RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780454|ref|YP_003064867.1| DNA polymerase III subunit beta [Candidatus Liberibacter asiaticus str. psy62] (385 letters) >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} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A* Length = 366 Score = 216 bits (550), Expect = 8e-57 Identities = 128/386 (33%), Positives = 212/386 (54%), Gaps = 21/386 (5%) Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-A 59 MK TVER +L+ L + + T+P+ ++LLQ DG L + + E+E+ + Sbjct: 1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV 60 Query: 60 SVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119 G+ TV A +DI R L +GA+I+ E E + + G S F L + P ++FP Sbjct: 61 QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGE---RMLVRSGRSRFSLSTLPAADFP 117 Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179 + + + F L + +K L+E T F+MA +++RYYLNG+ F E+L+ A TDGH Sbjct: 118 NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVA--TDGH 175 Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV 239 RLAV + I + S+IVPRK V E++R+L D+ ++V + + I ++ + Sbjct: 176 RLAVCSMPIGQSL-PSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS 234 Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299 +L+DG FP+Y+ V+P + DK L C L+QA R +I+S+ + + V+L +S ++L +T Sbjct: 235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITA 294 Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359 +NP+ +A E ++V Y+ M+I FN Y+L++++ + + V L S SSV I Sbjct: 295 NNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQI 349 Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMRI 385 +A YV+MPMR+ Sbjct: 350 EDAASQ---------SAAYVVMPMRL 366 >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} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 Length = 378 Score = 198 bits (504), Expect = 2e-51 Identities = 94/387 (24%), Positives = 186/387 (48%), Gaps = 24/387 (6%) 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 + + L IS G + F + + P EFP Sbjct: 73 EISGEARFVVPGDVIQKMVKVLPDEITELSLEGDAL----VISSGSTVFRITTMPADEFP 128 Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179 E +FE+ +S+L+ +VE+ FA A +E LNG+F+ +++ L+L A +DG Sbjct: 129 EITPAESGITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVA--SDGF 186 Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKV-SLSESRIHLNIESLSMS 238 RLA+AE I + S ++ K++ E+ +L + R+ L+ + Sbjct: 187 RLALAEEQIENEE--EASFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETV 244 Query: 239 VRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMT 298 +R++D EFP+Y+ VIP + ++ V+ LR+++ RV +++S ++VK + + + + Sbjct: 245 MRVVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLV 304 Query: 299 VDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVF 358 +PD G+ ++ + V + I FN K++ +++ +I + +E+ S S Sbjct: 305 SKSPDYGEVVDEVEVQKEGEDLVIAFNPKFIEDVLKHIET-----EEIEMNFVDSTSPCQ 359 Query: 359 IRGKDKDSKNNKDNKVNAFYVLMPMRI 385 I D Y++MP+R+ Sbjct: 360 INPLDIS---------GYLYIVMPIRL 377 >2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A* Length = 378 Score = 175 bits (443), Expect = 2e-44 Identities = 80/394 (20%), Positives = 166/394 (42%), Gaps = 27/394 (6%) Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60 ++ ++ R+ + L R I KN IP+ + ++ + + S +I I IP S Sbjct: 2 IQFSINRTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPVS 61 Query: 61 -------VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSF 113 + G+I + A +I+ L D + E ++ G S L+ Sbjct: 62 NENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVV---LTSGKSEITLKGK 118 Query: 114 PESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCA 173 ++P +E L + +LK+++ T FA + +E R L G+ ++ K Sbjct: 119 DVDQYPRLQEVSTENPLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNH--KDFK 176 Query: 174 VATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIE 233 + + + +++P K++ E + + +V+V S S+I E Sbjct: 177 AVATDSHRMSQRLITLDNTSADFMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSE 236 Query: 234 SLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSV-RIQAVKLSLSS 292 +S RL++G +P+ ++ + E+ N +LR A++R ++S+ + VKL ++ Sbjct: 237 HISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQ 296 Query: 293 DKLCMTVDNPDMGKAIESMN-VYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLD 351 + + V++P++GK E ++ V + + I FN YL+E + I S + V Sbjct: 297 NHISAHVNSPEVGKVNEDLDIVSQSGSDLTISFNPTYLIESLKAIKS-----ETVKIHFL 351 Query: 352 SSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385 S + D++ + ++ P+R Sbjct: 352 SPVRPFTLTPGDEEE--------SFIQLITPVRT 377 >3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Length = 798 Score = 75.5 bits (186), Expect = 2e-14 Identities = 39/223 (17%), Positives = 85/223 (38%), Gaps = 23/223 (10%) Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193 E + F + + + + F E+ + A D R+ + ++I + Sbjct: 12 FEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAVDDSRVLLVSLEIGVEAFQEYRCD 69 Query: 194 KMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIHLNIES------LSMSVRLIDGEF 246 ++ + ++ +ILR ++ D+ ++ + I L E S++L+D + Sbjct: 70 HPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDA 129 Query: 247 PNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMS-SVRIQA----VKLSLSSD--KLCMTV 299 + + D L + + + V +S +S S+ I +K D + + Sbjct: 130 DFLK-IEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVII 188 Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVV 342 + E+ + P+D+ F KYLL+II S + V Sbjct: 189 KPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRV 231 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 48.4 bits (115), Expect = 3e-06 Identities = 66/409 (16%), Positives = 125/409 (30%), Gaps = 183/409 (44%) Query: 26 TIPVSCHVLLQANDGLLEI-------KASG--P-EIE-----ITG---------AIPASV 61 +IP+SC ++ G++++ K G P E+ TG AI A Sbjct: 233 SIPISCPLI-----GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAI-AET 286 Query: 62 DVCGSITVSAHLLYDIVRKLQDGA-QISFFKENELGTEVNISHGDSNFYLQSFPESEFPS 120 D S + VRK A + FF +G + +++P + Sbjct: 287 DSWES-------FFVSVRK----AITVLFF----IGVR---CY-------EAYPNT---- 317 Query: 121 TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHR 180 L S+L++ +E N E Sbjct: 318 ----------SLPPSILEDSLE---------------NN------E--------GVPSPM 338 Query: 181 LAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSS---KDSSVKVSLSESRIHLNI----E 233 L+++ ++ ++ V + + +S V++SL +L + + Sbjct: 339 LSIS--NL------------TQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ 384 Query: 234 SL-SMSVRL--------IDGEFPNYQNVIPCSNDKELRVNCTN-------------LRQA 271 SL +++ L +D Q+ IP S K + +N L A Sbjct: 385 SLYGLNLTLRKAKAPSGLD------QSRIPFSERK---LKFSNRFLPVASPFHSHLLVPA 435 Query: 272 VDRVSIMSSVRIQAVKLSLSSDKLCM----TVDNPDMGKAIESMNVYYNECPMDICFNYK 327 D + + + +S ++ + + T D D+ S Sbjct: 436 SDLI----NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGS----------------- 474 Query: 328 YLLE-IIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKD----SKNNKD 371 + E I+D I V E + +++ F G + NKD Sbjct: 475 -ISERIVDCIIR-LPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKD 521 Score = 38.4 bits (89), Expect = 0.003 Identities = 45/266 (16%), Positives = 83/266 (31%), Gaps = 83/266 (31%) Query: 65 GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEE 124 GS+ + SFF ++L + F + PE ++ Sbjct: 14 GSLEHVLLVPTA-----------SFFIASQLQEQ---------F-NKILPEPTEGFAADD 52 Query: 125 EYVYSFELASSVLK---NLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRL 181 E EL L +LVE + + + L F E L D H L Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT--EF---ENCY-LE--GNDIHAL 104 Query: 182 AVAEVDIVAQIAKMPSII-VPRKAVGEILR-----ILSSKDSSVKVSLSESRIHLNIESL 235 A AK+ E+++ + +K K S S +L Sbjct: 105 A----------AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS---------AL 145 Query: 236 SMSVRLIDGEFPNY-----QNVIPCSND--KELR-VNCT---NLRQAVDRVSIMSSVRIQ 284 +V +G Q ++D +ELR + T + D + + + Sbjct: 146 FRAVG--EGNAQLVAIFGGQG---NTDDYFEELRDLYQTYHVLVG---DLIKFSAETLSE 197 Query: 285 AVKLSLSSDKLC---MTV----DNPD 303 ++ +L ++K+ + + +NP Sbjct: 198 LIRTTLDAEKVFTQGLNILEWLENPS 223 Score = 30.7 bits (69), Expect = 0.57 Identities = 37/166 (22%), Positives = 73/166 (43%), Gaps = 23/166 (13%) Query: 41 LLEIKASGPEIEITGAIPASVDVCG-SITVSAHL--LYDIVRKLQDGAQISFFKENELGT 97 L+E KA+ +++ G IPA G S+ A L L D++ ++ ++ F++ + Sbjct: 1738 LME-KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM-SIESLVEVVFYR--GMTM 1793 Query: 98 EVNISH---GDSNFYLQSF-PESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEI 153 +V + G SN+ + + P S +E Y E LVE ++ + E Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV--ENQ 1851 Query: 154 RYYLNGIFFHINEEDLKLCAVATDG-HRLAVAEVDIVAQIAKMPSI 198 +Y G DL+ T+ + + + ++DI+ ++ K S+ Sbjct: 1852 QYVAAG--------DLRALDTVTNVLNFIKLQKIDII-ELQKSLSL 1888 >1v1p_B Exotoxin 1; virulence factor, antigen presenting cell, secreted protein, SET1, superantigen, OB-fold, {beta}-grAsp; 2.7A {Staphylococcus aureus} SCOP: b.40.2.2 d.15.6.1 PDB: 1v1o_A 1v1p_A 2qej_C* Length = 213 Score = 27.9 bits (62), Expect = 3.7 Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 8/74 (10%) Query: 306 KAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKD 365 I ++ YY+ + + + + V F N +F+ GKDK+ Sbjct: 23 HDIRDLHRYYSSESFE--------YSNVSGKVENYNGSNVVRFNPKDQNHQLFLLGKDKE 74 Query: 366 SKNNKDNKVNAFYV 379 N F V Sbjct: 75 QYKEGLQGQNVFVV 88 >3jrs_A PYL1, putative uncharacterized protein AT5G46790; plant hormone receptor, abscisic acid; HET: A8S; 2.05A {Arabidopsis thaliana} Length = 208 Score = 27.2 bits (60), Expect = 7.0 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 2/47 (4%) Query: 209 LRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFP--NYQNVI 253 R ++ + E L+ + + GE NY++V Sbjct: 102 TRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVT 148 >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} Length = 296 Score = 26.8 bits (59), Expect = 8.5 Identities = 24/184 (13%), Positives = 57/184 (30%), Gaps = 18/184 (9%) Query: 203 KAVGEILRILSSKDSSVKVSLSESRIHL----NIESLSMSVRLIDGEFPNYQNVIPCSND 258 K +G+ + LS + + E + L + S F YQ P + Sbjct: 11 KVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDL 70 Query: 259 KELRVNCTNLRQAVDRV-SIMSSVRIQAVKLSLSSDKLCMTVDNPDMGK--------AIE 309 ++ + + + +V + L+ S +L + + + E Sbjct: 71 LRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNLSFQDCE 130 Query: 310 SMNVYYN--ECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSK 367 S+ ++ CP + + L E + S EV + + ++++ Sbjct: 131 SLQAVFDPASCPHMLRAPARVLGEAVLPFSP---ALAEVTLGIGRGRRVILRSYHEEEAD 187 Query: 368 NNKD 371 + Sbjct: 188 STAK 191 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.318 0.134 0.374 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,192,172 Number of extensions: 146348 Number of successful extensions: 375 Number of sequences better than 10.0: 1 Number of HSP's gapped: 365 Number of HSP's successfully gapped: 15 Length of query: 385 Length of database: 5,693,230 Length adjustment: 94 Effective length of query: 291 Effective length of database: 3,414,294 Effective search space: 993559554 Effective search space used: 993559554 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: 58 (26.2 bits)