------------------------------------------------------------ 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 3 sequences from file LAMBDA_PHAGE_CIII PATTERN CONSERVATION: CM: min Nr of Seqs to Match 3 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 LAMBDA_PHAGE_CIII.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RPC3_BPHK0 44 RPC3_BPP22 52 RPC3_LAMBD 54 Pratt run started at Thu Feb 6 20:10:17 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.0203 3( 3) E-x(0,1)-L-x(1,2)-R-x(4)-L-x(4)-K-x(5)-L 2: 23.5203 3( 3) L-x(2)-R-x(1,3)-K-x(0,1)-L-x(4)-K-x(5)-L 3: 23.5203 3( 3) E-S-x-L-x-R-x(0,2)-R-x(0,1)-K 4: 20.3503 3( 3) R-x(5)-R-x(3)-K-x-L-x(2,3)-L 5: 19.8503 3( 3) R-x(0,1)-K-x(0,1)-L-x(4)-K-x(5)-L 6: 19.8503 3( 3) R-x(4)-L-x(0,1)-R-x(2,3)-K-x(5)-L 7: 19.3503 3( 3) S-x-L-x-R-x(0,2)-R-x(0,1)-K 8: 16.1802 3( 3) R-x(3)-K-x-L-x(2,3)-L 9: 15.6802 3( 3) L-x(4)-K-x(1,2)-L-x(2,3)-L 10: 15.1802 4( 3) L-x-R-x(2,3)-K-x(0,2)-L 11: 15.1802 3( 3) K-x(1,3)-R-x(2,3)-K-x(5)-L 12: 15.1802 3( 3) R-x(2,3)-K-x-L-x(0,2)-I 13: 15.1802 3( 3) L-x-R-x(0,2)-R-x(0,1)-K 14: 12.5102 3( 3) L-x(3)-G-V 15: 12.5102 3( 3) M-x(4)-A-G 16: 12.0102 3( 3) K-x-L-x(2,3)-L 17: 11.5102 4( 3) K-x(1,2)-L-x(2,3)-L 18: 11.5102 4( 3) R-x(2,3)-K-x(1,2)-L 19: 11.5102 3( 3) K-x-L-x(0,2)-I 20: 11.5102 3( 3) A-G-x(0,2)-S Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 52.4548 3( 3) E-x(0,1)-L-x(1,2)-R-x-[TV]-[KR]-x-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] B 2: 48.1244 3( 3) L-x-[DER]-R-x(1,3)-K-x(0,1)-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] C 3: 46.0688 3( 3) R-[IV]-x-[QR]-x-[IL]-R-[AD]-[AG]-x-K-[QR]-L-x(2,3)-L-[CN]-[AQ] D 4: 45.1146 3( 3) R-x-[TV]-[KR]-x-L-x(0,1)-R-x(2,3)-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] E 5: 41.8647 3( 3) R-x(0,1)-K-x(0,1)-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] F 6: 37.1512 3( 3) R-x(2,3)-K-x-L-[AI]-[DR]-[AI]-[AL]-x(2)-[PQ]-[GL]-x-[AP]-x(2)-[ADG] G 7: 34.0246 3( 3) K-x(1,3)-R-x(2,3)-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] H 8: 32.2164 3( 3) R-[AD]-[AG]-x-K-[QR]-L-x(2,3)-L-[CN]-[AQ] I 9: 30.8391 3( 3) R-x(2,3)-K-[QR]-L-x(0,2)-I-x-[AN]-[AQ]-x(3)-[LP]-x(4)-[ACN] J 10: 27.5689 3( 3) M-x(2)-[AQ]-[IL]-A-G-x-[AGP]-x(2)-[GS]-[ACV] K 11: 27.1690 3( 3) K-[QR]-L-x(0,2)-I-x-[AN]-[AQ]-x(3)-[LP]-x(4)-[ACN] L 12: 26.1288 3( 3) E-S-x-L-[DES]-R-x(0,2)-R-x(0,1)-K M 13: 25.3093 3( 3) L-x(2)-[AG]-x-K-x(1,2)-L-x(2,3)-L-[CN]-[AQ] N 14: 24.7633 3( 3) L-x-R-x(2,3)-K-x(0,2)-L-[ER]-[AD]-[GL] O 15: 22.2540 3( 3) L-[AN]-[GQ]-[PS]-G-V P 16: 22.1002 3( 3) R-x-[TV]-[KR]-x-L-x(0,1)-R-x(2,3)-K Q 17: 21.9588 3( 3) S-x-L-[DES]-R-x(0,2)-R-x(0,1)-K R 18: 21.6400 3( 3) K-[QR]-L-x(2,3)-L-[CN]-[AQ] S 19: 17.9692 4( 3) K-x(1,2)-L-x(2,3)-L-[CN]-[AQ] T 20: 17.7887 3( 3) L-[DES]-R-x(0,2)-R-x(0,1)-K Best patterns with alignements: fitness hits(seqs) Pattern A 1: 52.4548 3( 3) E-x(0,1)-L-x(1,2)-R-x-[TV]-[KR]-x-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 21- 42: yphes E-Ls-RrVKqLirAaKKqLEALCA mk RPC3_BPP22 : 18- 41: vsqlh EsLldRiTRkLraGwKRlADILNQ pgvps RPC3_LAMBD : 16- 39: agcps EsLleRiTRkLrdGwKRlIDILNQ pgvpk B 2: 48.1244 3( 3) L-x-[DER]-R-x(1,3)-K-x(0,1)-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 22- 42: phese LsRRv--KqLirAaKKqLEALCA mk RPC3_BPP22 : 20- 41: qlhes LlDRitrK-LraGwKRlADILNQ pgvps RPC3_LAMBD : 18- 39: cpses LlERitrK-LrdGwKRlIDILNQ pgvpk C 3: 46.0688 3( 3) R-[IV]-x-[QR]-x-[IL]-R-[AD]-[AG]-x-K-[QR]-L-x(2,3)-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 25- 42: selsr RVkQlIRAAkKQLea-LCA mk RPC3_BPP22 : 23- 41: eslld RItRkLRAGwKRLadiLNQ pgvps RPC3_LAMBD : 21- 39: eslle RItRkLRDGwKRLidiLNQ pgvpk D 4: 45.1146 3( 3) R-x-[TV]-[KR]-x-L-x(0,1)-R-x(2,3)-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 24- 42: esels RrVKqLiRaa-KKqLEALCA mk RPC3_BPP22 : 23- 41: eslld RiTRkL-RagwKRlADILNQ pgvps RPC3_LAMBD : 21- 39: eslle RiTRkL-RdgwKRlIDILNQ pgvpk E 5: 41.8647 3( 3) R-x(0,1)-K-x(0,1)-L-x(2)-[AG]-x-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 25- 42: selsr RvKqLirAaKKqLEALCA mk RPC3_BPP22 : 26- 41: ldrit R-K-LraGwKRlADILNQ pgvps RPC3_LAMBD : 24- 39: lerit R-K-LrdGwKRlIDILNQ pgvpk F 6: 37.1512 3( 3) R-x(2,3)-K-x-L-[AI]-[DR]-[AI]-[AL]-x(2)-[PQ]-[GL]-x-[AP]-x(2)-[ADG] Occurences: 3(3) RPC3_BPHK0 : 24- 42: esels Rrv-KqLIRAAkkQLeAlcA mk RPC3_BPP22 : 29- 48: itrkl RagwKrLADILnqPGvPshD ycac RPC3_LAMBD : 27- 46: itrkl RdgwKrLIDILnqPGvPknG sntyg G 7: 34.0246 3( 3) K-x(1,3)-R-x(2,3)-K-[KR]-x-[AIL]-[DE]-[AI]-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 27- 42: lsrrv KqliRaa-KKqLEALCA mk RPC3_BPP22 : 27- 41: dritr Kl--RagwKRlADILNQ pgvps RPC3_LAMBD : 25- 39: eritr Kl--RdgwKRlIDILNQ pgvpk H 8: 32.2164 3( 3) R-[AD]-[AG]-x-K-[QR]-L-x(2,3)-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 31- 42: vkqli RAAkKQLea-LCA mk RPC3_BPP22 : 29- 41: itrkl RAGwKRLadiLNQ pgvps RPC3_LAMBD : 27- 39: itrkl RDGwKRLidiLNQ pgvpk I 9: 30.8391 3( 3) R-x(2,3)-K-[QR]-L-x(0,2)-I-x-[AN]-[AQ]-x(3)-[LP]-x(4)-[ACN] Occurences: 3(3) RPC3_BPHK0 : 24- 42: esels Rrv-KQL--IrAAkkqLealcA mk RPC3_BPP22 : 29- 50: itrkl RagwKRLadIlNQpgvPshdyC ac RPC3_LAMBD : 27- 48: itrkl RdgwKRLidIlNQpgvPkngsN tygyp J 10: 27.5689 3( 3) M-x(2)-[AQ]-[IL]-A-G-x-[AGP]-x(2)-[GS]-[ACV] Occurences: 3(3) RPC3_BPHK0 : 2- 14: m MhfQLAGsGvmSA fyphe RPC3_BPP22 : 1- 13: MiiAIAGsArmGV sqlhe RPC3_LAMBD : 1- 13: MqyAIAGwPvaGC psesl K 11: 27.1690 3( 3) K-[QR]-L-x(0,2)-I-x-[AN]-[AQ]-x(3)-[LP]-x(4)-[ACN] Occurences: 3(3) RPC3_BPHK0 : 27- 42: lsrrv KQL--IrAAkkqLealcA mk RPC3_BPP22 : 33- 50: lragw KRLadIlNQpgvPshdyC ac RPC3_LAMBD : 31- 48: lrdgw KRLidIlNQpgvPkngsN tygyp L 12: 26.1288 3( 3) E-S-x-L-[DES]-R-x(0,2)-R-x(0,1)-K Occurences: 3(3) RPC3_BPHK0 : 19- 27: afyph ESeLSR--RvK qlira RPC3_BPP22 : 18- 27: vsqlh ESlLDRitR-K lragw RPC3_LAMBD : 16- 25: agcps ESlLERitR-K lrdgw M 13: 25.3093 3( 3) L-x(2)-[AG]-x-K-x(1,2)-L-x(2,3)-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 29- 42: rrvkq LirAaKkqLea-LCA mk RPC3_BPP22 : 28- 41: ritrk LraGwKr-LadiLNQ pgvps RPC3_LAMBD : 26- 39: ritrk LrdGwKr-LidiLNQ pgvpk N 14: 24.7633 3( 3) L-x-R-x(2,3)-K-x(0,2)-L-[ER]-[AD]-[GL] Occurences: 3(3) RPC3_BPHK0 : 29- 40: rrvkq LiRaakKq-LEAL camk RPC3_BPHK0 : 29- 40: rrvkq LiRaa-KkqLEAL camk RPC3_BPP22 : 21- 31: lhesl LdRitrK--LRAG wkrla RPC3_LAMBD : 19- 29: psesl LeRitrK--LRDG wkrli O 15: 22.2540 3( 3) L-[AN]-[GQ]-[PS]-G-V Occurences: 3(3) RPC3_BPHK0 : 6- 11: mmhfq LAGSGV msafy RPC3_BPP22 : 39- 44: rladi LNQPGV pshdy RPC3_LAMBD : 37- 42: rlidi LNQPGV pkngs P 16: 22.1002 3( 3) R-x-[TV]-[KR]-x-L-x(0,1)-R-x(2,3)-K Occurences: 3(3) RPC3_BPHK0 : 24- 34: esels RrVKqLiRaa-K kqlea RPC3_BPP22 : 23- 33: eslld RiTRkL-RagwK rladi RPC3_LAMBD : 21- 31: eslle RiTRkL-RdgwK rlidi Q 17: 21.9588 3( 3) S-x-L-[DES]-R-x(0,2)-R-x(0,1)-K Occurences: 3(3) RPC3_BPHK0 : 20- 27: fyphe SeLSR--RvK qlira RPC3_BPP22 : 19- 27: sqlhe SlLDRitR-K lragw RPC3_LAMBD : 17- 25: gcpse SlLERitR-K lrdgw R 18: 21.6400 3( 3) K-[QR]-L-x(2,3)-L-[CN]-[AQ] Occurences: 3(3) RPC3_BPHK0 : 35- 42: iraak KQLea-LCA mk RPC3_BPP22 : 33- 41: lragw KRLadiLNQ pgvps RPC3_LAMBD : 31- 39: lrdgw KRLidiLNQ pgvpk S 19: 17.9692 4( 3) K-x(1,2)-L-x(2,3)-L-[CN]-[AQ] Occurences: 4(3) RPC3_BPHK0 : 34- 42: liraa KkqLea-LCA mk RPC3_BPHK0 : 35- 42: iraak Kq-Lea-LCA mk RPC3_BPP22 : 33- 41: lragw Kr-LadiLNQ pgvps RPC3_LAMBD : 31- 39: lrdgw Kr-LidiLNQ pgvpk T 20: 17.7887 3( 3) L-[DES]-R-x(0,2)-R-x(0,1)-K Occurences: 3(3) RPC3_BPHK0 : 22- 27: phese LSR--RvK qlira RPC3_BPP22 : 21- 27: lhesl LDRitR-K lragw RPC3_LAMBD : 19- 25: psesl LERitR-K lrdgw Number of patterns evaluated by Pratt:143 Total running time: 1 seconds