RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= 537021.9.peg.410_1 (952 letters) >1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B* Length = 1180 Score = 163 bits (412), Expect = 2e-40 Identities = 129/873 (14%), Positives = 278/873 (31%), Gaps = 114/873 (13%) Query: 96 LKEKLKKSQDEFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAKKKNCVLDFEDLIIN 155 K + + + D+ + L + K++ L F+D++ Sbjct: 298 TKAGGETPRHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSR 357 Query: 156 TNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRT 215 + + + + I +IDE QDT Q+ + R + H Sbjct: 358 LDSA-LRSESGEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWH--------HQPETA 408 Query: 216 LFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADILTVVD 275 L +GD KQ+IY+F GA+ ++ + L ++RS ++ V+ Sbjct: 409 LLLIGDPKQAIYAFRGADIFTYMKARSEVHAH----------YTLDTNWRSAPGMVNSVN 458 Query: 276 KVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDS 335 K+FS ++A E ++ + + + P + W +S Sbjct: 459 KLFSQTDDAFMFREIPFIPVKSAGK----------NQALRFVFKGETQPAMKMWLMEGES 508 Query: 336 LPQESSASILARRIAYTISNMI-----GTDTIFSNGKKRVIQAKDILVLVRKRKDTPLIT 390 S +A+ A I + + G + + R ++A DI VLVR R++ + Sbjct: 509 CGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVRSRQEAAQVR 568 Query: 391 FLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCMLKSPLFNFSE 450 L+ V ++R + + L ++++ L + +++ E + + L + + + Sbjct: 569 DALTLLEIPS---VYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALATSMMGLNA 625 Query: 451 DDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPHDFFTLILGA 510 DI + H + V E + + + + + S + +L Sbjct: 626 LDIETLNNDEHAWDVVVEEFDGYRQ--------IWRKRGVMPMLRALMSARNIAENLLAT 677 Query: 511 KKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSANHN 570 G ++ I L + L +E L + I E + + + ++ + Sbjct: 678 AGGERRLTDI---LHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESDKH 734 Query: 571 EVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPSLNDDPGIPIWIPQSKSRNN 630 V+I+T+H +KGLE P+V+L + + +D + N Sbjct: 735 LVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAF--------YHDRHSFEAVLD-----LN 781 Query: 631 IVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII--CKHSNTSNEKKSNQRTWYDMVYDS 688 + + + E RLLYV +TR+ + +KK + + Sbjct: 782 AAPESVDLAEAERLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRL 841 Query: 689 FHNDERVKKIKLTNSINKDEWIAYEWSTHH-PENTPLEREETIKQLMDEQKIPKKLFSPI 747 E L I W T +N P + + ++ + + + Sbjct: 842 LQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNW 901 Query: 748 K-----------NDINEPYILNPSTIDTKGKTNLESLLSDNQTF----NRGLIIHKLLQV 792 + + I + + + +E F + G +H L + Sbjct: 902 RVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFED 961 Query: 793 I-FTLPEHKR-----------------------KNFITSYCTKNAKLWPAKEYKNLLLSI 828 + FT P + + + +N + + Sbjct: 962 LDFTQPVDPNWVREKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEM 1021 Query: 829 TRLLENPMMTTAMSCDSYSEVSVSGKINCPKKD-----IIISGRIDQISISQQNIFIFEY 883 L A D+ CP + ++ G ID + + ++ +Y Sbjct: 1022 EFYLPISEPLIASQLDTLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDY 1081 Query: 884 KTHHHVPQEIEHIPYTHIAQLSIYEKILKDSYP 916 K+ + + ++ YT A + + Y Sbjct: 1082 KS-NWLGEDSSA--YTQQA---MAAAMQAHRYD 1108 >1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B* Length = 724 Score = 146 bits (369), Expect = 2e-35 Identities = 125/601 (20%), Positives = 228/601 (37%), Gaps = 119/601 (19%) Query: 81 QKNIITQEINKKSPDLKE-KLKKSQDEFIKIRDRFNTYKMFKSTLASLT--LAKYLNAHY 137 Q +++ + +K+ D K+ + + ++ + F ++ + + Y Sbjct: 121 QLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEY 180 Query: 138 EEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIR 197 ++ +N LDF+DLI+ T L + + + + +I IDE QDT+ Q+ +++ Sbjct: 181 QQRLLRNHSLDFDDLIMTTIQLFDRVP---DVLHYYQYKFQYIHIDEYQDTNRAQYTLVK 237 Query: 198 SLTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSI 257 L E F + + AVGD QSIY + GA+ + +L +R + Sbjct: 238 KLAERF----------QNICAVGDADQSIYRWRGADIQNILSFER--------DYPNAKV 279 Query: 258 IELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQ 317 I L ++RST IL ++V I H +R + + E Sbjct: 280 ILLEQNYRSTKRILQAANEV-----------------IEHNVNRKPKRIWTENPEGKPIL 322 Query: 318 HDSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDIL 377 + N E A+ +A I + ++ + +D Sbjct: 323 YYEAMNEADE------------------AQFVAGRIREAV---------ERGERRYRDFA 355 Query: 378 VLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSF 437 VL R + ++ LK + +VG +F D IKD++A R I + +DDLS Sbjct: 356 VLYRTNAQSRVME--EMLLKANIPYQIVGGLKFY--DRKEIKDILAYLRVIANPDDDLSL 411 Query: 438 VCMLKSPLFNFSEDDIFKICTQ-RHETETVYEYIQKFANCGIS-----KFQHVIKYIHEL 491 + ++ P I K+ +++E + + G+ + + Sbjct: 412 LRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQW 471 Query: 492 IHIAQFCSPHDFFTLILGAKKGRQQFISR---FGNEVIDVLDEFLNFTLRNEQ-NSYSSL 547 + ++ S + +L R+ + ++ LDEFL+ T E + SL Sbjct: 472 TQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSL 531 Query: 548 QELISELEQYPPTIKRA---HSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIK 604 +++L + +A + V +MT+H AKGLE PVVFL+ +F H Sbjct: 532 IAFLTDLALISDLDELDGTEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNR-- 589 Query: 605 KMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664 SL DD + EE RL YVG+TRA ++L++ Sbjct: 590 ------SLEDDDEM--------------------------EEERRLAYVGITRAEEELVL 617 Query: 665 C 665 Sbjct: 618 T 618 >2is6_A DNA helicase II; hydrolase/DNA complex; HET: DNA ADP; 2.20A {Escherichia coli} PDB: 2is2_A* 2is1_A* 2is4_A* Length = 680 Score = 135 bits (341), Expect = 4e-32 Identities = 111/601 (18%), Positives = 210/601 (34%), Gaps = 122/601 (20%) Query: 81 QKNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASL--TLAKYLNAHYE 138 Q ++ + I + D K+ + +I + + + + + Y+ Sbjct: 119 QLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQ 178 Query: 139 EAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRS 198 EA + ++DF +L++ ++L + I + +IL+DE QDT+ IQ+ IR Sbjct: 179 EACDRAGLVDFAELLLRAHELWLNKP---HILQHYRERFTNILVDEFQDTNNIQYAWIR- 234 Query: 199 LTEDFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSII 258 + VGD+ QSIY + GA+ N +R N I Sbjct: 235 ---------LLAGDTGKVMIVGDDDQSIYGWRGAQV--------ENIQRFLNDFPGAETI 277 Query: 259 ELPLSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQH 318 L ++RST++IL+ + + I + + R+G+ +LW Sbjct: 278 RLEQNYRSTSNILSAANAL-----------------IENNNGRLGK----KLWTD----- 311 Query: 319 DSQCNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDILV 378 + + S F+ L + AR + I + + Sbjct: 312 --GADGEPISLYCAFNELDE-------ARFVVNRIKTWQ----------DNGGALAECAI 352 Query: 379 LVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFV 438 L R + ++ L+ + G RF + IKD ++ R I+++ DD +F Sbjct: 353 LYRSNAQSRVLE--EALLQASMPYRIYGGMRFF--ERQEIKDALSYLRLIVNRNDDAAFE 408 Query: 439 CMLKSPLFNFSEDDIFKICTQRHETETVYEY----------IQKFANCGISKFQHVIKYI 488 ++ +P + + + + + + A + +F +I + Sbjct: 409 RVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDAL 468 Query: 489 HELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDVLDEFLN----FTLRNEQNSY 544 + D G + +Q G I+ L+E + F+ E Sbjct: 469 AQETADMPLHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDL 528 Query: 545 SSLQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIK 604 LQ +S + + V++MT+H+AKGLE P VF+V +F + Sbjct: 529 MPLQAFLSHAALE--AGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQM-- 584 Query: 605 KMHIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664 SL++ + EE RL YVG+TRA +L + Sbjct: 585 ------SLDEGGRL--------------------------EEERRLAYVGVTRAMQKLTL 612 Query: 665 C 665 Sbjct: 613 T 613 >1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 Length = 673 Score = 112 bits (280), Expect = 4e-25 Identities = 96/598 (16%), Positives = 182/598 (30%), Gaps = 121/598 (20%) Query: 82 KNIITQEINKKSPDLKEKLKKSQDEFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAK 141 K + I L++ + + ++ + Y Y+ Sbjct: 118 KELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCY--GLYDAHL 175 Query: 142 KKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTE 201 K VLDF+DLI+ LL+ + +R + +I ++L+DE QDT+ Q+ Sbjct: 176 KACNVLDFDDLILLPTLLLQANE---EVRKRWQNKIRYLLVDEYQDTNTSQY-------- 224 Query: 202 DFFVGKNTHSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELP 261 + K S VGD+ QSIYS+ GA P N + +I+L Sbjct: 225 --ELVKLLVGSRARFTVVGDDDQSIYSWRGARP--------QNLVLLSQDFPALKVIKLE 274 Query: 262 LSFRSTADILTVVDKVFSIPENAQGLSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQ 321 ++RS+ IL + + I + + +L + S Sbjct: 275 QNYRSSGRILKAANIL-----------------IANNPHVFEKRLFSELGYGAELKVLSA 317 Query: 322 CNPQQESWTSYFDSLPQESSASILARRIAYTISNMIGTDTIFSNGKKRVIQAKDILVLVR 381 N + E+ + + ++ Q KD +L R Sbjct: 318 NNEEHEAERVTGE---------------------------LIAHHFVNKTQYKDYAILYR 350 Query: 382 KRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALGRFILSQEDDLSFVCML 441 + + ++N + G F IKDL+A R + + +DD +F+ ++ Sbjct: 351 GNHQSRVFE--KFLMQNRIPYKISGGTSFF--SRPEIKDLLAYLRVLTNPDDDSAFLRIV 406 Query: 442 KSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPH 501 +P + K+ + + + H Sbjct: 407 NTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRL 466 Query: 502 DFFTLI---------------LGAKKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSS 546 I L + V + +E + + Sbjct: 467 AEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMT 526 Query: 547 LQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKM 606 L ++++ + ++V++MT+H +KGLE P V++V H+ Sbjct: 527 LTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQ----- 581 Query: 607 HIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLII 664 + + +E RL YVG+TRA +L Sbjct: 582 ------------------------------SSIDEDNIDEERRLAYVGITRAQKELTF 609 >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 = 76.5 bits (188), Expect = 2e-14 Identities = 106/706 (15%), Positives = 193/706 (27%), Gaps = 303/706 (42%) Query: 287 LSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCNPQQESWTSYFDSLPQESSASILA 346 LS S + + + + QL EQ P + D P + A ++ Sbjct: 11 LSHGSLEHVLLVPTASFFIAS-QLQEQFNKILPE---PTEGFA---ADDEP-TTPAELVG 62 Query: 347 RRIAYTISNMIGTDTIFSNGKKRVIQAKDILVLVRKRKDTPLITFLTRFLK-NDYKI-SV 404 + + Y + + Q +L L L F +L+ ND I ++ Sbjct: 63 KFLGYVS------SLVEPSKVG---QFDQVLNLC-------LTEFENCYLEGND--IHAL 104 Query: 405 VG-----NDRFILTDHLAIKD----LMALGRFILSQEDDLSFVCMLKSPLFNFSEDDIFK 455 ND ++ IK+ + R + + S LF + + Sbjct: 105 AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN---------SALFRAVGEGNAQ 155 Query: 456 I--------CTQRHETE-----TVY-----EYIQKFANC--GISK--------FQH---V 484 + T + E Y + I+ A + + F + Sbjct: 156 LVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215 Query: 485 IKYIHE---------------------LIHIAQFC--------SPHDFFTLILGAKKGRQ 515 ++++ +I +A + +P + + + GA G Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT-GHS 274 Query: 516 Q------FIS------RFGNEVIDVLDEFLNFT-LRNEQNSY--SSLQELISELEQYPPT 560 Q I+ F V + L F +R +Y +SL PP+ Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAI-TVLFFIGVRC-YEAYPNTSL----------PPS 322 Query: 561 IKRAHSANHNE--------VRIMTVHTAKGLESPVV--FLVDTGSQVFSHKHIKKMHIMP 610 I S +NE + L V ++ T S + + K + I Sbjct: 323 I-LEDSLENNEGVPSPMLSIS--------NLTQEQVQDYVNKTNSHLPAGKQV---EI-- 368 Query: 611 SLNDDPGIPIWIPQSKSRNNIVS-------DLIKHLKKSTQEEYNRLLYVGMTRASDQLI 663 SL + +N +VS L L+K DQ Sbjct: 369 SLVNGA-----------KNLVVSGPPQSLYGLNLTLRK-----------AKAPSGLDQSR 406 Query: 664 ICKHSNTSNEKKSNQRTWYDMVYDSFHNDERVKKIKLTNS---INKDEWIAYEWSTHHPE 720 I S +R K+K +N + ++ P Sbjct: 407 I-PFS---------ER-----------------KLKFSNRFLPV----------AS--PF 427 Query: 721 NTP-LER-EETIKQLMDEQKI---PKKLFSPIKNDINEPYILNPSTIDTKGKTNLESLLS 775 ++ L + I + + + + K + P+ Y DT ++L L S Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-------Y-------DTFDGSDLRVL-S 472 Query: 776 DNQTFNRGLIIHKLLQVIFTLPEHKRKNFITSYCTKNAKLWPAKEYKNLLLSITRLLE-N 834 + I +++ I LP W T +L+ Sbjct: 473 GS-------ISERIVDCIIRLPVK----------------WE----TTTQFKATHILDFG 505 Query: 835 PMMTTAMSCDSYSEVSVSG-----KINCPKKD-----IIISGRIDQ 870 P SG N KD +I++G +D Sbjct: 506 PG-------------GASGLGVLTHRN---KDGTGVRVIVAGTLDI 535 Score = 65.0 bits (158), Expect = 7e-11 Identities = 97/611 (15%), Positives = 169/611 (27%), Gaps = 265/611 (43%) Query: 1 LKNRFGLSLNESYELIYKDLWPLPYFQVSDIN---KYVSLSMETGNPTILKKAQTLQQAS 57 L+ +F L E E D P + K++ + + + Sbjct: 33 LQEQFNKILPEPTEGFAADDEP-----TTPAELVGKFLGY--------VSSLVEPSKVGQ 79 Query: 58 QTQC-------IEERF-------SLLSSFFLTQKFTP--QKNII----------TQEINK 91 Q E + +L + T K +I + +K Sbjct: 80 FDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK 139 Query: 92 KSPD-LKEKLKKSQDEFIKI-----------------RDRFNTYKMFKSTL---ASLTLA 130 KS L + + ++ RD + TY + L ++ TL+ Sbjct: 140 KSNSAL---FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196 Query: 131 KYLNAHYEEAKKKNCVLDFEDLIINTNDLLKKRDVSAWIRYKIDQ-EINHI--------L 181 + L +A+K + T L ++ W+ + + +++ L Sbjct: 197 E-LIRTTLDAEK-----------VFTQGL----NILEWLENPSNTPDKDYLLSIPISCPL 240 Query: 182 IDEVQDTSLIQWEV-----------IRSL----T------------------EDFFVGKN 208 I +Q L + V +RS T E FF + Sbjct: 241 IGVIQ---LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFF--VS 295 Query: 209 THSSPRTLFAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTA 268 + LF +G Y P L SI+E Sbjct: 296 VRKAITVLFFIGVRCYEAY------PNTSLPP---------------SILE--------- 325 Query: 269 DILTVVDKVFSIPENAQG-----LSEDSTTTIRHRSSRIGQVGTVQLWEQVVSQHDSQCN 323 D S+ EN +G LS I + + EQV + + N Sbjct: 326 D---------SL-ENNEGVPSPMLS------ISNLTQ-----------EQVQDYVN-KTN 357 Query: 324 PQQESWTSYFDSLPQESSASI-L--ARRIAYTISNMIGTDTIFS----NGKKRVIQAKDI 376 S+ LP I L + N++ + S N R +A Sbjct: 358 -------SH---LPAGKQVEISLVNGAK------NLVVSGPPQSLYGLNLTLRKAKAPSG 401 Query: 377 L----VLVRKRKDTPLITFLTRFLKNDYKISVVGNDRFILTDHLA------IKDLMALGR 426 L + +RK + RFL ++ F + L KDL Sbjct: 402 LDQSRIPFSERK--LKFS--NRFL----PVAS----PF-HSHLLVPASDLINKDL----- 443 Query: 427 FILSQEDDLSF-VCMLKSPLFN---------FSED---DIFK-ICTQR-H-ETETVYE-- 468 ++++SF ++ P+++ S I I ET T ++ Sbjct: 444 ----VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKAT 499 Query: 469 YIQKFANCGIS 479 +I F G S Sbjct: 500 HILDFGPGGAS 510 Score = 49.2 bits (117), Expect = 5e-06 Identities = 84/474 (17%), Positives = 142/474 (29%), Gaps = 213/474 (44%) Query: 10 NESY--EL-----IYKDLWPLPYFQVSDINKYVSLSMETGNPTILKKAQTLQQ-ASQTQC 61 + Y EL Y L V D+ I A+TL + T Sbjct: 166 TDDYFEELRDLYQTYHVL-------VGDL--------------IKFSAETLSELIRTTLD 204 Query: 62 IEERFS--------------------LLS---SF---FLTQ--KFTPQKNIITQEINKKS 93 E+ F+ LLS S + Q + ++T ++ + Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY-----VVTAKLLGFT 259 Query: 94 P-DLKEKLK----KSQD----EFIKIRDRFNTYKMFKSTLASLTLAKYLNAHYEEAKKKN 144 P +L+ LK SQ I D +++ F + +K Sbjct: 260 PGELRSYLKGATGHSQGLVTAVAIAETD---SWESF----------------FVSVRKAI 300 Query: 145 CVLDFEDLIINTNDLLKKRDVSAWIRYKIDQEINHILIDE--VQDTSLIQWE-------V 195 VL F +I + + + + ++D SL E Sbjct: 301 TVL-F------------------FIGVRCYEAYPNTSLPPSILED-SLENNEGVPSPMLS 340 Query: 196 IRSLTEDF---FVGK-NTH------------SSPRTLFAVGDEKQSIYSFHGAEPKRVLR 239 I +LT++ +V K N+H + + V QS+Y + LR Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN-LVVSGPPQSLYGLN-----LTLR 394 Query: 240 EKR----INQKRATNAGQK--FSIIELPLS--FRS------TADILTVV---DKVFS--- 279 + + ++Q R + +K FS LP++ F S + I + + F+ Sbjct: 395 KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKD 454 Query: 280 --IP-------ENAQGLSEDSTTTIRHRSSRIGQVGT--VQLWEQVV---SQH--DSQCN 323 IP + + LS + I + + V+ WE + H D Sbjct: 455 IQIPVYDTFDGSDLRVLSGSISERI------VDCIIRLPVK-WETTTQFKATHILD---- 503 Query: 324 PQQESWTSYFDSLPQESSA-SILARRIAYTISNMIGTDTIFSNGKKRVIQAKDI 376 F P +S +L R N GT RVI A + Sbjct: 504 ---------FG--PGGASGLGVLTHR------NKDGTGV-------RVIVAGTL 533 >1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D* Length = 608 Score = 46.6 bits (109), Expect = 3e-05 Identities = 15/119 (12%), Positives = 32/119 (26%), Gaps = 46/119 (38%) Query: 547 LQELISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKM 606 + + + +++ + H MTVH ++G E L+ Sbjct: 508 TRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHKSQGSEFDHAALI--------------- 552 Query: 607 HIMPSLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIIC 665 +P ++ L+Y +TRA +L + Sbjct: 553 ---------------LPSQRTP----------------VVTRELVYTAVTRARRRLSLY 580 >1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C* Length = 1122 Score = 45.6 bits (107), Expect = 5e-05 Identities = 45/365 (12%), Positives = 99/365 (27%), Gaps = 79/365 (21%) Query: 367 KKRVIQAKDILVLVRKRKD-TPLITFLTRFLKNDYKISVVGNDRFILTDHLAIKDLMALG 425 + + +DI+V+V +P I + D + +DR H ++ ++L Sbjct: 399 EDPTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAISDRRARQSHPVLEAFISLL 458 Query: 426 RFILSQEDDLSFVCMLKSPL----FNFSEDDIFKI------------------------- 456 S+ + +L P+ F+ +E+ + + Sbjct: 459 SLPDSRFVSEDVLALLDVPVLAARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPA 518 Query: 457 --------CTQRHETETVYEYIQKFANCGISKFQHVIKYIHELI-HIAQFCSPHDFFTLI 507 R E Q + + I EL+ H+A + + Sbjct: 519 TGQHTWRFGLTRMLLGYAMESAQGEWQ-SVLPYDESSGLIAELVGHLASLLMQLNIWRRG 577 Query: 508 LGAKKGRQQFISRFGN-----------------EVIDVLDEFLNFTLRNEQNSYSSLQEL 550 L ++ ++++ + + + L + L L Sbjct: 578 LAQERPLEEWLPVCRDMLNAFFLPDAETEAAMTLIEQQWQAIIAEGLGAQYGDAVPLSLL 637 Query: 551 ISELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMP 610 EL Q + + V I T+ + + VV L+ V+ + + Sbjct: 638 RDELAQRLDQERISQRFLAGPVNICTLMPMRSIPFKVVCLLGMNDGVYPRQLAPLGFDLM 697 Query: 611 SLNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNT 670 S G S +++ L + A +L I + Sbjct: 698 SQKPKRGDR----------------------SRRDDDRYLFLEALISAQQKLYISYIGRS 735 Query: 671 SNEKK 675 + Sbjct: 736 IQDNS 740 Score = 29.4 bits (65), Expect = 3.9 Identities = 12/128 (9%), Positives = 36/128 (28%), Gaps = 4/128 (3%) Query: 452 DIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCSPH--DFFTLILG 509 D + + ++ + ++ + + Q I + L Sbjct: 309 DYIYLLSDLESSQELDAFVDVTPDNLLHNIQSDILELENRAVAGVNIEEFSRSDNKRPLD 368 Query: 510 AKKGRQQFISRFG--NEVIDVLDEFLNFTLRNEQNSYSSLQELISELEQYPPTIKRAHSA 567 F EV + D L + + + ++++++ Y P I+ + Sbjct: 369 PLDSSITFHVCHSPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADIDSYSPFIQAVFGS 428 Query: 568 NHNEVRIM 575 + + Sbjct: 429 APADRYLP 436 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 33.6 bits (76), Expect = 0.20 Identities = 32/155 (20%), Positives = 62/155 (40%), Gaps = 26/155 (16%) Query: 157 NDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWEVIRSLTEDFFVGKNTHSSPRTL 216 N LK R + W+ K + ++ + +TS+++ IR + + F G N Sbjct: 865 NGNLKGRPYTGWVDSKTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKK---- 920 Query: 217 FAVGDEKQSIYSFHGAEPKRVLREKRINQKRATNAGQKFSIIELPLSFRSTADIL---TV 273 + Q + EP +E ++ G K I E+P + + +L T+ Sbjct: 921 ----EMIQEVIVEEDLEPFEASKETA--EQFKHQHGDKVDIFEIPETGEYSVKLLKGATL 974 Query: 274 -------VDKVFS--IPE--NAQ--GLSEDSTTTI 295 D++ + IP NA+ G+S+D + + Sbjct: 975 YIPKALRFDRLVAGQIPTGWNAKTYGISDDIISQV 1009 Score = 28.6 bits (63), Expect = 5.9 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 23/75 (30%) Query: 470 IQKFANCGISKFQHVIKYIHELIHIAQF--CSPHDFFTLILGAKKG-----RQQFISRFG 522 ++ F GI+ + KY +H+++ CS G+ G R F RF Sbjct: 1021 VEAFIASGITDPYEMYKY----VHVSEVGNCS---------GSGMGGVSALRGMFKDRFK 1067 Query: 523 NEVI--DVLDE-FLN 534 +E + D+L E F+N Sbjct: 1068 DEPVQNDILQESFIN 1082 >2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A Length = 624 Score = 33.5 bits (75), Expect = 0.22 Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 45/134 (33%) Query: 552 SELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPS 611 S L QY H+ + EV I +V +G E + L S V +++H + Sbjct: 511 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIIL----SCVRANEH----QGIGF 562 Query: 612 LNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTS 671 LND R L V +TRA +II + Sbjct: 563 LNDP---------------------------------RRLNVALTRARYGVIIVGNPKAL 589 Query: 672 NEKKSNQRTWYDMV 685 S Q W ++ Sbjct: 590 ----SKQPLWNHLL 599 >3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, structural genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum} Length = 174 Score = 31.9 bits (71), Expect = 0.63 Identities = 8/54 (14%), Positives = 21/54 (38%) Query: 556 QYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIM 609 + I+ + V ++ AKGLE V + + + + + +++ Sbjct: 86 EQVTLIQTENQRLAPGVIVVPSFLAKGLEFDAVIVWNANQENYQREDERQLLYT 139 >2wjy_A Regulator of nonsense transcripts 1; alternative splicing, nonsense mediated decay, zinc-finger, ATP-binding, polymorphism, metal-binding, UPF2; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800 Score = 32.1 bits (72), Expect = 0.66 Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 45/134 (33%) Query: 552 SELEQYPPTIKRAHSANHNEVRIMTVHTAKGLESPVVFLVDTGSQVFSHKHIKKMHIMPS 611 S L QY H+ + EV I +V +G E + L S V +++H + Sbjct: 687 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIIL----SCVRANEH----QGIGF 738 Query: 612 LNDDPGIPIWIPQSKSRNNIVSDLIKHLKKSTQEEYNRLLYVGMTRASDQLIICKHSNTS 671 LND R L V +TRA +II + Sbjct: 739 LNDP---------------------------------RRLNVALTRARYGVIIVGNPKAL 765 Query: 672 NEKKSNQRTWYDMV 685 S Q W ++ Sbjct: 766 ----SKQPLWNHLL 775 >3hhm_A Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform; PI3KCA, PI3K, PIK3R1, phosphatidilynositol 3,4,5- triphosphate, wortmannin, H1047R, ATP-binding, disease mutation, kinase; HET: KWT; 2.80A {Homo sapiens} PDB: 3hiz_A 2rd0_A 2enq_A Length = 1091 Score = 30.7 bits (69), Expect = 1.7 Identities = 17/121 (14%), Positives = 36/121 (29%), Gaps = 7/121 (5%) Query: 440 MLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYIHELIHIAQFCS 499 + PL +E + + + RH T+ E + K + + ++ L+ Sbjct: 558 STRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIK 617 Query: 500 PHDFFTLILGA---KKGRQQFISRFGNEVIDVLDEFLNF----TLRNEQNSYSSLQELIS 552 P L+ R + + D L+ EQ + L + Sbjct: 618 PEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLL 677 Query: 553 E 553 + Sbjct: 678 K 678 >3fg7_A Villin-1; actin binding protein, gelsolin, actin capping, actin-binding, calcium, cytoplasm, cytoskeleton, structural protein; 2.00A {Homo sapiens} Length = 398 Score = 30.8 bits (69), Expect = 1.7 Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 2/85 (2%) Query: 516 QFISRFGNEVIDVLDEFLNF-TLRNEQNSYSSLQELISELEQYPPTIKRAHSANHNEVRI 574 ISR +V+ E NF + Y++ + L E P + + + Sbjct: 239 DTISRTEKQVVVEGQEPANFWMALGGKAPYANTKRLQEENLVITPRLFECSNKTGRFLAT 298 Query: 575 MTVHTAKG-LESPVVFLVDTGSQVF 598 + LE VFL+D QVF Sbjct: 299 EIPDFNQDDLEEDDVFLLDVWDQVF 323 >3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Length = 574 Score = 30.6 bits (68), Expect = 1.7 Identities = 6/17 (35%), Positives = 9/17 (52%) Query: 649 RLLYVGMTRASDQLIIC 665 L+Y +TRA D+ Sbjct: 522 NLVYTALTRARDRFFSA 538 >3few_X Colicin S4; cell lysis, Y-RAY, cell killing, immune system; 2.45A {Escherichia coli} Length = 505 Score = 28.8 bits (64), Expect = 5.1 Identities = 12/129 (9%), Positives = 34/129 (26%), Gaps = 6/129 (4%) Query: 81 QKNIITQEINKKSPDLKEKLKKSQDEFIK-----IRDRFNTYKMFKSTLASLTLAKYLNA 135 K I ++IN K+P+ + + + + + + + + Sbjct: 164 AKAGIMEKINHKTPEEIYEALGFNKDESQRQEKAKQQAEDAWDRLPPNVRKFDVDVEQFH 223 Query: 136 HYEEAKKKNCVLDFE-DLIINTNDLLKKRDVSAWIRYKIDQEINHILIDEVQDTSLIQWE 194 + VL + K + E + + + Q + Sbjct: 224 YLVVLDDYGNVLSVTRTGVRPYVGSEKAKAGIMDKVDHKTPEEIYEALGFNNEEPQRQNQ 283 Query: 195 VIRSLTEDF 203 ++ + F Sbjct: 284 AKKAAYDVF 292 >3elb_A Ethanolamine-phosphate cytidylyltransferase; kennedy pathway, CMP, CTP, phosphoethanolamine, SGC, structural genomics consortium; HET: C5P; 2.00A {Homo sapiens} Length = 341 Score = 28.8 bits (64), Expect = 5.9 Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 18/100 (18%) Query: 670 TSNEKKSNQRTWY-DMVYDSFHND-----ERVKKI----KLTNSINKDEWIAYEWSTHHP 719 + E + + Y +D FH E+V ++ + ++ D+ + + ++P Sbjct: 190 SGKEPQPGETVIYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGKNYP 249 Query: 720 ENTPLEREETIKQL--------MDEQKIPKKLFSPIKNDI 751 ER ++ + +L S K D+ Sbjct: 250 IMNLHERTLSVLACRYVSEVVIGAPYAVTAELLSHFKVDL 289 >1zro_A Erythrocyte binding antigen region II; EBA-175, RII, DBL, invasion, HOST, malaria, disease, glycophorin, glycan, sialic acid; HET: SO4; 2.25A {Plasmodium falciparum} SCOP: a.264.1.1 a.264.1.1 PDB: 1zrl_A* Length = 602 Score = 28.9 bits (64), Expect = 6.1 Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 14/98 (14%) Query: 73 FLTQKFTPQKNIITQEINKKSPD---------LKEKLKKSQDEFIKIRDRFNTYK----- 118 + K + + + K D KE + K ++E+ K ++ Y+ Sbjct: 493 YCQDKTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNY 552 Query: 119 MFKSTLASLTLAKYLNAHYEEAKKKNCVLDFEDLIINT 156 S S+ YL + E+ N +F++ + + Sbjct: 553 KMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSD 590 >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C* Length = 1119 Score = 28.2 bits (62), Expect = 8.8 Identities = 24/180 (13%), Positives = 53/180 (29%), Gaps = 13/180 (7%) Query: 371 IQAKDILVLVRKRKDTPLITFLTRFL--KNDYKISVVGNDRFILTDHLAIKDLMALGRFI 428 ++ ++ + ++ PL+ L R L + +G + ++ LM F Sbjct: 176 VEPNGVVSMKVNKRKFPLVLLL-RVLGYDQETLARELGAYGEL------VQGLMDESVFA 228 Query: 429 LSQEDDLSFVCMLKSPLFNFSEDDIFKICTQRHETETVYEYIQKFANCGISKFQHVIKYI 488 + E+ L + L P D Y+ + G K + + Sbjct: 229 MRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEA----GRYKAEEKLGIR 284 Query: 489 HELIHIAQFCSPHDFFTLILGAKKGRQQFISRFGNEVIDVLDEFLNFTLRNEQNSYSSLQ 548 +A+F + L + + +D +D N +R + Sbjct: 285 LSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQF 344 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 0.319 0.134 0.385 Gapped Lambda K H 0.267 0.0450 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 7,915,164 Number of extensions: 371036 Number of successful extensions: 1150 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1126 Number of HSP's successfully gapped: 53 Length of query: 952 Length of database: 5,693,230 Length adjustment: 101 Effective length of query: 851 Effective length of database: 3,244,586 Effective search space: 2761142686 Effective search space used: 2761142686 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 (21.7 bits) S2: 61 (28.0 bits)