------------------------------------------------------------ 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 TEA_DOMAIN 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 TEA_DOMAIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ABAA_EMENI 796 SCAL_DROME 440 TEC1_YEAST 486 TEF1_HUMAN 426 TEF1_MOUSE 426 Pratt run started at Thu Feb 6 21:24:59 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 78.2310 5( 5) G-R-N-E-L-I-x(2)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 2: 74.0609 5( 5) R-N-E-L-I-x(2)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 3: 69.8909 5( 5) N-E-L-I-x(2)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 4: 65.7208 5( 5) E-L-I-x(2)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 5: 57.3807 5( 5) I-x(2)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 6: 57.3807 5( 5) L-x(3)-Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 7: 53.2107 5( 5) Y-I-x(0,1)-K-x(1,2)-T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 8: 41.7005 5( 5) T-x(3)-R-T-x-K-Q-x-S-S-H-x-Q-V 9: 37.5305 5( 5) R-T-x-K-Q-x-S-S-H-x-Q-V 10: 36.0305 8( 5) T-x(2,3)-R-x(0,2)-K-Q-x-S-S-H-x-Q-V 11: 35.5305 5( 5) K-x(2,4)-R-x(0,2)-K-Q-x-S-S-H-x-Q-V 12: 33.3604 5( 5) T-x-K-Q-x-S-S-H-x-Q-V 13: 32.3604 5( 5) R-x(0,1)-K-x(0,1)-Q-x-S-S-H-x-Q-V 14: 32.3604 9( 5) R-x(0,2)-K-Q-x-S-S-H-x-Q-V 15: 29.1904 5( 5) K-Q-x-S-S-H-x-Q-V 16: 28.6904 5( 5) L-x(1,2)-A-x(2)-I-x(5)-K-x(5)-Q-x(2)-S-x(2)-Q 17: 28.1904 5( 5) L-x(0,2)-A-x(2)-I-x(5)-K-x(5)-Q-x(2)-S-x(2)-Q 18: 28.1904 5( 5) G-x(1,3)-W-S-x(3)-E-x(2)-F-x(2)-A-L 19: 25.0203 5( 5) Q-x-S-S-H-x-Q-V 20: 25.0203 5( 5) W-S-x(3)-E-x(2)-F-x(2)-A-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 97.6542 5( 5) G-R-N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V B 2: 93.4841 5( 5) R-N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V C 3: 89.3141 5( 5) N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V D 4: 85.1440 5( 5) E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V E 5: 80.9740 5( 5) L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V F 6: 76.8039 5( 5) I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V G 7: 71.0363 5( 5) G-x(1,3)-W-S-[DEP]-[DEK]-[ILV]-E-[DEQ]-[AS]-F-x-[EQ]-A-L-x-[AIL]-x(4)-G-x(2)-K-x(3)-[RS]-[DGN]-x-[GNS]-x(3)-[GN]-[ER] H 8: 69.4547 5( 5) Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V I 9: 67.8663 5( 5) W-S-[DEP]-[DEK]-[ILV]-E-[DEQ]-[AS]-F-x-[EQ]-A-L-x-[AIL]-x(4)-G-x(2)-K-x(3)-[RS]-[DGN]-x-[GNS]-x(3)-[GN]-[ER] J 10: 57.9446 5( 5) T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V K 11: 53.2730 5( 5) L-x(1,2)-A-x(2)-I-x(3)-[QT]-x-K-x(2)-[NT]-[KR]-x-Q-x(2)-S-[HR]-[IL]-Q-x(2)-[ADE]-[RS]-x(4)-[DES] L 12: 52.7730 5( 5) L-x(0,2)-A-x(2)-I-x(3)-[QT]-x-K-x(2)-[NT]-[KR]-x-Q-x(2)-S-[HR]-[IL]-Q-x(2)-[ADE]-[RS]-x(4)-[DES] M 13: 47.2901 5( 5) R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V N 14: 43.1201 5( 5) T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V O 15: 42.5419 8( 5) T-x(2,3)-R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V P 16: 42.0419 5( 5) K-x(2,4)-R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V Q 17: 38.8719 5( 5) R-x(0,1)-K-x(0,1)-Q-[IV]-S-S-H-[IL]-Q-V R 18: 38.8719 9( 5) R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V S 19: 35.7018 5( 5) K-Q-[IV]-S-S-H-[IL]-Q-V T 20: 31.5318 5( 5) Q-[IV]-S-S-H-[IL]-Q-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 97.6542 5( 5) G-R-N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 171- 199: rgksy GRNELIAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 126- 154: egkmy GRNELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 163- 191: rnanf GRNELISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 68- 96: egkmy GRNELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 68- 96: egkmy GRNELIArYI-KlrTGKtRTRKQVSSHIQV larrk B 2: 93.4841 5( 5) R-N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 172- 199: gksyg RNELIAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 127- 154: gkmyg RNELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 164- 191: nanfg RNELISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 69- 96: gkmyg RNELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 69- 96: gkmyg RNELIArYI-KlrTGKtRTRKQVSSHIQV larrk C 3: 89.3141 5( 5) N-E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 173- 199: ksygr NELIAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 128- 154: kmygr NELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 165- 191: anfgr NELISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 70- 96: kmygr NELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 70- 96: kmygr NELIArYI-KlrTGKtRTRKQVSSHIQV larrk D 4: 85.1440 5( 5) E-L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 174- 199: sygrn ELIAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 129- 154: mygrn ELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 166- 191: nfgrn ELISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 71- 96: mygrn ELIArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 71- 96: mygrn ELIArYI-KlrTGKtRTRKQVSSHIQV larrk E 5: 80.9740 5( 5) L-I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 175- 199: ygrne LIAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 130- 154: ygrne LIArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 167- 191: fgrne LISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 72- 96: ygrne LIArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 72- 96: ygrne LIArYI-KlrTGKtRTRKQVSSHIQV larrk F 6: 76.8039 5( 5) I-[AS]-x-Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 176- 199: grnel IAeYIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 131- 154: grnel IArYI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 168- 191: grnel ISlYI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 73- 96: grnel IArYI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 73- 96: grnel IArYI-KlrTGKtRTRKQVSSHIQV larrk G 7: 71.0363 5( 5) G-x(1,3)-W-S-[DEP]-[DEK]-[ILV]-E-[DEQ]-[AS]-F-x-[EQ]-A-L-x-[AIL]-x(4)-G-x(2)-K-x(3)-[RS]-[DGN]-x-[GNS]-x(3)-[GN]-[ER] Occurences: 5(5) ABAA_EMENI : 136- 174: dtgkd GepvWSDELEDAFqQALeAnppmGrrKwseRGkSygrNE liaey SCAL_DROME : 91- 127: sadae Gv--WSPDIEQSFqEALsIyppcGrrKiilSDeGkmyGR nelia TEC1_YEAST : 128- 166: eswti GcdkWSEKVEEAFlEALrLimknGttKikiRNaNfgrNE lisly TEF1_HUMAN : 33- 69: dndae Gv--WSPDIEQSFqEALaIyppcGrrKiilSDeGkmyGR nelia TEF1_MOUSE : 33- 69: dndae Gv--WSPDIEQSFqEALaIyppcGrrKiilSDeGkmyGR nelia H 8: 69.4547 5( 5) Y-I-x(0,1)-K-x(1,2)-T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 179- 199: eliae YIyKl-TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 134- 154: eliar YI-KlrTGKtRTRKQVSSHIQV larrk TEC1_YEAST : 171- 191: elisl YI-KhkTNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 76- 96: eliar YI-KlrTGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 76- 96: eliar YI-KlrTGKtRTRKQVSSHIQV larrk I 9: 67.8663 5( 5) W-S-[DEP]-[DEK]-[ILV]-E-[DEQ]-[AS]-F-x-[EQ]-A-L-x-[AIL]-x(4)-G-x(2)-K-x(3)-[RS]-[DGN]-x-[GNS]-x(3)-[GN]-[ER] Occurences: 5(5) ABAA_EMENI : 140- 174: dgepv WSDELEDAFqQALeAnppmGrrKwseRGkSygrNE liaey SCAL_DROME : 93- 127: daegv WSPDIEQSFqEALsIyppcGrrKiilSDeGkmyGR nelia TEC1_YEAST : 132- 166: igcdk WSEKVEEAFlEALrLimknGttKikiRNaNfgrNE lisly TEF1_HUMAN : 35- 69: daegv WSPDIEQSFqEALaIyppcGrrKiilSDeGkmyGR nelia TEF1_MOUSE : 35- 69: daegv WSPDIEQSFqEALaIyppcGrrKiilSDeGkmyGR nelia J 10: 57.9446 5( 5) T-[GN]-[EK]-x-R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 184- 199: yiykl TGKrRTRKQVSSHLQV ldsfl SCAL_DROME : 139- 154: yiklr TGKtRTRKQVSSHIQV larrk TEC1_YEAST : 176- 191: yikhk TNEfRTKKQISSHIQV wkkti TEF1_HUMAN : 81- 96: yiklr TGKtRTRKQVSSHIQV larrk TEF1_MOUSE : 81- 96: yiklr TGKtRTRKQVSSHIQV larrk K 11: 53.2730 5( 5) L-x(1,2)-A-x(2)-I-x(3)-[QT]-x-K-x(2)-[NT]-[KR]-x-Q-x(2)-S-[HR]-[IL]-Q-x(2)-[ADE]-[RS]-x(4)-[DES] Occurences: 5(5) ABAA_EMENI : 175- 207: ygrne Li-AeyIyklTgKrrTRkQvsSHLQvlDSflkgD pdwer SCAL_DROME : 130- 162: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrklrE iqaki TEC1_YEAST : 347- 380: nkkai LesAkkIeieQrKiiNKyQriSRIQehESnpefS snsns TEF1_HUMAN : 72- 104: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrksrD fhskl TEF1_MOUSE : 72- 104: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrksrD fhskl L 12: 52.7730 5( 5) L-x(0,2)-A-x(2)-I-x(3)-[QT]-x-K-x(2)-[NT]-[KR]-x-Q-x(2)-S-[HR]-[IL]-Q-x(2)-[ADE]-[RS]-x(4)-[DES] Occurences: 5(5) ABAA_EMENI : 175- 207: ygrne Li-AeyIyklTgKrrTRkQvsSHLQvlDSflkgD pdwer SCAL_DROME : 130- 162: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrklrE iqaki TEC1_YEAST : 347- 380: nkkai LesAkkIeieQrKiiNKyQriSRIQehESnpefS snsns TEF1_HUMAN : 72- 104: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrksrD fhskl TEF1_MOUSE : 72- 104: ygrne Li-AryIklrTgKtrTRkQvsSHIQvlARrksrD fhskl M 13: 47.2901 5( 5) R-T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 188- 199: ltgkr RTRKQVSSHLQV ldsfl SCAL_DROME : 143- 154: rtgkt RTRKQVSSHIQV larrk TEC1_YEAST : 180- 191: ktnef RTKKQISSHIQV wkkti TEF1_HUMAN : 85- 96: rtgkt RTRKQVSSHIQV larrk TEF1_MOUSE : 85- 96: rtgkt RTRKQVSSHIQV larrk N 14: 43.1201 5( 5) T-[KR]-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 189- 199: tgkrr TRKQVSSHLQV ldsfl SCAL_DROME : 144- 154: tgktr TRKQVSSHIQV larrk TEC1_YEAST : 181- 191: tnefr TKKQISSHIQV wkkti TEF1_HUMAN : 86- 96: tgktr TRKQVSSHIQV larrk TEF1_MOUSE : 86- 96: tgktr TRKQVSSHIQV larrk O 15: 42.5419 8( 5) T-x(2,3)-R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 8(5) ABAA_EMENI : 184- 199: yiykl TgkrRtrKQVSSHLQV ldsfl SCAL_DROME : 139- 154: yiklr TgktRtrKQVSSHIQV larrk SCAL_DROME : 142- 154: lrtgk Trt-R--KQVSSHIQV larrk TEC1_YEAST : 176- 191: yikhk TnefRtkKQISSHIQV wkkti TEF1_HUMAN : 81- 96: yiklr TgktRtrKQVSSHIQV larrk TEF1_HUMAN : 84- 96: lrtgk Trt-R--KQVSSHIQV larrk TEF1_MOUSE : 81- 96: yiklr TgktRtrKQVSSHIQV larrk TEF1_MOUSE : 84- 96: lrtgk Trt-R--KQVSSHIQV larrk P 16: 42.0419 5( 5) K-x(2,4)-R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 186- 199: ykltg Krrt-R--KQVSSHLQV ldsfl SCAL_DROME : 141- 154: klrtg Ktrt-R--KQVSSHIQV larrk TEC1_YEAST : 175- 191: lyikh KtnefRtkKQISSHIQV wkkti TEF1_HUMAN : 83- 96: klrtg Ktrt-R--KQVSSHIQV larrk TEF1_MOUSE : 83- 96: klrtg Ktrt-R--KQVSSHIQV larrk Q 17: 38.8719 5( 5) R-x(0,1)-K-x(0,1)-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 190- 199: gkrrt R-K-QVSSHLQV ldsfl SCAL_DROME : 145- 154: gktrt R-K-QVSSHIQV larrk TEC1_YEAST : 180- 191: ktnef RtKkQISSHIQV wkkti TEF1_HUMAN : 87- 96: gktrt R-K-QVSSHIQV larrk TEF1_MOUSE : 87- 96: gktrt R-K-QVSSHIQV larrk R 18: 38.8719 9( 5) R-x(0,2)-K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 9(5) ABAA_EMENI : 188- 199: ltgkr RtrKQVSSHLQV ldsfl ABAA_EMENI : 190- 199: gkrrt R--KQVSSHLQV ldsfl SCAL_DROME : 143- 154: rtgkt RtrKQVSSHIQV larrk SCAL_DROME : 145- 154: gktrt R--KQVSSHIQV larrk TEC1_YEAST : 180- 191: ktnef RtkKQISSHIQV wkkti TEF1_HUMAN : 85- 96: rtgkt RtrKQVSSHIQV larrk TEF1_HUMAN : 87- 96: gktrt R--KQVSSHIQV larrk TEF1_MOUSE : 85- 96: rtgkt RtrKQVSSHIQV larrk TEF1_MOUSE : 87- 96: gktrt R--KQVSSHIQV larrk S 19: 35.7018 5( 5) K-Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 191- 199: krrtr KQVSSHLQV ldsfl SCAL_DROME : 146- 154: ktrtr KQVSSHIQV larrk TEC1_YEAST : 183- 191: efrtk KQISSHIQV wkkti TEF1_HUMAN : 88- 96: ktrtr KQVSSHIQV larrk TEF1_MOUSE : 88- 96: ktrtr KQVSSHIQV larrk T 20: 31.5318 5( 5) Q-[IV]-S-S-H-[IL]-Q-V Occurences: 5(5) ABAA_EMENI : 192- 199: rrtrk QVSSHLQV ldsfl SCAL_DROME : 147- 154: trtrk QVSSHIQV larrk TEC1_YEAST : 184- 191: frtkk QISSHIQV wkkti TEF1_HUMAN : 89- 96: trtrk QVSSHIQV larrk TEF1_MOUSE : 89- 96: trtrk QVSSHIQV larrk Number of patterns evaluated by Pratt:21798 Total running time: 9 seconds