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)