------------------------------------------------------------ Pratt version 2.1, Sept. 1996 Written by Inge Jonassen, University of Bergen Norway email: inge@ii.uib.no For more information, see http://www.ii.uib.no/~inge/Pratt.html ------------------------------------------------------------ Please quote: I.Jonassen, J.F.Collins, D.G.Higgins. Protein Science 1995;4(8):1587-1595. ------------------------------------------------------------ Pratt version 2.1 Analysing 7 sequences from file MAP PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 C%: min Percentage Seqs to Match 100.0 PATTERN RESTRICTIONS : PP: pos in seq [off,complete,start] off PL: max Pattern Length 50 PN: max Nr of Pattern Symbols 50 PX: max Nr of consecutive x's 5 FN: max Nr of flexible spacers 2 FL: max Flexibility 2 FP: max Flex.Product 10 BI: Input Pattern Symbol File off BN: Nr of Pattern Symbols Initial Search 20 PATTERN SCORING: S: Scoring [info,mdl,tree,dist,ppv] info SEARCH PARAMETERS: G: Pattern Graph from [seq,al,query] seq E: Search Greediness 3 R: Pattern Refinement on RG: Generalise ambiguous symbols off OUTPUT: OF: Output Filename MAP.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AMPM_BACST 51 AMPM_BACSU 248 AMPM_ECOLI 264 AMPM_HAEIN 268 AMPM_KLEPN 43 AMPM_SALTY 263 AMPM_YEAST 387 Pratt run started at Thu Feb 6 20:14:41 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 15.1802 10( 7) G-x(5)-L-x(0,2)-D-x(1,2)-I 2: 15.1802 7( 7) E-x(2,3)-I-V-x(1,3)-T 3: 12.0102 9( 7) T-x(3)-D-x(1,2)-I 4: 12.0102 8( 7) T-x(4)-D-x(0,1)-I 5: 12.0102 13( 7) T-x(3,4)-D-x-I 6: 12.0102 8( 7) E-x(4)-R-x(3,4)-I 7: 11.5102 8( 7) T-x(4,5)-I-x(2,3)-E 8: 11.5102 12( 7) K-x(1,2)-D-x(0,1)-I 9: 11.5102 9( 7) R-x(3,4)-I-x(1,2)-A 10: 11.5102 13( 7) L-x(0,1)-K-x(2,3)-I 11: 11.5102 7( 7) T-x(5)-I-x(3,5)-R 12: 11.5102 10( 7) I-V-x(1,3)-T 13: 11.5102 9( 7) T-x(3,4)-L-x(4,5)-E 14: 11.5102 8( 7) V-x(0,2)-K-x(2)-D 15: 11.5102 12( 7) V-x-T-x(1,3)-D 16: 11.5102 8( 7) T-x(0,2)-K-x(2)-D 17: 11.0102 10( 7) I-x(0,1)-S-x(1,3)-E 18: 11.0102 16( 7) D-x(1,2)-I-x(2,4)-I 19: 11.0102 12( 7) T-x(0,2)-K-x(1,2)-D 20: 11.0102 9( 7) E-x(0,1)-L-x(2,4)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 23.2054 9( 7) G-x-[EST]-x(2)-[ET]-L-x(0,2)-D-x(1,2)-I-[ACPV] B 2: 19.4390 10( 7) L-x(0,1)-K-x(2,3)-I-x-[ANP]-[GIL]-x-[STV] C 3: 17.4380 9( 7) T-x-[ER]-x-D-x(1,2)-I-[ACPV] D 4: 16.7966 9( 7) K-x(1,2)-D-x(0,1)-I-[APV]-[AEN] E 5: 16.7488 7( 7) V-x(0,2)-K-[DET]-x-D-x(4)-[ADE] F 6: 15.1802 7( 7) E-x(2,3)-I-V-x(1,3)-T G 7: 14.6852 8( 7) T-x(0,2)-K-[ET]-x-D H 8: 14.6306 7( 7) E-x(4)-R-x(3,4)-I-[APV] I 9: 14.2614 13( 7) T-x(3,4)-D-x-I-[ACPV] J 10: 14.1402 7( 7) T-x(4)-[AEG]-I-x(3,5)-R K 11: 13.7494 8( 7) T-x(3,4)-L-x(4,5)-E-x(2)-[AIPV] L 12: 12.0102 8( 7) T-x(4)-D-x(0,1)-I M 13: 11.5102 8( 7) T-x(4,5)-I-x(2,3)-E N 14: 11.5102 9( 7) R-x(3,4)-I-x(1,2)-A O 15: 11.5102 10( 7) I-V-x(1,3)-T P 16: 11.5102 12( 7) V-x-T-x(1,3)-D Q 17: 11.0102 10( 7) I-x(0,1)-S-x(1,3)-E R 18: 11.0102 16( 7) D-x(1,2)-I-x(2,4)-I S 19: 11.0102 12( 7) T-x(0,2)-K-x(1,2)-D T 20: 11.0102 9( 7) E-x(0,1)-L-x(2,4)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 23.2054 9( 7) G-x-[EST]-x(2)-[ET]-L-x(0,2)-D-x(1,2)-I-[ACPV] Occurences: 9(7) AMPM_BACST : 34- 44: nhirp GvTtkEL--Da-IA eevir AMPM_BACSU : 34- 44: khikp GiStkEL--Dq-IA erfik AMPM_ECOLI : 35- 45: pyvkp GvStgEL--Dr-IC ndyiv AMPM_ECOLI : 244- 257: vvtdn GcEilTLrkDdtIP aiish AMPM_HAEIN : 35- 45: pyvka GvTtgEL--Dr-IC heymv AMPM_KLEPN : 23- 36: vvtdn GcEilTLrkDdtIP aiish AMPM_SALTY : 34- 44: pyikp GvTtgEL--Dr-IC ndyiv AMPM_SALTY : 243- 256: vvten GcEilTLrkDdtIP aiith AMPM_YEAST : 159- 169: ahvrp GiTtdEL--De-IV hneti B 2: 19.4390 10( 7) L-x(0,1)-K-x(2,3)-I-x-[ANP]-[GIL]-x-[STV] Occurences: 10(7) AMPM_BACST : 27- 36: atlee L-Knh-IrPGvT tkeld AMPM_BACSU : 27- 36: lthee L-Kkh-IkPGiS tkeld AMPM_ECOLI : 87- 98: pddak LlKdgdIvNIdV tvikd AMPM_ECOLI : 88- 98: ddakl L-KdgdIvNIdV tvikd AMPM_ECOLI : 250- 261: ceilt LrKddtIpAIiS hde AMPM_HAEIN : 88- 98: sddkv L-KngdIvNIdV tvikd AMPM_KLEPN : 29- 40: ceilt LrKddtIpAIiS hne AMPM_SALTY : 87- 97: ddakh L-KdgdIvNIdV tvikd AMPM_SALTY : 249- 260: ceilt LrKddtIpAIiT hde AMPM_YEAST : 210- 220: pdktv L-KegdIvNLdV slyyq C 3: 17.4380 9( 7) T-x-[ER]-x-D-x(1,2)-I-[ACPV] Occurences: 9(7) AMPM_BACST : 37- 44: rpgvt TkElDa-IA eevir AMPM_BACSU : 37- 44: kpgis TkElDq-IA erfik AMPM_ECOLI : 38- 45: kpgvs TgElDr-IC ndyiv AMPM_ECOLI : 249- 257: gceil TlRkDdtIP aiish AMPM_HAEIN : 38- 45: kagvt TgElDr-IC heymv AMPM_KLEPN : 28- 36: gceil TlRkDdtIP aiish AMPM_SALTY : 37- 44: kpgvt TgElDr-IC ndyiv AMPM_SALTY : 248- 256: gceil TlRkDdtIP aiith AMPM_YEAST : 162- 169: rpgit TdElDe-IV hneti D 4: 16.7966 9( 7) K-x(1,2)-D-x(0,1)-I-[APV]-[AEN] Occurences: 9(7) AMPM_BACST : 38- 45: pgvtt KelDaIAE evirs AMPM_BACSU : 38- 45: pgist KelDqIAE rfikk AMPM_ECOLI : 89- 95: dakll KdgD-IVN idvtv AMPM_ECOLI : 252- 258: iltlr Kd-DtIPA iishd AMPM_HAEIN : 89- 95: ddkvl KngD-IVN idvtv AMPM_KLEPN : 31- 37: iltlr Kd-DtIPA iishn AMPM_SALTY : 88- 94: dakhl KdgD-IVN idvtv AMPM_SALTY : 251- 257: iltlr Kd-DtIPA iithd AMPM_YEAST : 211- 217: dktvl KegD-IVN ldvsl E 5: 16.7488 7( 7) V-x(0,2)-K-[DET]-x-D-x(4)-[ADE] Occurences: 7(7) AMPM_BACST : 35- 46: hirpg VttKElDaiaeE virsh AMPM_BACSU : 84- 94: ipgsr Vl-KDgDiisiD igakl AMPM_ECOLI : 223- 232: kdgwt V--KTkDrslsA qyeht AMPM_HAEIN : 224- 233: gdgwt V--KTkDrshsA qyehq AMPM_KLEPN : 2- 11: t V--KTkDrslsA qyeht AMPM_SALTY : 222- 231: kdgwt V--KTkDrslsA qyeht AMPM_YEAST : 209- 219: vpdkt Vl-KEgDivnlD vslyy F 6: 15.1802 7( 7) E-x(2,3)-I-V-x(1,3)-T Occurences: 7(7) AMPM_BACST : 15- 23: itlmr EagkIVsa-T leelk AMPM_BACSU : 15- 23: lgimr EagrIVal-T heelk AMPM_ECOLI : 235- 241: lsaqy Eht-IVv--T dngce AMPM_HAEIN : 236- 244: hsaqy EhqlIVte-T gcevm AMPM_KLEPN : 14- 20: lsaqy Eht-IVv--T dngce AMPM_SALTY : 234- 240: lsaqy Eht-IVv--T engce AMPM_YEAST : 164- 173: gittd EldeIVhneT ikrga G 7: 14.6852 8( 7) T-x(0,2)-K-[ET]-x-D Occurences: 8(7) AMPM_BACST : 36- 41: irpgv Tt-KElD aiaee AMPM_BACST : 37- 41: rpgvt T--KElD aiaee AMPM_BACSU : 37- 41: kpgis T--KElD qiaer AMPM_ECOLI : 222- 227: mkdgw Tv-KTkD rslsa AMPM_HAEIN : 223- 228: mgdgw Tv-KTkD rshsa AMPM_KLEPN : 1- 6: Tv-KTkD rslsa AMPM_SALTY : 221- 226: mkdgw Tv-KTkD rslsa AMPM_YEAST : 208- 214: gvpdk TvlKEgD ivnld H 8: 14.6306 7( 7) E-x(4)-R-x(3,4)-I-[APV] Occurences: 7(7) AMPM_BACST : 9- 20: cktah EitlmReagkIV satle AMPM_BACSU : 9- 20: cktpr ElgimReagrIV althe AMPM_ECOLI : 246- 257: tdngc EiltlRkddtIP aiish AMPM_HAEIN : 247- 257: tetgc EvmtiRdee-IA egris AMPM_KLEPN : 25- 36: tdngc EiltlRkddtIP aiish AMPM_SALTY : 245- 256: tengc EiltlRkddtIP aiith AMPM_YEAST : 118- 128: glpvs EqrndRlnn-IP iykkd I 9: 14.2614 13( 7) T-x(3,4)-D-x-I-[ACPV] Occurences: 13(7) AMPM_BACST : 36- 44: irpgv TtkelDaIA eevir AMPM_BACST : 37- 44: rpgvt Tkel-DaIA eevir AMPM_BACSU : 37- 44: kpgis Tkel-DqIA erfik AMPM_ECOLI : 38- 45: kpgvs Tgel-DrIC ndyiv AMPM_ECOLI : 249- 257: gceil TlrkdDtIP aiish AMPM_HAEIN : 37- 45: vkagv TtgelDrIC heymv AMPM_HAEIN : 38- 45: kagvt Tgel-DrIC heymv AMPM_KLEPN : 28- 36: gceil TlrkdDtIP aiish AMPM_SALTY : 36- 44: ikpgv TtgelDrIC ndyiv AMPM_SALTY : 37- 44: kpgvt Tgel-DrIC ndyiv AMPM_SALTY : 248- 256: gceil TlrkdDtIP aiith AMPM_YEAST : 161- 169: vrpgi TtdelDeIV hneti AMPM_YEAST : 162- 169: rpgit Tdel-DeIV hneti J 10: 14.1402 7( 7) T-x(4)-[AEG]-I-x(3,5)-R Occurences: 7(7) AMPM_BACST : 37- 49: rpgvt TkeldAIaeeviR sh AMPM_BACSU : 6- 18: miick TprelGImreagR ivalt AMPM_ECOLI : 241- 251: htivv TdngcEIltl--R kddti AMPM_HAEIN : 250- 260: gcevm TirdeEIaeg--R isrim AMPM_KLEPN : 20- 30: htivv TdngcEIltl--R kddti AMPM_SALTY : 240- 250: htivv TengcEIltl--R kddti AMPM_YEAST : 364- 374: htllv TehgvEIlta--R nkksp K 11: 13.7494 8( 7) T-x(3,4)-L-x(4,5)-E-x(2)-[AIPV] Occurences: 8(7) AMPM_BACST : 36- 48: irpgv Ttke-Ldaia-EevI rsh AMPM_BACSU : 126- 139: kllev Tees-LykglqEakP gerls AMPM_ECOLI : 225- 238: gwtvk TkdrsLsaqy-EhtI vvtdn AMPM_HAEIN : 37- 50: vkagv Ttge-LdrichEymV neqkv AMPM_KLEPN : 4- 17: tvk TkdrsLsaqy-EhtI vvtdn AMPM_SALTY : 224- 237: gwtvk TkdrsLsaqy-EhtI vvten AMPM_YEAST : 267- 280: mckpg TtfqeLgdhi-EkhA tenkc AMPM_YEAST : 268- 280: ckpgt Tfqe-Lgdhi-EkhA tenkc L 12: 12.0102 8( 7) T-x(4)-D-x(0,1)-I Occurences: 8(7) AMPM_BACST : 36- 43: irpgv TtkelDaI aeevi AMPM_BACSU : 238- 244: htiai TetgfD-I ltrv AMPM_ECOLI : 249- 256: gceil TlrkdDtI paiis AMPM_HAEIN : 37- 44: vkagv TtgelDrI cheym AMPM_KLEPN : 28- 35: gceil TlrkdDtI paiis AMPM_SALTY : 36- 43: ikpgv TtgelDrI cndyi AMPM_SALTY : 248- 255: gceil TlrkdDtI paiit AMPM_YEAST : 161- 168: vrpgi TtdelDeI vhnet M 13: 11.5102 8( 7) T-x(4,5)-I-x(2,3)-E Occurences: 8(7) AMPM_BACST : 37- 46: rpgvt TkeldaIae-E virsh AMPM_BACSU : 6- 15: miick TprelgImr-E agriv AMPM_ECOLI : 255- 264: lrkdd Tipai-IshdE AMPM_HAEIN : 38- 47: kagvt TgeldrIch-E ymvne AMPM_HAEIN : 140- 149: yvgir Tvkpd-IrlnE igkav AMPM_KLEPN : 34- 43: lrkdd Tipai-IshnE AMPM_SALTY : 254- 263: lrkdd Tipai-IthdE AMPM_YEAST : 162- 172: rpgit TdeldeIvhnE tikrg N 14: 11.5102 9( 7) R-x(3,4)-I-x(1,2)-A Occurences: 9(7) AMPM_BACST : 14- 22: eitlm ReagkIvsA tleel AMPM_BACSU : 14- 21: elgim ReagrIv-A lthee AMPM_BACSU : 142- 149: akpge Rlsn-IshA iqtyv AMPM_ECOLI : 251- 258: eiltl RkddtIp-A iishd AMPM_HAEIN : 146- 153: vkpdi Rlne-IgkA vqkyt AMPM_KLEPN : 30- 37: eiltl RkddtIp-A iishn AMPM_SALTY : 144- 150: vkpgi Rlrt-Ig-A aiqky AMPM_SALTY : 144- 151: vkpgi Rlrt-IgaA iqkya AMPM_SALTY : 250- 257: eiltl RkddtIp-A iithd AMPM_YEAST : 146- 153: acmlg RevldIa-A ahvrp AMPM_YEAST : 146- 154: acmlg RevldIaaA hvrpg O 15: 11.5102 10( 7) I-V-x(1,3)-T Occurences: 10(7) AMPM_BACST : 19- 23: reagk IVsa-T leelk AMPM_BACSU : 19- 23: reagr IVal-T heelk AMPM_ECOLI : 114- 119: tskmf IVgkpT imger AMPM_ECOLI : 238- 241: qyeht IVv--T dngce AMPM_HAEIN : 114- 119: nskmy IVggeT nirsk AMPM_HAEIN : 240- 244: yehql IVte-T gcevm AMPM_KLEPN : 17- 20: qyeht IVv--T dngce AMPM_SALTY : 113- 118: tskmf IVgkpT ilger AMPM_SALTY : 237- 240: qyeht IVv--T engce AMPM_YEAST : 168- 173: delde IVhneT ikrga P 16: 11.5102 12( 7) V-x-T-x(1,3)-D Occurences: 12(7) AMPM_BACST : 35- 41: hirpg VtTkelD aiaee AMPM_BACSU : 211- 216: agsry VkTla-D nwtvv AMPM_BACSU : 220- 224: adnwt VvTv--D gkkca AMPM_ECOLI : 36- 42: yvkpg VsTgelD ricnd AMPM_ECOLI : 223- 227: kdgwt VkTk--D rslsa AMPM_HAEIN : 36- 42: yvkag VtTgelD riche AMPM_HAEIN : 224- 228: gdgwt VkTk--D rshsa AMPM_HAEIN : 248- 253: etgce VmTir-D eeiae AMPM_KLEPN : 2- 6: t VkTk--D rslsa AMPM_SALTY : 35- 41: yikpg VtTgelD ricnd AMPM_SALTY : 222- 226: kdgwt VkTk--D rslsa AMPM_YEAST : 8- 12: tattt VtTs--D qashp Q 17: 11.0102 10( 7) I-x(0,1)-S-x(1,3)-E Occurences: 10(7) AMPM_BACST : 19- 25: reagk IvSatlE elknh AMPM_BACSU : 35- 39: hikpg I-Stk-E ldqia AMPM_ECOLI : 71- 75: pksvc I-Sin-E vvchg AMPM_ECOLI : 259- 264: dtipa IiShd-E AMPM_ECOLI : 260- 264: tipai I-Shd-E AMPM_HAEIN : 71- 75: pkatc I-Sin-E vvchg AMPM_KLEPN : 38- 43: dtipa IiShn-E AMPM_KLEPN : 39- 43: tipai I-Shn-E AMPM_SALTY : 70- 74: pksvc I-Sin-E vvchg AMPM_YEAST : 241- 244: yvgen I-Sk--E alntt R 18: 11.0102 16( 7) D-x(1,2)-I-x(2,4)-I Occurences: 16(7) AMPM_BACST : 41- 48: ttkel Da-IaeevI rsh AMPM_BACSU : 41- 48: stkel Dq-IaerfI kkqga AMPM_BACSU : 87- 93: srvlk DgdIis--I digak AMPM_BACSU : 87- 95: srvlk DgdIisidI gakln AMPM_BACSU : 89- 95: vlkdg Di-Isid-I gakln AMPM_ECOLI : 42- 49: stgel Dr-IcndyI vneqh AMPM_ECOLI : 90- 96: akllk DgdIvn--I dvtvi AMPM_ECOLI : 253- 259: ltlrk DdtIpa--I ishde AMPM_ECOLI : 253- 260: ltlrk DdtIpai-I shde AMPM_ECOLI : 254- 259: tlrkd Dt-Ipa--I ishde AMPM_ECOLI : 254- 260: tlrkd Dt-Ipai-I shde AMPM_HAEIN : 253- 261: vmtir DeeIaegrI srimv AMPM_KLEPN : 32- 38: ltlrk DdtIpa--I ishne AMPM_KLEPN : 32- 39: ltlrk DdtIpai-I shne AMPM_KLEPN : 33- 38: tlrkd Dt-Ipa--I ishne AMPM_KLEPN : 33- 39: tlrkd Dt-Ipai-I shne AMPM_SALTY : 41- 48: ttgel Dr-IcndyI vneqh AMPM_SALTY : 89- 95: akhlk DgdIvn--I dvtvi AMPM_SALTY : 252- 258: ltlrk DdtIpa--I ithde AMPM_SALTY : 252- 259: ltlrk DdtIpai-I thde AMPM_SALTY : 253- 258: tlrkd Dt-Ipa--I ithde AMPM_SALTY : 253- 259: tlrkd Dt-Ipai-I thde AMPM_YEAST : 133- 138: piykk Dq-Ikk--I rkacm S 19: 11.0102 12( 7) T-x(0,2)-K-x(1,2)-D Occurences: 12(7) AMPM_BACST : 36- 41: irpgv Tt-KelD aiaee AMPM_BACST : 37- 41: rpgvt T--KelD aiaee AMPM_BACSU : 37- 41: kpgis T--KelD qiaer AMPM_ECOLI : 222- 227: mkdgw Tv-KtkD rslsa AMPM_ECOLI : 249- 254: gceil TlrKd-D tipai AMPM_HAEIN : 140- 144: yvgir Tv-Kp-D irlne AMPM_HAEIN : 223- 228: mgdgw Tv-KtkD rshsa AMPM_KLEPN : 1- 6: Tv-KtkD rslsa AMPM_KLEPN : 28- 33: gceil TlrKd-D tipai AMPM_SALTY : 221- 226: mkdgw Tv-KtkD rslsa AMPM_SALTY : 248- 253: gceil TlrKd-D tipai AMPM_YEAST : 208- 214: gvpdk TvlKegD ivnld T 20: 11.0102 9( 7) E-x(0,1)-L-x(2,4)-R Occurences: 9(7) AMPM_BACST : 25- 32: vsatl EeLknhiR pgvtt AMPM_BACST : 26- 32: satle E-LknhiR pgvtt AMPM_BACSU : 9- 14: cktpr E-Lgim-R eagri AMPM_ECOLI : 131- 138: critq EsLylalR mvkpg AMPM_ECOLI : 246- 251: tdngc EiLtl--R kddti AMPM_HAEIN : 132- 139: veaaq EaLyvgiR tvkpd AMPM_KLEPN : 25- 30: tdngc EiLtl--R kddti AMPM_SALTY : 245- 250: tengc EiLtl--R kddti AMPM_YEAST : 369- 374: tehgv EiLta--R nkksp Number of patterns evaluated by Pratt:314 Total running time: 0 seconds