RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus
Liberibacter asiaticus str. psy62]
         (976 letters)



>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional.
          Length = 880

 Score = 1072 bits (2775), Expect = 0.0
 Identities = 406/987 (41%), Positives = 581/987 (58%), Gaps = 125/987 (12%)

Query: 4   ENHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63
              L L+DGSS ++RAFYA     R  DGLP  A+ GF NML KLL   ++E   +H AV
Sbjct: 1   MKTLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLL---KEEK-PTHVAV 56

Query: 64  IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123
            FD    TFR+E+YP+YKANRP +PE L  Q+PL+R   +A GIP +E++G+EADD+I T
Sbjct: 57  AFDAKGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGT 116

Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTV---KEEKIDIEHVIKKWGIPPEKMV 180
               AE  G+ V I++ DKDL+QLV     L DT+   K E++D E V++K+G+ PE+++
Sbjct: 117 LAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQII 176

Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
              AL GDS DNIPG+PGIG KTAA LLQEYG+L                E + E  +  
Sbjct: 177 DYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSL----------------EGLYENLDE- 219

Query: 241 RLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEFTKLIN--------RVATTY 292
                                              +K  +  KL          R   T 
Sbjct: 220 -----------------------------------IKGKKKEKLRENKEQAFLSRKLATI 244

Query: 293 DCDAANIEPVVLDINTTENKGIAIETEIDRDTTI---KTSQFSSLSDQTSKINSEQTPQK 349
             D     P+ +D+   E +        DR+  I   K  +F SL               
Sbjct: 245 KTDV----PLEVDLEDLELQ------PPDREKLIALFKELEFKSL--------------- 279

Query: 350 LFLERLQKLSQYPINNDSYTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAI 409
             L R       P++ + Y  I++ ++++ W+ KL+  G  +F   T ++D   ++ + +
Sbjct: 280 --LRRAAAAEAAPLDEEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGL 337

Query: 410 AISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNI 469
           + +            E  +I L           + L +E+L+ LK   E+    K+G N+
Sbjct: 338 SFAVEPG--------EAAYIPL-----------DQLDREVLAALKPLLEDPAIKKVGQNL 378

Query: 470 KYDKLVLHRYGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSI 528
           KYD  VL RYGI +RG   D ML SY+LD GR  H + S+A+++L +      +     +
Sbjct: 379 KYDLHVLARYGIELRGIAFDTMLASYLLDPGRR-HGLDSLAERYLGHKTISFEEVAGKQL 437

Query: 529 PIDKISDSQVQEHAIENSNVILQLWLLLRPKLIVE-KLLHVYERLDKPMIDVVSQMEITG 587
              ++   +  E+A E+++V L+L  +L+PKL+ E  LL +YE ++ P++ V+++ME  G
Sbjct: 438 TFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELPLVPVLARMERNG 497

Query: 588 IQIDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKT 647
           I++D++ LK++SAE+++ L  LE+ IY+L+GE+FN++SPKQLG+ILF KL  P G KTKT
Sbjct: 498 IKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEILFEKLGLPVGKKTKT 557

Query: 648 GQWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLAS 707
           G + T A+ LE++   D+PI   ILE+RQLSK+KSTY D+LP  IN  T R+HT ++   
Sbjct: 558 G-YSTDAEVLEKLA-DDHPIPDKILEYRQLSKLKSTYTDALPKLINPDTGRIHTSFNQTV 615

Query: 708 TMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPL 767
           T TGRL+S +PNLQNIPI+T+ G++IR+AF++P   KL+SADYSQIELRILAH++    L
Sbjct: 616 TATGRLSSSDPNLQNIPIRTEEGRRIRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGL 675

Query: 768 YQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSE 827
            + F    DIH   A+E+FGV +E+V+ + RR AK INF IIYG+S F LA QL I R E
Sbjct: 676 IEAFAEGEDIHTATASEVFGVPLEEVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKE 735

Query: 828 AADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAA 887
           A +YI RYF R+PG+ EY+E+T    R+ GYVET+FGRR +  +INS   + R   ERAA
Sbjct: 736 AKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPDINSRNGNRRAFAERAA 795

Query: 888 INAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHS 947
           INAPIQGSAADI + AMI V K+L++  L ++MLLQ+HDELVFEVPE+E+    +++   
Sbjct: 796 INAPIQGSAADIIKLAMIRVDKALKEEGLKSRMLLQVHDELVFEVPEDELEEVKKLVKEV 855

Query: 948 MEKACLPKINLRVPLKVNIKVSNNWQE 974
           ME A    + L VPL V++ V +NW E
Sbjct: 856 MENA----VELSVPLVVDVGVGDNWDE 878


>gnl|CDD|161944 TIGR00593, pola, DNA polymerase I.  This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 887

 Score =  823 bits (2129), Expect = 0.0
 Identities = 382/977 (39%), Positives = 549/977 (56%), Gaps = 101/977 (10%)

Query: 7   LFLVDGSSFIYRAFYA---TPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAV 63
           L L+DG S  +RA++A    PL + K  G P NA+ GF  ML KLL    KE   ++ AV
Sbjct: 1   LLLIDGHSLAFRAYFALKNKPLTNSK--GEPTNAVYGFTKMLLKLL----KEEKPTYVAV 54

Query: 64  IFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIAT 123
            FD    TFR+E Y +YKANR   PE L+ Q+PL++    A GIP +E++G+EADD+IAT
Sbjct: 55  AFDSGTPTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIAT 114

Query: 124 YTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDT---VKEEKIDIEHVIKKWGIPPEKMV 180
               AEKEG+ V IIS DKDL+QLVS    +          +I  E+V++K+G+ P+++V
Sbjct: 115 LAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTPDQLV 174

Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
            L+AL GDS DNIPG+ GIG KTAA LLQE+G+LENI  N  +IK  K RE ++ + E A
Sbjct: 175 DLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDA 234

Query: 241 RLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEFTKLINRVATTYDCDAANIE 300
            LS++L  + TDVP+ + LE L L + +  RL + L                        
Sbjct: 235 FLSKELATIVTDVPLEVDLEDLRLSEPDRERLYALL------------------------ 270

Query: 301 PVVLDINTTENKGIAIETEIDRDTTIKT--SQFSSLSDQTSKINSEQTPQKLFLERLQKL 358
                             E++  + +    +  S + D  + + +E+T      E    L
Sbjct: 271 -----------------QELEFKSLLDRLENLESPVIDDHAPVLTEKTSCAKESEEAAPL 313

Query: 359 SQYPINNDSYTKIVNTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKD 418
           +                       +   +G      + + +     K +A+A +T +Q  
Sbjct: 314 A--------------------NPAEKAEVG----GFVLERLLDQLKKALALAFATENQSY 349

Query: 419 DTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHR 478
              +  E   I L    + D                ++  NE   KIGH+ K+   +L R
Sbjct: 350 VA-YASEADGIPLLTILTDDK-------------FARWLLNEQIKKIGHDAKFLMHLLKR 395

Query: 479 YGISMRG-FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQ 537
            GI + G   D ML +Y+LD  + S  + ++A+++L        K              +
Sbjct: 396 EGIELGGVIFDTMLAAYLLDPAQVST-LDTLARRYLVEELILDEKIGGKLAKFAFPPLEE 454

Query: 538 VQEHAIENSNVILQLWLLLRPKLIVEKLLHVYERLDKPMIDVVSQMEITGIQIDQDLLKQ 597
             E+    +    +L   L  +L   KLL +Y  ++ P+  V+++ME TGI++D D L++
Sbjct: 455 ATEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQE 514

Query: 598 VSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDL 657
           +S E  + +  LEE IY+L+GE+FN++SPKQLG++LF KL  P G KTKTG + T A  L
Sbjct: 515 LSQEFGEEIADLEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTG-YSTDADVL 573

Query: 658 EQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLE 717
           E++    +PII  ILE+RQL+K+KSTY D LP  +N  T R+HT ++   T TGRL+S  
Sbjct: 574 EKLRE-KHPIIALILEYRQLTKLKSTYVDGLPELVNPDTGRIHTTFNQTGTATGRLSSSN 632

Query: 718 PNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDI 777
           PNLQNIPI+++ G+KIR+AF++     LISADYSQIELR+LAH+++   L + F+N  DI
Sbjct: 633 PNLQNIPIRSEEGRKIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDI 692

Query: 778 HRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFH 837
           H   A+ +FGV IE V+P MRR AKTINF ++YG+S F LA +L I R EA ++I+RYF 
Sbjct: 693 HTETASRLFGVEIEDVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFA 752

Query: 838 RFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAA 897
           R+PG+ +YIE T    R+ GYVET+FGRR +  +INS   ++R   ER AINAPIQGSAA
Sbjct: 753 RYPGVKDYIENTVEEARKKGYVETLFGRRRYIPDINSRNRNVREAAERMAINAPIQGSAA 812

Query: 898 DITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEKACLPKIN 957
           DI + AMI + K L++ KL  ++LLQ+HDEL+FE PEEE    + ++   ME A      
Sbjct: 813 DIMKIAMIKLDKRLKERKLKARLLLQVHDELIFEAPEEEAEEVAALVKEVMEHA----YP 868

Query: 958 LRVPLKVNIKVSNNWQE 974
           L VPL+V +    NW E
Sbjct: 869 LAVPLEVEVGTGKNWGE 885


>gnl|CDD|128751 smart00475, 53EXOc, 5'-3' exonuclease. 
          Length = 259

 Score =  315 bits (809), Expect = 4e-86
 Identities = 133/262 (50%), Positives = 178/262 (67%), Gaps = 10/262 (3%)

Query: 5   NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64
             L LVDGSS  +RA++A P L +   G P NA+ GF  ML KL+    KE   ++ AV+
Sbjct: 1   KKLLLVDGSSLAFRAYFALPPL-KNSKGEPTNAVYGFLRMLLKLI----KEEKPTYVAVV 55

Query: 65  FDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATY 124
           FD    TFR+E+YP+YKANRPK P+ LL Q+PL++    A GIP +E++G+EADD+IAT 
Sbjct: 56  FDAKGKTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATL 115

Query: 125 TYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEK----IDIEHVIKKWGIPPEKMV 180
              AE EG+ V I+S DKDL+QLVS    + D  K  K       E+VI+K+G+ PE+++
Sbjct: 116 AKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQII 175

Query: 181 CLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETA 240
             +AL GDS DNIPG+PGIG KTAA LL+E+G+LENIL N  ++K KK RE +L + E A
Sbjct: 176 DYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLK-KKLREKLLAHKEDA 234

Query: 241 RLSRKLVMLRTDVPITIPLEHL 262
           +LSRKL  + TDVP+ + LE L
Sbjct: 235 KLSRKLATIETDVPLEVDLEDL 256


>gnl|CDD|128758 smart00482, POLAc, DNA polymerase A domain. 
          Length = 206

 Score =  294 bits (755), Expect = 8e-80
 Identities = 111/206 (53%), Positives = 147/206 (71%)

Query: 730 GQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVN 789
           G++IRRAF++PP   L+SADYSQIELRILAH++    L + F N  DIH   AA++FGV 
Sbjct: 1   GREIRRAFVAPPGYVLVSADYSQIELRILAHLSGDENLLEAFNNGGDIHSKTAAQVFGVP 60

Query: 790 IEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKT 849
            E+V+ ++RR AK INF IIYG+    LA QL I  +EA + IK YF RFPG+  YI++T
Sbjct: 61  EEEVTKELRRAAKAINFGIIYGMGAKGLAEQLGISEAEAKELIKAYFARFPGVKRYIKRT 120

Query: 850 KNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRRAMISVHK 909
               R+ GYV T+FGRR +  +I+S    +R   ERAA+NAPIQGSAADI + AMI + +
Sbjct: 121 LEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAVNAPIQGSAADILKLAMIKMDE 180

Query: 910 SLEDHKLATKMLLQIHDELVFEVPEE 935
           +L++  L  ++LLQ+HDELVFEVPEE
Sbjct: 181 ALKEKGLRARLLLQVHDELVFEVPEE 206


>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase;
           Provisional.
          Length = 553

 Score =  273 bits (699), Expect = 2e-73
 Identities = 140/510 (27%), Positives = 233/510 (45%), Gaps = 53/510 (10%)

Query: 488 DIMLMSYVL--DSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIEN 545
           D+ML S +L    GR+   +++ A + L        K  ++S   D   + Q+  +A  +
Sbjct: 74  DLMLASQLLLGSEGRAGSSLSAAAARALGEGLD---KPPQTSALSDPPDEEQL-LYAAAD 129

Query: 546 SNVILQLWLLLRPKLIVEKLLHVYERLDKPMID-------VVSQMEITGIQIDQDLLKQV 598
           ++V+L+L+ +L  +L          RL + +           ++ME+ G+  D D+ + +
Sbjct: 130 ADVLLELYAVLADQLNRIAAAAHPGRL-RLLAAAESAGALAAAEMELAGLPWDTDVHEAL 188

Query: 599 SAEIS----------KNLLSLEENIYDLSGE-KFNLSSPKQLGDIL-FTKLKFPSGAKTK 646
            AE+             L  L   I +  G  + N  SP+Q+   L    ++ PS     
Sbjct: 189 LAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRAGIELPS----- 243

Query: 647 TGQWKTTAQDLEQINCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLA 706
           T +W     +L +I   D+P ++ +LE+R+LSK+ S    +  ++   R  R H  Y   
Sbjct: 244 TRKW-----ELREI---DHPAVEPLLEYRKLSKLLSANGWAWLDYWV-RDGRFHPEYVPG 294

Query: 707 STMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITP 766
             +TGR AS  PN Q IP      + IR AF++ P  KL+ AD SQIELR+LA  +    
Sbjct: 295 GVVTGRWASRGPNAQQIP------RDIRSAFVADPGWKLVVADASQIELRVLAAYSGDER 348

Query: 767 LYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRS 826
           + + F    D+HR+ A+  FG   E+   + R  AK  NF  IYG +   L    +    
Sbjct: 349 MIEAFRTGGDLHRLTASVGFGKPEEEK--EERALAKAANFGAIYGATSKGLQEYAK-NYG 405

Query: 827 EAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERA 886
           EAA  ++R    +P    ++E+      + G V T+ GR                   R 
Sbjct: 406 EAARLLERLRRAYPRAVGWVERAAREGERGGVVRTLLGRTSPPPGFAWRARRRARSRGRF 465

Query: 887 AINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVH 946
             N P+QG+AAD  + A+  + + L +  L  +++  +HDE+V E PEEE    +  I  
Sbjct: 466 TRNFPVQGTAADWAKLALALLRRRLAEG-LDAELVFFVHDEVVVECPEEEAEEVAAAIEE 524

Query: 947 SMEKACLPKINL-RVPLKVNIKVSNNWQEE 975
           +ME+A   ++    VP  V + V  ++ E 
Sbjct: 525 AMEEA--GRLLFGPVPFPVEVAVVESYAEA 552


>gnl|CDD|184939 PRK14976, PRK14976, 5'-3' exonuclease; Provisional.
          Length = 281

 Score =  222 bits (568), Expect = 4e-58
 Identities = 107/285 (37%), Positives = 159/285 (55%), Gaps = 11/285 (3%)

Query: 3   KENHLFLVDGSSFIYRAFYAT--PLLSRK-HDGLPVNAIAGFCNMLWKLLQNSRKESIAS 59
                 L+DG+S I+R++YAT       K + GLP NAI  F  M++K+L+        S
Sbjct: 1   MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNP----S 56

Query: 60  HFAVIFDYPAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADD 119
           +  + FD    TFR+++Y +YK  R K PE L+ Q+PL++   +  GI   E  G+EADD
Sbjct: 57  YILIAFDAGRKTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADD 116

Query: 120 IIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEH---VIKKWGIPP 176
           +I +      K+   V I S+DKDL+QLV+  T +    K     I +     + +GI P
Sbjct: 117 LIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFELYGIEP 176

Query: 177 EKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEY 236
           ++++  + L GDS DNI G+ GIG KTA  LL +YGN+ENI  N  +IK KK +  + E 
Sbjct: 177 KQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIK-KKIKNKLSEA 235

Query: 237 AETARLSRKLVMLRTDVPITIPLEHLILEDCNGPRLISFLKALEF 281
            E A LS+KL  ++TDVP+   +E + L+  + P L    + LE 
Sbjct: 236 KEKALLSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIFEELEL 280


>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
          Length = 256

 Score =  190 bits (484), Expect = 2e-48
 Identities = 90/264 (34%), Positives = 140/264 (53%), Gaps = 12/264 (4%)

Query: 5   NHLFLVDGSSFIYRAFYATPLLSRKHDGLPVNAIAGFCNMLWKLLQNSRKESIASHFAVI 64
           NHL ++D  + I R     P  S       V       +   KL+++S+     +H   +
Sbjct: 3   NHLLIIDALNLIRRIHAVQP--SPNDINACVETCQHALD---KLIRHSQ----PTHAVAV 53

Query: 65  FDY--PAVTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIA 122
           FD    +  +R+++ PDYKA R  +PE L   LP +R A +  GI +    G EADD+IA
Sbjct: 54  FDGDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIA 113

Query: 123 TYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCL 182
           T      + G   TI+STDK   QL+SPT  + D  ++  +D   + +++G+ P+++   
Sbjct: 114 TLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDAPFIEQEFGVEPQQLPDY 173

Query: 183 QALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILINASRIKQKKRRENILEYAETARL 242
             L G S   IPG+ GIG K+AA LL ++ +LENI  +   +  +K R+ + E+ E ARL
Sbjct: 174 WGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALP-EKWRKKLEEHKEMARL 232

Query: 243 SRKLVMLRTDVPITIPLEHLILED 266
            RKL  L+TD+P+   L+ L L  
Sbjct: 233 CRKLAQLQTDLPLGGNLQQLRLNR 256


>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease.  3\' -5' exonuclease
           proofreading domain present in DNA polymerase I, Werner
           syndrome helicase, RNase D and other enzymes.
          Length = 172

 Score = 80.9 bits (200), Expect = 2e-15
 Identities = 46/192 (23%), Positives = 87/192 (45%), Gaps = 24/192 (12%)

Query: 371 IVNTKDIQQWVQKLET-IGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFI 429
           + +++ +++ ++KL    G  +    T  ++++  K + I IS            E  FI
Sbjct: 4   VTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTG---------EGAFI 54

Query: 430 DLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMRGFEDI 489
              +              + L  LK   E+E   K+GHN K+D  VL R+GI +    D 
Sbjct: 55  IDPLAL-----------GDDLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDT 103

Query: 490 MLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVI 549
           ML +Y+L  G S H +A++ +    Y   E+ K  + S    +    +  ++A E+++ +
Sbjct: 104 MLAAYLLLGGPSKHGLATLLK---EYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADAL 160

Query: 550 LQLWLLLRPKLI 561
           L+L+  L  +L 
Sbjct: 161 LRLYEKLEKELE 172


>gnl|CDD|177280 PHA00439, PHA00439, exonuclease.
          Length = 286

 Score = 50.9 bits (122), Expect = 1e-06
 Identities = 37/144 (25%), Positives = 52/144 (36%), Gaps = 15/144 (10%)

Query: 70  VTFRNEIYPDYKANRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATYTYIAE 129
           V +R E+ P YKANR K     +     +          +I   G E DD++        
Sbjct: 75  VNWRKEVVPTYKANR-KAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPS 133

Query: 130 KEGFA-VTIISTDKDLMQLVSPTTCLYD--TVKEEKIDIEHVIKKWGIPPEKMVCLQALT 186
             GF    ++S DKD   +     C +   T             +W +        Q + 
Sbjct: 134 LFGFKKAVLVSCDKDFKTI---PNCDFLWCTTGNILTQTPETADRWHL-------FQTIK 183

Query: 187 GDSIDNIPGIPGIGYKTAALLLQE 210
           GDS D   GIPG G  TA   L+ 
Sbjct: 184 GDSTDGYSGIPGWG-DTAEAFLEN 206


>gnl|CDD|128575 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs.
           
          Length = 36

 Score = 50.9 bits (123), Expect = 1e-06
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 176 PEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEY 211
           PE+++    L GD  DNIPG+ GIG KTA  LL+E+
Sbjct: 1   PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36


>gnl|CDD|163388 TIGR03674, fen_arch, flap structure-specific endonuclease.
           Endonuclease that cleaves the 5'-overhanging flap
           structure that is generated by displacement synthesis
           when DNA polymerase encounters the 5'-end of a
           downstream Okazaki fragment. Has 5'-endo-/exonuclease
           and 5'-pseudo-Y-endonuclease activities. Cleaves the
           junction between single and double-stranded regions of
           flap DNA.
          Length = 338

 Score = 49.2 bits (118), Expect = 5e-06
 Identities = 33/89 (37%), Positives = 49/89 (55%), Gaps = 10/89 (11%)

Query: 150 PTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQ 209
           P   +Y  VK E I++E V+ + GI  E+++ +  L G   D   G+ GIG KTA  L++
Sbjct: 197 PGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVG--TDYNEGVKGIGPKTALKLIK 254

Query: 210 EYGNLENILINASRIKQKKRRENILEYAE 238
           E+G+LE +L        K R E+I  Y E
Sbjct: 255 EHGDLEKVL--------KARGEDIENYDE 275


>gnl|CDD|179693 PRK03980, PRK03980, flap endonuclease-1; Provisional.
          Length = 292

 Score = 48.3 bits (116), Expect = 1e-05
 Identities = 33/89 (37%), Positives = 50/89 (56%), Gaps = 10/89 (11%)

Query: 150 PTTCLYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQ 209
           P   +Y  VK E I++E V+K+ GI  E+++ +  L G   D  PGI GIG KTA  L++
Sbjct: 150 PGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIK 207

Query: 210 EYGNLENILINASRIKQKKRRENILEYAE 238
           ++G+LE +L        ++R   I  Y E
Sbjct: 208 KHGDLEKVL--------EERGFEIENYDE 228


>gnl|CDD|177397 PHA02567, rnh, RnaseH; Provisional.
          Length = 304

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 32/91 (35%), Positives = 42/91 (46%), Gaps = 13/91 (14%)

Query: 110 IEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCLYDTVKEEKIDIEHVI 169
           ++I   EADDIIA  T     EG  V I+S+D D  QL       Y  VK+       + 
Sbjct: 124 MKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHK-----YPGVKQ----WSPMQ 174

Query: 170 KKWGIP----PEKMVCLQALTGDSIDNIPGI 196
           KKW  P    PEK +  + + GD  D +  I
Sbjct: 175 KKWVKPKYGSPEKDLMTKIIKGDKKDGVASI 205


>gnl|CDD|185517 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
          Length = 393

 Score = 38.8 bits (91), Expect = 0.007
 Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 17/121 (14%)

Query: 106 GIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSPTTCL------YDTVK 159
           GIP IE    EA+   A    +  K+G    + + D D   L   T  L       +  K
Sbjct: 151 GIPVIEAPC-EAE---AQCAELV-KKGKVYAVATEDMD--ALTFGTPVLLRNLNFSEAKK 203

Query: 160 EE--KIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENI 217
               +I++  V+++ G+  ++ + L  L G   D    I GIG KTA  L+++Y ++E I
Sbjct: 204 RPIQEINLSTVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKSIEEI 261

Query: 218 L 218
           L
Sbjct: 262 L 262


>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
          Length = 665

 Score = 32.8 bits (76), Expect = 0.50
 Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)

Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
           GI  +G K A  L + +G+LE +   AS
Sbjct: 515 GIRHVGEKAAKALARHFGSLEAL-RAAS 541


>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
          Length = 773

 Score = 32.1 bits (74), Expect = 0.63
 Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
            +P +G   A  LL+ +G++E + + AS
Sbjct: 719 SLPDVGPVLARNLLEHFGSVEAV-MTAS 745


>gnl|CDD|182284 PRK10173, PRK10173, glucose-1-phosphatase/inositol phosphatase;
           Provisional.
          Length = 413

 Score = 30.5 bits (69), Expect = 2.5
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 668 IKNILEWRQLSKIKSTYADSL 688
           IK   +W+ LSK+K+ Y DSL
Sbjct: 253 IKTDQQWKVLSKLKNGYQDSL 273


>gnl|CDD|184786 PRK14671, uvrC, excinuclease ABC subunit C; Provisional.
          Length = 621

 Score = 30.1 bits (68), Expect = 2.6
 Identities = 11/23 (47%), Positives = 16/23 (69%)

Query: 195 GIPGIGYKTAALLLQEYGNLENI 217
            I GIG KTA  LL+ +G++E +
Sbjct: 573 DIAGIGEKTAEKLLEHFGSVEKV 595


>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional.
          Length = 689

 Score = 29.7 bits (67), Expect = 4.1
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 195 GIPGIGYKTAALLLQEYGNLENILI 219
           GIP +G  TA  L +E+G  E I+ 
Sbjct: 532 GIPEVGPTTARNLAREFGTFEAIMD 556


>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
          Length = 598

 Score = 29.3 bits (67), Expect = 4.7
 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 195 GIPGIGYKTAALLLQEYGNLENILINAS 222
            IPGIG K    LL+ +G+L+ I   AS
Sbjct: 547 DIPGIGPKRRKALLKHFGSLKAIK-EAS 573


>gnl|CDD|183710 PRK12737, gatY, tagatose-bisphosphate aldolase; Reviewed.
          Length = 284

 Score = 29.3 bits (66), Expect = 5.4
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 9/49 (18%)

Query: 793 VSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYIKRYFHRFPG 841
           V  +  + A      I  GI    +AT+L+I  S+A   +K+YF+  P 
Sbjct: 213 VPDEDVKKA------ISLGICKVNVATELKIAFSDA---VKKYFYENPK 252


>gnl|CDD|150116 pfam09340, NuA4, Histone acetyltransferase subunit NuA4.  The NuA4
           histone acetyltransferase (HAT) multisubunit complex is
           responsible for acetylation of histone H4 and H2A
           N-terminal tails in yeast. NuA4 complexes are highly
           conserved in eukaryotes and play primary roles in
           transcription, cellular response to DNA damage, and cell
           cycle control.
          Length = 80

 Score = 28.7 bits (65), Expect = 6.6
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 12/73 (16%)

Query: 593 DLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDIL-----FTKLKFPSGAKTKT 647
           +LL++   ++ K L +LE  IYD   E    SS    G+I+     + K    S      
Sbjct: 6   ELLQK-KKKLEKELAALERQIYDKETEYLEDSSS--GGNIIKGFDGYLK----SSKNGSA 58

Query: 648 GQWKTTAQDLEQI 660
            + K    D ++I
Sbjct: 59  QRRKRKFTDDDRI 71


>gnl|CDD|129319 TIGR00215, lpxB, lipid-A-disaccharide synthase.  Lipid-A precursor
           biosynthesis producing lipid A disaccharide in a
           condensation reaction. transcribed as part of an operon
           including lpxA.
          Length = 385

 Score = 28.7 bits (64), Expect = 7.1
 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 154 LYDTVKEEKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGN 213
           L D +   K D +   +K GI       L  L G     +  +  +  K A LL Q+  +
Sbjct: 167 LLDAIPLYKPDRKSAREKLGIDHNGE-TLALLPGSRGSEVEKLFPLFLKAAQLLEQQEPD 225

Query: 214 LENILINASRIKQKKRRENILEYAE 238
           L  +L   +  ++ +  +   EY  
Sbjct: 226 LRRVLPVVNFKRRLQFEQIKAEYGP 250


>gnl|CDD|173132 PRK14669, uvrC, excinuclease ABC subunit C; Provisional.
          Length = 624

 Score = 28.3 bits (63), Expect = 9.4
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 196 IPGIGYKTAALLLQEYGNLENI 217
           IPG+G KT   LL+ +G+LE +
Sbjct: 557 IPGVGAKTVQRLLKHFGSLERV 578


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 15,716,906
Number of extensions: 1040271
Number of successful extensions: 2085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2050
Number of HSP's successfully gapped: 45
Length of query: 976
Length of database: 5,994,473
Length adjustment: 103
Effective length of query: 873
Effective length of database: 3,768,849
Effective search space: 3290205177
Effective search space used: 3290205177
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 (27.6 bits)