RPS-BLAST 2.2.16 [Mar-25-2007]

Database: 95pdb09Oct16_0000; 95pdb09Oct16_0001; 95pdb09Oct16_0002;
95pdb09Oct16_0003 
           66,450 sequences; 15,983,541 total letters

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

Query= AAZ56054.1 tfus0 AAZ56054.1 GIB00263CH01 "Excinuclease ABC
subunit C"
         (656 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

2bggA [x.x.x] PROTEIN AF1318                                          202   3e-54
3c65A [x.x.x] UVRABC SYSTEM PROTEIN C                                 163   1e-42
2csdA [x.x.x] TOPOISOMERASE V                                         125   3e-31
1bgxT [c.120.1 - a.60.7 - c.55.3 - e.8.1] TAQ DNA POLYMERASE          125   3e-31
1dgsA [d.142.2 - b.40.4 - a.60.2] DNA LIGASE                          123   2e-30
2csbA [x.x.x] TOPOISOMERASE V                                         114   6e-28
2bhnA [x.x.x] XPF ENDONUCLEASE                                        108   4e-26
1cmwA [c.120.1 - a.60.7 - c.55.3 - e.8.1] PROTEIN (DNA POLYMERAS...   104   6e-25
1bvsB [b.40.4 - a.60.2 - a.5.1] PROTEIN (HOLLIDAY JUNCTION DNA H...    94   1e-21
1bvsA [b.40.4 - a.60.2 - a.5.1] PROTEIN (HOLLIDAY JUNCTION DNA H...    94   1e-21
1cukA [x.x.x] RUVA PROTEIN                                             94   2e-21
1dgtB [x.x.x] DNA LIGASE                                               94   2e-21
2bhnB [x.x.x] XPF ENDONUCLEASE                                         93   2e-21
3c1yA [x.x.x] DNA INTEGRITY SCANNING PROTEIN DISA                      92   5e-21
2bgwA [x.x.x] XPF ENDONUCLEASE                                         90   2e-20
2bgwB [x.x.x] XPF ENDONUCLEASE                                         86   2e-19
2bhnC [x.x.x] XPF ENDONUCLEASE                                         85   5e-19
1c7yA [b.40.4 - a.60.2 - a.5.1] HOLLIDAY JUNCTION DNA HELICASE RUVA    85   5e-19
1d8lA [b.40.4 - a.60.2] PROTEIN (HOLLIDAY JUNCTION DNA HELICASE ...    83   3e-18
2a1jB [x.x.x] DNA EXCISION REPAIR PROTEIN ERCC-1                       67   1e-13
3c5nA [x.x.x] TUBBY-RELATED PROTEIN 1                                  60   3e-11
3bz1U [x.x.x] PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN                  59   4e-11
1bqqT [b.40.3] METALLOPROTEINASE INHIBITOR 2                           58   9e-11
2a1jA [x.x.x] DNA REPAIR ENDONUCLEASE XPF                              56   2e-10
1b22A [a.60.4] DNA REPAIR PROTEIN RAD51                                56   3e-10
2duyA [x.x.x] COMPETENCE PROTEIN COMEA-RELATED PROTEIN                 53   3e-09
3egaA [x.x.x] PROTEIN PELLINO HOMOLOG 2                                51   1e-08
1cooA [x.x.x] RNA POLYMERASE ALPHA SUBUNIT                             50   2e-08
2eduA [x.x.x] KINESIN-LIKE PROTEIN KIF22                               50   3e-08
2axtU [x.x.x] PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN                  48   6e-08
3egbB [x.x.x] PROTEIN PELLINO HOMOLOG 2                                39   4e-05

>2bggA [x.x.x] PROTEIN AF1318
          Length = 395

 Score =  202 bits (514), Expect = 3e-54
 Identities = 24/418 (5%), Positives = 78/418 (18%), Gaps = 68/418 (16%)

Query: 233 IRDDIQALRTVMEKQAVVLGDSTDCDVIAIA---------EDQLEAAVQVFYVRGGRIRG 283
              +   L   +         S   + IA+                              
Sbjct: 12  PISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNI 71

Query: 284 ERGWVVDKVEDVSTGKLVEQFLAQTYGGADDEESTTAIPREVLVSAEPADRDAVVAWLSK 343
                +       +   ++  +           +       VL          + ++L  
Sbjct: 72  NISEFIYDSPHFDS---IKSQVDNAID------TGVDGIMLVLPEYNTPLYYKLKSYLI- 121

Query: 344 RRGAAVDVRVPQRGDKRALMETVLKNAEQTLARHKSQRASDLTTRSKXXXXXXXXXXXXX 403
                           R L   V     Q +++   +         K             
Sbjct: 122 -NSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKG------------ 168

Query: 404 XPLRIECFDISTLQGEHTVASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRR 463
               I     + +   +     +VF+             +  +E     + +  + +   
Sbjct: 169 -SDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLT-YLKSTIKKVVYG 226

Query: 464 FTRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLG 523
           F +   +                                 +      +    +     + 
Sbjct: 227 FKKSNPD----------------------------WDVEKLTLHVSGKRPKMKDGETKIL 258

Query: 524 IEDVAVCGLA-----KRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRK 578
            E V                +    E  P  +   ++     +R      +  ++  +  
Sbjct: 259 KETVEELKKQEMVSRDVKYAILHLNETHPFWVMEGTKVKLSSKRYLLTLLQPYVTPIKPL 318

Query: 579 RAKALTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYE 636
             + ++ +   +            + +   +       +  +       +  A  I  
Sbjct: 319 SVEIVSDNWTSEEYYHNVHEILDEIYYLSKM-NWRGFRSRNLPVTVNYPKLVAGIIAN 375


>3c65A [x.x.x] UVRABC SYSTEM PROTEIN C
          Length = 149

 Score =  163 bits (415), Expect = 1e-42
 Identities = 55/168 (32%), Positives = 85/168 (50%), Gaps = 31/168 (18%)

Query: 405 PLRIECFDISTLQGEHTVASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRF 464
           P RIE FD S + G   V+++VVF DG   K EYR++ ++   G + D     EV+ RR+
Sbjct: 13  PRRIEAFDNSNIYGADPVSALVVFLDGKPAKKEYRKYKVKTVAGPN-DYETR-EVVRRRY 70

Query: 465 TRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGI 524
           TR L+E                             P+L+++DGG+  ++A +  L++   
Sbjct: 71  TRVLKE-------------------------GLPLPDLIIIDGGKGHLSAVRDVLENELG 105

Query: 525 EDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAI 572
            DV + GL++ L         D + L R S+  YLLQR++DE HRFA+
Sbjct: 106 LDVPLAGLSELL----AGDPPDVVPLDRQSQEFYLLQRIQDEVHRFAV 149


>2csdA [x.x.x] TOPOISOMERASE V
          Length = 516

 Score =  125 bits (315), Expect = 3e-31
 Identities = 26/287 (9%), Positives = 65/287 (22%), Gaps = 48/287 (16%)

Query: 351 VRVPQRGDKRALMETVLKNAEQTLARHKSQRASDLTTRSKXXXXXXXXXXXXXXPLRIEC 410
           +   +R   R  +E  +      L      R       ++                 I  
Sbjct: 276 IVEHKRDIMRRYLEQRIVECALKLQDRYGIREDVALCLARAF------------DGSISM 323

Query: 411 FDISTLQG-EHTVASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLE 469
              +  +  +     + + E     ++        G   +      + E           
Sbjct: 324 IATTPYRTLKDVCPDLTLEEAKSVNRTLATLIDEHG--LSPDAADELIEHFESIAGIL-- 379

Query: 470 ESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIEDVAV 529
                                          +L  ++    +   ++ A        +A 
Sbjct: 380 -----------------------------ATDLEEIERMYEEGRLSEEAYRAAVEIQLAE 410

Query: 530 CGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKALTASVLD 589
               + +              P   + L     +   A    +     +       + L 
Sbjct: 411 LTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGY-ASLI 469

Query: 590 DIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYE 636
            I G+   R   LLK +G   ++ +A   E+    G+ +   + +  
Sbjct: 470 SIRGIDRERAERLLKKYGGYSKVREAGVEELR-EDGLTDAQIRELKG 515


>1bgxT [c.120.1 - a.60.7 - c.55.3 - e.8.1] TAQ DNA POLYMERASE
          Length = 828

 Score =  125 bits (315), Expect = 3e-31
 Identities = 28/233 (12%), Positives = 56/233 (24%), Gaps = 37/233 (15%)

Query: 405 PLRIECFDISTLQGEHTVASMVVFEDGL--ARKSEYRRFSIRGAEGADSDVAAMYEVISR 462
            +      +     E   A +VVF+      R   Y  +    A   + D      +I  
Sbjct: 43  AVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPE-DFPRQLALIKE 101

Query: 463 RFTRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDL 522
                                                  L V       V A+     + 
Sbjct: 102 LVDLL------------------------------GLARLEVPGYEADDVLASLAKKAEK 131

Query: 523 GIEDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKA 582
              +V +    K L ++      D I +      L     + ++       +   +    
Sbjct: 132 EGYEVRILTADKDLYQLL----SDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTG 187

Query: 583 LTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIY 635
             +  L  + G+G      LL+ +GS+  L +        +          + 
Sbjct: 188 DESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLK 240


>1dgsA [d.142.2 - b.40.4 - a.60.2] DNA LIGASE
          Length = 581

 Score =  123 bits (309), Expect = 2e-30
 Identities = 40/264 (15%), Positives = 68/264 (25%), Gaps = 51/264 (19%)

Query: 405 PLRIECFDISTLQG------------EHTVASMVVFEDGLARKSEYRRFSIRGAEGAD-- 450
               +      ++                   +V+  D L        ++ R    A   
Sbjct: 253 HCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLT-LWGELGYTARAPRFALAY 311

Query: 451 SDVAAMYEVISRRFTRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRP 510
              A   E         +  + RV           P G              V ++G   
Sbjct: 312 KFPAEEKETRLLDVVFQVGRTGRV----------TPVGV----------LEPVFIEGSEV 351

Query: 511 QVAAAQRALD----DLGIEDVAVCGLAKRLEEV-------WLPGEEDPIILPRTSEGLYL 559
                         D+ I D  +   A  +             G+E PI  P        
Sbjct: 352 SRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGH 411

Query: 560 LQRVRDEAHRFAISYHRRKRAKALTASV---LDDIPGLGPVRRAALLKH--FGSVRRLAQ 614
                 + HR        KR +A+         DI GLG      LL+      V  L  
Sbjct: 412 RLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYH 471

Query: 615 ATAAEIAEVPGIGERTAQTIYERL 638
               ++  +  +GE++AQ +  ++
Sbjct: 472 LRKEDLLGLERMGEKSAQNLLRQI 495


>2csbA [x.x.x] TOPOISOMERASE V
          Length = 511

 Score =  114 bits (287), Expect = 6e-28
 Identities = 30/283 (10%), Positives = 65/283 (22%), Gaps = 47/283 (16%)

Query: 359 KRALMETVLKNAEQTLARHKSQRASDLTTRSKXXXXXXXXXXXXXXPLRIECFDISTLQG 418
            R  +    ++  + L +   + A  L                         FD S    
Sbjct: 269 TRRWIVEHKRDIRRYLEQRIVECALKL--------QDRYGIREDVALCLARAFDGSISIA 320

Query: 419 EHTVASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLEESQRVGELD 478
                ++      L    E  +   R       D   +    +                 
Sbjct: 321 TTPYRTLKDVCPDLTL--EEAKSVNRTLATLI-DEHGLSPDAADELIE------------ 365

Query: 479 TLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIED-----VAVCGLA 533
                        ++       +L  ++       + +     + I+          G  
Sbjct: 366 -----------HFESIAGILATDLEEIERYEEGRLSEEAYRAAVEIQLAELTKKEGVGRK 414

Query: 534 KRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKALTASVLDDIPG 593
                +   G  + +        +  L  V     R   S            + L  I G
Sbjct: 415 TAERLLRAFGNPERVKQLAREFEIEKLASVEGVGERVLRSLVPGY-------ASLISIRG 467

Query: 594 LGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYE 636
           +   R   LLK +G   ++ +A   E+    G+ +   + +  
Sbjct: 468 IDRERAERLLKKYGGYSKVREAGVEEL-REDGLTDAQIRELKG 509


>2bhnA [x.x.x] XPF ENDONUCLEASE
          Length = 211

 Score =  108 bits (271), Expect = 4e-26
 Identities = 34/221 (15%), Positives = 71/221 (32%), Gaps = 20/221 (9%)

Query: 422 VASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLEESQRVGELDTLG 481
              + V E+     S      ++        +     ++S       + S    +     
Sbjct: 2   RVYVDVREERSPVPSILESLGVQVIP---KQLPMGDYLVSDSIIVERKTSSDFAK----- 53

Query: 482 ESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALD-DLGIEDVAVCGLAKRLEEVW 540
                        R     + +        +      +       + ++      L+  +
Sbjct: 54  --------SLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSLYAAMAALQLDY 105

Query: 541 LPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKALTAS---VLDDIPGLGPV 597
                + +    T+  +  L R+        I  H++ R   +      +L   PG+G  
Sbjct: 106 GIRLMNTMDPKGTALVIESLARLSTREGGQRIVIHKKPRLSDVREWQLYILQSFPGIGRR 165

Query: 598 RRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
               +L+ FGS+ R   A+ AEI++V GIGE+ A+ I + L
Sbjct: 166 TAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL 206


>1cmwA [c.120.1 - a.60.7 - c.55.3 - e.8.1] PROTEIN (DNA POLYMERASE
           I)
          Length = 817

 Score =  104 bits (261), Expect = 6e-25
 Identities = 29/234 (12%), Positives = 59/234 (25%), Gaps = 40/234 (17%)

Query: 405 PLRIECFDISTLQGEHTVASMVVFEDG--LARKSEYRRFSIRGAEGADSDVAAMYEVISR 462
            +      +     E   A +VVF+      R   Y  +    A   + D      +I  
Sbjct: 34  AVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPE-DFPRQLALIKE 92

Query: 463 RFTRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDL 522
                                                  L V       V A+     + 
Sbjct: 93  LV------------------------------DLLGLARLEVPGYEADDVLASLAKKAEK 122

Query: 523 GIEDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKA 582
              +V +    K L ++        I +      L     + ++       +   +    
Sbjct: 123 EGYEVRILTADKDLYQLLSDR----IHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTG 178

Query: 583 LTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYE 636
             +  L  + G+G      LL+ +GS+  L +     +     I E+    + +
Sbjct: 179 DESDNLPGVKGIGEKTARKLLEEWGSLEALLKNL-DRLKPA--IREKILAHMDD 229


>1bvsB [b.40.4 - a.60.2 - a.5.1] PROTEIN (HOLLIDAY JUNCTION DNA
           HELICASE RUVA)
          Length = 183

 Score = 94.0 bits (233), Expect = 1e-21
 Identities = 29/137 (21%), Positives = 43/137 (31%), Gaps = 14/137 (10%)

Query: 505 VDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVR 564
           +   R +V             D AV   A     V         +   +   L     VR
Sbjct: 2   IFSVRGEVLEVA--------LDHAVIEAAGIGYRVNATPSALATLNQGSQARLVTAMVVR 53

Query: 565 DEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGS---VRRLAQATAAEIA 621
           +++           R        L  + G+GP    A L    +    + LA +  A + 
Sbjct: 54  EDSMTLYGFSDAENRDL---FLALLSVSGVGPRLAMATLAVHDAAALRQALADSDVASLT 110

Query: 622 EVPGIGERTAQTIYERL 638
            VPGIG R A+ I   L
Sbjct: 111 RVPGIGRRGAERIVLEL 127


>1bvsA [b.40.4 - a.60.2 - a.5.1] PROTEIN (HOLLIDAY JUNCTION DNA
           HELICASE RUVA)
          Length = 183

 Score = 94.0 bits (233), Expect = 1e-21
 Identities = 29/141 (20%), Positives = 44/141 (31%), Gaps = 14/141 (9%)

Query: 505 VDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVR 564
           +   R +V        D  + + A  G       V         +   +   L     VR
Sbjct: 2   IFSVRGEVLEV---ALDHAVIEAAGIG-----YRVNATPSALATLNQGSQARLVTAMVVR 53

Query: 565 DEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHF---GSVRRLAQATAAEIA 621
           +++           R   L    L  + G+GP    A L         + LA +  A + 
Sbjct: 54  EDSMTLYGFSDAENRDLFL---ALLSVSGVGPRLAMATLAVHDAAALRQALADSDVASLT 110

Query: 622 EVPGIGERTAQTIYERLTSVE 642
            VPGIG R A+ I   L    
Sbjct: 111 RVPGIGRRGAERIVLELADKV 131


>1cukA [x.x.x] RUVA PROTEIN
          Length = 190

 Score = 93.5 bits (232), Expect = 2e-21
 Identities = 23/137 (16%), Positives = 49/137 (35%), Gaps = 13/137 (9%)

Query: 505 VDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVR 564
           +   R  +   Q  L  +   +V   G     E          +        ++    VR
Sbjct: 2   IGRLRGIIIEKQPPLVLI---EVGGVGY----EVHMPMTCFYELPEAGQEAIVFTHFVVR 54

Query: 565 DEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGS---VRRLAQATAAEIA 621
           ++A       ++++R        L    G+GP    A+L    +   V  + +     + 
Sbjct: 55  EDAQLLYGFNNKQERTLFKE---LIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALV 111

Query: 622 EVPGIGERTAQTIYERL 638
           ++PGIG++TA+ +   +
Sbjct: 112 KLPGIGKKTAERLIVEM 128


>1dgtB [x.x.x] DNA LIGASE
          Length = 660

 Score = 93.5 bits (232), Expect = 2e-21
 Identities = 36/297 (12%), Positives = 68/297 (22%), Gaps = 77/297 (25%)

Query: 405 PLRIECFDISTLQG------------EHTVASMVVFEDGLARKSEYRRFSIRGAEGAD-- 450
               +      ++                   +V+  D L        ++ R    A   
Sbjct: 253 HCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLT-LWGELGYTARAPRFALAY 311

Query: 451 SDVAAMYEVISRRFTRYLEESQRVGELDTLGESGAPQGAERKAPRFAYPPNLVVVDGGRP 510
              A   E         +  + RV  +  L                  P  +   +  R 
Sbjct: 312 KFPAEEKETRLLDVVFQVGRTGRVTPVGVLE-----------------PVFIEGSEVSRV 354

Query: 511 QVAAAQRALD-DLGIEDVAVCGLAKRLEEV-------WLPGEEDPIILPRTSEGLYLLQR 562
            +       + D+ I D  +   A  +             G+E PI  P           
Sbjct: 355 TLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLV 414

Query: 563 VRDEAHRFAISYHRRKRAKAL-----------------------------------TASV 587
              + HR        KR +A+                                       
Sbjct: 415 KEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRK 474

Query: 588 --LDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERLTSVE 642
             L  +  +G      LL+     +            +PG+GE  A+ +  R  +++
Sbjct: 475 EDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMD 531


>2bhnB [x.x.x] XPF ENDONUCLEASE
          Length = 199

 Score = 93.1 bits (230), Expect = 2e-21
 Identities = 36/222 (16%), Positives = 66/222 (29%), Gaps = 34/222 (15%)

Query: 422 VASMVVFEDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLEESQRVGELDTLG 481
              + V E+     S      ++        +     ++S       + S          
Sbjct: 2   RVYVDVREERSPVPSILESLGVQVIPK---QLPMGDYLVSDSIIVERKTSSD-------- 50

Query: 482 ESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIEDVAVCGLAKR--LEEV 539
                                 + DG   + A+      +     V    + +R    E 
Sbjct: 51  ------------------FAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRER 92

Query: 540 WLPGEEDPIILPRTSEGLYLLQRVRDEA---HRFAISYHRRKRAKALTASVLDDIPGLGP 596
            L      + L      +  +              +S  R    +     +L   PG+G 
Sbjct: 93  SLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTRRLSDVREWQLYILQSFPGIGR 152

Query: 597 VRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
                +L+ FGS+ R   A+ AEI++V GIGE+ A+ I + L
Sbjct: 153 RTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL 194


>3c1yA [x.x.x] DNA INTEGRITY SCANNING PROTEIN DISA
          Length = 349

 Score = 91.8 bits (227), Expect = 5e-21
 Identities = 16/117 (13%), Positives = 46/117 (39%), Gaps = 8/117 (6%)

Query: 538 EVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKAL-------TASVLDD 590
             +   E +        +     +     +    + Y  ++ A+            +L  
Sbjct: 234 MDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKT 293

Query: 591 IPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERLTSVEGGQRT 647
           +  +       +++ F ++ ++++A+  ++ +V GIGE+ A+ I E + S    ++T
Sbjct: 294 VARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESI-SSLKHRKT 349


>2bgwA [x.x.x] XPF ENDONUCLEASE
          Length = 219

 Score = 90.0 bits (222), Expect = 2e-20
 Identities = 37/230 (16%), Positives = 75/230 (32%), Gaps = 23/230 (10%)

Query: 416 LQGEHTVASMVVF---EDGLARKSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLEESQ 472
           +  +      V     E+     S      +   +     +     ++S       +   
Sbjct: 1   MLEDPGGRPRVYVDVREERSPVPSILESLGV---QVIPKQLPMGDYLVSDSIIVERKT-- 55

Query: 473 RVGELDTLGESGAPQG-AERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIEDVAVCG 531
                    +S       E+ +    +   + ++  G P     +     L    +A   
Sbjct: 56  ----SSDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRERSL-YAAMAALQ 110

Query: 532 LAKRLEEVWLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKA---LTASVL 588
           L   +  +     +   ++      +  L R+        I  H++ R          +L
Sbjct: 111 LDYGIRLMNTMDPKGTALV------IESLARLSTREGGQRIVIHKKPRLSDVREWQLYIL 164

Query: 589 DDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
              PG+G      +L+ FGS+ R   A+ AEI++V GIGE+ A+ I + L
Sbjct: 165 QSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL 214


>2bgwB [x.x.x] XPF ENDONUCLEASE
          Length = 200

 Score = 86.4 bits (213), Expect = 2e-19
 Identities = 35/225 (15%), Positives = 66/225 (29%), Gaps = 40/225 (17%)

Query: 424 SMVVFEDGLAR---KSEYRRFSIRGAEGADSDVAAMYEVISRRFTRYLEESQRVGELDTL 480
             V  +    R    S      ++        +     ++S       +           
Sbjct: 2   PRVYVDVREERSPVPSILESLGVQVIP---KQLPMGDYLVSDSIIVERKT---------- 48

Query: 481 GESGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVW 540
                           +     +       Q +      + + I  V    + +R     
Sbjct: 49  ---------------SSDFAKSLFDGRLFEQASRLAEHYETVFI-IVEGPPVPRR-YRGR 91

Query: 541 LPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKALTASV-------LDDIPG 593
                  +   +   G+ L+  +  +     I    R   K   + V       L   PG
Sbjct: 92  ERSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSTKPRLSDVREWQLYILQSFPG 151

Query: 594 LGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
           +G      +L+ FGS+ R   A+ AEI++V GIGE+ A+ I + L
Sbjct: 152 IGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL 196


>2bhnC [x.x.x] XPF ENDONUCLEASE
          Length = 194

 Score = 85.3 bits (210), Expect = 5e-19
 Identities = 32/219 (14%), Positives = 58/219 (26%), Gaps = 42/219 (19%)

Query: 427 VFEDGLARKSEYRRFSIR----GAEGADSDVAAMYEVISRRFTRYLEESQRVGELDTLGE 482
           V E+     S      ++         D  + +   ++ R+ +                 
Sbjct: 6   VREERSPVPSILESLGVQVIPKQLPMGD-YLVSDSIIVERKTS----------------- 47

Query: 483 SGAPQGAERKAPRFAYPPNLVVVDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEV--- 539
                             +             A R  +      + V G           
Sbjct: 48  -----------------SDFAKSLFDGRLFEQASRLAEHYETVFIIVEGPPVPRRYRGRE 90

Query: 540 WLPGEEDPIILPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRR 599
                    +       L      +  A             +     +L   PG+G    
Sbjct: 91  RSLYAAMAALQLDYGIRLMNTMDPKGTALVIESLARLSSDVREWQLYILQSFPGIGRRTA 150

Query: 600 AALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
             +L+ FGS+ R   A+ AEI++V GIGE+ A+ I + L
Sbjct: 151 ERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL 189


>1c7yA [b.40.4 - a.60.2 - a.5.1] HOLLIDAY JUNCTION DNA HELICASE RUVA
          Length = 199

 Score = 85.1 bits (210), Expect = 5e-19
 Identities = 24/138 (17%), Positives = 49/138 (35%), Gaps = 15/138 (10%)

Query: 505 VDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVWLPGEE-DPIILPRTSEGLYLLQRV 563
           +   R  +   Q  L  + +  V          EV +P      +        ++    V
Sbjct: 2   IGRLRGIIIEKQPPLVLIEVGGVG--------YEVHMPMTCFYELPEAGQEAIVFTHFVV 53

Query: 564 RDEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGS---VRRLAQATAAEI 620
           R++A      Y    + +      L    G+GP    A+L    +   V  + +     +
Sbjct: 54  REDAQLL---YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGAL 110

Query: 621 AEVPGIGERTAQTIYERL 638
            ++PGIG++TA+ +   +
Sbjct: 111 VKLPGIGKKTAERLIVEM 128


>1d8lA [b.40.4 - a.60.2] PROTEIN (HOLLIDAY JUNCTION DNA HELICASE
           RUVA)
          Length = 140

 Score = 82.8 bits (204), Expect = 3e-18
 Identities = 24/138 (17%), Positives = 51/138 (36%), Gaps = 15/138 (10%)

Query: 505 VDGGRPQVAAAQRALDDLGIEDVAVCGLAKRLEEVWLPGEED-PIILPRTSEGLYLLQRV 563
           +   R  +   Q  L  + +  V          EV +P      +        ++    V
Sbjct: 2   IGRLRGIIIEKQPPLVLIEVGGVG--------YEVHMPMTCFYELPEAGQEAIVFTHFVV 53

Query: 564 RDEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGS---VRRLAQATAAEI 620
           R++A       ++++R        L    G+GP    A+L    +   V  + +     +
Sbjct: 54  REDAQLLYGFNNKQERTLFKE---LIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGAL 110

Query: 621 AEVPGIGERTAQTIYERL 638
            ++PGIG++TA+ +   +
Sbjct: 111 VKLPGIGKKTAERLIVEM 128


>2a1jB [x.x.x] DNA EXCISION REPAIR PROTEIN ERCC-1
          Length = 79

 Score = 67.3 bits (164), Expect = 1e-13
 Identities = 14/68 (20%), Positives = 30/68 (44%)

Query: 571 AISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERT 630
            +     +   +     L  +  +       LL  FGS+ +L  A+  ++A  PG+G + 
Sbjct: 5   LLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQK 64

Query: 631 AQTIYERL 638
           A+ +++ L
Sbjct: 65  ARRLFDVL 72


>3c5nA [x.x.x] TUBBY-RELATED PROTEIN 1
          Length = 231

 Score = 59.5 bits (144), Expect = 3e-11
 Identities = 19/101 (18%), Positives = 31/101 (30%), Gaps = 5/101 (4%)

Query: 542 PGEEDPII---LPRTSEGLYLLQRVRDEAHRFAISYHRRKRAKAL--TASVLDDIPGLGP 596
           P  +   +   L R          +  E   F ++  +RKR+K      S+      +G 
Sbjct: 8   PAPQGRTVRCRLTRDKMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDPTNNFIGK 67

Query: 597 VRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYER 637
           +R   L   F                V  + +  A  IYE 
Sbjct: 68  LRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYET 108


>3bz1U [x.x.x] PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN
          Length = 97

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 6/79 (7%)

Query: 561 QRVRDEAHRFAISYHRRKRAKALTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEI 620
           + V     +   +Y  +        +      GL P     ++K+          +  ++
Sbjct: 1   ELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPY------ESVEDV 54

Query: 621 AEVPGIGERTAQTIYERLT 639
             +PG+ ER  Q + E L 
Sbjct: 55  LNIPGLTERQKQILRENLE 73


>1bqqT [b.40.3] METALLOPROTEINASE INHIBITOR 2
          Length = 184

 Score = 57.8 bits (139), Expect = 9e-11
 Identities = 17/148 (11%), Positives = 36/148 (24%), Gaps = 18/148 (12%)

Query: 32  YVGKAKNLRARLSSYFQDFSALHPRTQTMISTAADVDWTVVNTEVEALQLEYSWIKEYSP 91
            V +AK +  +      D           I         +     + ++  Y+       
Sbjct: 17  IVIRAKAVNKKEVDSGNDIY---GNPIKRIQYEIKQI-KMFKGPDQDIEFIYTAPAAAVC 72

Query: 92  RFNVRYRDDKSYPYLAVTLNEEFPRVQVMRGARRRGVRYFGPYSYAWAIRDTVDLLLRVF 151
             ++     K Y    +   +      +          +  P+    A +      L   
Sbjct: 73  GVSLDIGGKKEY----LIAGKAEGNGNMHITLC----DFIVPWDTLSATQKK---SLNHR 121

Query: 152 PVRTCSAGVFKRARSSGRPCLLGYIDKC 179
               C   +    R    PC +   D+C
Sbjct: 122 YQMGCECKIT---RCPMIPCYISSPDEC 146


>2a1jA [x.x.x] DNA REPAIR ENDONUCLEASE XPF
          Length = 62

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 586 SVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
             L  +PG+      +L+ H  ++  LA  +  E+  + G     A+ +Y+ +
Sbjct: 3   DFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILG-NAANAKQLYDFI 54


>1b22A [a.60.4] DNA REPAIR PROTEIN RAD51
          Length = 70

 Score = 56.0 bits (135), Expect = 3e-10
 Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 1/62 (1%)

Query: 578 KRAKALTASVLDDIPGLGPVRRAALLKH-FGSVRRLAQATAAEIAEVPGIGERTAQTIYE 636
           + +         +  G+       L +  F +V  +A A   E+  + GI E  A  I  
Sbjct: 2   EESFGPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILA 61

Query: 637 RL 638
             
Sbjct: 62  EA 63


>2duyA [x.x.x] COMPETENCE PROTEIN COMEA-RELATED PROTEIN
          Length = 64

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 6/48 (12%)

Query: 591 IPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
           +PG+GPV    +++          A   ++ +V GIG  T + +   L
Sbjct: 21  LPGIGPVLARRIVEGRPY------ARVEDLLKVKGIGPATLERLRPYL 62


>3egaA [x.x.x] PROTEIN PELLINO HOMOLOG 2
          Length = 214

 Score = 50.7 bits (120), Expect = 1e-08
 Identities = 8/68 (11%), Positives = 17/68 (25%)

Query: 1   MTVRPTLRPKPGSIPTDPGVYRFRDEHGRVIYVGKAKNLRARLSSYFQDFSALHPRTQTM 60
                T         + PGV+R     G V  + + ++ + R     +           +
Sbjct: 145 HDGLTTNGVLVHPRESQPGVWREISVCGDVYTLRETRSAQQRGKVESETNVLQDGSLIDL 204

Query: 61  ISTAADVD 68
                   
Sbjct: 205 CGATLLWR 212


>1cooA [x.x.x] RNA POLYMERASE ALPHA SUBUNIT
          Length = 81

 Score = 49.8 bits (119), Expect = 2e-08
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 590 DIPGLGPVRRAALLKH-FGSVRRLAQATAAEIAEVPGIGERTAQTIYERL 638
           D   L       L       +  L Q T  E+ + P +G+++   I + L
Sbjct: 10  DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVL 59


>2eduA [x.x.x] KINESIN-LIKE PROTEIN KIF22
          Length = 98

 Score = 49.5 bits (118), Expect = 3e-08
 Identities = 7/63 (11%), Positives = 21/63 (33%), Gaps = 2/63 (3%)

Query: 584 TASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAEIAEVPGIGERTAQTIYERLTSVEG 643
           +A  L  +  +GP +   ++         +     ++  V GI  +  ++  +       
Sbjct: 38  SARDLRSLQRIGPKKAQLIVGWRELHGPFS--QVEDLERVEGITGKQMESFLKANILGLA 95

Query: 644 GQR 646
             +
Sbjct: 96  AGQ 98


>2axtU [x.x.x] PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN
          Length = 98

 Score = 48.3 bits (115), Expect = 6e-08
 Identities = 12/91 (13%), Positives = 28/91 (30%), Gaps = 8/91 (8%)

Query: 561 QRVRDEAHRFAISYHRRKRAKA-LTASVLDDIPGLGPVRRAALLKHFGSVRRLAQATAAE 619
           + + +       + +  K        +      GL P     ++K+          +  +
Sbjct: 1   EELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAP------YESVED 54

Query: 620 IAEVPGIGERTAQTIYERLTSVEGGQRTQPE 650
           +  +PG+ ER  Q + E L         +  
Sbjct: 55  VLNIPGLTERQKQILRENL-EHFTVTEVETA 84


>3egbB [x.x.x] PROTEIN PELLINO HOMOLOG 2
          Length = 223

 Score = 39.1 bits (90), Expect = 4e-05
 Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 7/86 (8%)

Query: 4   RPTLRPKPGSIPTDPGVYRFRDEHGRVIYVGKAKNLRARLSSYFQDFSAL-------HPR 56
             T        P  PGV+R     G V  + + ++ + R      + + L          
Sbjct: 138 GLTTNGVLVMHPRQPGVWREISVCGDVYTLRETRSAQQRGKLVESETNVLQDGSLIDLCG 197

Query: 57  TQTMISTAADVDWTVVNTEVEALQLE 82
              +  TA  +  T     +EAL+ E
Sbjct: 198 ATLLWRTADGLFHTPTQKHIEALRQE 223


  Database: 95pdb09Oct16_0000
    Posted date:  Oct 27, 2009  4:27 PM
  Number of letters in database: 15,983,541
  Number of sequences in database:  66,450
  
Lambda     K      H
   0.329    0.141    0.368 

Gapped
Lambda     K      H
   0.267   0.0466    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 66450
Number of Hits to DB: 24,551,705
Number of extensions: 1517502
Number of successful extensions: 18712
Number of sequences better than 1.0e-03: 10
Number of HSP's gapped: 9048
Number of HSP's successfully gapped: 366
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)