------------------------------------------------------------ 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 UTEROGLOBIN_2 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 UTEROGLOBIN_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: CC10_HUMAN 91 CC10_MOUSE 96 CC10_RAT 96 FELA_FELCA 92 FELB_FELCA 88 UTER_LEPCA 91 UTER_RABIT 91 Pratt run started at Thu Feb 6 21:32:28 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.5203 7( 7) L-x(1,2)-K-I-x(2)-S-x-L-C 2: 20.8503 7( 7) K-I-x(2)-S-x-L-C 3: 19.3503 7( 7) K-x(5)-L-x(3,4)-R-x(0,2)-I-x-K 4: 16.6802 7( 7) I-x(2)-S-x-L-C 5: 15.6802 7( 7) K-x-L-x(2,3)-L-x(3,4)-R 6: 15.6802 7( 7) Q-x-K-x(1,2)-L-x(2,3)-L 7: 15.6802 7( 7) Q-x(1,2)-K-x-L-x(2,3)-L 8: 15.1802 7( 7) K-x(0,2)-E-x(3,4)-S-x-L 9: 15.1802 7( 7) L-x(3,4)-R-x(0,2)-I-x-K 10: 15.1802 8( 7) A-x(0,2)-Q-x-K-x(1,2)-L 11: 14.6802 7( 7) K-x(2)-E-x(0,2)-K-x(3,5)-L 12: 14.6802 7( 7) P-x(3)-R-x(3,5)-L-x(0,2)-T 13: 12.5102 7( 7) S-x-L-C 14: 12.5102 7( 7) I-C-P 15: 12.0102 7( 7) T-x(2)-L-x(0,1)-C 16: 12.0102 9( 7) L-x(1,2)-L-x(5)-S 17: 12.0102 7( 7) E-x(3,4)-S-x-L 18: 12.0102 7( 7) L-K-x(3,4)-D 19: 12.0102 7( 7) L-x(2,3)-C-x(2)-A 20: 12.0102 8( 7) L-x(2)-T-x(0,1)-P Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 102.4840 7( 7) I-C-P-x-[FV]-x(2)-[DV]-[ILV]-[DE]-x-[FL]-L-x-[DEG]-[ST]-[EP]-[DS]-[EGNS]-Y-x-[AET]-[AQS]-[LMV]-x(2)-[FY]-x-[AP]-x-[DPQS]-[ADTV]-[LMV]-x-[DEN]-[AN]-[AG]-x(2)-[LM]-K-x(2)-[LV]-D-[AST]-x(2)-[QT] B 2: 48.8054 7( 7) K-x-[LV]-[LPV]-[DV]-[STV]-L-x(3,4)-R-x(0,2)-I-[ILMV]-K-x(3)-[DK]-[AI]-x(2)-[ST]-[EPS]-x-[CD] C 3: 33.0568 7( 7) L-x(3,4)-R-x(0,2)-I-[ILMV]-K-x(3)-[DK]-[AI]-x(2)-[ST]-[EPS]-x-[CD] D 4: 27.7083 7( 7) L-x(1,2)-K-I-x(2)-S-[PS]-L-C E 5: 26.7588 7( 7) K-x-[LV]-[LPV]-[DV]-[STV]-L-x(3,4)-R-x(0,2)-I F 6: 26.3635 7( 7) L-x(2,3)-C-[SV]-[DPS]-A-x(2)-[DEGT]-x(2)-[DP]-x(4)-[LV] G 7: 25.9686 7( 7) P-[AQS]-x(2)-R-x(3,5)-L-x(0,2)-T-[EP]-x(4)-[AES]-x-[LMV] H 8: 25.7913 8( 7) A-x(0,2)-Q-x-K-x(1,2)-L-x-[DSTV]-x-[LP]-[EPQ]-[NQT] I 9: 25.7232 7( 7) L-x-[DG]-T-x(0,1)-P-[DQS]-[ES]-x(3)-[ANQS]-[ILMV] J 10: 24.0382 7( 7) K-I-x(2)-S-[PS]-L-C K 11: 22.0210 7( 7) Q-x-K-x(1,2)-L-x(2,3)-L-[EP]-[NQ] L 12: 22.0210 7( 7) Q-x(1,2)-K-x-L-x(2,3)-L-[EP]-[NQ] M 13: 21.5077 7( 7) K-[LM]-x-E-x(0,2)-K-x(3,5)-L-[CS] N 14: 19.8681 7( 7) I-x(2)-S-[PS]-L-C O 15: 19.4883 7( 7) L-K-x(3,4)-D-[ADT]-x(3)-[DEK]-x(3)-[ENQS] P 16: 18.3704 7( 7) K-x(0,2)-E-x(3,4)-S-x-L-[CD] Q 17: 16.8389 8( 7) L-x(1,2)-L-x(4)-[AEST]-S-[AGP] R 18: 15.6981 7( 7) S-[PS]-L-C S 19: 15.6802 7( 7) K-x-L-x(2,3)-L-x(3,4)-R T 20: 15.2313 7( 7) T-x-[AP]-L-x(0,1)-C Best patterns with alignements: fitness hits(seqs) Pattern A 1: 102.4840 7( 7) I-C-P-x-[FV]-x(2)-[DV]-[ILV]-[DE]-x-[FL]-L-x-[DEG]-[ST]-[EP]-[DS]-[EGNS]-Y-x-[AET]-[AQS]-[LMV]-x(2)-[FY]-x-[AP]-x-[DPQS]-[ADTV]-[LMV]-x-[DEN]-[AN]-[AG]-x(2)-[LM]-K-x(2)-[LV]-D-[AST]-x(2)-[QT] Occurences: 7(7) CC10_HUMAN : 23- 71: sasae ICPsFqrVIEtLLmDTPSSYeAAMelFsPdQDMrEAGaqLKklVDTlpQ kpres CC10_MOUSE : 23- 71: sassd ICPgFlqVLEaLLmESESGYvASLkpFnPgSDLqNAGtqLKrlVDTlpQ etrin CC10_RAT : 23- 71: sassd ICPgFlqVLEaLLlGSESNYeAALkpFnPaSDLqNAGtqLKrlVDTlpQ etrin FELA_FELCA : 24- 72: ggnce ICPaVkrDVDlFLtGTPDEYvEQVaqYkAlPVVlENAriLKncVDAkmT eedke FELB_FELCA : 20- 68: tadce ICPaVkrDVDlFLtGTPDEYvEQVaqYkAlPVVlENAriLKncVDAkmT eedke UTER_LEPCA : 23- 71: pasag ICPgFahVIEnLLlGTPSSYgTSLkeFqPdDAMkDAGmqMKkvLDTlpQ ttren UTER_RABIT : 23- 71: pasag ICPrFahVIEnLLlGTPSSYeTSLkeFePdDTMkDAGmqMKkvLDSlpQ ttren B 2: 48.8054 7( 7) K-x-[LV]-[LPV]-[DV]-[STV]-L-x(3,4)-R-x(0,2)-I-[ILMV]-K-x(3)-[DK]-[AI]-x(2)-[ST]-[EPS]-x-[CD] Occurences: 7(7) CC10_HUMAN : 63- 90: agaql KkLVDTLpqkpResIIKlmeKIaqSSlC n CC10_MOUSE : 63- 90: agtql KrLVDTLpqetRinIMKlteKIltSPlC kqdlr CC10_RAT : 63- 90: agtql KrLVDTLpqetRinIVKlteKIltSPlC eqdlr FELA_FELCA : 51- 75: qvaqy KaLPVVLena-R--ILKncvDAkmTEeD kenal FELB_FELCA : 47- 71: qvaqy KaLPVVLena-R--ILKncvDAkmTEeD kenal UTER_LEPCA : 63- 90: agmqm KkVLDTLpqttRenIIKlteKIvkSPlC m UTER_RABIT : 63- 90: agmqm KkVLDSLpqttRenIMKlteKIvkSPlC m C 3: 33.0568 7( 7) L-x(3,4)-R-x(0,2)-I-[ILMV]-K-x(3)-[DK]-[AI]-x(2)-[ST]-[EPS]-x-[CD] Occurences: 7(7) CC10_HUMAN : 69- 90: klvdt LpqkpResIIKlmeKIaqSSlC n CC10_MOUSE : 69- 90: rlvdt LpqetRinIMKlteKIltSPlC kqdlr CC10_RAT : 69- 90: rlvdt LpqetRinIVKlteKIltSPlC eqdlr FELA_FELCA : 57- 75: alpvv Lena-R--ILKncvDAkmTEeD kenal FELB_FELCA : 53- 71: alpvv Lena-R--ILKncvDAkmTEeD kenal UTER_LEPCA : 69- 90: kvldt LpqttRenIIKlteKIvkSPlC m UTER_RABIT : 69- 90: kvlds LpqttRenIMKlteKIvkSPlC m D 4: 27.7083 7( 7) L-x(1,2)-K-I-x(2)-S-[PS]-L-C Occurences: 7(7) CC10_HUMAN : 80- 90: esiik LmeKIaqSSLC n CC10_MOUSE : 80- 90: inimk LteKIltSPLC kqdlr CC10_RAT : 80- 90: inivk LteKIltSPLC eqdlr FELA_FELCA : 83- 92: nalsv Ld-KIytSPLC FELB_FELCA : 79- 88: nalsv Ld-KIytSPLC UTER_LEPCA : 80- 90: eniik LteKIvkSPLC m UTER_RABIT : 80- 90: enimk LteKIvkSPLC m E 5: 26.7588 7( 7) K-x-[LV]-[LPV]-[DV]-[STV]-L-x(3,4)-R-x(0,2)-I Occurences: 7(7) CC10_HUMAN : 63- 77: agaql KkLVDTLpqkpResI iklme CC10_MOUSE : 63- 77: agtql KrLVDTLpqetRinI mklte CC10_RAT : 63- 77: agtql KrLVDTLpqetRinI vklte FELA_FELCA : 51- 62: qvaqy KaLPVVLena-R--I lkncv FELB_FELCA : 47- 58: qvaqy KaLPVVLena-R--I lkncv UTER_LEPCA : 63- 77: agmqm KkVLDTLpqttRenI iklte UTER_RABIT : 63- 77: agmqm KkVLDSLpqttRenI mklte F 6: 26.3635 7( 7) L-x(2,3)-C-[SV]-[DPS]-A-x(2)-[DEGT]-x(2)-[DP]-x(4)-[LV] Occurences: 7(7) CC10_HUMAN : 12- 30: ltlvt LalcCSSAsaEicPsfqrV ietll CC10_MOUSE : 12- 30: itvvm LsicCSSAssDicPgflqV leall CC10_RAT : 12- 30: itvlm LsicCSSAssDicPgflqV leall FELA_FELCA : 63- 80: enari Lkn-CVDAkmTeeDkenaL svldk FELB_FELCA : 59- 76: enari Lkn-CVDAkmTeeDkenaL svldk UTER_LEPCA : 12- 30: lalvt LallCSPAsaGicPgfahV ienll UTER_RABIT : 12- 30: lalvt LallCSPAsaGicPrfahV ienll G 7: 25.9686 7( 7) P-[AQS]-x(2)-R-x(3,5)-L-x(0,2)-T-[EP]-x(4)-[AES]-x-[LMV] Occurences: 7(7) CC10_HUMAN : 25- 46: saeic PSfqRvietlLmdTPssyeAaM elfsp CC10_MOUSE : 70- 89: lvdtl PQetRinimkL--TEkiltSpL ckqdl CC10_RAT : 70- 89: lvdtl PQetRinivkL--TEkiltSpL ceqdl FELA_FELCA : 26- 47: nceic PAvkRdvdlfLtgTPdeyvEqV aqyka FELB_FELCA : 22- 43: dceic PAvkRdvdlfLtgTPdeyvEqV aqyka UTER_LEPCA : 70- 89: vldtl PQttReniikL--TEkivkSpL cm UTER_RABIT : 70- 89: vldsl PQttRenimkL--TEkivkSpL cm H 8: 25.7913 8( 7) A-x(0,2)-Q-x-K-x(1,2)-L-x-[DSTV]-x-[LP]-[EPQ]-[NQT] Occurences: 8(7) CC10_HUMAN : 58- 71: qdmre AgaQlKk-LvDtLPQ kpres CC10_HUMAN : 60- 71: mreag A--QlKk-LvDtLPQ kpres CC10_MOUSE : 58- 71: sdlqn AgtQlKr-LvDtLPQ etrin CC10_RAT : 58- 71: sdlqn AgtQlKr-LvDtLPQ etrin FELA_FELCA : 48- 59: yveqv A--QyKa-LpVvLEN arilk FELB_FELCA : 44- 55: yveqv A--QyKa-LpVvLEN arilk UTER_LEPCA : 58- 72: damkd AgmQmKkvLdTlPQT treni UTER_RABIT : 58- 72: dtmkd AgmQmKkvLdSlPQT treni I 9: 25.7232 7( 7) L-x-[DG]-T-x(0,1)-P-[DQS]-[ES]-x(3)-[ANQS]-[ILMV] Occurences: 7(7) CC10_HUMAN : 35- 46: vietl LmDT-PSSyeaAM elfsp CC10_MOUSE : 65- 77: tqlkr LvDTlPQEtriNI mklte CC10_RAT : 65- 77: tqlkr LvDTlPQEtriNI vklte FELA_FELCA : 36- 47: dvdlf LtGT-PDEyveQV aqyka FELB_FELCA : 32- 43: dvdlf LtGT-PDEyveQV aqyka UTER_LEPCA : 35- 46: vienl LlGT-PSSygtSL kefqp UTER_RABIT : 35- 46: vienl LlGT-PSSyetSL kefep J 10: 24.0382 7( 7) K-I-x(2)-S-[PS]-L-C Occurences: 7(7) CC10_HUMAN : 83- 90: iklme KIaqSSLC n CC10_MOUSE : 83- 90: mklte KIltSPLC kqdlr CC10_RAT : 83- 90: vklte KIltSPLC eqdlr FELA_FELCA : 85- 92: lsvld KIytSPLC FELB_FELCA : 81- 88: lsvld KIytSPLC UTER_LEPCA : 83- 90: iklte KIvkSPLC m UTER_RABIT : 83- 90: mklte KIvkSPLC m K 11: 22.0210 7( 7) Q-x-K-x(1,2)-L-x(2,3)-L-[EP]-[NQ] Occurences: 7(7) CC10_HUMAN : 61- 71: reaga QlKk-LvdtLPQ kpres CC10_MOUSE : 61- 71: qnagt QlKr-LvdtLPQ etrin CC10_RAT : 61- 71: qnagt QlKr-LvdtLPQ etrin FELA_FELCA : 49- 59: veqva QyKa-LpvvLEN arilk FELB_FELCA : 45- 55: veqva QyKa-LpvvLEN arilk UTER_LEPCA : 61- 71: kdagm QmKkvLdt-LPQ ttren UTER_RABIT : 61- 71: kdagm QmKkvLds-LPQ ttren L 12: 22.0210 7( 7) Q-x(1,2)-K-x-L-x(2,3)-L-[EP]-[NQ] Occurences: 7(7) CC10_HUMAN : 61- 71: reaga Ql-KkLvdtLPQ kpres CC10_MOUSE : 61- 71: qnagt Ql-KrLvdtLPQ etrin CC10_RAT : 61- 71: qnagt Ql-KrLvdtLPQ etrin FELA_FELCA : 49- 59: veqva Qy-KaLpvvLEN arilk FELB_FELCA : 45- 55: veqva Qy-KaLpvvLEN arilk UTER_LEPCA : 61- 71: kdagm QmkKvLdt-LPQ ttren UTER_RABIT : 61- 71: kdagm QmkKvLds-LPQ ttren M 13: 21.5077 7( 7) K-[LM]-x-E-x(0,2)-K-x(3,5)-L-[CS] Occurences: 7(7) CC10_HUMAN : 79- 90: resii KLmE--KiaqssLC n CC10_MOUSE : 79- 90: rinim KLtE--KiltspLC kqdlr CC10_RAT : 79- 90: riniv KLtE--KiltspLC eqdlr FELA_FELCA : 70- 81: ncvda KMtEedKena--LS vldki FELB_FELCA : 66- 77: ncvda KMtEedKena--LS vldki UTER_LEPCA : 79- 90: renii KLtE--KivkspLC m UTER_RABIT : 79- 90: renim KLtE--KivkspLC m N 14: 19.8681 7( 7) I-x(2)-S-[PS]-L-C Occurences: 7(7) CC10_HUMAN : 84- 90: klmek IaqSSLC n CC10_MOUSE : 84- 90: kltek IltSPLC kqdlr CC10_RAT : 84- 90: kltek IltSPLC eqdlr FELA_FELCA : 86- 92: svldk IytSPLC FELB_FELCA : 82- 88: svldk IytSPLC UTER_LEPCA : 84- 90: kltek IvkSPLC m UTER_RABIT : 84- 90: kltek IvkSPLC m O 15: 19.4883 7( 7) L-K-x(3,4)-D-[ADT]-x(3)-[DEK]-x(3)-[ENQS] Occurences: 7(7) CC10_HUMAN : 62- 76: eagaq LKklv-DTlpqKpreS iiklm CC10_MOUSE : 62- 76: nagtq LKrlv-DTlpqEtriN imklt CC10_RAT : 62- 76: nagtq LKrlv-DTlpqEtriN ivklt FELA_FELCA : 63- 77: enari LKncv-DAkmtEedkE nalsv FELB_FELCA : 59- 73: enari LKncv-DAkmtEedkE nalsv UTER_LEPCA : 46- 61: sygts LKefqpDDamkDagmQ mkkvl UTER_RABIT : 46- 61: syets LKefepDDtmkDagmQ mkkvl P 16: 18.3704 7( 7) K-x(0,2)-E-x(3,4)-S-x-L-[CD] Occurences: 7(7) CC10_HUMAN : 79- 90: resii KlmEkiaqSsLC n CC10_MOUSE : 79- 90: rinim KltEkiltSpLC kqdlr CC10_RAT : 79- 90: riniv KltEkiltSpLC eqdlr FELA_FELCA : 76- 84: mteed K--Enal-SvLD kiyts FELB_FELCA : 72- 80: mteed K--Enal-SvLD kiyts UTER_LEPCA : 79- 90: renii KltEkivkSpLC m UTER_RABIT : 79- 90: renim KltEkivkSpLC m Q 17: 16.8389 8( 7) L-x(1,2)-L-x(4)-[AEST]-S-[AGP] Occurences: 8(7) CC10_HUMAN : 9- 19: avtlt LvtLalccSSA saeic CC10_HUMAN : 12- 21: ltlvt La-LccssASA eicps CC10_MOUSE : 31- 41: gflqv LeaLlmesESG yvasl CC10_RAT : 10- 19: ititv Lm-LsiccSSA ssdic FELA_FELCA : 80- 90: dkena LsvLdkiyTSP lc FELB_FELCA : 76- 86: dkena LsvLdkiyTSP lc UTER_LEPCA : 12- 21: lalvt La-LlcspASA gicpg UTER_RABIT : 12- 21: lalvt La-LlcspASA gicpr R 18: 15.6981 7( 7) S-[PS]-L-C Occurences: 7(7) CC10_HUMAN : 87- 90: ekiaq SSLC n CC10_MOUSE : 87- 90: ekilt SPLC kqdlr CC10_RAT : 87- 90: ekilt SPLC eqdlr FELA_FELCA : 89- 92: dkiyt SPLC FELB_FELCA : 85- 88: dkiyt SPLC UTER_LEPCA : 87- 90: ekivk SPLC m UTER_RABIT : 87- 90: ekivk SPLC m S 19: 15.6802 7( 7) K-x-L-x(2,3)-L-x(3,4)-R Occurences: 7(7) CC10_HUMAN : 63- 74: agaql KkLvdtLpqkpR esiik CC10_MOUSE : 63- 74: agtql KrLvdtLpqetR inimk CC10_RAT : 63- 74: agtql KrLvdtLpqetR inivk FELA_FELCA : 51- 61: qvaqy KaLpvvLena-R ilknc FELB_FELCA : 47- 57: qvaqy KaLpvvLena-R ilknc UTER_LEPCA : 64- 74: gmqmk KvLdt-LpqttR eniik UTER_RABIT : 64- 74: gmqmk KvLds-LpqttR enimk T 20: 15.2313 7( 7) T-x-[AP]-L-x(0,1)-C Occurences: 7(7) CC10_HUMAN : 11- 15: tltlv TlAL-C cssas CC10_HUMAN : 11- 16: tltlv TlALcC ssasa CC10_MOUSE : 86- 90: tekil TsPL-C kqdlr CC10_RAT : 86- 90: tekil TsPL-C eqdlr FELA_FELCA : 88- 92: ldkiy TsPL-C FELB_FELCA : 84- 88: ldkiy TsPL-C UTER_LEPCA : 11- 16: tlalv TlALlC spasa UTER_RABIT : 11- 16: tlalv TlALlC spasa Number of patterns evaluated by Pratt:426 Total 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