------------------------------------------------------------ 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 8 sequences from file CLAT_ADAPTOR_M_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 8 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 CLAT_ADAPTOR_M_1.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AP47_CAEEL 422 AP47_MOUSE 423 AP50_CAEEL 441 AP50_RAT 435 AP50_SCHPO 446 AP54_YEAST 474 AP70_YEAST 605 YB8C_YEAST 483 Pratt run started at Thu Feb 6 19:07:50 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 37.5305 8( 8) I-x-F-I-P-P-D-G-x(3)-L-x(2)-Y 2: 33.3604 8( 8) F-I-P-P-D-G-x(3)-L-x(2)-Y 3: 29.1904 8( 8) I-P-P-D-G-x(3)-L-x(2)-Y 4: 25.0203 8( 8) P-P-D-G-x(3)-L-x(2)-Y 5: 20.8503 8( 8) P-D-G-x(3)-L-x(2)-Y 6: 19.3503 10( 8) I-x(1,2)-F-x(0,2)-P-x-G-x(3)-L 7: 19.3503 8( 8) L-x-D-x(0,2)-E-x(2)-D-x(0,1)-G 8: 18.8503 10( 8) I-x(2,4)-L-L-x(0,2)-E-x(2)-D 9: 18.8503 8( 8) I-x(0,2)-L-L-x(0,2)-E-x(2)-D 10: 16.6802 8( 8) D-G-x(3)-L-x(2)-Y 11: 15.6802 10( 8) I-x(0,2)-I-x(3)-G-x(3)-L 12: 15.6802 8( 8) G-x(2,3)-V-x(1,2)-Y-L 13: 15.6802 11( 8) I-P-x(0,1)-P-x(0,1)-D 14: 15.6802 11( 8) I-x(1,2)-I-P-x(0,1)-P 15: 15.6802 8( 8) F-x(0,1)-Q-x(0,1)-V-x-L 16: 15.6802 8( 8) L-x(0,1)-L-x(0,1)-D-x(3)-D 17: 15.6802 8( 8) L-x(0,1)-L-x(0,1)-E-x(2)-D 18: 15.6802 8( 8) I-x(0,1)-E-x(3)-E-x(2,3)-D 19: 15.1802 9( 8) S-x(3,5)-V-x(2)-L-x(3,4)-E 20: 15.1802 12( 8) I-x(1,3)-F-x(0,1)-I-P Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 44.6378 8( 8) I-[EST]-F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] B 2: 41.5389 9( 8) I-x(1,2)-F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] C 3: 37.8688 8( 8) F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] D 4: 37.3688 8( 8) I-x(1,2)-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] E 5: 36.8688 8( 8) I-x(0,2)-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] F 6: 34.3028 8( 8) L-x-D-x(0,2)-E-x(2)-D-x(0,1)-G-x(2)-[QS]-x-[ST]-[DEN]-x(3)-[IL]-x(3)-[GIV] G 7: 33.6988 8( 8) I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] H 8: 32.1988 9( 8) I-x(1,2)-F-x(0,2)-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] I 9: 29.5287 8( 8) P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] J 10: 27.9188 8( 8) I-x(0,1)-E-x(2)-[DEP]-E-x(2,3)-D-x-[DGS]-x(4)-[AST]-[ADET]-[APST] K 11: 25.3587 8( 8) P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] L 12: 23.9641 10( 8) I-x(2,4)-L-L-x(0,2)-E-x-[FILM]-D-x-[CDG] M 13: 23.9641 8( 8) I-x(0,2)-L-L-x(0,2)-E-x-[FILM]-D-x-[CDG] N 14: 21.1886 8( 8) D-G-x(3)-L-x-[ENQRS]-Y-[ERS] O 15: 20.7940 8( 8) L-x(0,1)-L-x(0,1)-E-x-[FILM]-D-x-[CDG] P 16: 18.8708 8( 8) L-x(0,1)-L-x(0,1)-D-[ES]-x(2)-D Q 17: 18.8504 8( 8) G-x(2,3)-V-x(1,2)-Y-L-x(3)-[EP] R 18: 15.6802 11( 8) I-P-x(0,1)-P-x(0,1)-D S 19: 15.6802 11( 8) I-x(1,2)-I-P-x(0,1)-P T 20: 15.6802 8( 8) F-x(0,1)-Q-x(0,1)-V-x-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 44.6378 8( 8) I-[EST]-F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 252- 267: dtdrt ISFIPPDGafeLmSYR lttvv AP47_MOUSE : 253- 268: endrt ISFIPPDGefeLmSYR lnthv AP50_CAEEL : 267- 282: eteha ISFIPPDGeyeLmRYR ttkdi AP50_RAT : 263- 278: dsers ISFIPPDGefeLmRYR ttkdi AP50_SCHPO : 276- 291: enehr ITFIPPDGeveLmSYR sheni AP54_YEAST : 292- 307: eneki ITFIPPDGkfdLmNYR lstti AP70_YEAST : 367- 382: tdare IEFIPPDGefvLcQYE lkrhv YB8C_YEAST : 288- 303: fspsn ITFIPPDGkfrLlEYS vdlss B 2: 41.5389 9( 8) I-x(1,2)-F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 9(8) AP47_CAEEL : 252- 267: dtdrt Is-FIPPDGafeLmSYR lttvv AP47_MOUSE : 253- 268: endrt Is-FIPPDGefeLmSYR lnthv AP50_CAEEL : 267- 282: eteha Is-FIPPDGeyeLmRYR ttkdi AP50_RAT : 263- 278: dsers Is-FIPPDGefeLmRYR ttkdi AP50_SCHPO : 276- 291: enehr It-FIPPDGeveLmSYR sheni AP54_YEAST : 291- 307: fenek IitFIPPDGkfdLmNYR lstti AP54_YEAST : 292- 307: eneki It-FIPPDGkfdLmNYR lstti AP70_YEAST : 367- 382: tdare Ie-FIPPDGefvLcQYE lkrhv YB8C_YEAST : 288- 303: fspsn It-FIPPDGkfrLlEYS vdlss C 3: 37.8688 8( 8) F-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 254- 267: drtis FIPPDGafeLmSYR lttvv AP47_MOUSE : 255- 268: drtis FIPPDGefeLmSYR lnthv AP50_CAEEL : 269- 282: ehais FIPPDGeyeLmRYR ttkdi AP50_RAT : 265- 278: ersis FIPPDGefeLmRYR ttkdi AP50_SCHPO : 278- 291: ehrit FIPPDGeveLmSYR sheni AP54_YEAST : 294- 307: ekiit FIPPDGkfdLmNYR lstti AP70_YEAST : 369- 382: areie FIPPDGefvLcQYE lkrhv YB8C_YEAST : 290- 303: psnit FIPPDGkfrLlEYS vdlss D 4: 37.3688 8( 8) I-x(1,2)-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 252- 267: dtdrt IsfIPPDGafeLmSYR lttvv AP47_MOUSE : 253- 268: endrt IsfIPPDGefeLmSYR lnthv AP50_CAEEL : 267- 282: eteha IsfIPPDGeyeLmRYR ttkdi AP50_RAT : 263- 278: dsers IsfIPPDGefeLmRYR ttkdi AP50_SCHPO : 276- 291: enehr ItfIPPDGeveLmSYR sheni AP54_YEAST : 292- 307: eneki ItfIPPDGkfdLmNYR lstti AP70_YEAST : 367- 382: tdare IefIPPDGefvLcQYE lkrhv YB8C_YEAST : 288- 303: fspsn ItfIPPDGkfrLlEYS vdlss E 5: 36.8688 8( 8) I-x(0,2)-I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 252- 267: dtdrt IsfIPPDGafeLmSYR lttvv AP47_MOUSE : 253- 268: endrt IsfIPPDGefeLmSYR lnthv AP50_CAEEL : 267- 282: eteha IsfIPPDGeyeLmRYR ttkdi AP50_RAT : 263- 278: dsers IsfIPPDGefeLmRYR ttkdi AP50_SCHPO : 276- 291: enehr ItfIPPDGeveLmSYR sheni AP54_YEAST : 292- 307: eneki ItfIPPDGkfdLmNYR lstti AP70_YEAST : 367- 382: tdare IefIPPDGefvLcQYE lkrhv YB8C_YEAST : 288- 303: fspsn ItfIPPDGkfrLlEYS vdlss F 6: 34.3028 8( 8) L-x-D-x(0,2)-E-x(2)-D-x(0,1)-G-x(2)-[QS]-x-[ST]-[DEN]-x(3)-[IL]-x(3)-[GIV] Occurences: 8(8) AP47_CAEEL : 113- 135: vviye LlD--EmmDfGfpQtTEsriLqeyI tqegq AP47_MOUSE : 113- 135: viiye LlD--ElmDfGypQtTDskiLqeyI tqegh AP50_CAEEL : 111- 133: vliye LlD--EilDfGypQnTDpgvLktfI tqqgv AP50_RAT : 111- 133: vliye LlD--EilDfGypQnSEtgaLktfI tqqgi AP50_SCHPO : 110- 132: sfife LlD--EmiDyGiiQtTEpdaLarsV sitav AP54_YEAST : 114- 136: viiye LlD--EvmDyGipQiTEtkmLkqyI tqksf AP70_YEAST : 114- 136: llvle LiD--EciDfGivQvTDpsiIkdyI rvkvn YB8C_YEAST : 272- 295: igips LhDcvEinD-GvfSpSNitfIppdG kfrll G 7: 33.6988 8( 8) I-P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 255- 267: rtisf IPPDGafeLmSYR lttvv AP47_MOUSE : 256- 268: rtisf IPPDGefeLmSYR lnthv AP50_CAEEL : 270- 282: haisf IPPDGeyeLmRYR ttkdi AP50_RAT : 266- 278: rsisf IPPDGefeLmRYR ttkdi AP50_SCHPO : 279- 291: hritf IPPDGeveLmSYR sheni AP54_YEAST : 295- 307: kiitf IPPDGkfdLmNYR lstti AP70_YEAST : 370- 382: reief IPPDGefvLcQYE lkrhv YB8C_YEAST : 291- 303: snitf IPPDGkfrLlEYS vdlss H 8: 32.1988 9( 8) I-x(1,2)-F-x(0,2)-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 9(8) AP47_CAEEL : 252- 267: dtdrt Is-FipPDGafeLmSYR lttvv AP47_MOUSE : 253- 268: endrt Is-FipPDGefeLmSYR lnthv AP50_CAEEL : 267- 282: eteha Is-FipPDGeyeLmRYR ttkdi AP50_RAT : 263- 278: dsers Is-FipPDGefeLmRYR ttkdi AP50_SCHPO : 276- 291: enehr It-FipPDGeveLmSYR sheni AP54_YEAST : 291- 307: fenek IitFipPDGkfdLmNYR lstti AP54_YEAST : 292- 307: eneki It-FipPDGkfdLmNYR lstti AP70_YEAST : 367- 382: tdare Ie-FipPDGefvLcQYE lkrhv YB8C_YEAST : 288- 303: fspsn It-FipPDGkfrLlEYS vdlss I 9: 29.5287 8( 8) P-P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 256- 267: tisfi PPDGafeLmSYR lttvv AP47_MOUSE : 257- 268: tisfi PPDGefeLmSYR lnthv AP50_CAEEL : 271- 282: aisfi PPDGeyeLmRYR ttkdi AP50_RAT : 267- 278: sisfi PPDGefeLmRYR ttkdi AP50_SCHPO : 280- 291: ritfi PPDGeveLmSYR sheni AP54_YEAST : 296- 307: iitfi PPDGkfdLmNYR lstti AP70_YEAST : 371- 382: eiefi PPDGefvLcQYE lkrhv YB8C_YEAST : 292- 303: nitfi PPDGkfrLlEYS vdlss J 10: 27.9188 8( 8) I-x(0,1)-E-x(2)-[DEP]-E-x(2,3)-D-x-[DGS]-x(4)-[AST]-[ADET]-[APST] Occurences: 8(8) AP47_CAEEL : 110- 128: dnfvv IyEllDEmm-DfGfpqtTES rilqe AP47_MOUSE : 110- 128: dnfvi IyEllDElm-DfGypqtTDS kilqe AP50_CAEEL : 108- 126: nnfvl IyEllDEil-DfGypqnTDP gvlkt AP50_RAT : 108- 126: nnfvl IyEllDEil-DfGypqnSET galkt AP50_SCHPO : 107- 125: dnvsf IfEllDEmi-DyGiiqtTEP dalar AP54_YEAST : 111- 129: dnfvi IyEllDEvm-DyGipqiTET kmlkq AP70_YEAST : 344- 362: dsint I-EkdEEknsDdDaglqAAT darei YB8C_YEAST : 145- 163: lyvnk IkEavPErs-DlSkfisSTA hnlqq K 11: 25.3587 8( 8) P-D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 257- 267: isfip PDGafeLmSYR lttvv AP47_MOUSE : 258- 268: isfip PDGefeLmSYR lnthv AP50_CAEEL : 272- 282: isfip PDGeyeLmRYR ttkdi AP50_RAT : 268- 278: isfip PDGefeLmRYR ttkdi AP50_SCHPO : 281- 291: itfip PDGeveLmSYR sheni AP54_YEAST : 297- 307: itfip PDGkfdLmNYR lstti AP70_YEAST : 372- 382: iefip PDGefvLcQYE lkrhv YB8C_YEAST : 293- 303: itfip PDGkfrLlEYS vdlss L 12: 23.9641 10( 8) I-x(2,4)-L-L-x(0,2)-E-x-[FILM]-D-x-[CDG] Occurences: 10(8) AP47_CAEEL : 110- 121: dnfvv Iye--LLd-EmMDfG fpqtt AP47_MOUSE : 109- 121: rdnfv Iiye-LLd-ElMDfG ypqtt AP47_MOUSE : 110- 121: dnfvi Iye--LLd-ElMDfG ypqtt AP50_CAEEL : 108- 119: nnfvl Iye--LLd-EiLDfG ypqnt AP50_RAT : 108- 119: nnfvl Iye--LLd-EiLDfG ypqns AP50_SCHPO : 107- 118: dnvsf Ife--LLd-EmIDyG iiqtt AP54_YEAST : 110- 122: rdnfv Iiye-LLd-EvMDyG ipqit AP54_YEAST : 111- 122: dnfvi Iye--LLd-EvMDyG ipqit AP70_YEAST : 104- 118: ltknv IldniLLvlElIDeC idfgi YB8C_YEAST : 96- 107: tflet Idri-LL--EyFDkD klsik M 13: 23.9641 8( 8) I-x(0,2)-L-L-x(0,2)-E-x-[FILM]-D-x-[CDG] Occurences: 8(8) AP47_CAEEL : 110- 121: dnfvv IyeLLd-EmMDfG fpqtt AP47_MOUSE : 110- 121: dnfvi IyeLLd-ElMDfG ypqtt AP50_CAEEL : 108- 119: nnfvl IyeLLd-EiLDfG ypqnt AP50_RAT : 108- 119: nnfvl IyeLLd-EiLDfG ypqns AP50_SCHPO : 107- 118: dnvsf IfeLLd-EmIDyG iiqtt AP54_YEAST : 111- 122: dnfvi IyeLLd-EvMDyG ipqit AP70_YEAST : 108- 118: vildn I--LLvlElIDeC idfgi YB8C_YEAST : 99- 107: etidr I--LL--EyFDkD klsik N 14: 21.1886 8( 8) D-G-x(3)-L-x-[ENQRS]-Y-[ERS] Occurences: 8(8) AP47_CAEEL : 258- 267: sfipp DGafeLmSYR lttvv AP47_MOUSE : 259- 268: sfipp DGefeLmSYR lnthv AP50_CAEEL : 273- 282: sfipp DGeyeLmRYR ttkdi AP50_RAT : 269- 278: sfipp DGefeLmRYR ttkdi AP50_SCHPO : 282- 291: tfipp DGeveLmSYR sheni AP54_YEAST : 298- 307: tfipp DGkfdLmNYR lstti AP70_YEAST : 373- 382: efipp DGefvLcQYE lkrhv YB8C_YEAST : 294- 303: tfipp DGkfrLlEYS vdlss O 15: 20.7940 8( 8) L-x(0,1)-L-x(0,1)-E-x-[FILM]-D-x-[CDG] Occurences: 8(8) AP47_CAEEL : 113- 121: vviye L-LdEmMDfG fpqtt AP47_MOUSE : 113- 121: viiye L-LdElMDfG ypqtt AP50_CAEEL : 111- 119: vliye L-LdEiLDfG ypqnt AP50_RAT : 111- 119: vliye L-LdEiLDfG ypqns AP50_SCHPO : 110- 118: sfife L-LdEmIDyG iiqtt AP54_YEAST : 114- 122: viiye L-LdEvMDyG ipqit AP70_YEAST : 110- 118: ldnil LvL-ElIDeC idfgi YB8C_YEAST : 100- 107: tidri L-L-EyFDkD klsik P 16: 18.8708 8( 8) L-x(0,1)-L-x(0,1)-D-[ES]-x(2)-D Occurences: 8(8) AP47_CAEEL : 113- 119: vviye L-L-DEmmD fgfpq AP47_MOUSE : 113- 119: viiye L-L-DElmD fgypq AP50_CAEEL : 111- 117: vliye L-L-DEilD fgypq AP50_RAT : 111- 117: vliye L-L-DEilD fgypq AP50_SCHPO : 110- 116: sfife L-L-DEmiD ygiiq AP54_YEAST : 114- 120: viiye L-L-DEvmD ygipq AP70_YEAST : 112- 120: nillv LeLiDEciD fgivq YB8C_YEAST : 41- 48: ttcpq L-LeDSssD dyldh Q 17: 18.8504 8( 8) G-x(2,3)-V-x(1,2)-Y-L-x(3)-[EP] Occurences: 8(8) AP47_CAEEL : 388- 398: yftts Giq-Vr-YLkiiE krgyq AP47_MOUSE : 389- 399: yftts Giq-Vr-YLkiiE ksgyq AP50_CAEEL : 404- 414: pfaps Glk-Vr-YLkvfE pklny AP50_RAT : 398- 408: pfaps Glk-Vr-YLkvfE pklny AP50_SCHPO : 411- 421: mftss Glh-Vq-YLrvsE psnsk AP54_YEAST : 439- 449: yftts Gmq-Vr-YLkinE klqyk AP70_YEAST : 570- 580: yctcs Glk-Ve-YLkveE pqlqy YB8C_YEAST : 242- 254: tgsih GivdVrsYLndnP lvavk R 18: 15.6802 11( 8) I-P-x(0,1)-P-x(0,1)-D Occurences: 11(8) AP47_CAEEL : 255- 258: rtisf IP-P-D gafel AP47_CAEEL : 313- 318: nveii IPvPsD adspk AP47_MOUSE : 256- 259: rtisf IP-P-D gefel AP47_MOUSE : 314- 319: nveih IPvPnD adspk AP50_CAEEL : 270- 273: haisf IP-P-D geyel AP50_RAT : 266- 269: rsisf IP-P-D gefel AP50_SCHPO : 279- 282: hritf IP-P-D gevel AP54_YEAST : 295- 298: kiitf IP-P-D gkfdl AP54_YEAST : 353- 357: nveil IPvP-D dadtp AP54_YEAST : 353- 358: nveil IPvPdD adtpt AP70_YEAST : 370- 373: reief IP-P-D gefvl YB8C_YEAST : 291- 294: snitf IP-P-D gkfrl S 19: 15.6802 11( 8) I-x(1,2)-I-P-x(0,1)-P Occurences: 11(8) AP47_CAEEL : 252- 257: dtdrt IsfIP-P dgafe AP47_CAEEL : 311- 316: annve Ii-IPvP sdads AP47_MOUSE : 253- 258: endrt IsfIP-P dgefe AP47_MOUSE : 312- 317: annve Ih-IPvP ndads AP50_CAEEL : 267- 272: eteha IsfIP-P dgeye AP50_RAT : 263- 268: dsers IsfIP-P dgefe AP50_SCHPO : 276- 281: enehr ItfIP-P dgeve AP54_YEAST : 292- 297: eneki ItfIP-P dgkfd AP54_YEAST : 351- 356: atnve Il-IPvP ddadt AP70_YEAST : 367- 372: tdare IefIP-P dgefv YB8C_YEAST : 288- 293: fspsn ItfIP-P dgkfr T 20: 15.6802 8( 8) F-x(0,1)-Q-x(0,1)-V-x-L Occurences: 8(8) AP47_CAEEL : 237- 243: ledvk FhQcVrL srfdt AP47_MOUSE : 238- 244: ledvk FhQcVrL srfen AP50_CAEEL : 252- 258: iddcq FhQcVkL tkfet AP50_RAT : 248- 254: iddct FhQcVrL skfds AP50_SCHPO : 261- 267: ledcq FhQcVrL pefen AP54_YEAST : 277- 283: ledlk FhQcVrL skfen AP70_YEAST : 332- 338: msnss FhQcVsL dsint YB8C_YEAST : 479- 483: tqtgn F-Q-VrL Number of patterns evaluated by Pratt:11582 Total running time: 9 seconds