TBLASTN 2.2.25+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Database: lm_genome.fasta 12 sequences; 2,945,078 total letters Query= P42412 Length=487 Score E Sequences producing significant alignments: (Bits) Value embl|AL591975|AL591975 Listeria monocytogenes strain EGD, compl... 842 0.0 embl|AL591977|AL591977 Listeria monocytogenes strain EGD, compl... 268 6e-73 embl|AL591978|AL591978 Listeria monocytogenes strain EGD, compl... 44.3 2e-05 > embl|AL591975|AL591975 Listeria monocytogenes strain EGD, complete genome, segment 3/12 Length=280050 Score = 842 bits (2174), Expect = 0.0, Method: Compositional matrix adjust. Identities = 396/481 (83%), Positives = 443/481 (93%), Gaps = 0/481 (0%) Frame = +2 Query 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 MA++RKLKNYI+GEWVESKTD+YEDV+NPAT EVLCQVPIST+ ++D AA A +AF+ W Sbjct 46637 MADVRKLKNYIDGEWVESKTDKYEDVINPATGEVLCQVPISTRAELDQAAVIAEQAFEKW 46816 Query 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPS 120 S+VAVPRRAR+LF FQQLL QHKEELA LIT+ENGKN EA GEV RGIENVEFAAGAP+ Sbjct 46817 SQVAVPRRARVLFGFQQLLIQHKEELARLITLENGKNLSEARGEVQRGIENVEFAAGAPT 46996 Query 121 LMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSER 180 LMMGDSLASIATDVEAANYRYP+GVVGGIAPFNFPMMVPCWMFPMAIALGN+FILKPSER Sbjct 46997 LMMGDSLASIATDVEAANYRYPVGVVGGIAPFNFPMMVPCWMFPMAIALGNSFILKPSER 47176 Query 181 TPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKG 240 TPLL EKLVELF +AGLPKGVFNVVYGAHDVVNGILE+ IKA+SFVGSKPVGEYVYK G Sbjct 47177 TPLLMEKLVELFSEAGLPKGVFNVVYGAHDVVNGILENEIIKAVSFVGSKPVGEYVYKTG 47356 Query 241 SENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 S NLKRVQ+LTGAKNHTIVLNDA+LEDTVTN++ AAFGSAGERCMACAVVTVEEGIADEF Sbjct 47357 SANLKRVQALTGAKNHTIVLNDADLEDTVTNVISAAFGSAGERCMACAVVTVEEGIADEF 47536 Query 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDD 360 + L+ ++KIGNGLDDGVFLGPVIRE+N+KRT++YIEKG+EEGA+L DGRE + Sbjct 47537 LEALRTAAQNVKIGNGLDDGVFLGPVIREENQKRTIAYIEKGIEEGAKLTVDGRETGLSE 47716 Query 361 GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSN 420 G+FVGPTI ++VTT+MTIWKDEIFAPVLSVIRVKNL+EA+ +AN+SEFANGAC+FT+N+ Sbjct 47717 GHFVGPTILEDVTTDMTIWKDEIFAPVLSVIRVKNLQEAVRVANQSEFANGACIFTNNAK 47896 Query 421 AIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480 AIRYFRE IDAGMLG+NLGVPAPMAFFPFSGWKSSF+GTLHANGKDSVDFYT KKVVTAR Sbjct 47897 AIRYFREKIDAGMLGVNLGVPAPMAFFPFSGWKSSFYGTLHANGKDSVDFYTHKKVVTAR 48076 Query 481 Y 481 Y Sbjct 48077 Y 48079 > embl|AL591977|AL591977 Listeria monocytogenes strain EGD, complete genome, segment 5/12 Length=270050 Score = 268 bits (685), Expect = 6e-73, Method: Compositional matrix adjust. Identities = 162/481 (34%), Positives = 265/481 (56%), Gaps = 11/481 (2%) Frame = +2 Query 6 KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 + K +ING+W + + +D+VNPA +V+ ++ + + A + A +AF W+K+ + Sbjct 58787 QTKLFINGKWTDGDNKETKDIVNPANGDVIAKIAQAGPSETKKAIKAAKDAFPDWAKMEL 58966 Query 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125 R ++L L+ + + LA ++T+E GK KE+ GEV G+EN FAA + G+ Sbjct 58967 ADRVKLLHKIADLMEEKADTLAKIMTLEQGKPLKESKGEVLTGVENFRFAAEEARRLYGE 59146 Query 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185 ++ + + PIGVV I P+NFP + A+A GNT +LKPS TPL Sbjct 59147 TIPAPNNHAFIVK-KQPIGVVAAITPWNFPGGMVTRKLAPALATGNTIVLKPSGDTPLSA 59323 Query 186 EKLVELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKKGSENL 244 + E+FE+AGLPKGV N+V G+ + L + +++ ++F GS VG+ ++K+ ++ L Sbjct 59324 LAIFEIFEEAGLPKGVANIVMGSSKEIGETLTDSDDVRKLTFTGSTKVGQTLFKQSADTL 59503 Query 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 K++ G IV +DANL+ V ++V A F + G+ C++ + V + I ++F L Sbjct 59504 KKISLELGGHAPFIVFDDANLDAAVNDLVAAKFRNNGQVCVSPNRIFVAKEIKEKFTKAL 59683 Query 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDD---G 361 KV +K+GNGLDD V +GP+IRED + ++ E+GA+++ G D G Sbjct 59684 VAKVEQLKVGNGLDD-VNVGPLIREDAIDKIDKQLKNATEKGAKVLTGGGRLTGSDYDKG 59860 Query 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421 F PT+ DNVT +M I+ +E F PV+ +I + EAIE+AN SEF + +T + Sbjct 59861 NFYKPTVLDNVTRKMDIFYEETFGPVIPLITFETEDEAIEMANDSEFGLASYFYTKDLAR 60040 Query 422 IRYFRENIDAGMLGIN-LGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480 + ++ GM+G N + + P PF G K S FG NG ++ Y + K + + Sbjct 60041 VEKVGAALEYGMVGANEIAISNPET--PFGGVKHSGFG--RENGHYGMEEYIQVKFINLK 60208 Query 481 Y 481 Y Sbjct 60209 Y 60211 > embl|AL591978|AL591978 Listeria monocytogenes strain EGD, complete genome, segment 6/12 Length=250050 Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust. Identities = 86/372 (24%), Positives = 142/372 (39%), Gaps = 37/372 (9%) Frame = +1 Query 44 EDIDYAAQTAAEAFKTWSKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG 103 + +D A Q A A ++ + ++ R ++ ++ L E +A E G +G Sbjct 31663 DTVDEAVQAAVIAQNSYKEKSLEERRNVVKAIREALYPEIESIAARAVAETG------MG 31824 Query 104 EVGRGI-ENVEFAAGAPSLMMGDSLASIAT-DVEAANYRY-PIGVVGGIAPFNFPM-MVP 159 V I +N P + D +AT D Y P GV+G +AP P + Sbjct 31825 NVADKILKNTLAIEKTPGVE--DLYTEVATGDNGMTLYELSPYGVIGAVAPSTNPTETLI 31998 Query 160 CWMFPMAIALGNTFILKPSERTPLLTEKLVE-----LFEKAGLPKGVFNVVYGAHDVVNG 214 C M +A GN P ++ L+E + E G+ V V + Sbjct 31999 CNTIGM-LAAGNAVFYSPHPGAKNISLWLIEKLNTIVRESCGVDNLVVTVEKPSIQAAQE 32175 Query 215 ILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVG 274 ++ HP++ + G G V + ++ K+V +IV AN+E +IV Sbjct 32176 MMNHPKVPLLVITG----GPGVVLQAMQSGKKVIGAGAGNPPSIVDETANIEKAAADIVD 32343 Query 275 AAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVADIKIGNGLDDGVFLGPVIRED---N 331 A C+A V + IAD M ++ EK + + N D + + N Sbjct 32344 GASFDHNILCIAEKSVVAVDSIADFLMFQM-EKNGALHVTNPSDIQKLEKVAVTDKGVTN 32520 Query 332 KKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVI 391 KK + L+E A + CD F I E+ P++ V+ Sbjct 32521 KKLVGKSASEILKE-AGIACD----------FSPRLIIVETEKTHPFATVELLMPIVPVV 32667 Query 392 RVKNLKEAIEIA 403 RV N +EA+E+A Sbjct 32668 RVPNFEEALEVA 32703 Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust. Identities = 64/300 (22%), Positives = 119/300 (40%), Gaps = 35/300 (11%) Frame = +2 Query 142 PIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKP---SERTPLLTEKLV-ELFEKAGL 197 P+GVV G+ P P + ++I GN+ + P + + L T +++ E EKAG Sbjct 47432 PLGVVAGLIPSTNPTSTVIYKTLISIKAGNSIVFSPHPNALKAILETVRIISEAAEKAGC 47611 Query 198 PKGVFN-VVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQSLTGAKNH 256 PKG + + + +++H + I G + + Y G+ + + Sbjct 47612 PKGAISCMTVPTIQGTDQLMKHKDTAVILATGGSAMVKAAYSSGTPAI----GVGPGNGP 47779 Query 257 TIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVADIKIGNG 316 + AN+ V +I+ + G C + V VE + +A+ +++ A Sbjct 47780 AFIERSANIPRAVKHILDSKTFDNGTICASEQSVVVERVNKEAVIAEFRKQGAHF----- 47944 Query 317 LDD--GVFLGPVIREDNKKRTLSYIEKGLEEGARLV-----CDGRENVSDDGYFVGPTIF 369 L D V LG I N + + K ++ A L D R ++++ VG I Sbjct 47945 LSDAEAVQLGKFILRPNGSMNPAIVGKSVQHIANLAGLTVPADARVLIAEETK-VGAKIP 48121 Query 370 DNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGA----CLFTSNSNAIRYF 425 + E AP+L+ + +EA E++ + GA + + + IR F Sbjct 48122 ---------YSREKLAPILAFYTAETWQEACELSMDILYHEGAGHTLIIHSEDKEIIREF 48274 Lambda K H 0.318 0.136 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Effective search space used: 391273764 Database: lm_genome.fasta Posted date: Nov 18, 2012 10:02 PM Number of letters in database: 2,945,078 Number of sequences in database: 12 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Neighboring words threshold: 13 Window for multiple hits: 40