------------------------------------------------------------ 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 5 sequences from file ENT_VIR_OMP_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 5 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 ENT_VIR_OMP_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AIL_YEREN 178 OMPX_ECOLI 171 OMPX_ENTCL 172 PAGC_SALTY 188 VLOM_LAMBD 206 Pratt run started at Thu Feb 6 19:26:11 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 40.7005 5( 5) A-G-x-Q-x-N-P-x(3,4)-V-x(1,2)-D-x(2)-Y-E-x-S 2: 36.5305 5( 5) G-x-Q-x-N-P-x(3,4)-V-x(1,2)-D-x(2)-Y-E-x-S 3: 32.8604 5( 5) G-x-N-x-K-Y-R-Y-E-x(1,2)-D 4: 32.3604 5( 5) Q-x-N-P-x(3,4)-V-x(1,2)-D-x(2)-Y-E-x-S 5: 32.3604 6( 5) G-x(1,2)-N-x-K-Y-R-Y-E-x(1,2)-D 6: 28.6904 5( 5) N-x-K-Y-R-Y-E-x(1,2)-D 7: 28.1904 5( 5) N-P-x(3,4)-V-x(1,2)-D-x(2)-Y-E-x-S 8: 24.5203 5( 5) K-Y-R-Y-E-x(1,2)-D 9: 24.0203 5( 5) P-x(3,4)-V-x(1,2)-D-x(2)-Y-E-x-S 10: 20.3503 6( 5) V-x(1,2)-D-x(2)-Y-E-x-S 11: 20.3503 5( 5) Y-R-Y-E-x(1,2)-D 12: 19.3503 9( 5) G-x(1,3)-Q-x-N-P-x(3,4)-V 13: 18.8503 5( 5) K-x(0,2)-G-x-N-x(2,4)-Y-R 14: 16.6802 5( 5) G-x-G-Y-x-F 15: 16.6802 5( 5) D-x(2)-Y-E-x-S 16: 16.1802 7( 5) G-x(3,4)-G-x-G-x(2)-F 17: 16.1802 5( 5) S-x(5)-Y-x(1,2)-A-G 18: 16.1802 7( 5) G-x-G-Y-x(1,2)-F 19: 16.1802 5( 5) R-Y-E-x(1,2)-D 20: 15.6802 7( 5) G-V-x(0,1)-G-x(1,2)-F Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 88.6785 5( 5) A-G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F B 2: 84.5085 5( 5) G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F C 3: 77.9438 5( 5) Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F D 4: 71.0790 5( 5) N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F E 5: 66.9090 5( 5) P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F F 6: 63.2389 6( 5) V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F G 7: 59.5689 5( 5) D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F H 8: 46.7642 5( 5) G-[FIV]-N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] I 9: 43.6307 6( 5) G-x(1,2)-N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] J 10: 39.9607 5( 5) N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] K 11: 38.1848 5( 5) S-[DK]-x(4)-Y-x(1,2)-A-G-[LMV]-[AGQ]-x-[NSV]-x(2)-[EPST]-x(4)-[DS]-x-[QRS]-x-[EGT] L 12: 33.2797 5( 5) A-G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D M 13: 32.6069 5( 5) K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] N 14: 30.0022 9( 5) G-x(1,3)-Q-[FIM]-N-P-x(3,4)-V-[AIV]-x-[ADV]-x(4)-[GQS] O 15: 29.1097 5( 5) G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D P 16: 28.4368 5( 5) Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Q 17: 26.7842 5( 5) G-x(3,4)-G-[AV]-G-Y-[KR]-F R 18: 25.2058 5( 5) K-x(0,2)-G-[FI]-N-x(2,4)-Y-R-[FY] S 19: 24.2668 5( 5) R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] T 20: 23.1142 5( 5) G-[AV]-G-Y-[KR]-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 88.6785 5( 5) A-G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 141- 178: smayg AGVQFNPlpnfVi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 134- 171: gfsyg AGLQFNPmen-ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 135- 172: gfsyg AGMQFNPien-ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 151- 188: gfawg AGVQMNPleniVv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 169- 206: svaws AGIQINPaasvVv-DiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 169- 206: svaws AGIQINPaas-VvvDiAYEgSgsgDwRtDGFiVGVGYKF B 2: 84.5085 5( 5) G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 142- 178: mayga GVQFNPlpnfVi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 135- 171: fsyga GLQFNPmen-ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 136- 172: fsyga GMQFNPien-ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 152- 188: fawga GVQMNPleniVv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 170- 206: vawsa GIQINPaasvVv-DiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 170- 206: vawsa GIQINPaas-VvvDiAYEgSgsgDwRtDGFiVGVGYKF C 3: 77.9438 5( 5) Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 144- 178: ygagv QFNPlpnfVi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 137- 171: ygagl QFNPmen-ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 138- 172: ygagm QFNPien-ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 154- 188: wgagv QMNPleniVv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 172- 206: wsagi QINPaasvVv-DiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 172- 206: wsagi QINPaas-VvvDiAYEgSgsgDwRtDGFiVGVGYKF D 4: 71.0790 5( 5) N-P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 146- 178: agvqf NPlpnfVi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 139- 171: aglqf NPmen-ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 140- 172: agmqf NPien-ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 156- 188: agvqm NPleniVv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 174- 206: agiqi NPaasvVv-DiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 174- 206: agiqi NPaas-VvvDiAYEgSgsgDwRtDGFiVGVGYKF E 5: 66.9090 5( 5) P-x(3,4)-V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 147- 178: gvqfn PlpnfVi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 140- 171: glqfn Pmen-ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 141- 172: gmqfn Pien-ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 157- 188: gvqmn PleniVv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 175- 206: giqin PaasvVv-DiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 175- 206: giqin Paas-VvvDiAYEgSgsgDwRtDGFiVGVGYKF F 6: 63.2389 6( 5) V-x(1,2)-D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 6(5) AIL_YEREN : 152- 178: plpnf Vi-DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 144- 171: npmen ValDfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 145- 172: npien ValDfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 162- 188: pleni Vv-DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 179- 206: npaas VvvDiAYEgSgsgDwRtDGFiVGVGYKF VLOM_LAMBD : 180- 206: paasv Vv-DiAYEgSgsgDwRtDGFiVGVGYKF G 7: 59.5689 5( 5) D-x-[AGS]-Y-E-x-S-x(3)-[DNS]-x-[DKR]-x-[DGN]-[GT]-[FW]-x-[ALV]-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 154- 178: pnfvi DaSYEySkldSiKvGTWmLGAGYRF OMPX_ECOLI : 147- 171: enval DfSYEqSrirSvDvGTWiAGVGYRF OMPX_ENTCL : 148- 172: enval DfSYEqSrirNvDvGTWiAGVGYRF PAGC_SALTY : 164- 188: enivv DvGYEgSnisStKiNGFnVGVGYRF VLOM_LAMBD : 182- 206: asvvv DiAYEgSgsgDwRtDGFiVGVGYKF H 8: 46.7642 5( 5) G-[FIV]-N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 5(5) AIL_YEREN : 51- 68: dndpk GFNLKYRYEldDNwGviG sfayt OMPX_ECOLI : 46- 62: mnkmg GFNLKYRYEe-DNsPlgV igsft OMPX_ENTCL : 46- 62: mnktn GFNLKYRYEq-DNnPlgV igsft PAGC_SALTY : 48- 64: fknir GVNVKYRYEd-DSpVsfI sslsy VLOM_LAMBD : 57- 74: vshlk GINVKYRYEltDSvGvmA slgfa I 9: 43.6307 6( 5) G-x(1,2)-N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 6(5) AIL_YEREN : 51- 68: dndpk Gf-NLKYRYEldDNwGviG sfayt OMPX_ECOLI : 45- 62: qmnkm GgfNLKYRYEe-DNsPlgV igsft OMPX_ECOLI : 46- 62: mnkmg Gf-NLKYRYEe-DNsPlgV igsft OMPX_ENTCL : 46- 62: mnktn Gf-NLKYRYEq-DNnPlgV igsft PAGC_SALTY : 48- 64: fknir Gv-NVKYRYEd-DSpVsfI sslsy VLOM_LAMBD : 57- 74: vshlk Gi-NVKYRYEltDSvGvmA slgfa J 10: 39.9607 5( 5) N-[LV]-K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 5(5) AIL_YEREN : 53- 68: dpkgf NLKYRYEldDNwGviG sfayt OMPX_ECOLI : 48- 62: kmggf NLKYRYEe-DNsPlgV igsft OMPX_ENTCL : 48- 62: ktngf NLKYRYEq-DNnPlgV igsft PAGC_SALTY : 50- 64: nirgv NVKYRYEd-DSpVsfI sslsy VLOM_LAMBD : 59- 74: hlkgi NVKYRYEltDSvGvmA slgfa K 11: 38.1848 5( 5) S-[DK]-x(4)-Y-x(1,2)-A-G-[LMV]-[AGQ]-x-[NSV]-x(2)-[EPST]-x(4)-[DS]-x-[QRS]-x-[EGT] Occurences: 5(5) AIL_YEREN : 133- 158: esisa SKtsmaYg-AGVQfNplPnfviDaSyE yskld OMPX_ECOLI : 126- 151: ykhdt SDygfsYg-AGLQfNpmEnvalDfSyE qsrir OMPX_ENTCL : 127- 152: rtasn SDygfsYg-AGMQfNpiEnvalDfSyE qsrir PAGC_SALTY : 107- 133: payrl SDnfslYalAGVGtVkaTfkehStQdG dsfsn VLOM_LAMBD : 115- 141: pvlqi SKqvsaYamAGVAhSrwSgstmDyRkT eitpg L 12: 33.2797 5( 5) A-G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D Occurences: 5(5) AIL_YEREN : 141- 154: smayg AGVQFNPlpnfVi-D asyey OMPX_ECOLI : 134- 147: gfsyg AGLQFNPmen-ValD fsyeq OMPX_ENTCL : 135- 148: gfsyg AGMQFNPien-ValD fsyeq PAGC_SALTY : 151- 164: gfawg AGVQMNPleniVv-D vgyeg VLOM_LAMBD : 169- 182: svaws AGIQINPaasvVv-D iayeg VLOM_LAMBD : 169- 182: svaws AGIQINPaas-VvvD iayeg M 13: 32.6069 5( 5) K-Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 5(5) AIL_YEREN : 55- 68: kgfnl KYRYEldDNwGviG sfayt OMPX_ECOLI : 50- 62: ggfnl KYRYEe-DNsPlgV igsft OMPX_ENTCL : 50- 62: ngfnl KYRYEq-DNnPlgV igsft PAGC_SALTY : 52- 64: rgvnv KYRYEd-DSpVsfI sslsy VLOM_LAMBD : 61- 74: kginv KYRYEltDSvGvmA slgfa N 14: 30.0022 9( 5) G-x(1,3)-Q-[FIM]-N-P-x(3,4)-V-[AIV]-x-[ADV]-x(4)-[GQS] Occurences: 9(5) AIL_YEREN : 140- 160: tsmay GagvQFNPlpnfVIdAsyeyS kldsi AIL_YEREN : 142- 160: mayga Gv--QFNPlpnfVIdAsyeyS kldsi OMPX_ECOLI : 133- 152: ygfsy GaglQFNPmen-VAlDfsyeQ srirs OMPX_ECOLI : 135- 152: fsyga Gl--QFNPmen-VAlDfsyeQ srirs OMPX_ENTCL : 134- 153: ygfsy GagmQFNPien-VAlDfsyeQ srirn OMPX_ENTCL : 136- 153: fsyga Gm--QFNPien-VAlDfsyeQ srirn PAGC_SALTY : 150- 170: tgfaw GagvQMNPleniVVdVgyegS nisst PAGC_SALTY : 152- 170: fawga Gv--QMNPleniVVdVgyegS nisst VLOM_LAMBD : 170- 187: vawsa Gi--QINPaas-VVvDiayeG sgsgd O 15: 29.1097 5( 5) G-[ILMV]-Q-[FIM]-N-P-x(3,4)-V-x(1,2)-D Occurences: 5(5) AIL_YEREN : 142- 154: mayga GVQFNPlpnfVi-D asyey OMPX_ECOLI : 135- 147: fsyga GLQFNPmen-ValD fsyeq OMPX_ENTCL : 136- 148: fsyga GMQFNPien-ValD fsyeq PAGC_SALTY : 152- 164: fawga GVQMNPleniVv-D vgyeg VLOM_LAMBD : 170- 182: vawsa GIQINPaasvVv-D iayeg VLOM_LAMBD : 170- 182: vawsa GIQINPaas-VvvD iayeg P 16: 28.4368 5( 5) Y-R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 5(5) AIL_YEREN : 56- 68: gfnlk YRYEldDNwGviG sfayt OMPX_ECOLI : 51- 62: gfnlk YRYEe-DNsPlgV igsft OMPX_ENTCL : 51- 62: gfnlk YRYEq-DNnPlgV igsft PAGC_SALTY : 53- 64: gvnvk YRYEd-DSpVsfI sslsy VLOM_LAMBD : 62- 74: ginvk YRYEltDSvGvmA slgfa Q 17: 26.7842 5( 5) G-x(3,4)-G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 168- 178: dsikv GtwmlGAGYRF OMPX_ECOLI : 161- 171: rsvdv GtwiaGVGYRF OMPX_ENTCL : 162- 172: rnvdv GtwiaGVGYRF PAGC_SALTY : 179- 188: stkin Gfnv-GVGYRF VLOM_LAMBD : 197- 206: dwrtd Gfiv-GVGYKF R 18: 25.2058 5( 5) K-x(0,2)-G-[FI]-N-x(2,4)-Y-R-[FY] Occurences: 5(5) AIL_YEREN : 50- 58: ldndp K--GFNlk--YRY elddn OMPX_ECOLI : 43- 53: qgqmn KmgGFNlk--YRY eedns OMPX_ENTCL : 43- 53: qgvmn KtnGFNlk--YRY eqdnn PAGC_SALTY : 176- 188: nisst KinGFNvgvgYRF VLOM_LAMBD : 56- 64: gvshl K--GINvk--YRY eltds S 19: 24.2668 5( 5) R-Y-E-x(1,2)-D-[NS]-x-[GPV]-x(2)-[AGIV] Occurences: 5(5) AIL_YEREN : 57- 68: fnlky RYEldDNwGviG sfayt OMPX_ECOLI : 52- 62: fnlky RYEe-DNsPlgV igsft OMPX_ENTCL : 52- 62: fnlky RYEq-DNnPlgV igsft PAGC_SALTY : 54- 64: vnvky RYEd-DSpVsfI sslsy VLOM_LAMBD : 63- 74: invky RYEltDSvGvmA slgfa T 20: 23.1142 5( 5) G-[AV]-G-Y-[KR]-F Occurences: 5(5) AIL_YEREN : 173- 178: gtwml GAGYRF OMPX_ECOLI : 166- 171: gtwia GVGYRF OMPX_ENTCL : 167- 172: gtwia GVGYRF PAGC_SALTY : 183- 188: ngfnv GVGYRF VLOM_LAMBD : 201- 206: dgfiv GVGYKF Number of patterns evaluated by Pratt:3007 Total running time: 1 seconds