------------------------------------------------------------ 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 6 sequences from file GALANIN PATTERN CONSERVATION: CM: min Nr of Seqs to Match 6 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 GALANIN.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: GALA_BOVIN 123 GALA_CHICK 29 GALA_HUMAN 107 GALA_PIG 123 GALA_RAT 124 GALA_SHEEP 29 Pratt run started at Thu Feb 6 19:31:15 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 91.7411 6( 6) G-W-T-L-N-S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 2: 87.5711 6( 6) W-T-L-N-S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 3: 83.4010 6( 6) T-L-N-S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 4: 79.2310 6( 6) L-N-S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 5: 75.0609 6( 6) N-S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 6: 70.8909 6( 6) S-A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 7: 66.7208 6( 6) A-G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 8: 62.5508 6( 6) G-Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 9: 58.3807 6( 6) Y-L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 10: 54.2107 6( 6) L-L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 11: 50.0406 6( 6) L-G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 12: 45.8706 6( 6) G-P-H-A-x(3)-H-R-S-F-x-D-K-x-G 13: 41.7005 6( 6) P-H-A-x(3)-H-R-S-F-x-D-K-x-G 14: 37.5305 6( 6) H-A-x(3)-H-R-S-F-x-D-K-x-G 15: 33.3604 6( 6) A-x(3)-H-R-S-F-x-D-K-x-G 16: 29.1904 6( 6) H-R-S-F-x-D-K-x-G 17: 25.0203 6( 6) R-S-F-x-D-K-x-G 18: 20.8503 6( 6) S-F-x-D-K-x-G 19: 16.6802 6( 6) F-x-D-K-x-G 20: 15.6802 7( 6) A-x(1,3)-D-x(2)-R-S Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 107.3300 6( 6) G-W-T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] B 2: 103.1599 6( 6) W-T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] C 3: 98.9899 6( 6) T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] D 4: 94.8198 6( 6) L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] E 5: 90.6498 6( 6) N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] F 6: 86.4797 6( 6) S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] G 7: 82.3097 6( 6) A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] H 8: 78.1396 6( 6) G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] I 9: 73.9696 6( 6) Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] J 10: 69.7995 6( 6) L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] K 11: 65.6295 6( 6) L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] L 12: 61.4594 6( 6) G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] M 13: 57.2894 6( 6) P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] N 14: 53.1193 6( 6) H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] O 15: 48.9493 6( 6) A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] P 16: 35.6564 6( 6) H-R-S-F-x-D-K-x-G-[FL]-[AT] Q 17: 31.4864 6( 6) R-S-F-x-D-K-x-G-[FL]-[AT] R 18: 27.3163 6( 6) S-F-x-D-K-x-G-[FL]-[AT] S 19: 23.1463 6( 6) F-x-D-K-x-G-[FL]-[AT] T 20: 18.8768 7( 6) A-x(1,3)-D-x-[EH]-R-S Best patterns with alignements: fitness hits(seqs) Pattern A 1: 107.3300 6( 6) G-W-T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 33- 61: vkekr GWTLNSAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 1- 29: GWTLNSAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 17- 45: akekr GWTLNSAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 33- 61: vkekr GWTLNSAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 33- 61: tkekr GWTLNSAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 1- 29: GWTLNSAGYLLGPHAIDNHRSFhDKhGLA B 2: 103.1599 6( 6) W-T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 34- 61: kekrg WTLNSAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 2- 29: g WTLNSAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 18- 45: kekrg WTLNSAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 34- 61: kekrg WTLNSAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 34- 61: kekrg WTLNSAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 2- 29: g WTLNSAGYLLGPHAIDNHRSFhDKhGLA C 3: 98.9899 6( 6) T-L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 35- 61: ekrgw TLNSAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 3- 29: gw TLNSAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 19- 45: ekrgw TLNSAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 35- 61: ekrgw TLNSAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 35- 61: ekrgw TLNSAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 3- 29: gw TLNSAGYLLGPHAIDNHRSFhDKhGLA D 4: 94.8198 6( 6) L-N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 36- 61: krgwt LNSAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 4- 29: gwt LNSAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 20- 45: krgwt LNSAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 36- 61: krgwt LNSAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 36- 61: krgwt LNSAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 4- 29: gwt LNSAGYLLGPHAIDNHRSFhDKhGLA E 5: 90.6498 6( 6) N-S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 37- 61: rgwtl NSAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 5- 29: gwtl NSAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 21- 45: rgwtl NSAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 37- 61: rgwtl NSAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 37- 61: rgwtl NSAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 5- 29: gwtl NSAGYLLGPHAIDNHRSFhDKhGLA F 6: 86.4797 6( 6) S-A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 38- 61: gwtln SAGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 6- 29: gwtln SAGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 22- 45: gwtln SAGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 38- 61: gwtln SAGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 38- 61: gwtln SAGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 6- 29: gwtln SAGYLLGPHAIDNHRSFhDKhGLA G 7: 82.3097 6( 6) A-G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 39- 61: wtlns AGYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 7- 29: wtlns AGYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 23- 45: wtlns AGYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 39- 61: wtlns AGYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 39- 61: wtlns AGYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 7- 29: wtlns AGYLLGPHAIDNHRSFhDKhGLA H 8: 78.1396 6( 6) G-Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 40- 61: tlnsa GYLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 8- 29: tlnsa GYLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 24- 45: tlnsa GYLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 40- 61: tlnsa GYLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 40- 61: tlnsa GYLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 8- 29: tlnsa GYLLGPHAIDNHRSFhDKhGLA I 9: 73.9696 6( 6) Y-L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 41- 61: lnsag YLLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 9- 29: lnsag YLLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 25- 45: lnsag YLLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 41- 61: lnsag YLLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 41- 61: lnsag YLLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 9- 29: lnsag YLLGPHAIDNHRSFhDKhGLA J 10: 69.7995 6( 6) L-L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 42- 61: nsagy LLGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 10- 29: nsagy LLGPHAVDNHRSFnDKhGFT GALA_HUMAN : 26- 45: nsagy LLGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 42- 61: nsagy LLGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 42- 61: nsagy LLGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 10- 29: nsagy LLGPHAIDNHRSFhDKhGLA K 11: 65.6295 6( 6) L-G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 43- 61: sagyl LGPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 11- 29: sagyl LGPHAVDNHRSFnDKhGFT GALA_HUMAN : 27- 45: sagyl LGPHAVGNHRSFsDKnGLT skrel GALA_PIG : 43- 61: sagyl LGPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 43- 61: sagyl LGPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 11- 29: sagyl LGPHAIDNHRSFhDKhGLA L 12: 61.4594 6( 6) G-P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 44- 61: agyll GPHALDSHRSFqDKhGLA gkrel GALA_CHICK : 12- 29: agyll GPHAVDNHRSFnDKhGFT GALA_HUMAN : 28- 45: agyll GPHAVGNHRSFsDKnGLT skrel GALA_PIG : 44- 61: agyll GPHAIDNHRSFhDKyGLA gkrel GALA_RAT : 44- 61: agyll GPHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 12- 29: agyll GPHAIDNHRSFhDKhGLA M 13: 57.2894 6( 6) P-H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 45- 61: gyllg PHALDSHRSFqDKhGLA gkrel GALA_CHICK : 13- 29: gyllg PHAVDNHRSFnDKhGFT GALA_HUMAN : 29- 45: gyllg PHAVGNHRSFsDKnGLT skrel GALA_PIG : 45- 61: gyllg PHAIDNHRSFhDKyGLA gkrel GALA_RAT : 45- 61: gyllg PHAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 13- 29: gyllg PHAIDNHRSFhDKhGLA N 14: 53.1193 6( 6) H-A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 46- 61: yllgp HALDSHRSFqDKhGLA gkrel GALA_CHICK : 14- 29: yllgp HAVDNHRSFnDKhGFT GALA_HUMAN : 30- 45: yllgp HAVGNHRSFsDKnGLT skrel GALA_PIG : 46- 61: yllgp HAIDNHRSFhDKyGLA gkrel GALA_RAT : 46- 61: yllgp HAIDNHRSFsDKhGLT gkrel GALA_SHEEP : 14- 29: yllgp HAIDNHRSFhDKhGLA O 15: 48.9493 6( 6) A-[ILV]-[DG]-[NS]-H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 47- 61: llgph ALDSHRSFqDKhGLA gkrel GALA_CHICK : 15- 29: llgph AVDNHRSFnDKhGFT GALA_HUMAN : 31- 45: llgph AVGNHRSFsDKnGLT skrel GALA_PIG : 47- 61: llgph AIDNHRSFhDKyGLA gkrel GALA_RAT : 47- 61: llgph AIDNHRSFsDKhGLT gkrel GALA_SHEEP : 15- 29: llgph AIDNHRSFhDKhGLA P 16: 35.6564 6( 6) H-R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 51- 61: halds HRSFqDKhGLA gkrel GALA_CHICK : 19- 29: havdn HRSFnDKhGFT GALA_HUMAN : 35- 45: havgn HRSFsDKnGLT skrel GALA_PIG : 51- 61: haidn HRSFhDKyGLA gkrel GALA_RAT : 51- 61: haidn HRSFsDKhGLT gkrel GALA_SHEEP : 19- 29: haidn HRSFhDKhGLA Q 17: 31.4864 6( 6) R-S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 52- 61: aldsh RSFqDKhGLA gkrel GALA_CHICK : 20- 29: avdnh RSFnDKhGFT GALA_HUMAN : 36- 45: avgnh RSFsDKnGLT skrel GALA_PIG : 52- 61: aidnh RSFhDKyGLA gkrel GALA_RAT : 52- 61: aidnh RSFsDKhGLT gkrel GALA_SHEEP : 20- 29: aidnh RSFhDKhGLA R 18: 27.3163 6( 6) S-F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 53- 61: ldshr SFqDKhGLA gkrel GALA_CHICK : 21- 29: vdnhr SFnDKhGFT GALA_HUMAN : 37- 45: vgnhr SFsDKnGLT skrel GALA_PIG : 53- 61: idnhr SFhDKyGLA gkrel GALA_RAT : 53- 61: idnhr SFsDKhGLT gkrel GALA_SHEEP : 21- 29: idnhr SFhDKhGLA S 19: 23.1463 6( 6) F-x-D-K-x-G-[FL]-[AT] Occurences: 6(6) GALA_BOVIN : 54- 61: dshrs FqDKhGLA gkrel GALA_CHICK : 22- 29: dnhrs FnDKhGFT GALA_HUMAN : 38- 45: gnhrs FsDKnGLT skrel GALA_PIG : 54- 61: dnhrs FhDKyGLA gkrel GALA_RAT : 54- 61: dnhrs FsDKhGLT gkrel GALA_SHEEP : 22- 29: dnhrs FhDKhGLA T 20: 18.8768 7( 6) A-x(1,3)-D-x-[EH]-R-S Occurences: 7(6) GALA_BOVIN : 47- 53: llgph Al--DsHRS fqdkh GALA_BOVIN : 117- 123: ptaes Ae--DaERS GALA_CHICK : 15- 21: llgph Av--DnHRS fndkh GALA_HUMAN : 99- 107: dlpaa AsseDiERS GALA_PIG : 47- 53: llgph Ai--DnHRS fhdky GALA_RAT : 47- 53: llgph Ai--DnHRS fsdkh GALA_SHEEP : 15- 21: llgph Ai--DnHRS fhdkh Number of patterns evaluated by Pratt:810 Total running time: 0 seconds