------------------------------------------------------------ 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 11 sequences from file HEMERYTHRINS PATTERN CONSERVATION: CM: min Nr of Seqs to Match 11 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 HEMERYTHRINS.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: HEM1_PHAGO 119 HEMH_THETS 18 HEMM_NERDI 120 HEMM_THEZO 118 HEMT_LINUN 117 HEMT_PHAGO 113 HEMT_SIPCU 113 HEMT_THEDY 113 HEMT_THEZO 113 HEMU_LINUN 117 MP2_NERDI 119 Pratt run started at Thu Feb 6 19:52:45 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.8503 11( 11) P-x-P-x(2)-W-x(3)-F-x(3)-Y 2: 16.6802 11( 11) P-x(2)-W-x(3)-F-x(3)-Y 3: 12.5102 11( 11) W-x(3)-F-x(3)-Y 4: 10.5102 17( 11) D-x(0,2)-F-x(0,2)-K 5: 8.3401 11( 11) F-x(3)-Y 6: 7.8401 21( 11) F-x(0,1)-Y 7: 7.8401 19( 11) F-x(2,3)-F 8: 7.8401 12( 11) S-x(0,1)-F 9: 7.8401 13( 11) W-x(1,2)-S 10: 7.8401 21( 11) F-x(2,3)-E 11: 7.8401 18( 11) I-x(3,4)-F 12: 7.3401 17( 11) K-x(0,2)-Y 13: 7.3401 23( 11) F-x(0,2)-K 14: 7.3401 20( 11) E-x(1,3)-K 15: 7.3401 12( 11) D-x(2,4)-F Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 33.0063 11( 11) P-x-P-[FY]-x-W-[DNT]-x-[DS]-F-x-[TV]-x-Y B 2: 28.8363 11( 11) P-[FY]-x-W-[DNT]-x-[DS]-F-x-[TV]-x-Y C 3: 21.4817 11( 11) W-[DNT]-x-[DS]-F-x-[TV]-x-Y D 4: 19.7636 11( 11) I-x(3,4)-F-x-[WY]-[DKR]-[EG]-x-[FIL] E 5: 14.1845 11( 11) S-x(0,1)-F-x-[TV]-x-[HY] F 6: 13.1084 13( 11) D-x(0,2)-F-x(0,2)-K-[GLV] G 7: 11.5120 11( 11) F-x-[TV]-x-Y H 8: 10.4323 13( 11) W-x(1,2)-S-x(2)-[PTV] I 9: 10.0634 18( 11) F-x(0,1)-Y-[DEKR] J 10: 9.9384 17( 11) F-x(0,2)-K-[GLV] K 11: 7.8401 19( 11) F-x(2,3)-F L 12: 7.8401 21( 11) F-x(2,3)-E M 13: 7.3401 17( 11) K-x(0,2)-Y N 14: 7.3401 20( 11) E-x(1,3)-K O 15: 7.3401 12( 11) D-x(2,4)-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 33.0063 11( 11) P-x-P-[FY]-x-W-[DNT]-x-[DS]-F-x-[TV]-x-Y Occurences: 11(11) HEM1_PHAGO : 5- 18: pfdi PePYvWDeSFrVfY dnldd HEMH_THETS : 4- 17: ydi PePFrWDeSFkVfY e HEMM_NERDI : 5- 18: gfev PePFkWDeSFqVfY dklde HEMM_THEZO : 5- 18: gwei PePYvWDeSFrVfY eqlde HEMT_LINUN : 4- 17: vkv PePFaWNeSFaTsY knidl HEMT_PHAGO : 5- 18: gfpi PdPYvWDpSFrTfY siidd HEMT_SIPCU : 5- 18: gfpv PdPFiWDaSFkTfY ddldn HEMT_THEDY : 5- 18: gfpi PdPYcWDiSFrTfY tivdd HEMT_THEZO : 5- 18: gfpi PdPYgWDpSFrTfY siidd HEMU_LINUN : 4- 17: mki PvPYaWTpDFkTtY enids MP2_NERDI : 5- 18: gfei PePYkWDeSFqVfY eklde B 2: 28.8363 11( 11) P-[FY]-x-W-[DNT]-x-[DS]-F-x-[TV]-x-Y Occurences: 11(11) HEM1_PHAGO : 7- 18: fdipe PYvWDeSFrVfY dnldd HEMH_THETS : 6- 17: ydipe PFrWDeSFkVfY e HEMM_NERDI : 7- 18: fevpe PFkWDeSFqVfY dklde HEMM_THEZO : 7- 18: weipe PYvWDeSFrVfY eqlde HEMT_LINUN : 6- 17: vkvpe PFaWNeSFaTsY knidl HEMT_PHAGO : 7- 18: fpipd PYvWDpSFrTfY siidd HEMT_SIPCU : 7- 18: fpvpd PFiWDaSFkTfY ddldn HEMT_THEDY : 7- 18: fpipd PYcWDiSFrTfY tivdd HEMT_THEZO : 7- 18: fpipd PYgWDpSFrTfY siidd HEMU_LINUN : 6- 17: mkipv PYaWTpDFkTtY enids MP2_NERDI : 7- 18: feipe PYkWDeSFqVfY eklde C 3: 21.4817 11( 11) W-[DNT]-x-[DS]-F-x-[TV]-x-Y Occurences: 11(11) HEM1_PHAGO : 10- 18: pepyv WDeSFrVfY dnldd HEMH_THETS : 9- 17: pepfr WDeSFkVfY e HEMM_NERDI : 10- 18: pepfk WDeSFqVfY dklde HEMM_THEZO : 10- 18: pepyv WDeSFrVfY eqlde HEMT_LINUN : 9- 17: pepfa WNeSFaTsY knidl HEMT_PHAGO : 10- 18: pdpyv WDpSFrTfY siidd HEMT_SIPCU : 10- 18: pdpfi WDaSFkTfY ddldn HEMT_THEDY : 10- 18: pdpyc WDiSFrTfY tivdd HEMT_THEZO : 10- 18: pdpyg WDpSFrTfY siidd HEMU_LINUN : 9- 17: pvpya WTpDFkTtY enids MP2_NERDI : 10- 18: pepyk WDeSFqVfY eklde D 4: 19.7636 11( 11) I-x(3,4)-F-x-[WY]-[DKR]-[EG]-x-[FIL] Occurences: 11(11) HEM1_PHAGO : 108- 119: wlvqh IkttdFkYKGkL HEMH_THETS : 3- 13: yd Ipep-FrWDEsF kvfye HEMM_NERDI : 109- 120: wlvnh IkgtdFtYKGkL HEMM_THEZO : 107- 118: wlvnh IkgtdFkYKGkL HEMT_LINUN : 106- 117: wlvnh IptedFkYKGkL HEMT_PHAGO : 102- 113: wlvnh IktidFkYKGkI HEMT_SIPCU : 102- 113: wltqh IktidFkYKGkL HEMT_THEDY : 102- 113: wlvnh IktidFkYRGkI HEMT_THEZO : 102- 113: wlvnh IktidFkYKGkI HEMU_LINUN : 106- 117: wlanh IptedFkYKGkL MP2_NERDI : 108- 119: wlvnh IkgtdFgYKGkL E 5: 14.1845 11( 11) S-x(0,1)-F-x-[TV]-x-[HY] Occurences: 11(11) HEM1_PHAGO : 13- 18: yvwde S-FrVfY dnldd HEMH_THETS : 12- 17: frwde S-FkVfY e HEMM_NERDI : 13- 18: fkwde S-FqVfY dklde HEMM_THEZO : 13- 18: yvwde S-FrVfY eqlde HEMT_LINUN : 12- 17: fawne S-FaTsY knidl HEMT_PHAGO : 13- 18: yvwdp S-FrTfY siidd HEMT_SIPCU : 13- 18: fiwda S-FkTfY ddldn HEMT_THEDY : 13- 18: ycwdi S-FrTfY tivdd HEMT_THEZO : 13- 18: ygwdp S-FrTfY siidd HEMU_LINUN : 35- 41: glfal SeFnTqH qlnaa MP2_NERDI : 13- 18: ykwde S-FqVfY eklde F 6: 13.1084 13( 11) D-x(0,2)-F-x(0,2)-K-[GLV] Occurences: 13(11) HEM1_PHAGO : 80- 85: kqmhk D--FlaKL gglka HEM1_PHAGO : 112- 117: hiktt D--FkyKG kl HEMH_THETS : 10- 15: epfrw DesF--KV fye HEMM_NERDI : 113- 118: hikgt D--FtyKG kl HEMM_THEZO : 111- 116: hikgt D--FkyKG kl HEMT_LINUN : 110- 115: hipte D--FkyKG kl HEMT_PHAGO : 106- 111: hikti D--FkyKG ki HEMT_SIPCU : 106- 111: hikti D--FkyKG kl HEMT_THEDY : 78- 84: hkkah Dd-FihKL dtwdg HEMT_THEDY : 79- 84: kkahd D--FihKL dtwdg HEMT_THEZO : 106- 111: hikti D--FkyKG ki HEMU_LINUN : 110- 115: hipte D--FkyKG kl MP2_NERDI : 112- 117: hikgt D--FgyKG kl G 7: 11.5120 11( 11) F-x-[TV]-x-Y Occurences: 11(11) HEM1_PHAGO : 14- 18: vwdes FrVfY dnldd HEMH_THETS : 13- 17: rwdes FkVfY e HEMM_NERDI : 14- 18: kwdes FqVfY dklde HEMM_THEZO : 14- 18: vwdes FrVfY eqlde HEMT_LINUN : 13- 17: awnes FaTsY knidl HEMT_PHAGO : 14- 18: vwdps FrTfY siidd HEMT_SIPCU : 14- 18: iwdas FkTfY ddldn HEMT_THEDY : 14- 18: cwdis FrTfY tivdd HEMT_THEZO : 14- 18: gwdps FrTfY siidd HEMU_LINUN : 13- 17: awtpd FkTtY enids MP2_NERDI : 14- 18: kwdes FqVfY eklde H 8: 10.4323 13( 11) W-x(1,2)-S-x(2)-[PTV] Occurences: 13(11) HEM1_PHAGO : 10- 16: pepyv WdeSfrV fydnl HEMH_THETS : 9- 15: pepfr WdeSfkV fye HEMM_NERDI : 10- 16: pepfk WdeSfqV fydkl HEMM_THEZO : 10- 16: pepyv WdeSfrV fyeql HEMT_LINUN : 9- 15: pepfa WneSfaT sykni HEMT_PHAGO : 10- 16: pdpyv WdpSfrT fysii HEMT_PHAGO : 93- 99: kgdvk WakSwlV nhikt HEMT_SIPCU : 10- 16: pdpfi WdaSfkT fyddl HEMT_THEDY : 10- 16: pdpyc WdiSfrT fytiv HEMT_THEZO : 10- 16: pdpyg WdpSfrT fysii HEMT_THEZO : 93- 99: kgdvk WakSwlV nhikt HEMU_LINUN : 86- 91: dtmrg Wq-SpvP qkalk MP2_NERDI : 10- 16: pepyk WdeSfqV fyekl I 9: 10.0634 18( 11) F-x(0,1)-Y-[DEKR] Occurences: 18(11) HEM1_PHAGO : 17- 19: esfrv F-YD nldde HEM1_PHAGO : 113- 116: ikttd FkYK gkl HEMH_THETS : 16- 18: esfkv F-YE HEMM_NERDI : 17- 19: esfqv F-YD kldee HEMM_NERDI : 114- 117: ikgtd FtYK gkl HEMM_THEZO : 17- 19: esfrv F-YE qldee HEMM_THEZO : 112- 115: ikgtd FkYK gkl HEMT_LINUN : 111- 114: ipted FkYK gkl HEMT_PHAGO : 69- 71: asqyq F-YD ehkke HEMT_PHAGO : 107- 110: iktid FkYK gki HEMT_SIPCU : 17- 19: asfkt F-YD dldnq HEMT_SIPCU : 107- 110: iktid FkYK gkl HEMT_THEDY : 107- 110: iktid FkYR gki HEMT_THEZO : 69- 71: asqyq F-YD ehkka HEMT_THEZO : 107- 110: iktid FkYK gki HEMU_LINUN : 111- 114: ipted FkYK gkl MP2_NERDI : 17- 19: esfqv F-YE kldee MP2_NERDI : 113- 116: ikgtd FgYK gkl J 10: 9.9384 17( 11) F-x(0,2)-K-[GLV] Occurences: 17(11) HEM1_PHAGO : 29- 31: ehkgl F--KG vfnca HEM1_PHAGO : 81- 85: qmhkd FlaKL gglka HEM1_PHAGO : 113- 117: ikttd FkyKG kl HEMH_THETS : 13- 15: rwdes F--KV fye HEMM_NERDI : 17- 21: esfqv FydKL deehk HEMM_NERDI : 114- 118: ikgtd FtyKG kl HEMM_THEZO : 29- 31: ehkki F--KG ifdci HEMM_THEZO : 112- 116: ikgtd FkyKG kl HEMT_LINUN : 111- 115: ipted FkyKG kl HEMT_PHAGO : 107- 111: iktid FkyKG ki HEMT_SIPCU : 80- 84: aahee FlgKV kggsa HEMT_SIPCU : 107- 111: iktid FkyKG kl HEMT_THEDY : 80- 84: kahdd FihKL dtwdg HEMT_THEZO : 107- 111: iktid FkyKG ki HEMU_LINUN : 111- 115: ipted FkyKG kl MP2_NERDI : 17- 21: esfqv FyeKL deehk MP2_NERDI : 113- 117: ikgtd FgyKG kl K 11: 7.8401 19( 11) F-x(2,3)-F Occurences: 19(11) HEM1_PHAGO : 14- 17: vwdes Frv-F ydnld HEM1_PHAGO : 29- 33: ehkgl FkgvF ncaad HEMH_THETS : 13- 16: rwdes Fkv-F ye HEMM_NERDI : 14- 17: kwdes Fqv-F ydkld HEMM_NERDI : 29- 33: ehkqi FnaiF alggg HEMM_THEZO : 14- 17: vwdes Frv-F yeqld HEMM_THEZO : 29- 33: ehkki FkgiF dcird HEMT_LINUN : 28- 32: ehrtl FnglF alsef HEMT_LINUN : 50- 54: ackev FvmhF rdeqg HEMT_PHAGO : 14- 17: vwdps Frt-F ysiid HEMT_PHAGO : 29- 33: ehktl FngiF hlaid HEMT_SIPCU : 14- 17: iwdas Fkt-F yddld HEMT_THEDY : 14- 17: cwdis Frt-F ytivd HEMT_THEZO : 14- 17: gwdps Frt-F ysiid HEMT_THEZO : 29- 33: ehktl FngiF hlaid HEMU_LINUN : 28- 32: ehrtl FnglF alsef HEMU_LINUN : 50- 54: aaiev FtlhF hdeqg MP2_NERDI : 14- 17: kwdes Fqv-F yekld MP2_NERDI : 29- 33: ehkqi FnaiF alcgg L 12: 7.8401 21( 11) F-x(2,3)-E Occurences: 21(11) HEM1_PHAGO : 2- 6: p FdipE pyvwd HEM1_PHAGO : 56- 59: vttth Frn-E eammd HEM1_PHAGO : 56- 60: vttth FrneE ammda HEMH_THETS : 7- 11: dipep FrwdE sfkvf HEMM_NERDI : 2- 6: g FevpE pfkwd HEMM_NERDI : 8- 12: evpep FkwdE sfqvf HEMM_NERDI : 55- 58: vtanh Fad-E eamml HEMM_NERDI : 55- 59: vtanh FadeE ammla HEMM_THEZO : 55- 58: vttnh Fth-E eammd HEMM_THEZO : 55- 59: vttnh FtheE ammda HEMT_LINUN : 7- 11: kvpep FawnE sfats HEMT_LINUN : 32- 36: lfngl FalsE fntrd HEMT_LINUN : 54- 57: vfvmh Frd-E qgqme HEMT_LINUN : 97- 100: qkdik Fgm-E wlvnh HEMT_PHAGO : 55- 58: ctgkh Fln-E qvlmq HEMT_PHAGO : 69- 72: asqyq Fyd-E hkkeh HEMT_SIPCU : 55- 58: clvah Flf-E eaamq HEMT_SIPCU : 55- 59: clvah FlfeE aamqv HEMT_THEDY : 55- 58: ctgkh Fln-E qqlmq HEMT_THEZO : 55- 59: ctgkh FlnqE vlmqa HEMT_THEZO : 69- 72: asqyq Fyd-E hkkah HEMU_LINUN : 32- 36: lfngl FalsE fntqh HEMU_LINUN : 54- 57: vftlh Fhd-E qgqmi MP2_NERDI : 2- 6: g FeipE pykwd MP2_NERDI : 55- 58: vtanh Fad-E eamlk MP2_NERDI : 55- 59: vtanh FadeE amlka M 13: 7.3401 17( 11) K-x(0,2)-Y Occurences: 17(11) HEM1_PHAGO : 67- 68: mmdaa K--Y envvp HEM1_PHAGO : 114- 115: kttdf K--Y kgkl HEMH_THETS : 14- 17: wdesf KvfY e HEMM_NERDI : 97- 100: pvpnd KllY akdwl HEMM_THEZO : 66- 67: mmdaa K--Y sevvp HEMM_THEZO : 113- 114: kgtdf K--Y kgkl HEMT_LINUN : 63- 66: qgqme KanY ehfee HEMT_LINUN : 112- 113: ptedf K--Y kgkl HEMT_PHAGO : 108- 109: ktidf K--Y kgki HEMT_SIPCU : 15- 18: wdasf KtfY ddldn HEMT_SIPCU : 66- 67: amqva K--Y ggyga HEMT_SIPCU : 108- 109: ktidf K--Y kgkl HEMT_THEDY : 108- 109: ktidf K--Y rgki HEMT_THEZO : 108- 109: ktidf K--Y kgki HEMU_LINUN : 14- 17: wtpdf KttY enids HEMU_LINUN : 112- 113: ptedf K--Y kgkl MP2_NERDI : 96- 99: pvpqd KinY akewl N 14: 7.3401 20( 11) E-x(1,3)-K Occurences: 20(11) HEM1_PHAGO : 24- 26: dnldd Eh--K glfkg HEMH_THETS : 11- 14: pfrwd Esf-K vfye HEMM_NERDI : 6- 9: gfevp Epf-K wdesf HEMM_NERDI : 23- 26: ydkld Eeh-K qifna HEMM_NERDI : 24- 26: dklde Eh--K qifna HEMM_THEZO : 23- 26: yeqld Eeh-K kifkg HEMM_THEZO : 23- 27: yeqld EehkK ifkgi HEMM_THEZO : 24- 26: eqlde Eh--K kifkg HEMM_THEZO : 24- 27: eqlde Ehk-K ifkgi HEMT_LINUN : 109- 112: nhipt Edf-K ykgkl HEMT_PHAGO : 24- 26: siidd Eh--K tlfng HEMT_PHAGO : 72- 74: yqfyd Eh--K keheg HEMT_PHAGO : 72- 75: yqfyd Ehk-K ehegf HEMT_SIPCU : 79- 83: kaahe EflgK vkggs HEMT_THEDY : 24- 26: tivdd Eh--K tlfng HEMT_THEDY : 72- 74: yagya Eh--K kahdd HEMT_THEDY : 72- 75: yagya Ehk-K ahddf HEMT_THEZO : 24- 26: siidd Eh--K tlfng HEMT_THEZO : 72- 74: yqfyd Eh--K kahee HEMT_THEZO : 72- 75: yqfyd Ehk-K aheef HEMU_LINUN : 109- 112: nhipt Edf-K ykgkl MP2_NERDI : 6- 9: gfeip Epy-K wdesf MP2_NERDI : 23- 26: yekld Eeh-K qifna MP2_NERDI : 24- 26: eklde Eh--K qifna MP2_NERDI : 59- 63: hfade EamlK asasy O 15: 7.3401 12( 11) D-x(2,4)-F Occurences: 12(11) HEM1_PHAGO : 11- 14: epyvw Des--F rvfyd HEMH_THETS : 2- 7: y DipepF rwdes HEMH_THETS : 10- 13: epfrw Des--F kvfye HEMM_NERDI : 11- 14: epfkw Des--F qvfyd HEMM_THEZO : 11- 14: epyvw Des--F rvfye HEMT_LINUN : 94- 97: pvaqk Dik--F gmewl HEMT_PHAGO : 11- 14: dpyvw Dps--F rtfys HEMT_SIPCU : 11- 14: dpfiw Das--F ktfyd HEMT_THEDY : 11- 14: dpycw Dis--F rtfyt HEMT_THEZO : 11- 14: dpygw Dps--F rtfys HEMU_LINUN : 74- 79: tkeht DihngF mdtmr MP2_NERDI : 11- 14: epykw Des--F qvfye Number of patterns evaluated by Pratt:31 Total running time: 0 seconds