RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780454|ref|YP_003064867.1| DNA polymerase III subunit
beta [Candidatus Liberibacter asiaticus str. psy62]
         (385 letters)



>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication,
           DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}
           (A:)
          Length = 798

 Score =  160 bits (405), Expect = 2e-40
 Identities = 52/409 (12%), Positives = 128/409 (31%), Gaps = 45/409 (11%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
             +++  S+  +++    ++ +  N +     +   A+  +                  S
Sbjct: 408 STLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETS 467

Query: 61  VDVC----GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPES 116
           + +       +T  A  L DI++      ++     +E       +    +         
Sbjct: 468 IKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSE-----APALFQFDLKSGFLQFF 522

Query: 117 EFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVAT 176
             P   +E        + ++     E + F    +  +  +  + F   E+ +     A 
Sbjct: 523 LAPKFNDEGSNSQASNSGALEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAV 580

Query: 177 DGHRLAVAEVDIVA------QIAKMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIH 229
           D  R+ +  ++I        +     ++ +   ++ +ILR  ++ D+ ++    +   I 
Sbjct: 581 DDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSII 640

Query: 230 LNIESLSM------SVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRI 283
           L  E          S++L+D +    + +     D  L +  +   + V  +S +S    
Sbjct: 641 LLFEDTKKDRIAEYSLKLMDIDADFLK-IEELQYDSTLSLPSSEFSKIVRDLSQLSDSIN 699

Query: 284 QAV-------KLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNI 336
             +                 + +      +  E+      + P+D+ F  KYLL+II   
Sbjct: 700 IMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGS 759

Query: 337 SSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
           S       + V    SS +    +   K             + L P   
Sbjct: 760 SL-----SDRVGIRLSSEAPALFQFDLKSG--------FLQFFLAPKFN 795



 Score =  112 bits (280), Expect = 7e-26
 Identities = 47/411 (11%), Positives = 124/411 (30%), Gaps = 33/411 (8%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
             +++  S+  +++    ++ +  N +     +   A+  +                  S
Sbjct: 141 STLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETS 200

Query: 61  VDVC----GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPES 116
           + +       +T  A  L DI++      ++     +E       +    +         
Sbjct: 201 IKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSE-----APALFQFDLKSGFLQFF 255

Query: 117 EFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVAT 176
             P   +E        + ++     E + F    +  +  +  + F   E+ +     A 
Sbjct: 256 LAPKFNDEGSNSQSNGSGALEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAV 313

Query: 177 DGHRLAVAEVDIVA------QIAKMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIH 229
           D  R+ +  ++I        +     ++ +   ++ +ILR  ++ D+ ++    +   I 
Sbjct: 314 DDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSII 373

Query: 230 LNIES-----LSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRV-------SI 277
           L  E      ++     +     ++  +     D  L +  +   + V  +       +I
Sbjct: 374 LLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINI 433

Query: 278 MSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNIS 337
           M +                + +      +  E+      + P+D+ F  KYLL+II   S
Sbjct: 434 MITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSS 493

Query: 338 SDEVV---DDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
             + V          L   +            K N +   +       +  
Sbjct: 494 LSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEGSNSQASNSGALEA 544



 Score = 59.3 bits (142), Expect = 9e-10
 Identities = 33/220 (15%), Positives = 74/220 (33%), Gaps = 21/220 (9%)

Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193
             E + F    +  +  +  + F   E+ +     A D  R+ +  ++I        +  
Sbjct: 12  FEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAVDDSRVLLVSLEIGVEAFQEYRCD 69

Query: 194 KMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIHLNIESLSMSVRL-----IDGEFP 247
              ++ +   ++ +ILR  ++ D+ ++    +   I L  E             +     
Sbjct: 70  HPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDA 129

Query: 248 NYQNVIPCSND-------KELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVD 300
           ++  +     D        E      +L Q  D ++IM +                + + 
Sbjct: 130 DFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIK 189

Query: 301 NPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDE 340
                +  E+      + P+D+ F  KYLL+II   S  +
Sbjct: 190 PFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSD 229


>1vpk_A DNA polymerase III, beta subunit; TM0262, structural
           genomics, joint center for structural genomics, JCSG,
           protein structure initiative; HET: DNA; 2.00A
           {Thermotoga maritima MSB8} (A:144-207,A:256-378)
          Length = 187

 Score =  155 bits (394), Expect = 8e-39
 Identities = 54/251 (21%), Positives = 102/251 (40%), Gaps = 65/251 (25%)

Query: 135 SVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAK 194
           S+L+ +VE+  FA A +E    LNG+F+ +      L  VA+DG RLA+AE  I  +   
Sbjct: 1   SLLEEMVEKVIFAAAKDEFMRNLNGVFWEL--HKNLLRLVASDGFRLALAEEQIENEEEA 58

Query: 195 MPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIP 254
             S ++  K V                                               IP
Sbjct: 59  --SFLLSLKRV-----------------------------------------------IP 69

Query: 255 CSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVY 314
            +   ++ V+   LR+++ RV +++S   ++VK  +  + + +   +PD G+ ++ + V 
Sbjct: 70  ETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPDYGEVVDEVEVQ 129

Query: 315 YNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKV 374
                + I FN K++ +++ +I +     +E+      S S   I   D           
Sbjct: 130 KEGEDLVIAFNPKFIEDVLKHIET-----EEIEMNFVDSTSPCQINPLDIS--------- 175

Query: 375 NAFYVLMPMRI 385
              Y++MP+R+
Sbjct: 176 GYLYIVMPIRL 186


>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp,
           replication, transferase; HET: DNA; 2.00A {Streptococcus
           pyogenes} PDB: 2awa_A* (A:140-204,A:253-378)
          Length = 191

 Score =  146 bits (370), Expect = 5e-36
 Identities = 47/252 (18%), Positives = 96/252 (38%), Gaps = 65/252 (25%)

Query: 136 VLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKM 195
           +LK+++  T FA + +E R  L G+   +        AVATD HR++   + +    A  
Sbjct: 2   LLKSIIAETAFAASLQESRPILTGVHIVL-SNHKDFKAVATDSHRMSQRLITLDNTSADF 60

Query: 196 PSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPC 255
             +++P +                                                ++  
Sbjct: 61  -MVVLPDR------------------------------------------------LLMT 71

Query: 256 SNDKELRVNCTNLRQAVDRVSIMSS-VRIQAVKLSLSSDKLCMTVDNPDMGKAIESMN-V 313
             + E+  N  +LR A++R  ++S+  +   VKL ++ + +   V++P++GK  E ++ V
Sbjct: 72  EFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQNHISAHVNSPEVGKVNEDLDIV 131

Query: 314 YYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNK 373
             +   + I FN  YL+E +  I S     + V     S      +   D++        
Sbjct: 132 SQSGSDLTISFNPTYLIESLKAIKS-----ETVKIHFLSPVRPFTLTPGDEEE------- 179

Query: 374 VNAFYVLMPMRI 385
            +   ++ P+R 
Sbjct: 180 -SFIQLITPVRT 190



 Score = 26.6 bits (59), Expect = 5.5
 Identities = 11/97 (11%), Positives = 32/97 (32%), Gaps = 10/97 (10%)

Query: 2   KITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEI-EITGAIPAS 60
           ++      +   +  A  I        V   +        +    + PE+ ++   +   
Sbjct: 76  EVVFNTQSLRHAMERAFLISNATQNGTVKLEI----TQNHISAHVNSPEVGKVNEDLDI- 130

Query: 61  VDVCG---SITVSAHLLYDIVRKLQ-DGAQISFFKEN 93
           V   G   +I+ +   L + ++ ++ +  +I F    
Sbjct: 131 VSQSGSDLTISFNPTYLIESLKAIKSETVKIHFLSPV 167


>1rwz_A DNA polymerase sliding clamp; torus, processivity factor,
           replication; HET: DNA; 1.80A {Archaeoglobus fulgidus}
           (A:)
          Length = 245

 Score =  143 bits (362), Expect = 3e-35
 Identities = 41/258 (15%), Positives = 84/258 (32%), Gaps = 27/258 (10%)

Query: 137 LKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------ 190
           +  ++        T  I   ++    H  E+   L + A D   +A+  VDI        
Sbjct: 2   IDVIMTGELLKTVTRAIVALVSEARIHFLEK--GLHSRAVDPANVAMVIVDIPKDSFEVY 59

Query: 191 QIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQ 250
            I +  +I V    + +I + +S+KD    +   ES + +   S+   V LID      +
Sbjct: 60  NIDEEKTIGVDMDRIFDISKSISTKDLVELIVEDESTLKVKFGSVEYKVALIDPSAIRKE 119

Query: 251 NVIP-CSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAI- 308
             IP      ++ ++    ++A+     +       V      +   +            
Sbjct: 120 PRIPELELPAKIVMDAGEFKKAIAAADKI----SDQVIFRSDKEGFRIEAKGDVDSIVFH 175

Query: 309 --ESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDS 366
             E+  + +N       F+  YL E      S      +++     +N  V +  +    
Sbjct: 176 MTETELIEFNGGEARSMFSVDYLKEFCKVAGS-----GDLLTIHLGTNYPVRLVFELVGG 230

Query: 367 KNNKDNKVNAFYVLMPMR 384
           +          Y+L P  
Sbjct: 231 RA------KVEYILAPRI 242


>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1;
           protein-peptide complex, DNA replication, DNA-binding,
           nucleus, DNA binding protein; 2.00A {Arabidopsis
           thaliana} PDB: 2zvw_A (A:)
          Length = 276

 Score =  142 bits (358), Expect = 8e-35
 Identities = 31/291 (10%), Positives = 76/291 (26%), Gaps = 38/291 (13%)

Query: 113 FPESEFPSTKEEEYVYSFELASSVLKN-LVERTHFAMATEEIRYYLNGIFFHINEEDLKL 171
                                S +L+  LV+ +      E I+  +N   F  +      
Sbjct: 2   GSSHHHHHHSSGL----VPRGSHMLELRLVQGSLLKKVLESIKDLVNDANFDCSST--GF 55

Query: 172 CAVATDGHRLAVAEVDIVA------QIAKMPSIIVPRKAVGEILRILSS-KDSSVKVSLS 224
              A D   +A+  + + +      +  +  S+ +    + ++L+   +    ++K    
Sbjct: 56  SLQAMDSSHVALVSLLLRSEGFEHYRCDRNLSMGMNLGNMSKMLKCAGNDDIITIKADDG 115

Query: 225 ESRIHLNIESLSMSV-----RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMS 279
              +    ES +          +      +  +        +R+      +    +S + 
Sbjct: 116 GDTVTFMFESPTQDKIADFEMKLMDIDSEHLGIPDAEYHSIVRMPSNEFSRICKDLSSIG 175

Query: 280 SV-------RIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEI 332
                           +       + +         E   V   + P+ + F  +Y+   
Sbjct: 176 DTVVISVTKEGVKFSTAGDIGTANIVLRQNTTVDKPEDAIVIEMKEPVSLSFALRYMNSF 235

Query: 333 IDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPM 383
                       + V    SS   V +  K  +    +       Y L P 
Sbjct: 236 TKATPL-----SDTVTISLSSELPVVVEYKVAEMGYIR-------YYLAPK 274


>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding,
           nuclear protein, DNA replication, processivity factor;
           2.30A {Saccharomyces cerevisiae} (A:)
          Length = 258

 Score =  139 bits (351), Expect = 6e-34
 Identities = 41/269 (15%), Positives = 87/269 (32%), Gaps = 36/269 (13%)

Query: 137 LKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------ 190
                E + F    +  +  +  + F   E+ +     A D  R+ +  ++I        
Sbjct: 3   EAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAVDDSRVLLVSLEIGVEAFQEY 60

Query: 191 QIAKMPSIIVPRKAVGEILRILSSK-DSSVKVSLSESRIHLNIESLSM------SVRLID 243
           +     ++ +   ++ +ILR  ++    ++    +   I L  E          S++L+D
Sbjct: 61  RCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMD 120

Query: 244 GEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAV-------KLSLSSDKLC 296
            +    + +     D  L +  +   + V  +S +S      +                 
Sbjct: 121 IDADFLK-IEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGS 179

Query: 297 MTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSS 356
           + +      +  E+      + P+D+ F  KYLL+II   S      D V  RL S   +
Sbjct: 180 VIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSL----SDRVGIRLSSEAPA 235

Query: 357 VFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
           +F                   + L P   
Sbjct: 236 LFQFDLKSG---------FLQFFLAPKFN 255


>3fds_D DNA polymerase sliding clamp C; protein-protein complex,
           cytoplasm, DNA damage, DNA repair, DNA replication,
           DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus
           solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B
           2hii_B* 2izo_B* (D:)
          Length = 245

 Score =  138 bits (348), Expect = 1e-33
 Identities = 22/256 (8%), Positives = 75/256 (29%), Gaps = 23/256 (8%)

Query: 137 LKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI---- 192
              +++   F+     +  +L+   F + +E +++     D  R+   ++ + +      
Sbjct: 3   KAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRV--SGIDPSRVVFLDIFLPSSYFEGF 60

Query: 193 ---AKMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIHLNIESLSMSVRLIDGEFPN 248
               +   I    + V +IL+ +   D+  +  + S+  +  + E        +      
Sbjct: 61  EVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVEST 120

Query: 249 YQNVIPCSNDKELRVNCTNLRQAVDRVSI-MSSVRIQAVKLSLSSDKLCMTVDNPDMGKA 307
               +      + ++        +D +S     + I + +  L  + +            
Sbjct: 121 QPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELST 180

Query: 308 IESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSK 367
                +  +   +   +  +Y+        +      + +     S   + +R K     
Sbjct: 181 DNGTLLEASGADVSSSYGMEYVANTTKMRRA-----SDSMELYFGSQIPLKLRFKLPQEG 235

Query: 368 NNKDNKVNAFYVLMPM 383
                     + + P 
Sbjct: 236 YGD-------FYIAPR 244


>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA
           repair, exonuclease, hydrolase, nuclease, nucleus,
           phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A
           {Homo sapiens} PDB: 3ggr_A (A:)
          Length = 266

 Score =  135 bits (340), Expect = 1e-32
 Identities = 30/272 (11%), Positives = 70/272 (25%), Gaps = 41/272 (15%)

Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------- 192
                    A   +    + ++    E+ L L     +  R A A               
Sbjct: 7   GGNVKVLGKAVHSLSRIGDELYLEPLEDGLSL--RTVNSSRSAYACFLFAPLFFQQYQAA 64

Query: 193 ---AKMPSIIVPRKAVGEILRILSSKDSS-----VKVSLSESRIHLNIESLSMSVRLIDG 244
                +    +  K+   + R L+  + +     + ++   SR+ + +       +  + 
Sbjct: 65  TPGQDLLRCKILXKSFLSVFRSLAXLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNL 124

Query: 245 EFPNYQNVIPCSNDKE----LRVNCTNLRQAVDRVSIMSSV---------RIQAVKLSLS 291
            F + +++    +       LR     L +AV   S   +          R+        
Sbjct: 125 SFQDCESLQAVFDPASCPHXLRAPARVLGEAVLPFSPALAEVTLGIGRGRRVILRSYHEE 184

Query: 292 SDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLD 351
                      +     E       +  + I F  K    ++    S    +  +    D
Sbjct: 185 EADSTAKAXVTEXCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAES---ANLNLSIHFD 241

Query: 352 SSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPM 383
           +         KD           +  +VL  +
Sbjct: 242 APGRPAIFTIKDSLL--------DGHFVLATL 265


>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA
           replication, DNA binding protein; HET: DNA; 1.68A
           {Sulfolobus tokodaii} (A:)
          Length = 245

 Score =  131 bits (330), Expect = 1e-31
 Identities = 28/257 (10%), Positives = 84/257 (32%), Gaps = 31/257 (12%)

Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193
             +        + +   ++   F I  E ++L  VA D   +++ ++++         + 
Sbjct: 5   YDDVRDLKAIIQALLKLVDEALFDIKPEGIQL--VAIDKAHISLIKIELPKEMFKEYDVP 62

Query: 194 KMPSIIVPRKAVGEILRILSSK-DSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNV 252
           +        + + ++L+    K +  +     E        +L+    + + E    +  
Sbjct: 63  EEFKFGFNTQYMSKLLKAAKRKEEIIIDADSPEVVKLTLSGALNRVFNVNNIEVLPPEVP 122

Query: 253 IPCSN-DKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDM-----GK 306
                 D +  +N + L+ A+  ++ ++      + +S + +K+ +  +  +       K
Sbjct: 123 EVNLEFDIKATINASGLKNAIGEIAEVAD----TLLISGNEEKVVVKGEGENKVEVEFSK 178

Query: 307 AIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDS 366
              S+            ++ +YL +II           + V    +    + +    +  
Sbjct: 179 DTGSLADIEFNKESSSAYDVEYLNDIISLTKL-----SDYVKVAFADQKPMQLEFNMEGG 233

Query: 367 KNNKDNKVNAFYVLMPM 383
                      Y+L P 
Sbjct: 234 G-------KVTYLLAPK 243


>1iz5_A Proliferating cell nuclear antigen; DNA, replication,
           processivity, sliding clamp, DNA binding protein; 1.80A
           {Pyrococcus furiosus} (A:)
          Length = 249

 Score =  131 bits (330), Expect = 1e-31
 Identities = 30/262 (11%), Positives = 82/262 (31%), Gaps = 34/262 (12%)

Query: 137 LKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------ 190
                    FA   +     ++   F + E+ + +   A D  R+ + ++++ +      
Sbjct: 4   EIVFEGAKEFAQLIDTASKLIDEAAFKVTEDGISM--RAMDPSRVVLIDLNLPSSIFSKY 61

Query: 191 QIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHL---NIESLSMSVRLIDGEFP 247
           ++ +  +I V    + +IL+   +KD ++ +   E           +       +     
Sbjct: 62  EVVEPETIGVNLDHLKKILKRGKAKD-TLILKKGEENFLEITIQGTATRTFRVPLIDVEE 120

Query: 248 NYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPD---- 303
              ++       ++ V    L+ AV   S++S     ++K     ++  M  +       
Sbjct: 121 MEVDLPELPFTAKVVVLGEVLKAAVKAASLVSD----SIKFIARENEFIMKAEGETQEVE 176

Query: 304 --MGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRG 361
             +    E +     +      +   YL +++  +       DEV  +  +         
Sbjct: 177 IKLTLEDEGLLDIEVQEETKSAYGVSYLSDMVKGLG----KADEVTIKFGNEMPMQMEYY 232

Query: 362 KDKDSKNNKDNKVNAFYVLMPM 383
              +            ++L P 
Sbjct: 233 IRDEG--------RLTFLLAPR 246


>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit,
           protein-protein interaction, PCNA123 heterotrimer, DNA
           binding protein; HET: DNA; 1.90A {Sulfolobus
           solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C* (A:)
          Length = 244

 Score =  129 bits (324), Expect = 8e-31
 Identities = 25/253 (9%), Positives = 78/253 (30%), Gaps = 23/253 (9%)

Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193
             +        + +   ++       ++ ++L  VA D   +++  V++         + 
Sbjct: 5   YDDVRVLKDIIQALARLVDEAVLKFKQDSVEL--VALDRAHISLISVNLPREMFKEYDVN 62

Query: 194 KMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNV 252
                    + + +IL++   K++  +     +S I   I S +    + + E    +  
Sbjct: 63  DEFKFGFNTQYLMKILKVAKRKEAIEIASESPDSVIINIIGSTNREFNVRNLEVSEQEIP 122

Query: 253 IP-CSNDKELRVNCTNLRQAVDRVSIMSS-VRIQAVKLSLSSDKLCMTVDNPDMGKAIES 310
                 D    ++    + A+  VS ++  V ++  +  +       +    +  K    
Sbjct: 123 EINLQFDISATISSDGFKSAISEVSTVTDNVVVEGHEDRILIKAEGESEVEVEFSKDTGG 182

Query: 311 MNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNK 370
           +            ++ +YL +++           + V     +   + +    +      
Sbjct: 183 LQDLEFSKESKNSYSAEYLDDVLSLTKL-----SDYVKISFGNQKPLQLFFNMEGG---- 233

Query: 371 DNKVNAFYVLMPM 383
                  Y+L P 
Sbjct: 234 ---GKVTYLLAPK 243


>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding
           clamp, DNA processing, FEN1, PIP- BOX, replication;
           1.88A {Homo sapiens} (A:)
          Length = 261

 Score =  125 bits (315), Expect = 8e-30
 Identities = 24/263 (9%), Positives = 75/263 (28%), Gaps = 33/263 (12%)

Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193
           LV+ +      E ++  +N   + I+   + L   + D   +++ ++ + +      +  
Sbjct: 6   LVQGSILKKVLEALKDLINEACWDISSSGVNL--QSMDSSHVSLVQLTLRSEGFDTYRCD 63

Query: 194 KMPSIIVPRKAVGEILRIL-SSKDSSVKVSLSESRIHLNIESLSMSV-----RLIDGEFP 247
           +  ++ V   ++ +IL+   +    +++   +   + L  E+ +          +     
Sbjct: 64  RNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDV 123

Query: 248 NYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAV-------KLSLSSDKLCMTVD 300
               +        +++      +    +S +    + +          S       + + 
Sbjct: 124 EQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLS 183

Query: 301 NPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIR 360
                   E         P+ + F  +YL            +   V   + +    V   
Sbjct: 184 QTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATP----LSSTVTLSMSADVPLVVEY 239

Query: 361 GKDKDSKNNKDNKVNAFYVLMPM 383
                         +  Y L P 
Sbjct: 240 KIADMG--------HLKYYLAPK 254


>1vpk_A DNA polymerase III, beta subunit; TM0262, structural
           genomics, joint center for structural genomics, JCSG,
           protein structure initiative; HET: DNA; 2.00A
           {Thermotoga maritima MSB8} (A:1-143,A:208-255)
          Length = 191

 Score =  108 bits (272), Expect = 1e-24
 Identities = 31/141 (21%), Positives = 61/141 (43%), Gaps = 5/141 (3%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
           MK+TV   ++ + +  A + + +K+  P+    L +  DG   I A+  E  +   + A+
Sbjct: 13  MKVTVTTLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAA 72

Query: 61  -VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
            +       V   ++  +V+ L D        E +    + IS G + F + + P  EFP
Sbjct: 73  EISGEARFVVPGDVIQKMVKVLPDE-ITELSLEGD---ALVISSGSTVFRITTMPADEFP 128

Query: 120 STKEEEYVYSFELASSVLKNL 140
                E   +FE+ +  +K +
Sbjct: 129 EITPAESGITFEVDTKSMKEV 149



 Score = 32.5 bits (74), Expect = 0.10
 Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 189 VAQIAKMPSIIVPRKAVGEILRILSSKDSS-VKVSLSESRIHLNIESLSMSVRLIDGEFP 247
           +       +  V  K++ E+  +L +     + V     R+ L+   +   +R++D EFP
Sbjct: 130 ITPAESGITFEVDTKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMRVVDAEFP 189

Query: 248 NY 249
           +Y
Sbjct: 190 DY 191


>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding
           clamp, DNA replication, rational drug design, antibiotic
           target, transferase; HET: DNA 322; 1.64A {Escherichia
           coli} (A:1-131,A:198-244)
          Length = 178

 Score =  107 bits (269), Expect = 3e-24
 Identities = 41/138 (29%), Positives = 68/138 (49%), Gaps = 4/138 (2%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
           MK TVER  +L+ L      +  + T+P+  ++LLQ  DG L +  +  E+E+   +   
Sbjct: 1   MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV 60

Query: 61  VDVC-GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
                G+ TV A   +DI R L +GA+I+   E E    + +  G S F L + P ++FP
Sbjct: 61  QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGE---RMLVRSGRSRFSLSTLPAADFP 117

Query: 120 STKEEEYVYSFELASSVL 137
           +  + +    F L   V+
Sbjct: 118 NLDDWQSEVEFTLPKGVI 135



 Score = 53.3 bits (128), Expect = 6e-08
 Identities = 14/47 (29%), Positives = 28/47 (59%)

Query: 203 KAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNY 249
           K V E++R+L   D+ ++V +  + I  ++     + +L+DG FP+Y
Sbjct: 132 KGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDY 178


>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp,
           replication, transferase; HET: DNA; 2.00A {Streptococcus
           pyogenes} PDB: 2awa_A* (A:1-139,A:205-252)
          Length = 187

 Score =  101 bits (253), Expect = 1e-22
 Identities = 32/149 (21%), Positives = 59/149 (39%), Gaps = 12/149 (8%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
           ++ ++ R+  +  L    R I  KN IP+   + ++     + +  S  +I I   IP S
Sbjct: 2   IQFSINRTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPVS 61

Query: 61  VDVC-------GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSF 113
            +         G+I + A    +I+  L D +      E      V ++ G S   L+  
Sbjct: 62  NENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQ---VVLTSGKSEITLKGK 118

Query: 114 PESEFPSTKEEEYVYSFELASSVLKNLVE 142
              ++P  +E        L +S  K+L E
Sbjct: 119 DVDQYPRLQEVSTENPLILKTS--KSLRE 145



 Score = 44.8 bits (106), Expect = 2e-05
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 198 IIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFP 247
           I+   K++ E   + +    +V+V  S S+I    E +S   RL++G +P
Sbjct: 136 ILKTSKSLREFSAVFTDDIETVEVFFSPSQILFRSEHISFYTRLLEGNYP 185


>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA
           binding clamp, DNA damage, DNA repair, exonuclease,
           hydrolase, nuclease, nucleus, phosphoprotein; 2.90A
           {Homo sapiens} (A:)
          Length = 296

 Score = 94.5 bits (234), Expect = 2e-20
 Identities = 32/268 (11%), Positives = 69/268 (25%), Gaps = 41/268 (15%)

Query: 144 THFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI----------A 193
                A   +    + ++    E+   L     +  R A A                   
Sbjct: 11  KVLGKAVHSLSRIGDELYLEPLED--GLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQ 68

Query: 194 KMPSIIVPRKAVGEILRILSSKDSSV-----KVSLSESRIHLNIESLSMSVRLIDGEFPN 248
            +    +  K+   + R L+  + +V      ++   SR+ + +       +  +  F +
Sbjct: 69  DLLRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNLSFQD 128

Query: 249 YQNVIP----CSNDKELRVNCTNLRQAVDRVSIMS-----SVRIQAVKLSLSSD----KL 295
            +++       S    LR     L +AV   S         +      +  S        
Sbjct: 129 CESLQAVFDPASCPHMLRAPARVLGEAVLPFSPALAEVTLGIGRGRRVILRSYHEEEADS 188

Query: 296 CMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNS 355
                  +M    E       +  + I F  K    ++    S    +  +    D+   
Sbjct: 189 TAKAMVTEMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAES---ANLNLSIHFDAPGR 245

Query: 356 SVFIRGKDKDSKNNKDNKVNAFYVLMPM 383
                 KD              +VL  +
Sbjct: 246 PAIFTIKDSLLD--------GHFVLATL 265


>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding
           clamp, DNA replication, rational drug design, antibiotic
           target, transferase; HET: DNA 322; 1.64A {Escherichia
           coli} (A:132-197,A:245-260,A:333-366)
          Length = 116

 Score = 80.0 bits (197), Expect = 4e-16
 Identities = 36/95 (37%), Positives = 55/95 (57%), Gaps = 6/95 (6%)

Query: 135 SVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAK 194
           + +K L+E T F+MA +++RYYLNG+ F    E+L+   VATDGHRLAV  + I   +  
Sbjct: 2   ATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRT--VATDGHRLAVCSMPIGQSLPS 59

Query: 195 MPSIIVPRKAVGEILRILSSKDSS---VKVSLSES 226
             S+IVPR+ V         +      V++ L++S
Sbjct: 60  H-SVIVPRRRVLPKNPDKHLEAGCCENVRMMLTDS 93



 Score = 40.3 bits (94), Expect = 4e-04
 Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 9/45 (20%)

Query: 341 VVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
              + V   L  S SSV I               +A YV+MPMR+
Sbjct: 81  GCCENVRMMLTDSVSSVQIEDAASQ---------SAAYVVMPMRL 116


>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding
           clamp, DNA replication, rational drug design, antibiotic
           target, transferase; HET: DNA 322; 1.64A {Escherichia
           coli} (A:261-332)
          Length = 72

 Score = 70.4 bits (173), Expect = 4e-13
 Identities = 23/69 (33%), Positives = 47/69 (68%)

Query: 268 LRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYK 327
           L+QA  R +I+S+ + + V+L +S ++L +T +NP+  +A E ++V Y+   M+I FN  
Sbjct: 3   LKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVS 62

Query: 328 YLLEIIDNI 336
           Y+L++++ +
Sbjct: 63  YVLDVLNAL 71


>2wan_A Pullulanase; hydrolase, glycoside hydrolase, polysaccharide,
           amylase, starch, carbohydrate; 1.65A {Bacillus
           acidopullulyticus} (A:1-162,A:262-310)
          Length = 211

 Score = 26.9 bits (59), Expect = 4.0
 Identities = 11/49 (22%), Positives = 14/49 (28%), Gaps = 5/49 (10%)

Query: 77  IVRKLQDGAQ---ISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTK 122
           IVRK     +        +   G EV I  GD   Y          +  
Sbjct: 65  IVRKNDWSEKNTPNDLHIDLAKGHEVWIVQGDPTIYYN--LSDAQAAAI 111


>3df6_A ORF99; archaeal virus, extremophiles, protein fold,
           lipothrixviridae, viral protein, unknown function; 2.05A
           {Acidianus filamentous virus 1} PDB: 3djw_A (A:)
          Length = 99

 Score = 25.8 bits (56), Expect = 9.4
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 4/52 (7%)

Query: 335 NISSDEVVDDEVVFRLDSSNSS----VFIRGKDKDSKNNKDNKVNAFYVLMP 382
           N + DE+  +E++ + DSSNS+    +FI     D+  N   K+   YV  P
Sbjct: 30  NTTLDELEFEELIGKPDSSNSAENNGIFIDEYSYDASENAXKKLFVEYVRQP 81


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.318    0.134    0.374 

Gapped
Lambda     K      H
   0.267   0.0609    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,782,263
Number of extensions: 122342
Number of successful extensions: 381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 315
Number of HSP's successfully gapped: 42
Length of query: 385
Length of database: 4,956,049
Length adjustment: 90
Effective length of query: 295
Effective length of database: 1,913,599
Effective search space: 564511705
Effective search space used: 564511705
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.2 bits)