------------------------------------------------------------ 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 9 sequences from file TRANSTHYRETIN_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 9 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 TRANSTHYRETIN_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: TTHY_CHICK 150 TTHY_HUMAN 147 TTHY_MACEU 149 TTHY_MOUSE 147 TTHY_RABIT 127 TTHY_RANCA 18 TTHY_RAT 147 TTHY_SHEEP 147 TTHY_TILRU 150 Pratt run started at Thu Feb 6 21:28:59 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 53.2107 9( 9) G-x(2,3)-S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V 2: 49.5406 9( 9) S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V 3: 45.3706 9( 9) K-C-x(0,1)-L-M-V-K-V-L-D-A-V 4: 41.2005 9( 9) C-x(0,1)-L-M-V-K-V-L-D-A-V 5: 37.5305 9( 9) L-M-V-K-V-L-D-A-V 6: 33.3604 9( 9) M-V-K-V-L-D-A-V 7: 29.1904 9( 9) V-K-V-L-D-A-V 8: 25.0203 9( 9) K-V-L-D-A-V 9: 20.8503 9( 9) V-L-D-A-V 10: 18.8503 9( 9) E-x-D-x(0,2)-S-x(0,2)-K-x-L 11: 16.6802 9( 9) L-D-A-V 12: 14.6802 9( 9) D-x(0,2)-S-x(0,2)-K-x-L 13: 12.5102 9( 9) D-A-V 14: 11.5102 9( 9) A-x(1,3)-S-x(4)-V 15: 11.5102 12( 9) G-x(3,4)-S-x(4,5)-V 16: 11.5102 9( 9) H-x(0,1)-E-x(0,1)-A 17: 11.5102 11( 9) T-x(1,3)-G-E 18: 11.5102 9( 9) T-x(2,3)-A-x(1,2)-S 19: 8.3401 25( 9) A-V 20: 8.3401 10( 9) A-D Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 53.2107 9( 9) G-x(2,3)-S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V B 2: 49.5406 9( 9) S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V C 3: 45.3706 9( 9) K-C-x(0,1)-L-M-V-K-V-L-D-A-V D 4: 41.2005 9( 9) C-x(0,1)-L-M-V-K-V-L-D-A-V E 5: 37.5305 9( 9) L-M-V-K-V-L-D-A-V F 6: 36.2960 9( 9) E-x-D-x(0,2)-S-x(0,2)-K-[ACGST]-L-x-[ILV]-x-[PV]-[FL]-[DH]-[AE] G 7: 34.8599 10( 9) T-x(1,3)-G-E-[AIL]-[DH]-[EGS]-x-[CT]-x(4)-[FV]-x-[DEQ]-[AG]-[ILV] H 8: 33.3604 9( 9) M-V-K-V-L-D-A-V I 9: 32.1260 9( 9) D-x(0,2)-S-x(0,2)-K-[ACGST]-L-x-[ILV]-x-[PV]-[FL]-[DH]-[AE] J 10: 30.0489 9( 9) H-x(0,1)-E-x(0,1)-A-[DE]-[SV]-x(4)-[NV]-[DK]-[ASV]-[GL] K 11: 29.1904 9( 9) V-K-V-L-D-A-V L 12: 26.7976 9( 9) T-x(2,3)-A-x(1,2)-S-x(4)-[SV]-x-[TV]-[AL]-x-[AV]-[STV] M 13: 25.0203 9( 9) K-V-L-D-A-V N 14: 21.2706 10( 9) G-x(3,4)-S-x(4,5)-V-[HK]-x(2)-[DG]-[AE] O 15: 20.8503 9( 9) V-L-D-A-V P 16: 19.8503 9( 9) G-x(2,3)-S-K-C-x(0,1)-L Q 17: 18.6397 9( 9) A-x(1,3)-S-x-[ACT]-[AILV]-x-V-x(3)-[DGSV] R 18: 16.6802 9( 9) L-D-A-V S 19: 16.1802 9( 9) S-K-C-x(0,1)-L T 20: 14.6802 9( 9) E-x-D-x(0,2)-S-x(0,2)-K Best patterns with alignements: fitness hits(seqs) Pattern A 1: 53.2107 9( 9) G-x(2,3)-S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 27- 43: plvsh GsvdSKCpLMVKVLDAV rgspa TTHY_HUMAN : 24- 40: eagpt GtgeSKCpLMVKVLDAV rgspa TTHY_MACEU : 27- 42: avhhe Geh-SKCpLMVKVLDAV rgrpa TTHY_MOUSE : 24- 40: eagpa GageSKCpLMVKVLDAV rgspa TTHY_RABIT : 4- 20: gpv GtgdSKCpLMVKVLDAV rgspa TTHY_RANCA : 3- 18: th GeadSKC-LMVKVLDAV TTHY_RAT : 24- 40: eagpg GageSKCpLMVKVLDAV rgspa TTHY_SHEEP : 24- 40: easpa GageSKCpLMVKVLDAV rgspa TTHY_TILRU : 27- 43: plvsh GsidSKCpLMVKVLDAV rgrpa B 2: 49.5406 9( 9) S-K-C-x(0,1)-L-M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 31- 43: hgsvd SKCpLMVKVLDAV rgspa TTHY_HUMAN : 28- 40: tgtge SKCpLMVKVLDAV rgspa TTHY_MACEU : 30- 42: hegeh SKCpLMVKVLDAV rgrpa TTHY_MOUSE : 28- 40: agage SKCpLMVKVLDAV rgspa TTHY_RABIT : 8- 20: vgtgd SKCpLMVKVLDAV rgspa TTHY_RANCA : 7- 18: hgead SKC-LMVKVLDAV TTHY_RAT : 28- 40: ggage SKCpLMVKVLDAV rgspa TTHY_SHEEP : 28- 40: agage SKCpLMVKVLDAV rgspa TTHY_TILRU : 31- 43: hgsid SKCpLMVKVLDAV rgrpa C 3: 45.3706 9( 9) K-C-x(0,1)-L-M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 32- 43: gsvds KCpLMVKVLDAV rgspa TTHY_HUMAN : 29- 40: gtges KCpLMVKVLDAV rgspa TTHY_MACEU : 31- 42: egehs KCpLMVKVLDAV rgrpa TTHY_MOUSE : 29- 40: gages KCpLMVKVLDAV rgspa TTHY_RABIT : 9- 20: gtgds KCpLMVKVLDAV rgspa TTHY_RANCA : 8- 18: geads KC-LMVKVLDAV TTHY_RAT : 29- 40: gages KCpLMVKVLDAV rgspa TTHY_SHEEP : 29- 40: gages KCpLMVKVLDAV rgspa TTHY_TILRU : 32- 43: gsids KCpLMVKVLDAV rgrpa D 4: 41.2005 9( 9) C-x(0,1)-L-M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 33- 43: svdsk CpLMVKVLDAV rgspa TTHY_HUMAN : 30- 40: tgesk CpLMVKVLDAV rgspa TTHY_MACEU : 32- 42: gehsk CpLMVKVLDAV rgrpa TTHY_MOUSE : 30- 40: agesk CpLMVKVLDAV rgspa TTHY_RABIT : 10- 20: tgdsk CpLMVKVLDAV rgspa TTHY_RANCA : 9- 18: eadsk C-LMVKVLDAV TTHY_RAT : 30- 40: agesk CpLMVKVLDAV rgspa TTHY_SHEEP : 30- 40: agesk CpLMVKVLDAV rgspa TTHY_TILRU : 33- 43: sidsk CpLMVKVLDAV rgrpa E 5: 37.5305 9( 9) L-M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 35- 43: dskcp LMVKVLDAV rgspa TTHY_HUMAN : 32- 40: eskcp LMVKVLDAV rgspa TTHY_MACEU : 34- 42: hskcp LMVKVLDAV rgrpa TTHY_MOUSE : 32- 40: eskcp LMVKVLDAV rgspa TTHY_RABIT : 12- 20: dskcp LMVKVLDAV rgspa TTHY_RANCA : 10- 18: adskc LMVKVLDAV TTHY_RAT : 32- 40: eskcp LMVKVLDAV rgspa TTHY_SHEEP : 32- 40: eskcp LMVKVLDAV rgspa TTHY_TILRU : 35- 43: dskcp LMVKVLDAV rgrpa F 6: 36.2960 9( 9) E-x-D-x(0,2)-S-x(0,2)-K-[ACGST]-L-x-[ILV]-x-[PV]-[FL]-[DH]-[AE] Occurences: 9(9) TTHY_CHICK : 95- 112: gvyrv EfDtsSywKGLgLsPFHE yadvv TTHY_HUMAN : 92- 109: giykv EiDtkSywKALgIsPFHE haevv TTHY_MACEU : 94- 111: glykv EfDtiSywKALgVsPFHE yadvv TTHY_MOUSE : 92- 109: gvyrv ElDtkSywKTLgIsPFHE fadvv TTHY_RABIT : 72- 89: gvykv ElDtkSywKALgIsPFHE yaevv TTHY_RANCA : 4- 17: thg EaD--S--KCLmVkVLDA v TTHY_RAT : 92- 109: gvyrv ElDtkSywKALgIsPFHE yaevv TTHY_SHEEP : 92- 109: glykv ElDtkSywKSLgIsPFHE yaevv TTHY_TILRU : 95- 112: glykv EfDtsSywKALgVsPFHE yadvv G 7: 34.8599 10( 9) T-x(1,3)-G-E-[AIL]-[DH]-[EGS]-x-[CT]-x(4)-[FV]-x-[DEQ]-[AG]-[ILV] Occurences: 10(9) TTHY_CHICK : 72- 91: fatgk TtefGEIHElTteeqFvEGV yrvef TTHY_CHICK : 73- 91: atgkt Tef-GEIHElTteeqFvEGV yrvef TTHY_HUMAN : 69- 88: fasgk TsesGELHGlTteeeFvEGI ykvei TTHY_MACEU : 71- 90: faagk TndnGEIHElTtddkFgEGL ykvef TTHY_MOUSE : 69- 88: fasgk TaesGELHGlTtdekFvEGV yrvel TTHY_RABIT : 49- 68: fasgk TsktGELHGlTtsekFvEGV ykvel TTHY_RANCA : 1- 18: Th--GEADSkClmvkVlDAV TTHY_RAT : 69- 88: fasgk TaesGELHGlTtdekFtEGV yrvel TTHY_SHEEP : 69- 88: fasgk TsdsGELHGlTtedkFvEGL ykvel TTHY_TILRU : 72- 91: fangk TnefGEIHElTtdeqFvQGL ykvef H 8: 33.3604 9( 9) M-V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 36- 43: skcpl MVKVLDAV rgspa TTHY_HUMAN : 33- 40: skcpl MVKVLDAV rgspa TTHY_MACEU : 35- 42: skcpl MVKVLDAV rgrpa TTHY_MOUSE : 33- 40: skcpl MVKVLDAV rgspa TTHY_RABIT : 13- 20: skcpl MVKVLDAV rgspa TTHY_RANCA : 11- 18: dskcl MVKVLDAV TTHY_RAT : 33- 40: skcpl MVKVLDAV rgspa TTHY_SHEEP : 33- 40: skcpl MVKVLDAV rgspa TTHY_TILRU : 36- 43: skcpl MVKVLDAV rgrpa I 9: 32.1260 9( 9) D-x(0,2)-S-x(0,2)-K-[ACGST]-L-x-[ILV]-x-[PV]-[FL]-[DH]-[AE] Occurences: 9(9) TTHY_CHICK : 97- 112: yrvef DtsSywKGLgLsPFHE yadvv TTHY_HUMAN : 94- 109: ykvei DtkSywKALgIsPFHE haevv TTHY_MACEU : 96- 111: ykvef DtiSywKALgVsPFHE yadvv TTHY_MOUSE : 94- 109: yrvel DtkSywKTLgIsPFHE fadvv TTHY_RABIT : 74- 89: ykvel DtkSywKALgIsPFHE yaevv TTHY_RANCA : 6- 17: thgea D--S--KCLmVkVLDA v TTHY_RAT : 94- 109: yrvel DtkSywKALgIsPFHE yaevv TTHY_SHEEP : 94- 109: ykvel DtkSywKSLgIsPFHE yaevv TTHY_TILRU : 97- 112: ykvef DtsSywKALgVsPFHE yadvv J 10: 30.0489 9( 9) H-x(0,1)-E-x(0,1)-A-[DE]-[SV]-x(4)-[NV]-[DK]-[ASV]-[GL] Occurences: 9(9) TTHY_CHICK : 111- 124: glspf H-EyADVvftaNDSG hrhyt TTHY_HUMAN : 108- 121: gispf H-EhAEVvftaNDSG prryt TTHY_MACEU : 110- 123: gvspf H-EyADVvftaNDAG hrhyt TTHY_MOUSE : 108- 121: gispf H-EfADVvftaNDSG hrhyt TTHY_RABIT : 88- 101: gispf H-EyAEVvftaNDSG hrsyt TTHY_RANCA : 2- 15: t HgE-ADSkclmVKVL dav TTHY_RAT : 108- 121: gispf H-EyAEVvftaNDSG hrhyt TTHY_SHEEP : 108- 121: gispf H-EyAEVvftaNDSG lrhyt TTHY_TILRU : 111- 124: gvspf H-EyADVvfsaNDSG hrhyt K 11: 29.1904 9( 9) V-K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 37- 43: kcplm VKVLDAV rgspa TTHY_HUMAN : 34- 40: kcplm VKVLDAV rgspa TTHY_MACEU : 36- 42: kcplm VKVLDAV rgrpa TTHY_MOUSE : 34- 40: kcplm VKVLDAV rgspa TTHY_RABIT : 14- 20: kcplm VKVLDAV rgspa TTHY_RANCA : 12- 18: skclm VKVLDAV TTHY_RAT : 34- 40: kcplm VKVLDAV rgspa TTHY_SHEEP : 34- 40: kcplm VKVLDAV rgspa TTHY_TILRU : 37- 43: kcplm VKVLDAV rgrpa L 12: 26.7976 9( 9) T-x(2,3)-A-x(1,2)-S-x(4)-[SV]-x-[TV]-[AL]-x-[AV]-[STV] Occurences: 9(9) TTHY_CHICK : 129- 146: ghrhy Tia-AllSpfsyStTAvVS dpqe TTHY_HUMAN : 126- 143: gprry Tia-AllSpysyStTAvVT npke TTHY_MACEU : 128- 145: ghrhy Tia-AllSpysfStTAiVS npte TTHY_MOUSE : 126- 143: ghrhy Tia-AllSpysyStTAvVS npqn TTHY_RABIT : 106- 123: ghrsy Tia-AllSpfsyStTAvVS npqe TTHY_RANCA : 1- 18: ThgeAd-SkclmVkVLdAV TTHY_RAT : 126- 143: ghrhy Tia-AllSpysyStTAvVS npqn TTHY_SHEEP : 126- 143: glrhy Tia-AllSpysyStTAlVS spke TTHY_TILRU : 129- 146: ghrhy Tia-AllSpfsyStTAvVS dpke M 13: 25.0203 9( 9) K-V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 38- 43: cplmv KVLDAV rgspa TTHY_HUMAN : 35- 40: cplmv KVLDAV rgspa TTHY_MACEU : 37- 42: cplmv KVLDAV rgrpa TTHY_MOUSE : 35- 40: cplmv KVLDAV rgspa TTHY_RABIT : 15- 20: cplmv KVLDAV rgspa TTHY_RANCA : 13- 18: kclmv KVLDAV TTHY_RAT : 35- 40: cplmv KVLDAV rgspa TTHY_SHEEP : 35- 40: cplmv KVLDAV rgspa TTHY_TILRU : 38- 43: cplmv KVLDAV rgrpa N 14: 21.2706 10( 9) G-x(3,4)-S-x(4,5)-V-[HK]-x(2)-[DG]-[AE] Occurences: 10(9) TTHY_CHICK : 27- 42: plvsh Gsvd-SkcplmVKvlDA vrgsp TTHY_HUMAN : 24- 39: eagpt Gtge-SkcplmVKvlDA vrgsp TTHY_MACEU : 13- 28: llcla GlafvSetaa-VHheGE hskcp TTHY_MOUSE : 24- 39: eagpa Gage-SkcplmVKvlDA vrgsp TTHY_RABIT : 4- 19: gpv Gtgd-SkcplmVKvlDA vrgsp TTHY_RANCA : 3- 17: th Gead-Skclm-VKvlDA v TTHY_RAT : 23- 39: seagp GgageSkcplmVKvlDA vrgsp TTHY_RAT : 24- 39: eagpg Gage-SkcplmVKvlDA vrgsp TTHY_SHEEP : 24- 39: easpa Gage-SkcplmVKvlDA vrgsp TTHY_TILRU : 27- 42: plvsh Gsid-SkcplmVKvlDA vrgrp O 15: 20.8503 9( 9) V-L-D-A-V Occurences: 9(9) TTHY_CHICK : 39- 43: plmvk VLDAV rgspa TTHY_HUMAN : 36- 40: plmvk VLDAV rgspa TTHY_MACEU : 38- 42: plmvk VLDAV rgrpa TTHY_MOUSE : 36- 40: plmvk VLDAV rgspa TTHY_RABIT : 16- 20: plmvk VLDAV rgspa TTHY_RANCA : 14- 18: clmvk VLDAV TTHY_RAT : 36- 40: plmvk VLDAV rgspa TTHY_SHEEP : 36- 40: plmvk VLDAV rgspa TTHY_TILRU : 39- 43: plmvk VLDAV rgrpa P 16: 19.8503 9( 9) G-x(2,3)-S-K-C-x(0,1)-L Occurences: 9(9) TTHY_CHICK : 27- 35: plvsh GsvdSKCpL mvkvl TTHY_HUMAN : 24- 32: eagpt GtgeSKCpL mvkvl TTHY_MACEU : 27- 34: avhhe Geh-SKCpL mvkvl TTHY_MOUSE : 24- 32: eagpa GageSKCpL mvkvl TTHY_RABIT : 4- 12: gpv GtgdSKCpL mvkvl TTHY_RANCA : 3- 10: th GeadSKC-L mvkvl TTHY_RAT : 24- 32: eagpg GageSKCpL mvkvl TTHY_SHEEP : 24- 32: easpa GageSKCpL mvkvl TTHY_TILRU : 27- 35: plvsh GsidSKCpL mvkvl Q 17: 18.6397 9( 9) A-x(1,3)-S-x-[ACT]-[AILV]-x-V-x(3)-[DGSV] Occurences: 9(9) TTHY_CHICK : 42- 55: vkvld AvrgSpAAnVavkV fkkaa TTHY_HUMAN : 39- 52: vkvld AvrgSpAInVavhV frkaa TTHY_MACEU : 15- 27: clagl Afv-SeTAaVhheG ehskc TTHY_MOUSE : 39- 52: vkvld AvrgSpAVdVavkV fkkts TTHY_RABIT : 19- 32: vkvld AvrgSpAVdVsvhV fkkaa TTHY_RANCA : 5- 16: thge Ad--SkCLmVkvlD av TTHY_RAT : 39- 52: vkvld AvrgSpAVdVavkV fkkta TTHY_SHEEP : 39- 52: vkvld AvrgSpAAnVgvkV fkkaa TTHY_TILRU : 48- 59: vrgrp At--SiAVkVskmS eegdw R 18: 16.6802 9( 9) L-D-A-V Occurences: 9(9) TTHY_CHICK : 40- 43: lmvkv LDAV rgspa TTHY_HUMAN : 37- 40: lmvkv LDAV rgspa TTHY_MACEU : 39- 42: lmvkv LDAV rgrpa TTHY_MOUSE : 37- 40: lmvkv LDAV rgspa TTHY_RABIT : 17- 20: lmvkv LDAV rgspa TTHY_RANCA : 15- 18: lmvkv LDAV TTHY_RAT : 37- 40: lmvkv LDAV rgspa TTHY_SHEEP : 37- 40: lmvkv LDAV rgspa TTHY_TILRU : 40- 43: lmvkv LDAV rgrpa S 19: 16.1802 9( 9) S-K-C-x(0,1)-L Occurences: 9(9) TTHY_CHICK : 31- 35: hgsvd SKCpL mvkvl TTHY_HUMAN : 28- 32: tgtge SKCpL mvkvl TTHY_MACEU : 30- 34: hegeh SKCpL mvkvl TTHY_MOUSE : 28- 32: agage SKCpL mvkvl TTHY_RABIT : 8- 12: vgtgd SKCpL mvkvl TTHY_RANCA : 7- 10: hgead SKC-L mvkvl TTHY_RAT : 28- 32: ggage SKCpL mvkvl TTHY_SHEEP : 28- 32: agage SKCpL mvkvl TTHY_TILRU : 31- 35: hgsid SKCpL mvkvl T 20: 14.6802 9( 9) E-x-D-x(0,2)-S-x(0,2)-K Occurences: 9(9) TTHY_CHICK : 95- 103: gvyrv EfDtsSywK glgls TTHY_HUMAN : 92- 100: giykv EiDtkSywK algis TTHY_MACEU : 94- 102: glykv EfDtiSywK algvs TTHY_MOUSE : 92- 100: gvyrv ElDtkSywK tlgis TTHY_RABIT : 72- 80: gvykv ElDtkSywK algis TTHY_RANCA : 4- 8: thg EaD--S--K clmvk TTHY_RAT : 92- 100: gvyrv ElDtkSywK algis TTHY_SHEEP : 92- 100: glykv ElDtkSywK slgis TTHY_TILRU : 95- 103: glykv EfDtsSywK algvs Number of patterns evaluated by Pratt:145 Total running time: 1 seconds