RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780834|ref|YP_003065247.1| DNA primase [Candidatus Liberibacter asiaticus str. psy62] (648 letters) >2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Length = 407 Score = 219 bits (559), Expect = 1e-57 Identities = 138/428 (32%), Positives = 204/428 (47%), Gaps = 37/428 (8%) Query: 6 DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF 65 I +L I I ++I +Y++ ++ +N Y CPFH + TPSF+ + SK + CF Sbjct: 5 SDIDELRREIDIVDVISEYLNLEKVGSN-----YRTNCPFHPDDTPSFYVSPSKQIFKCF 59 Query: 66 SCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVAT 125 C V GD + F+S S+ E+ LA G L + ++K + ++ Sbjct: 60 GCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYV------ALDRVC 113 Query: 126 DFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE 185 DF+ SL R+ Y+ RGID F LGYAP S ++ L++ E + Sbjct: 114 DFYRESLLKNREAS--EYVKSRGIDPKVARKFDLGYAPSSEALVK-VLKENDLLEAYLET 170 Query: 186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKG 245 LL D F R++ PI+ RG+VI FGGR + + +S KY+NSP++ +F KG Sbjct: 171 KNLLSPTKGV--YRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKG 228 Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305 +NL+ + A Y F ILVEGY D+L L G++NVV+ LGTALT+ Sbjct: 229 ENLFGLYEAKEY----------IKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQN 278 Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365 Q LL K + ++ + +DGDD G +A AI L G V V L G DPD FI+ Sbjct: 279 QANLLSKFTKKVYILYDGDDAGRKAMKSAIP---LLLSAGVEVYPVYLPEGYDPDEFIKE 335 Query: 366 YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYS 425 +GK +LI S L + L K EN T + R + I D R+ + Sbjct: 336 FGKEELRRLINSSGELFETLIKTARENLEEKTREFRYY--------LGFISDGVRRFALA 387 Query: 426 QAIRDRLQ 433 + + Sbjct: 388 SEFHTKYK 395 >1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Length = 338 Score = 210 bits (536), Expect = 6e-55 Identities = 110/321 (34%), Positives = 177/321 (55%), Gaps = 12/321 (3%) Query: 117 LIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQK 176 L +L++ F+ SL+ YL++RG+ I F +G+AP ++ + Sbjct: 21 LYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGN 80 Query: 177 GFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNS 236 + + +I+AG+L+ D SYDRFR R++FPIR RG+VI FGGR L ++ KYLNS Sbjct: 81 PENRQSLIDAGMLVTNDQG-RSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 138 Query: 237 PETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVS 296 PET +FHKG+ LY + + +++VEGYMDV++L Q G+ V+ Sbjct: 139 PETDIFHKGRQLYGLY----------EAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVA 188 Query: 297 SLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356 SLGT+ T ++LL++ + ++ C+DGD G AA++A++ L ++ G ++ F+ L G Sbjct: 189 SLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDG 248 Query: 357 EDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIK 416 EDPD+ +R GK AFE + +++PL L+ +TPD RA L I+ + Sbjct: 249 EDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP 308 Query: 417 DQKLRYYYSQAIRDRLQQLFQ 437 + LR Y Q + ++L L Sbjct: 309 GETLRIYLRQELGNKLGILDD 329 >1d0q_A DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus stearothermophilus} SCOP: g.41.3.2 Length = 103 Score = 92.7 bits (230), Expect = 2e-19 Identities = 39/102 (38%), Positives = 58/102 (56%), Gaps = 5/102 (4%) Query: 3 YPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFY 62 P + I+ + + I ++IG+YV R+ N Y+ CPFH EKTPSF + K + Sbjct: 5 IPEETIEAIRRGVDIVDVIGEYVQLKRQGRN-----YFGLCPFHGEKTPSFSVSPEKQIF 59 Query: 63 YCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVD 104 +CF C G+ +FL + G F+E+ +RLAA AGV L V + Sbjct: 60 HCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYE 101 >1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Length = 503 Score = 84.6 bits (208), Expect = 7e-17 Identities = 33/211 (15%), Positives = 67/211 (31%), Gaps = 40/211 (18%) Query: 171 EHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGES 230 L +G S+E +AG I + + R G +++ R K + Sbjct: 16 SALTARGISKETCQKAGYWIAKVDG-------VMYQVADYRDQNGNIVSQKVRDKDK--N 66 Query: 231 VKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG 290 K S K L+ N I++ EG +D+L++ + Sbjct: 67 FKTTGSH------KSDALFGKHLW--------------NGGKKIVVTEGEIDMLTVMELQ 106 Query: 291 VQNVVSSLGTALTEYQLRLLWKLSP------RIVLCFDGDDPGLRAAYKAIDLVLCHLIP 344 + +I+L FD D+ G +A +A ++P Sbjct: 107 DCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEA-----AQVLP 161 Query: 345 GNRVNFVLLSRGEDPDSFIRCYGKTAFEKLI 375 +V +L + + + + + E++ Sbjct: 162 AGKVRVAVLPCKDANECHLNGHDREIMEQVW 192 >1t6t_1 Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} SCOP: c.136.1.1 Length = 118 Score = 80.1 bits (197), Expect = 1e-15 Identities = 29/129 (22%), Positives = 53/129 (41%), Gaps = 19/129 (14%) Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305 K N K++++ S +ILVEG D +L + ++NV+ G + Sbjct: 3 KEPRNLSEW--------IKELKKASREAVILVEGKNDKKALSKFSIKNVIDLSGKRYADV 54 Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365 L K +++L FD D G R K +L+ G V+ E+ +F++ Sbjct: 55 VDMLEGK-WEKVILLFDLDTHGERINQKMKELLSSQ---GFLVD-------ENFRNFLKK 103 Query: 366 YGKTAFEKL 374 + E++ Sbjct: 104 WNIIHIEEI 112 >2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Length = 119 Score = 66.5 bits (162), Expect = 2e-11 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 3/68 (4%) Query: 274 IILVEGYMDVLSLCQAGVQNVVSSL-GTALTEYQLRLLWKLS--PRIVLCFDGDDPGLRA 330 +I+VEG D + + VV +++ +L L + L D D+ G + Sbjct: 7 VIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLLADADEAGEKL 66 Query: 331 AYKAIDLV 338 + + Sbjct: 67 RRQFRRMF 74 >1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Length = 255 Score = 64.2 bits (155), Expect = 8e-11 Identities = 36/340 (10%), Positives = 73/340 (21%), Gaps = 112/340 (32%) Query: 49 KTPSFHCNDSKGF-------YYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLP 101 P +C S G +C+ C Sbjct: 14 HIPCDNCGSSDGNSLFSDGHTFCYVCEKWTA----------------------------- 44 Query: 102 VVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGY 161 ++ + R ++ + L RGI + Sbjct: 45 ------GNEDTKERASKRKPSGGKPGTYNVWNFGESNGRYSALTARGISKETCQKAGYWI 98 Query: 162 APDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFG 221 + + R G +++ Sbjct: 99 ------------------------------------AKVDGVMYQVADYRDQNGNIVSQK 122 Query: 222 GRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYM 281 R K K+ F L K I++ EG + Sbjct: 123 VRDKDK----------NFKTTGSHKSDALFGKHLWNGGK------------KIVVTEGEI 160 Query: 282 DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSP------RIVLCFDGDDPGLRAAYKAI 335 D+L++ + + +I+L FD D+ G +A +A Sbjct: 161 DMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAA 220 Query: 336 DLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLI 375 ++P +V +L +D + + + Sbjct: 221 Q-----VLPAGKVRVAVLP-CKDANECHLNGHDREIMEQV 254 >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 = 53.0 bits (127), Expect = 2e-07 Identities = 107/598 (17%), Positives = 180/598 (30%), Gaps = 218/598 (36%) Query: 121 IEVATD-FFHHS-LKNARDKRLHYYLDERGID---SHAIEM---FKLGY-----APDSRY 167 + V T FF S L+ +K L + D + E+ F LGY P Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF-LGYVSSLVEPSKVG 78 Query: 168 SLREHLRQ--KGFSEEKIIE--------AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQV 217 + L F E +E A LL + D + LI ++ Sbjct: 79 QFDQVLNLCLTEF-ENCYLEGNDIHALAAKLLQENDTTLVK----TKELI---KN----- 125 Query: 218 IAFGGRTLSKGESVKYLNSPETILFH---KGK-NLYNFFG----ALNYLQ---------K 260 R ++K K + LF +G L FG +Y + Sbjct: 126 -YITARIMAKRPFDK---KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH 181 Query: 261 SIRKD-VRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSL----GTALTEYQLRLLWKLSP 315 + D ++ ++ + L+ +D + G+ N++ L T +Y L LS Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGL-NILEWLENPSNTPDKDY----L--LSI 234 Query: 316 RIVLCFDGDDP--GLRAAYKAIDL----VLCHLI---PGN-RVNF-------------VL 352 I P G+ I L V L+ PG R V Sbjct: 235 PISC------PLIGV------IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVA 282 Query: 353 LSRGEDPDSFIRCYGKTAFEKL--I-VESLPLVDMLWKRETENRSFNTPDERAELEIHLK 409 ++ + +SF + A L I V E + P + Sbjct: 283 IAETDSWESFFVS-VRKAITVLFFIGVRCY---------EAYPNTSLPPSILED------ 326 Query: 410 NCINHIKDQK---LRYYYSQAIRD-RLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQR 465 + + + L +I + +Q+ Q Y+ + N H P+ + Sbjct: 327 -SLENNEGVPSPML------SISNLTQEQV-QDYVNKT---------N-SHL----PAGK 364 Query: 466 LMQSSLVKGK----LSKKP-SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWS 520 ++ SLV G +S P SL L L P+ L +Q + I + +KL Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGL-DQ----SRIPFSE---RKL-- 414 Query: 521 FLFSDFVEQKYFLP--------------EEIHQRLCERGF-------------------- 546 F + FLP + I++ L + Sbjct: 415 ----KFSNR--FLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL 468 Query: 547 ----GELLKQLDRQV-RDAGLWSATTEAN---IVDVRQGYQQALALYKRFRLLSRQKE 596 G + +++ + R W TT+ I+D G L + L R K+ Sbjct: 469 RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGV-----LTHRNKD 521 Score = 50.7 bits (121), Expect = 1e-06 Identities = 76/499 (15%), Positives = 130/499 (26%), Gaps = 208/499 (41%) Query: 5 RDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYC 64 +++ IH + L+ + T + Y Sbjct: 93 NCYLEGNDIHALAAKLLQ-----ENDTTLVKTKE-LIKN------------------YI- 127 Query: 65 FSCHVKGDHLSFL--SALLGCSFIESVQ----RLAAIAG------------VPL-----P 101 + + SAL +V +L AI G L Sbjct: 128 TARIMAKRPFDKKSNSALF-----RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV 182 Query: 102 VVDPKIEKKEKIQTDLIRLIEVATDFFHHS------LKNARDKR---------------- 139 +V I+ + ++LIR A F L+N Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN-PSNTPDKDYLLSIPISCPLI 241 Query: 140 -----LHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLR-QKGFSEEKIIEAGLLIDGD 193 HY + + LG+ P LR +L+ G S + ++ A + Sbjct: 242 GVIQLAHYV-----VTAKL-----LGFTPG---ELRSYLKGATGHS-QGLVTAVAI---- 283 Query: 194 NSATSYDRF-RN-----RLIFPIRSSRGQVIAFGGRTLS---------KGE-------SV 231 S++ F + ++F I R A+ +L E S+ Sbjct: 284 AETDSWESFFVSVRKAITVLFFI-GVRCY-EAYPNTSLPPSILEDSLENNEGVPSPMLSI 341 Query: 232 KYLNSPETILFHKGKNLYNFFGALN-YLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG 290 L + + ++ N +L ++ I LV G Sbjct: 342 SNLTQEQ---------VQDYVNKTNSHLPAG-----KQVE---ISLVNGA---------- 374 Query: 291 VQN-VVSSLGTALTEYQL-RLLWKLS----------------PRIVLCFDGDD------- 325 +N VVS G + Y L L K + F Sbjct: 375 -KNLVVS--GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF----LPVASPF 427 Query: 326 --PGLRAAYKAI--DLVLCHL-IPGNRVNF-VLLSR-GEDPDSFIRCYGKTAFEKLIVES 378 L A I DLV ++ + V + G D +R + I E Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSGS-----ISER 478 Query: 379 LPLVDML------WKRETE 391 +VD + W+ T+ Sbjct: 479 --IVDCIIRLPVKWETTTQ 495 Score = 49.9 bits (119), Expect = 2e-06 Identities = 84/473 (17%), Positives = 130/473 (27%), Gaps = 218/473 (46%) Query: 3 YPRDFIKDL----------LIHIP--ISNLIGQYVD---W--DRRKTNAVKGDYWACCPF 45 Y + DL LI + Q ++ W + T DY P Sbjct: 180 Y-HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK--DYLLSIPI 236 Query: 46 HDEKTPSF---------HCNDSKGFYYCFSCHVKGDH----LSFLSALLGCSFIESVQRL 92 S H Y + + G S+L G S Q L Sbjct: 237 ------SCPLIGVIQLAH--------YVVTAKLLGFTPGELRSYLKGATGHS-----QGL 277 Query: 93 ---AAIA----------------------GV------P---LP--VVDPKIEKKEKIQTD 116 AIA GV P LP +++ +E E + + Sbjct: 278 VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP 337 Query: 117 LIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSH-------AIEM------FKLGYAP 163 ++ S+ N +++ Y+++ +SH I + + P Sbjct: 338 ML------------SISNLTQEQVQDYVNK--TNSHLPAGKQVEISLVNGAKNLVVSGPP 383 Query: 164 DSRYSLREHLRQKGFSEEKI-IEAGLLIDGDNSATSYD----RFRNRLIFPIRSSRGQVI 218 S Y L LR K +GL D S + +F NR + P+ Sbjct: 384 QSLYGLNLTLR-------KAKAPSGL----DQSRIPFSERKLKFSNRFL-PV-------- 423 Query: 219 AFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKS---IRKDVRRNS----- 270 SP FH + L + I KD+ +N+ Sbjct: 424 ----------------ASP----FHS-----------HLLVPASDLINKDLVKNNVSFNA 452 Query: 271 SSFIILVEGY-----MDVLSLCQAGVQNVVSSLGTALTEYQLRLLW----KLSPRIVLCF 321 I V Y D+ L ++ + + L + W + +L F Sbjct: 453 KDIQIPV--YDTFDGSDLRVLS----GSISERIVDCIIR--LPVKWETTTQFKATHILDF 504 Query: 322 D-GDDPGLRAAYKAIDLVLCHLIP---GNRVNFVL---LSRGEDPDSFIRCYG 367 G GL VL H G RV ++ L D D YG Sbjct: 505 GPGGASGLG--------VLTHRNKDGTGVRV--IVAGTLDINPDDD-----YG 542 Score = 28.4 bits (63), Expect = 5.0 Identities = 32/179 (17%), Positives = 51/179 (28%), Gaps = 76/179 (42%) Query: 496 AILQEQYQELADIRYDNNELQ---KLW-SFLFSDFV-----------------------E 528 IL E + A ++E +L FL +V E Sbjct: 39 KILPEPTEGFAA----DDEPTTPAELVGKFL--GYVSSLVEPSKVGQFDQVLNLCLTEFE 92 Query: 529 QKYFLPEEIH---QRLCERGFGELLKQLD----------------RQVRDAGLWSATTE- 568 Y +IH +L + L+K + + ++ L+ A E Sbjct: 93 NCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG 152 Query: 569 -ANIVDV--RQG----YQQALA-LY---------------KRFRLLSRQKEEIEKQIAQ 604 A +V + QG Y + L LY + L R + EK Q Sbjct: 153 NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ 211 >3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Score = 35.3 bits (81), Expect = 0.046 Identities = 10/33 (30%), Positives = 11/33 (33%), Gaps = 1/33 (3%) Query: 43 CPFHDEKTPSFHCNDSKGFYYCFSC-HVKGDHL 74 CP P S+G C C V D L Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKL 56 >3dwc_A TCMCP-1, metallocarboxypeptidase; cowrin family of metallocarboxypeptidases, hydrolase; 2.10A {Trypanosoma cruzi} Length = 505 Score = 31.2 bits (70), Expect = 0.68 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 3/61 (4%) Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587 L +H + L+++ ++ V D AN+ ++R+ ++ L + Sbjct: 44 AAMAELQLHMHDTITAPKIRALIEEAEKSVGD---LEKLQRANLREMRRAWELENLLPEE 100 Query: 588 F 588 F Sbjct: 101 F 101 >3hoa_A Thermostable carboxypeptidase 1; proline-rich loop, hydrolase; 2.10A {Thermus thermophilus HB27} PDB: 1wgz_A Length = 509 Score = 30.8 bits (69), Expect = 0.94 Identities = 20/114 (17%), Positives = 40/114 (35%), Gaps = 6/114 (5%) Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALA---- 583 Q L +HQR+ + GE L++++ S N+ + RQ Y++A A Sbjct: 45 RQMAALARLLHQRMTDPRIGEWLEKVEGSPLVQDPLSDAA-VNVREWRQAYERARAIPER 103 Query: 584 LYKRFRLLSRQKEEI-EKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEA 636 L + E E+ + +G + ++ E + + Sbjct: 104 LAVELAQAESEAESFWEEARPRDDWRGFLPYLKRVYALTKEKAEVLFALPPAPG 157 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 30.7 bits (68), Expect = 1.1 Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 10/34 (29%) Query: 304 EYQ-LRLLWKLSPRIVLCFDGDD--PGLRAAYKA 334 E Q L+ KL + L + DD P L A KA Sbjct: 18 EKQALK---KLQASLKL-Y-ADDSAPAL--AIKA 44 >1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus} Length = 501 Score = 29.0 bits (64), Expect = 3.1 Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 24/112 (21%) Query: 534 PEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSR 593 PE+ + L R K L I+ +Q+ L ++ R L Sbjct: 50 PEDAARALDLRKGELRSKDLPG---------------IIST---WQELRQLREQIRSLEE 91 Query: 594 QKEEIEKQIAQVTAKGEAEKTAI------LISILHEVHIQIHQIESQEAMIE 639 +KE + + + + + + L + E+ Q+ + +EA +E Sbjct: 92 EKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLE 143 >1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1 Length = 245 Score = 28.8 bits (63), Expect = 3.5 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 9/78 (11%) Query: 446 YGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPA---ILQEQY 502 +G W A+ R + GP R++Q++L + K L A L + A ++QE Y Sbjct: 2 HGEQWNTTAKVRPKNGPPYRVLQANLQRKK------LATAELAIEAATRKAAIALIQEPY 55 Query: 503 QELADIRYDNNELQKLWS 520 A ++ S Sbjct: 56 VGGAKSMKGFRGVRVFQS 73 >3hrp_A Uncharacterized protein; NP_812590.1, structural genomics protein of unknown function, structural genomics; HET: MSE; 1.70A {Bacteroides thetaiotaomicron vpi-5482} Length = 409 Score = 28.8 bits (64), Expect = 3.6 Identities = 11/68 (16%), Positives = 21/68 (30%), Gaps = 5/68 (7%) Query: 187 GLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE-----SVKYLNSPETIL 241 G+ +D D + D F+ + + G V G+ + N P I Sbjct: 327 GMTVDEDGNFYIVDGFKGYCLRKLDILDGYVSTVAGQVDVASQIDGTPLEATFNYPYDIC 386 Query: 242 FHKGKNLY 249 + + Sbjct: 387 YDGEGGYW 394 >1sjj_A Actinin; 3-helix bundle, calponin homology domain, calmodulin-like domain, actin binding protein, contractIle protein; 20.00A {Gallus gallus} SCOP: i.15.1.1 Length = 863 Score = 28.7 bits (63), Expect = 3.6 Identities = 28/244 (11%), Positives = 73/244 (29%), Gaps = 9/244 (3%) Query: 371 FEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRD 430 + + + P + + + + E++ QAI Sbjct: 487 YLEYAKRAAPFNNWMEGAMEDLQDTFIVHTIEEIQGLTTAHEQFKATLPDADKERQAILG 546 Query: 431 RLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLT 490 ++ + T H + + + + + + A Sbjct: 547 IHNEVSKIVQTYHVNMAG--TNPYTTITPQEINGKWEHVRQLVPRRDQALMEEHARQQQN 604 Query: 491 LINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELL 550 + I+ E+ ++ + +Q L + + + + L Sbjct: 605 ERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLEDQLNHLRQYEKSIVNYKPKIDQL 664 Query: 551 KQLDRQVRDAG-LWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKG 609 + +Q+++A + T + +R G++Q L ++R E+E QI AKG Sbjct: 665 EGDHQQIQEALIFDNKHTNYTMEHIRVGWEQLLTT------IARTINEVENQILTRDAKG 718 Query: 610 EAEK 613 +++ Sbjct: 719 ISQE 722 >1ka2_A M32 carboxypeptidase; hexxh motif, M32 family, metallopeptidase; 2.20A {Pyrococcus furiosus} SCOP: d.92.1.5 PDB: 1k9x_A 1ka4_A Length = 499 Score = 28.8 bits (64), Expect = 3.9 Identities = 9/83 (10%), Positives = 26/83 (31%), Gaps = 14/83 (16%) Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587 + L H+ L F L+++ + + + + + + A A Sbjct: 48 VAQGELSVLSHELLLHPEFVNLVEKA----KGLENLNEYERGIVRVLDRSIRIARAFP-- 101 Query: 588 FRLLSRQKEEIEKQIAQVTAKGE 610 E +++++ T+ Sbjct: 102 --------PEFIREVSETTSLAT 116 >3hq2_A Bacillus subtilis M32 carboxypeptidase; hydrolase, metal-binding, metalloprotease, protease, zinc; 2.90A {Bacillus subtilis} Length = 501 Score = 28.8 bits (64), Expect = 3.9 Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 3/61 (4%) Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587 E L +I EL+ L + D + + ++ Y++ + + Sbjct: 45 ESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTK---KAVELAKKEYEENKKIPEA 101 Query: 588 F 588 Sbjct: 102 E 102 >2gz4_A Hypothetical protein ATU1052; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.50A {Agrobacterium tumefaciens str} SCOP: a.211.1.1 Length = 207 Score = 28.4 bits (63), Expect = 5.5 Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 13/89 (14%) Query: 530 KYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDV--------RQGYQQA 581 + H + E F + L E I D+ GY+ Sbjct: 51 DHAFTVAQHCLIVETIFCRMCPGATPDEMQMALLHDAPEYVIGDMISPFKSVVGGGYKTV 110 Query: 582 -----LALYKRFRLLSRQKEEIEKQIAQV 605 A++ RF L E++ +I + Sbjct: 111 EKRLEAAVHLRFGLPPHASRELKDRIKKA 139 >3d5l_A Regulatory protein RECX; PSI-II, NYSGXRC, DNA repair, 10123K, structural genomics, protein structure initiative; 2.35A {Lactobacillus reuteri 100-23} Length = 221 Score = 28.3 bits (63), Expect = 6.3 Identities = 22/123 (17%), Positives = 34/123 (27%), Gaps = 40/123 (32%) Query: 106 KIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHY-------------YLDERGIDSH 152 ++ K ++ I I A A + L Y L E Sbjct: 39 RLMKGTELDEKQIAAIATADQQ-----AKAYSRMLDYLSYQMRTESDIVKKLKEIDTPEE 93 Query: 153 AIE-----MFKLGYAPDSRYS-----------------LREHLRQKGFSEEKIIEAGLLI 190 +E + D Y+ +R+HLRQKG E I +A Sbjct: 94 FVEPILKKLRGQQLIDDHAYAASYVRTMINTDLKGPGIIRQHLRQKGIGESDIDDALTQF 153 Query: 191 DGD 193 + Sbjct: 154 TPE 156 >3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83 Score = 28.1 bits (62), Expect = 6.5 Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 1/38 (2%) Query: 38 DYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLS 75 W D+ + YC++C KG H Sbjct: 23 SIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKG-HFG 59 >2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A Length = 455 Score = 28.2 bits (62), Expect = 6.8 Identities = 17/112 (15%), Positives = 39/112 (34%), Gaps = 34/112 (30%) Query: 534 PEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSR 593 PE + L +RG E +K +D + L L +R + Sbjct: 11 PELVKNDLIKRGELEKVKWVD-------------------------EILKLDTEWRTKLK 45 Query: 594 QKEEIE-------KQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMI 638 + + +I + + + E L++ E+ +I ++E++ + Sbjct: 46 EINRLRHERNKIAVEIGK--RRKKGEPVDELLAKSREIVKRIGELENEVEEL 95 >1pj3_A NAD-dependent malic enzyme, mitochondrial; oxidative decarboxylase, oxidoreductase; HET: NAD; 2.10A {Homo sapiens} SCOP: c.2.1.7 c.58.1.3 PDB: 1pj2_A* 1do8_A* 1pj4_A* 1qr6_A* 1efl_A* 1pjl_A* 1efk_A* 1gz4_A* 1gz3_A* Length = 564 Score = 27.9 bits (62), Expect = 7.2 Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 16/63 (25%) Query: 397 TPDERAELEIH--LKNCINHIKDQKLRYY--------------YSQAIRDRLQQLFQKYI 440 T ER L + L I Q LR++ Y I++R ++LF + + Sbjct: 21 TLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRIL 80 Query: 441 TEH 443 + Sbjct: 81 QDD 83 >3i4r_B Nuclear pore complex protein NUP133; protein transport,structural protein, kinetochore, mRNA transport, nucleus, phosphoprotein, translocation; 3.53A {Homo sapiens} Length = 644 Score = 27.5 bits (61), Expect = 9.6 Identities = 16/131 (12%), Positives = 42/131 (32%), Gaps = 16/131 (12%) Query: 421 RYYYSQAIRDRLQQLFQ-------KYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVK 473 R+Y + R +L ++ H W ++ + L+ + ++ Sbjct: 391 RWYLEKGKRGKLLSQPISQHGQLANFLQAHEHLS--WLHEINSQELEKAHATLLGLANME 448 Query: 474 GKL--SKKPSLREAAL-LLTLINHPAILQEQY----QELADIRYDNNELQKLWSFLFSDF 526 + KK L + L L +LQE+ ++ + + ++L + + Sbjct: 449 TRYFAKKKTLLGLSKLAALASDFSEDMLQEKIEEMAEQERFLLHQETLPEQLLAEKQLNL 508 Query: 527 VEQKYFLPEEI 537 ++ Sbjct: 509 SAMPVLTAPQL 519 >3e3v_A Regulatory protein RECX; PSI-II, NYSGXRC, structural genomics, protein structure initiative; 2.04A {Lactobacillus salivarius UCC118} Length = 177 Score = 27.6 bits (61), Expect = 9.7 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 7/63 (11%) Query: 159 LGYAPDSRYSLREHLRQKGFSEEKI-------IEAGLLIDGDNSATSYDRFRNRLIFPIR 211 L Y +R + + LR E+ I I+ L+ D + + + N + Sbjct: 28 LSYQLRTRKEVEDKLRSLDIHEDYISEIINKLIDLDLINDKNYAESYVRTMMNTSDKGPK 87 Query: 212 SSR 214 + Sbjct: 88 VIK 90 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 0.322 0.139 0.413 Gapped Lambda K H 0.267 0.0522 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 5,712,998 Number of extensions: 273789 Number of successful extensions: 1143 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1121 Number of HSP's successfully gapped: 47 Length of query: 648 Length of database: 5,693,230 Length adjustment: 98 Effective length of query: 550 Effective length of database: 3,317,318 Effective search space: 1824524900 Effective search space used: 1824524900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 60 (27.4 bits)