS 347 >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 = 59.6 bits (144), Expect = 4e-09 Identities = 36/110 (32%), Positives = 61/110 (55%), Gaps = 2/110 (1%) Query: 450 LSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASI 508 L LK E+E LK+G N+KYD+ +L Y I +RG D ML +Y+L+S D+ S+ Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSL 101 Query: 509 AQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRP 558 ++WL + + +S + ++ + +A E+++V LQ+ L L P Sbjct: 102 VERWLGHKLIK-FESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150 >gnl|CDD|29030 cd00128, XPG, Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.. Length = 316 Score = 51.0 bits (122), Expect = 1e-06 Identities = 44/132 (33%), Positives = 68/132 (51%), Gaps = 14/132 (10%) Query: 103 QAFGIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKE-- 160 + GIP I +EA+ A Y+ K+G II+ D DL+ +P Sbjct: 138 RLMGIPYIVA-PYEAE---AQCAYL-AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAK 192 Query: 161 --EKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENIL 218 E+ID+E ++K+ G+ EK++ L L G D GIPGIG TA L+++YG++E + Sbjct: 193 PVEEIDLEKILKELGLTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDI 250 Query: 219 INASRIKQKKRR 230 R+K+K R Sbjct: 251 ---ERLKKKLYR 259 >gnl|CDD|37730 KOG2519, KOG2519, KOG2519, 5'-3' exonuclease [Replication, recombination and repair]. Length = 449 Score = 44.2 bits (104), Expect = 2e-04 Identities = 30/124 (24%), Positives = 50/124 (40%), Gaps = 17/124 (13%) Query: 130 KEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEK------IDIEHVIKKWGIPPEKMVCLQ 183 K G + + D D + +P + D+ +++ G+ E + L Sbjct: 164 KAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLC 223 Query: 184 ALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLS 243 L G D P I GIG K A L++++G++ENIL + ++ EY S Sbjct: 224 LLLG--CDYCPTIRGIGPKKALKLIRQHGDIENIL---------EINSDLKEYPIPEDWS 272 Query: 244 RKLV 247 KL Sbjct: 273 YKLA 276 >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 = 38.7 bits (91), Expect = 0.007 Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%) Query: 453 LKKFFENEHFLKIGHNIKYDKLVLHR-YGISMRGFEDI 489 LK+ E+ LK+G IK D L R +GI +RG D+ Sbjct: 65 LKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDL 102 >gnl|CDD|176478 cd08641, DNA_pol_gammaA, Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. 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 gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). 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. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases. Length = 425 Score = 36.5 bits (85), Expect = 0.034 Identities = 46/194 (23%), Positives = 73/194 (37%), Gaps = 50/194 (25%) Query: 776 DIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGIS-PF--RLATQL--RIPRSEAAD 830 D+H A I G++ R HAK N+ IYG PF RL Q R+ +EA + Sbjct: 189 DLHSK-TASILGIS--------RDHAKVFNYGRIYGAGQPFAERLLMQFNPRLTPAEATE 239 Query: 831 YIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINS--------------PK 876 K+ + GI I+++ R +F R S P+ Sbjct: 240 KAKQMYAATKGIRIAIQRSTKGKR-------LFKRPFWSGGSESIMFNKLEEIAAQSQPR 292 Query: 877 SS------IRNINERAA---------INAPIQGSAADITRRAMISVHKSLEDHKLATKML 921 + + E IN +Q SA D ++S+ +E + + + Sbjct: 293 TPVLGACITSALLEPNLVKNEFMTSRINWVVQSSAVDYLHLMLVSMRWLIEKYDIDARFC 352 Query: 922 LQIHDELVFEVPEE 935 + IHDE+ + V EE Sbjct: 353 ISIHDEVRYLVKEE 366 >gnl|CDD|38861 KOG3657, KOG3657, KOG3657, Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]. Length = 1075 Score = 35.4 bits (81), Expect = 0.080 Identities = 53/272 (19%), Positives = 97/272 (35%), Gaps = 73/272 (26%) Query: 729 LGQKIRRAFISPPTKKLISADYSQIELRIL-----AHIAKI---TPLYQVF-----ENSL 775 +G +++ +PP +L+ AD EL I A + T + + Sbjct: 719 IGSELKAMVQAPPGYRLVGADVDSQELWIAALLGDASAEGVHGKTAFGWMTLAGSKSDGT 778 Query: 776 DIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGI-SPF--RLATQL--RIPRSEAAD 830 D+H A+++ +S R HAK N++ IYG F +L + + +SEA Sbjct: 779 DLHSKTASQL------GIS---RNHAKVFNYARIYGAGQTFAEKLLMRFNPSLTQSEAKS 829 Query: 831 ---------------YIKRYFH-----------RFPGIHEYIEKTKNFVR-----QNGYV 859 +K GI+ +N V G Sbjct: 830 KASQLFKLTKGDRAKRLKVEVRMVENSLVCKILTIDGIYLIYSIYENEVEPRRLWVGGTE 889 Query: 860 ETIFGRRIHYDEINSPKS---------SIRNINERAA------INAPIQGSAADITRRAM 904 ++F + + P++ S+ + E IN +Q SA D + Sbjct: 890 SSMFNKLESIATAHDPRTPVLGCQISRSLEKLPEGEPKFLPSRINWVVQSSAVDFLHLLL 949 Query: 905 ISVHKSLEDHKLATKMLLQIHDELVFEVPEEE 936 +S+ + +K+ + + IHDE+ + V EE+ Sbjct: 950 VSMQWLCDTYKIDARFCISIHDEVRYLVKEED 981 >gnl|CDD|37729 KOG2518, KOG2518, KOG2518, 5'-3' exonuclease [Replication, recombination and repair]. Length = 556 Score = 34.2 bits (78), Expect = 0.18 Identities = 55/261 (21%), Positives = 94/261 (36%), Gaps = 39/261 (14%) Query: 10 VDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVIFD--- 66 VDG +++R A + G P + F KLL + + I ++FD Sbjct: 29 VDGYCWLHRG--ALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPI-----LVFDGDP 81 Query: 67 YPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFG-------------IPAIEIQ 113 P+ + + E LL A + F I + Q Sbjct: 82 LPSKKETERKRRERRKKNLDAAEQLL-AEGKESNARECFQRCVDITPEMAHKLIQYLRSQ 140 Query: 114 GFEADDIIATYTYIA-----EKEGFAVTIISTDKDLMQLVSPT--TCLYDTVKEEKIDIE 166 E I+A Y A E+EG II+ D DL+ + +I+ Sbjct: 141 NVEY--IVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEINRS 198 Query: 167 HVIKKWGI----PPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINAS 222 + + + EK + L+G D + +PG+G TA LL +Y + ++I+ Sbjct: 199 KLPECKPLGDKFTEEKFRRMCILSG--CDYLSSLPGVGLATAHKLLSKYNTPDRVIISHL 256 Query: 223 RIKQKKRRENILEYAETARLS 243 K+ ++ +E E A L+ Sbjct: 257 LKKKLTVPDDYIENFERANLT 277 >gnl|CDD|132972 cd06641, STKc_MST3, Catalytic domain of the Protein Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 3. Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 3 (MST3) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. It may also regulate paxillin and consequently, cell migration. MST3 is present in human placenta, where it plays an essential role in the oxidative stress-induced apoptosis of trophoblasts in normal spontaneous delivery. Dysregulation of trophoblast apoptosis may result in pregnancy complications such as preeclampsia and intrauterine growth retardation. Length = 277 Score = 31.2 bits (70), Expect = 1.5 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 6/79 (7%) Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435 D ++ KLE IG SF + +D K +AI I L++ +D ++E I +++V + Sbjct: 1 DPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAED---EIEDIQQEITVLS 57 Query: 436 SQDSTGKNTLTKEILSYLK 454 DS +TK SYLK Sbjct: 58 QCDSP---YVTKYYGSYLK 73 >gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]. Length = 667 Score = 30.9 bits (70), Expect = 1.5 Identities = 10/24 (41%), Positives = 14/24 (58%) Query: 195 GIPGIGYKTAALLLQEYGNLENIL 218 GI +G TA L + +G LE +L Sbjct: 515 GIRHVGETTAKSLARHFGTLEALL 538 >gnl|CDD|31234 COG1031, COG1031, Uncharacterized Fe-S oxidoreductase [Energy production and conversion]. Length = 560 Score = 30.3 bits (68), Expect = 2.9 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 11/95 (11%) Query: 225 KQKKRRENILEYAETARLSRKLVMLRTDVPITIPLEHLILEDCNG-----------PRLI 273 K +K ++ + R L ML+ VP L + +E G P L+ Sbjct: 418 KAEKHKKLFAAFKRKVREEIDLPMLKRVVPKGTVLRDVRVEVYEGGLTFGRQLGSYPLLV 477 Query: 274 SFLKALEFTKLINRVATTYDCDAANIEPVVLDINT 308 LE + ++ V + + PV LD+N+ Sbjct: 478 GIPGRLELGRYVDVVVVDHGARSVTAIPVPLDVNS 512 >gnl|CDD|30715 COG0366, AmyA, Glycosidases [Carbohydrate transport and metabolism]. Length = 505 Score = 30.3 bits (67), Expect = 2.9 Identities = 16/102 (15%), Positives = 29/102 (28%), Gaps = 1/102 (0%) Query: 802 KTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGY-VE 860 + F + G+ FRL I + + IHEY+ + V G + Sbjct: 182 DVVKFWLDKGVDGFRLDAAKHISKDFGLPPSEENLTFLEEIHEYLREENPDVLIYGEAIT 241 Query: 861 TIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRR 902 + E + +S N + G + Sbjct: 242 DVGEAPGAVKEDFADNTSFTNPELSMLFDFSHVGLDFEALAP 283 >gnl|CDD|146299 pfam03586, Herpes_UL36, Herpesvirus UL36 tegument protein. The UL36 open reading frame (ORF) encodes the largest herpes simplex virus type 1 (HSV-1) protein, a 270-kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells. This family only covers a small central part of this large protein. Length = 253 Score = 30.0 bits (68), Expect = 3.1 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 8/81 (9%) Query: 783 AEIFGVNIEKVSPQMR------RHAKTINFSIIYGISPFRLATQL-RIPR-SEAADYIKR 834 +FGV++E + +R HA +I Y + L+ L +P ++ D+ +R Sbjct: 106 ETLFGVDVEPLMRLLRIAGGILEHAAAGGGNIDYYDAVGTLSGDLLAVPELAKYVDFYRR 165 Query: 835 YFHRFPGIHEYIEKTKNFVRQ 855 + F +E + V Q Sbjct: 166 GYEEFEEELARLEALRADVLQ 186 >gnl|CDD|35422 KOG0201, KOG0201, KOG0201, Serine/threonine protein kinase [Signal transduction mechanisms]. Length = 467 Score = 30.0 bits (67), Expect = 3.5 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%) Query: 383 KLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGK 442 KLE IG SF + +D K +AI I L++ +D ++E I ++SV + DS Sbjct: 17 KLELIGRGSFGEVYKAIDNKTKKVVAIKIIDLEEAED---EIEDIQQEISVLSQCDSP-- 71 Query: 443 NTLTKEILSYLKKF 456 +T+ SYLK Sbjct: 72 -NITEYYGSYLKGT 84 >gnl|CDD|37415 KOG2204, KOG2204, KOG2204, Mannosyl-oligosaccharide alpha-1,2-mannosidase and related glycosyl hydrolases [Carbohydrate transport and metabolism]. Length = 625 Score = 29.6 bits (66), Expect = 4.3 Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%) Query: 606 LLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAK 644 LLS Y LSGE+ L ++GD L P+G Sbjct: 271 LLSA----YALSGEEMFLEKAPEIGDKLLPAFNTPTGIP 305 >gnl|CDD|37048 KOG1837, KOG1837, KOG1837, Uncharacterized conserved protein [Function unknown]. Length = 1621 Score = 29.6 bits (66), Expect = 4.4 Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 1/90 (1%) Query: 298 NIEPVVLDINTTENKGIAIETEIDRDTTIKT-SQFSSLSDQTSKINSEQTPQKLFLERLQ 356 E +LDI ++ I++ + I+ ++ +++ Q + + Sbjct: 445 LKEYQILDIIQFASEAISLTQSEESIEIIEEELPSCKKIKLSASERAQKLAQLSIFAKRE 504 Query: 357 KLSQYPINNDSYTKIVNTKDIQQWVQKLET 386 + PIN + + N D +W+ Sbjct: 505 VFNGDPINKATEGLMGNPWDKVEWLSNEMA 534 >gnl|CDD|132971 cd06640, STKc_MST4, Catalytic domain of the Protein Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 4. Serine/threonine kinases (STKs), mammalian Ste20-like protein kinase 4 (MST4) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MST4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MST4 is sometimes referred to as MASK (MST3 and SOK1-related kinase). It plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. It influences cell growth and transformation by modulating the extracellular signal-regulated kinase (ERK) pathway. MST4 may also play a role in tumor formation and progression. It localizes in the Golgi apparatus by interacting with the Golgi matrix protein GM130 and may play a role in cell migration. Length = 277 Score = 29.6 bits (66), Expect = 4.7 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 6/79 (7%) Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435 D ++ KLE IG SF + +D + +AI I L++ +D ++E I +++V + Sbjct: 1 DPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAED---EIEDIQQEITVLS 57 Query: 436 SQDSTGKNTLTKEILSYLK 454 DS +TK SYLK Sbjct: 58 QCDSP---YVTKYYGSYLK 73 >gnl|CDD|38827 KOG3621, KOG3621, KOG3621, WD40 repeat-containing protein [General function prediction only]. Length = 726 Score = 29.6 bits (66), Expect = 4.7 Identities = 10/54 (18%), Positives = 18/54 (33%) Query: 157 TVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQE 210 T +++I + E+ +C L S+ P G+G E Sbjct: 455 TQPPRRVEIFKRAGEMDGGFEQSICHTTLEKTSVGEPPFASGVGIVEIGHETHE 508 >gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]. Length = 436 Score = 29.4 bits (66), Expect = 5.0 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 1/58 (1%) Query: 195 GIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARLSRKLVMLRTD 252 G PG G T A L+ N ++A K I+E A RL + +L D Sbjct: 55 GPPGTGKTTLARLIAGTTNAAFEALSAV-TSGVKDLREIIEEARKNRLLGRRTILFLD 111 >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 = 5.1 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 21/94 (22%) Query: 402 FHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEH 461 FH K ++I+ D KV T+ KE+L + E ++ Sbjct: 50 FH-KVVSISAL-YRDDDGGFLKVRTLD-GAD-------------EKELLEDFFQLIEKKN 93 Query: 462 FLKIGHNIK-YDKLVLH----RYGISMRGFEDIM 490 + N + +D VLH +G+S + D+ Sbjct: 94 PRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLG 127 >gnl|CDD|132973 cd06642, STKc_STK25-YSK1, Catalytic domain of the Protein Serine/Threonine Kinase, STK25 or Yeast Sps1/Ste20-related kinase 1. Serine/threonine kinases (STKs), STK25 subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The STK25 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. STK25 is also called Ste20/oxidant stress response kinase 1 (SOK1) or yeast Sps1/Ste20-related kinase 1 (YSK1). STK25 is localized in the Golgi apparatus through its interaction with the Golgi matrix protein GM130. It may play a role in the regulation of cell migration and polarization. STK25 binds and phosphorylates CCM3 (cerebral cavernous malformation 3), also called PCD10 (programmed cell death 10), and may play a role in apoptosis. Human STK25 is a candidate gene responsible for pseudopseudohypoparathyroidism (PPHP), a disease that shares features with the Albright hereditary osteodystrophy (AHO) phenotype. Length = 277 Score = 28.9 bits (64), Expect = 8.3 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%) Query: 376 DIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHT 435 D ++ KLE IG SF + +D + +AI I L++ +D ++E I +++V + Sbjct: 1 DPEELFTKLERIGKGSFGEVYKGIDNRTKEVVAIKIIDLEEAED---EIEDIQQEITVLS 57 Query: 436 SQDSTGKNTLTKEILSYLK 454 DS +T+ SYLK Sbjct: 58 QCDSP---YITRYYGSYLK 73 >gnl|CDD|36279 KOG1061, KOG1061, KOG1061, Vesicle coat complex AP-1/AP-2/AP-4, beta subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 734 Score = 28.3 bits (63), Expect = 9.9 Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 4/93 (4%) Query: 511 KWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLLRPKLIVEKLLHVYE 570 K+L + + K + S+S++Q A+ N N+ILQ RP+++ ++ + Sbjct: 268 KYLKQVNELLFKKVAPPLVTLLSSESEIQYVALRNINLILQ----KRPEILKVEIKVFFC 323 Query: 571 RLDKPMIDVVSQMEITGIQIDQDLLKQVSAEIS 603 + + P+ + ++EI + L QV AE+ Sbjct: 324 KYNDPIYVKLEKLEILIELANDANLAQVLAELK 356 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 0.135 0.381 Gapped Lambda K H 0.267 0.0657 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 11,448,157 Number of extensions: 614262 Number of successful extensions: 1591 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1537 Number of HSP's successfully gapped: 65 Length of query: 976 Length of database: 6,263,737 Length adjustment: 103 Effective length of query: 873 Effective length of database: 4,038,010 Effective search space: 3525182730 Effective search space used: 3525182730 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 (21.7 bits) S2: 62 (27.8 bits)