RPS-BLAST 2.2.16 [Mar-25-2007]

Database: 40scop73nmM 
           9549 sequences; 1,678,726 total letters

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

Query= AAZ21022.1 pubi0 polA GIB00256CH01 "DNA polymerase I"
         (924 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1bgxT4 [e.8.1.1] TAQ DNA POLYMERASE T:423 -- 832                      439   e-126
1skrA2 [e.8.1.1] DNA POLYMERASE A:211 -- 704                          338   5e-96
2hbjA2 [c.55.3.5] EXOSOME COMPLEX EXONUCLEASE RRP6 A:129 -- 420       158   7e-42
1exnA2 [c.120.1.2] 5'-EXONUCLEASE A:20 -- 185                         141   1e-36
1q40B [d.17.4.2] MRNA EXPORT FACTOR MEX67                             137   2e-35
1d8yA1 [c.55.3.5] DNA POLYMERASE I A:324 -- 518                       134   2e-34
1a76A2 [c.120.1.2] FLAP ENDONUCLEASE-1 PROTEIN A:2 -- 208             117   1e-29
1yt3A3 [c.55.3.5] RIBONUCLEASE D A:1 -- 193                           113   3e-28
1tfrA2 [c.120.1.2] T4 RNASE H A:12 -- 180                             112   8e-28
1exnA1 [a.60.7.1] 5'-EXONUCLEASE A:186 -- 290                         102   7e-25
1l3sA1 [c.55.3.5] DNA POLYMERASE I A:297 -- 468                       101   1e-24
1i3qH [b.40.4.8] DNA-DIRECTED RNA POLYMERASE II 14.5KD                101   2e-24
1bgxT1 [a.60.7.1] TAQ DNA POLYMERASE T:174 -- 289                     100   3e-24
1skrA1 [c.55.3.5] DNA POLYMERASE A:1 -- 210                            93   4e-22
1ul1X1 [a.60.7.1] FLAP ENDONUCLEASE-1 X:218 -- 357                     90   4e-21
2i5hA1 [e.71.1.1] HYPOTHETICAL PROTEIN AF1531 A:16 -- 195              88   1e-20
1dgsA1 [a.60.2.2] DNA LIGASE A:401 -- 581                              69   6e-15
1vk0A [c.55.3.5] HYPOTHETICAL PROTEIN                                  67   4e-14
1a76A1 [a.60.7.1] FLAP ENDONUCLEASE-1 PROTEIN A:209 -- 316             62   8e-13
2j9uB1 [g.41.11.1] VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 3...    62   1e-12
1z00B1 [a.60.2.5] DNA REPAIR ENDONUCLEASE XPF B:823 -- 905             61   2e-12
1j53A [c.55.3.5] DNA POLYMERASE III, EPSILON CHAIN                     52   8e-10
2a1jA1 [a.60.2.5] DNA REPAIR ENDONUCLEASE XPF A:837 -- 898             39   9e-06
1keaA [a.96.1.2] POSSIBLE G-T MISMATCHES REPAIR ENZYME                 35   1e-04
2csbA4 [a.60.2.4] TOPOISOMERASE V A:465 -- 519                         34   3e-04
1d5aA1 [c.55.3.5] PROTEIN (DNA POLYMERASE) A:1 -- 347                  33   4e-04
1bgxT2 [c.120.1.2] TAQ DNA POLYMERASE T:1 -- 173                       33   5e-04

>1bgxT4 [e.8.1.1] TAQ DNA POLYMERASE T:423 -- 832
          Length = 406

 Score =  439 bits (1131), Expect = e-126
 Identities = 164/417 (39%), Positives = 268/417 (64%), Gaps = 14/417 (3%)

Query: 509 EKLTNIYEIFEKPLIKILAFMEIEGIKIDNKFLKVLSEKFEKKISKLEKEVFKISKKEFN 568
           E+L  +Y   E+PL  +LA ME  G+++D  +L+ LS +  ++I++LE EVF+++   FN
Sbjct: 2   ERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFN 61

Query: 569 IASPKQLGEIIYNDLKIAVLKKTRK-GSFATNASVLEDLAFKGHEFPKLILDWRQVSKLK 627
           + S  QL  +++++L +  + KT K G  +T+A+VLE L    H   + IL +R+++KLK
Sbjct: 62  LNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREA-HPIVEKILQYRELTKLK 120

Query: 628 NTYSDALPEHINPNTKRVHTSFLLAATTTGRLASSDPNLQNIPIKSEDGKDIRKAFIAEK 687
           +TY D LP+ I+P T R+HT F   AT TGRL+SSDPNLQNIP+++  G+ IR+AFIAE+
Sbjct: 121 STYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEE 180

Query: 688 GFTLISADYNQIEMRILADLAEVKELKKAFSNNEDIHSLTASQVFNVDIKKVDQDMRRKA 747
           G+ L++ DY+QIE+R+LA L+  + L + F    DIH+ TAS +F V  + VD  MRR A
Sbjct: 181 GWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAA 240

Query: 748 KAINFGIIYGISQYGLAKQINVSNHEADEFLNAYFLKFPEIKIYMDNTIKFCRKSGYVTN 807
           K INFG++YG+S + L++++ +   EA  F+  YF  FP+++ +++ T++  R+ GYV  
Sbjct: 241 KTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVET 300

Query: 808 IFGRRSHFNGINDKNFNVRNFQERAAINAPIQGSASEIMRLAMIRLNKKFESIKNNKSKI 867
           +FGRR +   +  +  +VR   ER A N P+QG+A+++M+LAM++L  +   ++   +++
Sbjct: 301 LFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPR---LEEMGARM 357

Query: 868 LLQIHDELIFEVPVKEVKNITEIIKDEMTSVTESDLHTFSTPLTVDVNTGDNWGILH 924
           LLQ+HDEL+ E      + +  + K+ M  V        + PL V+V  G++W    
Sbjct: 358 LLQVHDELVLEA----AEAVARLAKEVMEGVYP-----LAVPLEVEVGIGEDWLSAK 405


>1skrA2 [e.8.1.1] DNA POLYMERASE A:211 -- 704
          Length = 465

 Score =  338 bits (868), Expect = 5e-96
 Identities = 89/481 (18%), Positives = 159/481 (33%), Gaps = 58/481 (12%)

Query: 471 KKEINFSDVELDKAMEYAAEDADITYRLYKIFSKNLKLEKLTNIYEIFEKPLIKILAFME 530
           K+E N    +     E   E A     L         L KLT  +  + +P      F  
Sbjct: 16  KQERNGFPFDTKAIEELYVELAARRSEL---------LRKLTETFGSWYQPKGGTEMFCH 66

Query: 531 IEGIKIDNKFLKVLSEKF--EKKISKLEKEVF-KISKKEFNIASPKQLGEIIYNDLKIAV 587
               K   K+ ++ + K         +    +  +    FN +S   + + +     +  
Sbjct: 67  PRTGKPLPKYPRIKTPKVGGIDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPT 126

Query: 588 LKKTRKGSFATNASVLEDLAFKG---HEFPKLILDWRQVSKLKNTYSDA--LPEHINPNT 642
            K T KG+   +  VLE +            LI ++  + K     ++            
Sbjct: 127 -KYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAED 185

Query: 643 KRVHTSFLLAATTTGRLASSDPNLQNIP-IKSEDGKDIRKAFIAE--------KGFTLIS 693
            ++H S       TGR   + PNL  IP ++S  G+  R AF AE        K +    
Sbjct: 186 GKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAG 245

Query: 694 ADYNQIEMRILADLAEVKELKKAFSNNEDIHSLTASQVFNVDIKKVDQDMRRKAKAINFG 753
            D + +E+R LA           F N E  H +    +   +    +   R  AK   +G
Sbjct: 246 IDASGLELRCLAHFMA------RFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYG 299

Query: 754 IIYGISQYGLAKQINVSNHEADEFLNAYFLKFPEIKIYMD---NTIKFCRKSGYVTNIFG 810
            +YG     + + +        E    +    P I    +    T+    K  ++  + G
Sbjct: 300 FLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVEKWKRRWIKGLDG 359

Query: 811 RRSHFNGINDKNFNVRNFQERAAINAPIQGSASEIMRLAMIRLNKKFE-----SIKNNKS 865
           R+ H                 AA+N  +Q + + I +L +I+  +           +   
Sbjct: 360 RKVHVRS------------PHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDF 407

Query: 866 KILLQIHDELIFEVPVKEVKNITEIIKDEMTSVTE--SDLHTFSTPLTVDVNTGDNWGIL 923
             +  +HDE+      +E+    +++ +          D   F   L  +   G NW I 
Sbjct: 408 AYMAWVHDEIQVGCRTEEIA---QVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAIC 464

Query: 924 H 924
           H
Sbjct: 465 H 465


>2hbjA2 [c.55.3.5] EXOSOME COMPLEX EXONUCLEASE RRP6 A:129 -- 420
          Length = 292

 Score =  158 bits (400), Expect = 7e-42
 Identities = 36/320 (11%), Positives = 85/320 (26%), Gaps = 31/320 (9%)

Query: 229 EIKQNKRRETLIENKDKAIISKKLVTLMKDAPVERKLEEFHLK-KIDKNKLYKFLREMEF 287
           E  Q K +  +  ++    I           P+   L           +  + +  E++ 
Sbjct: 2   EKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNPSHYPHPYEYEIDH 61

Query: 288 NRLLSSVISAYGEPLLXXXXXXXXXXXXHQNISKKNYHLITNEKEIDEWINEAEEAGELA 347
                 ++    E                ++        +    E++  + + +   E+A
Sbjct: 62  QEYSPEILQIREEIPS-------------KSWDDSVPIWVDTSTELESMLEDLKNTKEIA 108

Query: 348 IDTETSSLDAHQTDLVGISLSTKIGQACYIPIGHKFKGCLKKETVIKKLKPLLEDKSVKK 407
           +D E     ++   +  + +ST+        +  +          +  L  +  + S+ K
Sbjct: 109 VDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLREN--------LHILNEVFTNPSIVK 160

Query: 408 IGQNIKFDFIVLYKQGINMN-SMEDTMLMSYVLDAGKNRHNMDTLSEIHLQHKTISFKEI 466
           +      D I L +        + DT   S  +     RH++  L E     KT    ++
Sbjct: 161 VFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLP--RHSLAYLLENFANFKTSKKYQL 218

Query: 467 VGTGKKEINFSDVELDKAMEYAAEDADITYRLYKIFSKNLKLEKLTNIYEIFEKPLIKIL 526
                + +             A  D      +Y      L             + + K  
Sbjct: 219 ADWRIRPL------SKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKRR 272

Query: 527 AFMEIEGIKIDNKFLKVLSE 546
                      +  +    E
Sbjct: 273 FEYSKYRPLTPSSEVYSPIE 292


>1exnA2 [c.120.1.2] 5'-EXONUCLEASE A:20 -- 185
          Length = 166

 Score =  141 bits (357), Expect = 1e-36
 Identities = 33/180 (18%), Positives = 57/180 (31%), Gaps = 26/180 (14%)

Query: 9   HFYLIDGSGYIFRAYYALPPLTRKSDGLPVGAVSGFCSMLFKLLEDSKSNENLQKPTHFA 68
           +  ++DG+   FR  +            P  +   + S +  L +               
Sbjct: 2   NLXIVDGTNLGFRFKHNNS-------KKPFAS--SYVSTIQSLAKS-------YSARTTI 45

Query: 69  VIFDAARKTFRNEIYSDYKANRSEAPDDLAPQFEYIRKS----------VVAFNLPSVDL 118
           V+ D  +  FR E   +YK NR E       + + + +           +     P+  +
Sbjct: 46  VLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTI 105

Query: 119 PNYEADDLIATYVEQILAKGAKVTIVSSDKDLMQLYRKDVRIFDPMKNKFITPEDIVTKF 178
              EADD  A  V+ I      V ++S+D D   L    V  F     +     D     
Sbjct: 106 RGVEADDXAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDXYEHH 165


>1q40B [d.17.4.2] MRNA EXPORT FACTOR MEX67
          Length = 186

 Score =  137 bits (346), Expect = 2e-35
 Identities = 18/205 (8%), Positives = 42/205 (20%), Gaps = 27/205 (13%)

Query: 515 YEIFEKPLIKILAFMEIEGIKIDNKFLKVLSEKFEKKISKLEKEVFKISKKEFNIASPKQ 574
             +     I     +       +   L +L +                S      +    
Sbjct: 2   RNL-ATNFIANYLKLW----DANRSELXILYQNES-----QFSXQVDSSHPHLIESGSTD 51

Query: 575 LGEIIYNDLKIAVLK------KTRKGSFATNASVLEDLAFKGHEFPKLILDWRQVSKLKN 628
            G  + N   +  +                     + L    H+       +        
Sbjct: 52  FGYYLNNSRNLTRVSSIKARXAKLSIGQEQIYKSFQQLPKTRHDIIATPELFSXEVYKFP 111

Query: 629 TYSDALPEHINPNTKRVHTSFLLAATTTGRLASSDPNLQNIPIKSEDGKDIRKAFIAEKG 688
           T +                        +     S P  + IP      K   + F+   G
Sbjct: 112 TLNGI----XITLHGSFDEVAQPEVDGSASRYHSGPKHKRIP---LSKKSFDRTFVVIPG 164

Query: 689 FTLISADYNQIEMRILADLAEVKEL 713
             ++++D     + I    ++    
Sbjct: 165 SXIVASD----TLLIRPYTSDFPWK 185


>1d8yA1 [c.55.3.5] DNA POLYMERASE I A:324 -- 518
          Length = 195

 Score =  134 bits (337), Expect = 2e-34
 Identities = 80/193 (41%), Positives = 121/193 (62%), Gaps = 4/193 (2%)

Query: 319 ISKKNYHLITNEKEIDEWINEAEEAGELAIDTETSSLDAHQTDLVGISLSTKIGQACYIP 378
           IS  NY  I +E+ +  WI + E+A   A  T T SLD    +LVG+S + + G A YIP
Sbjct: 2   ISYDNYVTILDEETLKAWIAKLEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIP 61

Query: 379 IGHKFKGC---LKKETVIKKLKPLLEDKSVKKIGQNIKFDFIVLYKQGINMNS-MEDTML 434
           + H +      + +E  ++ LKPLLED+   K+GQN+K+D  +L   GI +     DTML
Sbjct: 62  VAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTML 121

Query: 435 MSYVLDAGKNRHNMDTLSEIHLQHKTISFKEIVGTGKKEINFSDVELDKAMEYAAEDADI 494
            SY+L++   RH+MD+L+E  L+HKTI+F+EI G GK ++ F+ + L++A  YAAEDAD+
Sbjct: 122 ESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADV 181

Query: 495 TYRLYKIFSKNLK 507
           T +L+     +L+
Sbjct: 182 TLQLHLKMWPDLQ 194


>1a76A2 [c.120.1.2] FLAP ENDONUCLEASE-1 PROTEIN A:2 -- 208
          Length = 207

 Score =  117 bits (295), Expect = 1e-29
 Identities = 25/197 (12%), Positives = 50/197 (25%), Gaps = 44/197 (22%)

Query: 12  LIDGSGYIFRAYYALP----PLTRKSDGLPVGAVSGFCSMLFKLLEDSKSNENLQKPTHF 67
            IDG   +++   ++        R   G    A +G       LLE+             
Sbjct: 24  AIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLEN---------DITP 74

Query: 68  AVIFDAARKTFRNEI-----------------------YSDYKANRSEAPDDLAPQFEYI 104
             +FD      + +                        + +                E  
Sbjct: 75  IWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLTPKMVENC 134

Query: 105 RKSVVAFNLPSVDLPNYEADDLIATYVEQILAKGAKVTIVSSDKDLMQLYRKDVRIFDPM 164
           +  +    +P V+ P  E +   +   +    KG    +VS D D +      V      
Sbjct: 135 KYLLSLMGIPYVEAP-SEGEAQASYMAK----KGDVWAVVSQDYDALLYGAPRVVRNLTT 189

Query: 165 KNK---FITPEDIVTKF 178
             +    I   +++   
Sbjct: 190 TKEMPELIELNEVLEDL 206


>1yt3A3 [c.55.3.5] RIBONUCLEASE D A:1 -- 193
          Length = 193

 Score =  113 bits (283), Expect = 3e-28
 Identities = 31/204 (15%), Positives = 57/204 (27%), Gaps = 18/204 (8%)

Query: 323 NYHLITNEKEIDEWINEAEEAGELAIDTETSSLDAHQTDLVGISLSTKIGQACYIPIGHK 382
           NY +IT +  +            +A+DTE      +   L  I L      A   P+G  
Sbjct: 2   NYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGIT 61

Query: 383 FKGCLKKETVIKKLKPLLEDKSVKKIGQNIKFDFIVLYKQGINM-NSMEDTMLMSYVLDA 441
                        LK +L D S+ K       D  V       +   + DT +++     
Sbjct: 62  ---------DWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGR 112

Query: 442 GKNRHNMDTLSEIHLQHKTISFKEIVGTGKKEINFSDVELDKAMEYAAEDADITYRLYKI 501
                   ++ E +        +       + +       ++  EYAA D      +   
Sbjct: 113 PM-SWGFASMVEEYSGVTLDKSESRTDWLARPLT------ERQCEYAAADVWYLLPITAK 165

Query: 502 FSKNL-KLEKLTNIYEIFEKPLIK 524
                     L    +      ++
Sbjct: 166 LMVETEASGWLPAALDECRLMQMR 189


>1tfrA2 [c.120.1.2] T4 RNASE H A:12 -- 180
          Length = 160

 Score =  112 bits (280), Expect = 8e-28
 Identities = 32/162 (19%), Positives = 56/162 (34%), Gaps = 9/162 (5%)

Query: 8   DHFYLIDGSGYIFRAYYALPPLT-RKSDGLPVGAVSGFCSMLFKLLEDSKSNENLQKPTH 66
           +   LID S           P   + +  +    +        K  +           T 
Sbjct: 2   EGICLIDFSQIALSTALVNFPDKEKINLSMVRHLILNSIKFNVKKAKTLG-------YTK 54

Query: 67  FAVIFDAARKTFRNEIYSDYKANRSEAPDDLAPQFEYIRKSVVAFNLPSVDLPNYEADDL 126
             +  D A+  +    ++ Y     +         + I +         +D+  YEADD 
Sbjct: 55  IVLCIDNAKSGYWRRDFAYYYKKTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDH 114

Query: 127 IATYVEQILAKGAKVTIVSSDKDLMQLYRKDVRI-FDPMKNK 167
           IA  V++   +G K+ I+SSD D  QL++      + PM  K
Sbjct: 115 IAVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSPMHKK 156


>1exnA1 [a.60.7.1] 5'-EXONUCLEASE A:186 -- 290
          Length = 105

 Score =  102 bits (255), Expect = 7e-25
 Identities = 20/101 (19%), Positives = 41/101 (40%)

Query: 182 PEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELINKYGTLEKLLDNAQEIKQNKRRETLIE 241
            E+ I ++++ GD  DN+ GV GIG K    +I ++G +  ++D      + K  + L  
Sbjct: 4   VEQFISLKAIXGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNA 63

Query: 242 NKDKAIISKKLVTLMKDAPVERKLEEFHLKKIDKNKLYKFL 282
           +++    +  LV L              +       + +  
Sbjct: 64  SEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIA 104


>1l3sA1 [c.55.3.5] DNA POLYMERASE I A:297 -- 468
          Length = 172

 Score =  101 bits (252), Expect = 1e-24
 Identities = 31/182 (17%), Positives = 62/182 (34%), Gaps = 14/182 (7%)

Query: 327 ITNEKEIDEWINEAEEAGELAIDTETSSLDAHQTDLVGISLSTKIGQACYIPIGHKFKGC 386
                  D    E     + A+  E    + H   +VGI++  + G+    P        
Sbjct: 2   KMAFTLADRVTEEMLA-DKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETAL---- 56

Query: 387 LKKETVIKKLKPLLEDKSVKKIGQNIKFDFIVLYKQGINM-NSMEDTMLMSYVLDAGKNR 445
                   +    L D++ KK   + K   + L  +GI +     D +L +Y+LD  +  
Sbjct: 57  -----ADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGV 111

Query: 446 HNMDTLSEIHLQHKTISFKEIVGTGKKEINFSDVELDKAMEYAAEDADITYRLYKIFSKN 505
            ++   +++         + + G G K       +     E+    A   + L + F   
Sbjct: 112 DDVAAAAKMKQYEAVRPDEAVYGKGAKRA---VPDEPVLAEHLVRKAAAIWELERPFLDE 168

Query: 506 LK 507
           L+
Sbjct: 169 LR 170


>1i3qH [b.40.4.8] DNA-DIRECTED RNA POLYMERASE II 14.5KD
          Length = 133

 Score =  101 bits (252), Expect = 2e-24
 Identities = 13/139 (9%), Positives = 32/139 (23%), Gaps = 16/139 (11%)

Query: 460 TISFKEIVG-TGKKEINFSDVELDKAMEYAAEDADITYRLYKIFSKNLKLEKLTNIYEIF 518
              F +I   +      ++ V   +A     +   +T  +          + L       
Sbjct: 2   NTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSL------- 54

Query: 519 EKPLIKILAFMEIEGIKIDNKFLKVLS-------EKFEKKISKLEKEVFKISKKEFNIAS 571
              +   L          D                KFE+    L    +        +  
Sbjct: 55  TVTIASSLTRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEG 114

Query: 572 PKQ-LGEIIYNDLKIAVLK 589
             + L  +   +  + + +
Sbjct: 115 NYRNLNNLKQENAYLLIRR 133


>1bgxT1 [a.60.7.1] TAQ DNA POLYMERASE T:174 -- 289
          Length = 116

 Score =  100 bits (250), Expect = 3e-24
 Identities = 41/112 (36%), Positives = 65/112 (58%), Gaps = 3/112 (2%)

Query: 180 VGPEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELINKYGTLEKLLDNAQEIKQNKRRETL 239
           + P++  D ++L GD SDN+PGV GIG KTA +L+ ++G+LE LL N   +K    RE +
Sbjct: 1   LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKP-AIREKI 59

Query: 240 IENKDKAIISKKLVTLMKDAPVERKLEEFHLKKIDKNKLYKFLREMEFNRLL 291
           + + D   +S  L  +  D P+E    +   ++ D+ +L  FL  +EF  LL
Sbjct: 60  LAHMDDLKLSWDLAKVRTDLPLEVDFAK--RREPDRERLRAFLERLEFGSLL 109


>1skrA1 [c.55.3.5] DNA POLYMERASE A:1 -- 210
          Length = 204

 Score = 93.2 bits (230), Expect = 4e-22
 Identities = 24/205 (11%), Positives = 55/205 (26%), Gaps = 34/205 (16%)

Query: 346 LAIDTETSSLDAHQTDLVGISLSTKIGQACYIPIGHKFKGCLKKETVIKKLKPLLEDKSV 405
           +  D E ++L    T      +               F         +  L+  +    +
Sbjct: 2   IVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDF------GAYLDALEAEVARGGL 55

Query: 406 KKIGQNIKFDFIVLYKQ---------GINMNSMEDTMLMSYVLDAGKNRHNMDTLSEIHL 456
                  K+D   L K           +   +  DT+++S ++ +     +M  L    L
Sbjct: 56  IVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKL 115

Query: 457 QHKTISFKEIVGTGKKEINF------------------SDVELDKAMEYAAEDADITYRL 498
                ++   +G  K E                          ++ M+Y  +D  +T  L
Sbjct: 116 PGALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKAL 175

Query: 499 YKIFSKNLK-LEKLTNIYEIFEKPL 522
            +    +        +  ++     
Sbjct: 176 LEKLLSDKHYFPPEIDFTDVGYTTF 200


>1ul1X1 [a.60.7.1] FLAP ENDONUCLEASE-1 X:218 -- 357
          Length = 140

 Score = 89.6 bits (222), Expect = 4e-21
 Identities = 23/111 (20%), Positives = 49/111 (44%), Gaps = 11/111 (9%)

Query: 180 VGPEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELINKYGTLEKLLDNAQEIKQNKRRETL 239
           +  E+ +D+  L G  SD    + GIG K A +LI K+ ++E+++      K       L
Sbjct: 1   LNQEQFVDLCILLG--SDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWL 58

Query: 240 IENKDKAIISKKLVTLMKDAPVERKLEEFHLKKIDKNKLYKFL-REMEFNR 289
            +   +  +  +++          +  E    + ++ +L KF+  E +F+ 
Sbjct: 59  HKEAHQLFLEPEVLDP--------ESVELKWSEPNEEELIKFMCGEKQFSE 101


>2i5hA1 [e.71.1.1] HYPOTHETICAL PROTEIN AF1531 A:16 -- 195
          Length = 178

 Score = 88.2 bits (218), Expect = 1e-20
 Identities = 20/184 (10%), Positives = 52/184 (28%), Gaps = 14/184 (7%)

Query: 79  RNEIYSDYKANRSEAPDDLAPQFEYIRKSVVAFNLPSVDLPNYEADDLIATYVEQILAKG 138
                 D+             +    R+  +A  +   +    E                
Sbjct: 2   DYAYVLDFMPYG-----HPDDKRPIHRREPLAQVVGERNFTLLEVSIRKGKQP----LVM 52

Query: 139 AKVTIVSSDKDLMQLYRKDVRIFDPMKNKFITPEDIVT--KFGVGPEKVIDVQSLAGDSS 196
            +V I   ++D++   ++ +R  D           ++         + V           
Sbjct: 53  DRVYIGKGERDVVYKIKRRLRYEDLTPAAKTELPYVIEHIIKQDEKKYVDFFNDSITTRM 112

Query: 197 DNVPGVPGIGVKTAAELINKYGTLEKLLDNAQEIKQNKR-RETLIENKDKAIISKKLVTL 255
             +  +PG+G K    +I +    ++  ++ ++I Q  +  +   +     II +     
Sbjct: 113 HQLELLPGVGKKMMWAIIEERK--KRPFESFEDIAQRVKGIQRPEKLIVSRIIYEIKNPQ 170

Query: 256 MKDA 259
            K  
Sbjct: 171 TKYK 174


>1dgsA1 [a.60.2.2] DNA LIGASE A:401 -- 581
          Length = 181

 Score = 69.3 bits (169), Expect = 6e-15
 Identities = 19/135 (14%), Positives = 41/135 (30%), Gaps = 5/135 (3%)

Query: 100 QFEYIRKSVVAFNLPSVDLPNYEADDLIATYVEQILAKGAKVTIVSSDKDLMQLYRKDVR 159
                   +V                           K   +  +        L +  VR
Sbjct: 5   ACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVR 64

Query: 160 ----IFDPMKNKFITPEDIVTK-FGVGPEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELI 214
               ++   K   +  E +  K       ++ + +    +      G+PG+G   A  L 
Sbjct: 65  DVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLA 124

Query: 215 NKYGTLEKLLDNAQE 229
            ++GT+++LL+ + E
Sbjct: 125 RRFGTMDRLLEASLE 139


>1vk0A [c.55.3.5] HYPOTHETICAL PROTEIN
          Length = 200

 Score = 66.5 bits (161), Expect = 4e-14
 Identities = 17/203 (8%), Positives = 49/203 (24%), Gaps = 33/203 (16%)

Query: 326 LITNEKEIDEWINEAEEAGELAIDTETSSLDAHQTDLVGISLSTKIGQA----------- 374
              +  +  +  + +    +      ++ +  + + +   S+                  
Sbjct: 2   ASFDGPKF-KXTDGSYVQTKTIDVGSSTDISPYLSLIREDSILNGNRAVIFDVYWDVGFT 60

Query: 375 -------CYIPIGH-----KFKGCLKKETVIKKLKPLLEDKSVKKIGQNIKFDFIVLYKQ 422
                    + +         +        +K L      K V  +G  I+ D  +L + 
Sbjct: 61  KTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLREN 120

Query: 423 -GINMNSM--EDTMLMSYVLDAGKNRHNMDTLSEIHLQHKTISFKEIVGTGKKEINFSDV 479
            G+ + +      +                 L+   L         I    +K      +
Sbjct: 121 HGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQL 180

Query: 480 ELDKAMEYAAEDADITYRLYKIF 502
                 E AA +  +   ++   
Sbjct: 181 ------EAAAIEGWLIVNVWDQL 197


>1a76A1 [a.60.7.1] FLAP ENDONUCLEASE-1 PROTEIN A:209 -- 316
          Length = 108

 Score = 62.1 bits (151), Expect = 8e-13
 Identities = 28/109 (25%), Positives = 40/109 (36%), Gaps = 22/109 (20%)

Query: 182 PEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELINKYGTLEKLLDNAQEIKQNKRRETLIE 241
            + +ID+    G +  N  GV GIG K A EL+      + L    +   + KR      
Sbjct: 3   LDDLIDIAIFMG-TDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVEYYDEIKR------ 55

Query: 242 NKDKAIISKKLVTLMKDAPVERKLEEFHLKKIDKNKLYKFL-REMEFNR 289
                        + K+  V        LK  DK  + KFL  E +FN 
Sbjct: 56  -------------IFKEPKVTDN-YSLSLKLPDKEGIIKFLVDENDFNY 90


>2j9uB1 [g.41.11.1] VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36
           B:115 -- 161
          Length = 47

 Score = 61.7 bits (150), Expect = 1e-12
 Identities = 3/42 (7%), Positives = 10/42 (23%)

Query: 69  VIFDAARKTFRNEIYSDYKANRSEAPDDLAPQFEYIRKSVVA 110
             +        NE   ++  +    P  +        +   +
Sbjct: 2   STWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKS 43


>1z00B1 [a.60.2.5] DNA REPAIR ENDONUCLEASE XPF B:823 -- 905
          Length = 83

 Score = 61.0 bits (148), Expect = 2e-12
 Identities = 9/83 (10%), Positives = 27/83 (32%), Gaps = 2/83 (2%)

Query: 182 PEKVIDVQSLAGDSSDNVPGVPGIGVKTAAELINKYGTLEKLLD-NAQEIKQNKRRETLI 240
            E + + +       D +  +PG+  K    L++    + +L   +  E+          
Sbjct: 2   SETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANA 61

Query: 241 ENKDKAIISKKLVTLMKDAPVER 263
           + +    I      ++     ++
Sbjct: 62  K-QLYDFIHTSFAEVVSKGKGKK 83


>1j53A [c.55.3.5] DNA POLYMERASE III, EPSILON CHAIN
          Length = 174

 Score = 52.1 bits (124), Expect = 8e-10
 Identities = 17/184 (9%), Positives = 40/184 (21%), Gaps = 41/184 (22%)

Query: 346 LAIDTETSSLDAHQTDLVG---ISLSTKIGQACYIPIGH--------------------- 381
           + +DTET+ ++       G   I +         +   +                     
Sbjct: 3   IVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGI 62

Query: 382 ---KFKGCLKKETVIKKLKPLLEDKSVKKIGQNIKFDFIVLYKQGINMNSMEDTMLMSYV 438
                        V  +    +     + +  N  FD   +  +                
Sbjct: 63  ADEFLLDKPTFAEVADEFMDYIRG--AELVIHNAAFDIGFMDYE------FSLLKRDIPK 114

Query: 439 LDAGKNRHNMDTLSEIHLQHKTISFKEIVGTGKKEINFSDVELDKAMEYAAEDADITYRL 498
            +      +   ++      K  S   +         +      + +  A  DA I   +
Sbjct: 115 TNTFCKVTDSLAVARKMFPGKRNSLDALCAR------YEIDNSKRTLHGALLDAQILAEV 168

Query: 499 YKIF 502
           Y   
Sbjct: 169 YLAM 172


>2a1jA1 [a.60.2.5] DNA REPAIR ENDONUCLEASE XPF A:837 -- 898
          Length = 62

 Score = 38.7 bits (90), Expect = 9e-06
 Identities = 7/34 (20%), Positives = 16/34 (47%)

Query: 196 SDNVPGVPGIGVKTAAELINKYGTLEKLLDNAQE 229
            D +  +PG+  K    L++    + +L   +Q+
Sbjct: 2   QDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQD 35


>1keaA [a.96.1.2] POSSIBLE G-T MISMATCHES REPAIR ENZYME
          Length = 217

 Score = 34.7 bits (79), Expect = 1e-04
 Identities = 30/186 (16%), Positives = 60/186 (32%), Gaps = 38/186 (20%)

Query: 117 DLPNYEADDLIATYVEQILAKGAKVTIVSSDKDLMQLYRKDVRIFDPMKNKFITPEDIVT 176
           D P     D     + +IL +      V              +I+D    K+   EDI+ 
Sbjct: 24  DFPWRHTRDPYVILITEILLRRTTAGHVK-------------KIYDKFFVKYKCFEDILK 70

Query: 177 -----------KFGVGPEKVIDVQSLAG-----------DSSDNVPGVPGIGVKTA-AEL 213
                      + G+  ++   ++ LA             +   +  +PG+G  T  A +
Sbjct: 71  TPKSEIAKDIKEIGLSNQRAEQLKELARVVINDYGGRVPRNRKAILDLPGVGKYTCAAVM 130

Query: 214 INKYGTLEKLLDNAQEIKQNKRRETLIENKDKAIISKKLVTLMKDAPVERKLEEFHLKKI 273
              +G    ++D      +   R      ++     K L  L +      K  +F+L  +
Sbjct: 131 CLAFGKKAAMVD--ANFVRVINRYFGGSYENLNYNHKALWELAETLVPGGKCRDFNLGLM 188

Query: 274 DKNKLY 279
           D + + 
Sbjct: 189 DFSAII 194


>2csbA4 [a.60.2.4] TOPOISOMERASE V A:465 -- 519
          Length = 55

 Score = 33.5 bits (77), Expect = 3e-04
 Identities = 9/29 (31%), Positives = 14/29 (48%)

Query: 201 GVPGIGVKTAAELINKYGTLEKLLDNAQE 229
            + GI  + A  L+ KYG   K+ +   E
Sbjct: 8   SIRGIDRERAERLLKKYGGYSKVREAGVE 36


>1d5aA1 [c.55.3.5] PROTEIN (DNA POLYMERASE) A:1 -- 347
          Length = 347

 Score = 33.3 bits (76), Expect = 4e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 15/87 (17%)

Query: 443 KNRHNMDTLSEIHLQHKTISFK------EIVGTGKKEINFSDV--------ELDKAMEYA 488
           K R + D    I       ++        + G   +++   ++         L++   Y+
Sbjct: 253 KGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASGEGLERVARYS 312

Query: 489 AEDADITYRLY-KIFSKNLKLEKLTNI 514
            EDA  TY L  + F    +L +L   
Sbjct: 313 MEDAKATYELGKEFFPMEAQLSRLVGQ 339


>1bgxT2 [c.120.1.2] TAQ DNA POLYMERASE T:1 -- 173
          Length = 173

 Score = 33.0 bits (74), Expect = 5e-04
 Identities = 56/168 (33%), Positives = 85/168 (50%), Gaps = 10/168 (5%)

Query: 12  LIDGSGYIFRAYYALPPLTRKSDGLPVGAVSGFCSMLFKLLEDSKSNENLQKPTHFAVIF 71
           L+DG    +R ++AL  LT    G PV AV GF   L K           +      V+F
Sbjct: 16  LVDGHHLAYRTFHALKGLTTS-RGEPVQAVYGFAKSLLK--------ALKEDGDAVIVVF 66

Query: 72  DAARKTFRNEIYSDYKANRSEAPDDLAPQFEYIRKSVVAFNLPSVDLPNYEADDLIATYV 131
           DA   +FR+E Y  YKA R+  P+D   Q   I++ V    L  +++P YEADD++A+  
Sbjct: 67  DAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLA 126

Query: 132 EQILAKGAKVTIVSSDKDLMQLYRKDVRIFDPMKNKFITPEDIVTKFG 179
           ++   +G +V I+++DKDL QL    + +  P      TP  +  K+G
Sbjct: 127 KKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLI-TPAWLWEKYG 173


  Database: 40scop73nmM
    Posted date:  Nov 2, 2009 11:39 AM
  Number of letters in database: 1,678,726
  Number of sequences in database:  9549
  
Lambda     K      H
   0.333    0.149    0.449 

Gapped
Lambda     K      H
   0.267   0.0583    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 15,755,999
Number of extensions: 1155663
Number of successful extensions: 6023
Number of sequences better than 1.0e-03: 9
Number of HSP's gapped: 5510
Number of HSP's successfully gapped: 513
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)