------------------------------------------------------------ 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 PROTEIN_SPLICING 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 PROTEIN_SPLICING.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: DPOL_THELI 1702 RECA_MYCLE 711 RECA_MYCTU 790 VATA_CANTR 1088 VATA_YEAST 1071 Pratt run started at Thu Feb 6 20:53:56 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.0203 5( 5) P-x(2)-Q-x(5)-L-x(1,2)-K-x(2)-S-x(1,2)-E 2: 24.0203 5( 5) I-x-G-x(3,4)-G-K-T-x(0,1)-V 3: 23.5203 5( 5) A-x(5)-I-x(3)-I-x(1,3)-E-x(4,5)-G-x(2)-V 4: 23.5203 5( 5) K-x-G-x-D-x(5)-V-x(3,5)-D-x(3,4)-Q 5: 20.3503 5( 5) A-x-E-x(2,3)-K-x-I-K 6: 19.8503 5( 5) L-G-I-x(2)-V-x(2,4)-D 7: 19.8503 5( 5) A-x(0,1)-E-x(2,3)-K-x-I-K 8: 19.8503 5( 5) A-x(0,1)-E-x(4)-I-x(3)-L-x(0,1)-G 9: 19.8503 5( 5) D-x(2,3)-E-I-x(5)-E-x(0,1)-L 10: 19.8503 5( 5) Q-x(5)-L-x(1,2)-K-x(2)-S-x(1,2)-E 11: 19.8503 7( 5) E-x(1,2)-E-x(5)-V-x(2,3)-A-x(3)-S 12: 19.8503 5( 5) E-x(5)-G-x(2,3)-V-x(2,3)-A-x(3)-S 13: 19.8503 5( 5) V-x(2,3)-E-x(2)-G-x(2,3)-G-D 14: 19.8503 5( 5) D-x(3,4)-L-x(5)-L-x(3,4)-G-x-S 15: 19.8503 5( 5) A-x(0,1)-L-x(0,1)-D-x(3)-I-x(4)-A 16: 19.8503 5( 5) E-x(2,3)-E-x(0,1)-A-x(2)-L-x(5)-L 17: 19.8503 5( 5) G-x(2)-A-L-x(3)-D-x(1,3)-L 18: 19.8503 5( 5) L-x(2,3)-S-x(3)-T-x(3)-A-x(0,1)-L 19: 19.8503 5( 5) L-x(5)-D-x(4)-A-x(3,4)-A-x(1,2)-L 20: 19.8503 5( 5) G-x(3,4)-G-K-T-x(0,1)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 59.9280 5( 5) K-[ILV]-G-x-D-[NST]-x-[SV]-x(2)-V-x(3,5)-D-x(3,4)-Q-[ATV]-x-[ER]-x(2)-[ADN]-x(4)-[GNS]-x-[AIP]-[LPV]-x(3)-[GLV]-x-[DP]-x(2)-[AGV]-x(3)-[PQ] B 2: 53.2738 5( 5) I-x-G-x(3,4)-G-K-T-x(0,1)-V-x(3)-[ADS]-[ALV]-[ASV]-x(2)-[QRS]-x(3)-[AGLV]-[GIV]-x(2)-[FV]-x-[CDV]-x(3)-[AGI]-x-[DENQ]-x(3)-[AD] C 3: 49.1038 5( 5) G-x(3,4)-G-K-T-x(0,1)-V-x(3)-[ADS]-[ALV]-[ASV]-x(2)-[QRS]-x(3)-[AGLV]-[GIV]-x(2)-[FV]-x-[CDV]-x(3)-[AGI]-x-[DENQ]-x(3)-[AD] D 4: 47.3281 5( 5) A-x(0,1)-L-x(0,1)-D-x-[DSV]-x-I-[DET]-x(3)-A-x(2)-[GIP]-[EKR]-x-[DEH]-x(2)-[GQT]-x(2)-[GV]-x-[DS]-x(3)-[ALV]-x(3)-[FIL] E 5: 37.4706 5( 5) D-x(2,3)-E-I-x(3)-[AIL]-x-E-x(0,1)-L-x(3)-[AGV]-x-[ILV]-[STV]-[DGN]-x(4)-[DNPS]-[DEGT] F 6: 35.6047 5( 5) G-x-[EQS]-A-L-[EST]-x-[ADS]-D-x(1,3)-L-x(3)-[GPT]-[ALV]-[ILP] G 7: 34.3733 5( 5) E-x(3)-[DEK]-x-G-x(2,3)-V-x(2,3)-A-[DR]-x(2)-S-x(3)-[ER]-x-[ILM]-x(4)-[GNS] H 8: 31.3785 5( 5) A-x(5)-I-x(3)-I-x(1,3)-E-x(4,5)-G-x(2)-V-x(3)-[ADP]-x(2)-[DPS]-[GST] I 9: 30.9704 5( 5) A-x(0,1)-E-x(4)-I-x-[EGS]-[KR]-L-x(0,1)-G-x(3)-[ALV]-x(2)-[DEG] J 10: 26.6471 5( 5) P-x(2)-Q-[AGP]-x(4)-L-x(1,2)-K-x(2)-S-x(1,2)-E K 11: 25.6641 5( 5) E-x(2,3)-E-x(0,1)-A-x(2)-L-x-[DER]-x-[GP]-x-L L 12: 25.6517 5( 5) L-x(2,3)-S-[DQS]-x(2)-T-[GL]-x(2)-A-x(0,1)-L M 13: 25.1667 7( 5) E-x(1,2)-E-x(2)-[DGV]-x(2)-V-x(2,3)-A-x(3)-S-[DGQ] N 14: 25.1554 5( 5) V-x(2,3)-E-x(2)-G-x(2,3)-G-D-[GPS]-x(4)-[DGQ] O 15: 25.1157 5( 5) L-G-I-[GST]-[AQS]-V-x(2,4)-D P 16: 23.0308 5( 5) L-x(5)-D-x-[GS]-x(2)-A-x(3,4)-A-x(1,2)-L Q 17: 22.4771 5( 5) Q-[AGP]-x(4)-L-x(1,2)-K-x(2)-S-x(1,2)-E R 18: 20.3503 5( 5) A-x-E-x(2,3)-K-x-I-K S 19: 19.8503 5( 5) A-x(0,1)-E-x(2,3)-K-x-I-K T 20: 19.8503 5( 5) V-x(2,3)-E-x(2)-G-x(2,3)-G-D Best patterns with alignements: fitness hits(seqs) Pattern A 1: 59.9280 5( 5) K-[ILV]-G-x-D-[NST]-x-[SV]-x(2)-V-x(3,5)-D-x(3,4)-Q-[ATV]-x-[ER]-x(2)-[ADN]-x(4)-[GNS]-x-[AIP]-[LPV]-x(3)-[GLV]-x-[DP]-x(2)-[AGV]-x(3)-[PQ] Occurences: 5(5) DPOL_THELI : 913- 960: gissv KIGfDSgVyrVyine-DlqfpQTsRekNtyysNlIPkeiLrDvfGkefQ knmtf RECA_MYCLE : 107- 152: peyak KLGvDTdSllVsqp--Dtge-QAlEiaDmlirSgALdivViDsvAalvP raele RECA_MYCTU : 107- 152: pdyak KLGvDTdSllVsqp--Dtge-QAlEiaDmlirSgALdivViDsvAalvP raele VATA_CANTR : 51- 99: myelv KVGhDNlVgeViringDkatiQVyEetAgvtvGdPVlrtGkPlsVelgP glmet VATA_YEAST : 51- 99: myelv KVGhDNlVgeViridgDkatiQVyEetAgltvGdPVlrtGkPlsVelgP glmet B 2: 53.2738 5( 5) I-x-G-x(3,4)-G-K-T-x(0,1)-V-x(3)-[ADS]-[ALV]-[ASV]-x(2)-[QRS]-x(3)-[AGLV]-[GIV]-x(2)-[FV]-x-[CDV]-x(3)-[AGI]-x-[DENQ]-x(3)-[AD] Occurences: 5(5) DPOL_THELI : 54- 92: eeika IkGerh-GKT-VrvlDAVkvRkkfLGreVeVwklIfEhpqD vpamr RECA_MYCLE : 65- 105: grive IyGpessGKTtValhAVAnaQavgGVaaFiDaehAlEpeyA kklgv RECA_MYCTU : 65- 105: grvie IyGpessGKTtValhAVAnaQaagGVaaFiDaehAlDpdyA kklgv VATA_CANTR : 255- 294: ggttc IpGafgcGKT-VisqSLSkfSnsdVIiyVgCftkGtQvmmA dgadk VATA_YEAST : 255- 294: ggttc IpGafgcGKT-VisqSLSkySnsdAIiyVgCfakGtNvlmA dgsie C 3: 49.1038 5( 5) G-x(3,4)-G-K-T-x(0,1)-V-x(3)-[ADS]-[ALV]-[ASV]-x(2)-[QRS]-x(3)-[AGLV]-[GIV]-x(2)-[FV]-x-[CDV]-x(3)-[AGI]-x-[DENQ]-x(3)-[AD] Occurences: 5(5) DPOL_THELI : 56- 92: ikaik Gerh-GKT-VrvlDAVkvRkkfLGreVeVwklIfEhpqD vpamr RECA_MYCLE : 67- 105: iveiy GpessGKTtValhAVAnaQavgGVaaFiDaehAlEpeyA kklgv RECA_MYCTU : 67- 105: vieiy GpessGKTtValhAVAnaQaagGVaaFiDaehAlDpdyA kklgv VATA_CANTR : 257- 294: ttcip GafgcGKT-VisqSLSkfSnsdVIiyVgCftkGtQvmmA dgadk VATA_YEAST : 257- 294: ttcip GafgcGKT-VisqSLSkySnsdAIiyVgCfakGtNvlmA dgsie D 4: 47.3281 5( 5) A-x(0,1)-L-x(0,1)-D-x-[DSV]-x-I-[DET]-x(3)-A-x(2)-[GIP]-[EKR]-x-[DEH]-x(2)-[GQT]-x(2)-[GV]-x-[DS]-x(3)-[ALV]-x(3)-[FIL] Occurences: 5(5) DPOL_THELI : 40- 75: qpyiy AlLkDdSaIEeikAikGErHgkTvrVlDavkVrkkF lgrev RECA_MYCLE : 138- 171: lirsg A-L-DiVvIDsvaAlvPRaEleGemGdSyvgLqarL msqal RECA_MYCTU : 138- 171: lirsg A-L-DiVvIDsvaAlvPRaEleGemGdShvgLqarL msqal VATA_CANTR : 978- 1012: lvgks A-LsDsDkITldvAtlIKeDflQqnGySsydAfcpI wktfd VATA_YEAST : 961- 995: lvgks A-LsDsDkITldvAtlIKeDflQqnGyStydAfcpI wktfd E 5: 37.4706 5( 5) D-x(2,3)-E-I-x(3)-[AIL]-x-E-x(0,1)-L-x(3)-[AGV]-x-[ILV]-[STV]-[DGN]-x(4)-[DNPS]-[DEGT] Occurences: 5(5) DPOL_THELI : 1257- 1283: lstgk Dae-EIkqkLlEpLktyGvISNyypkNE kgdfn RECA_MYCLE : 680- 707: llena DvanEIekkIkEkLgigAvVTDddilPT pvdf RECA_MYCTU : 755- 782: lvena DvadEIekkIkEkLgigAvVTDdpsnDG vlpap VATA_CANTR : 955- 981: fpqlr DkirEIlsnAeE-LeqvVqLVGksalSD sdkit VATA_YEAST : 938- 964: fpvlr DrmkEIlsnAeE-LeqvVqLVGksalSD sdkit F 6: 35.6047 5( 5) G-x-[EQS]-A-L-[EST]-x-[ADS]-D-x(1,3)-L-x(3)-[GPT]-[ALV]-[ILP] Occurences: 5(5) DPOL_THELI : 1123- 1141: ycile GvEALTlDDdgkLvwkPVP yvmrh RECA_MYCLE : 123- 139: sqpdt GeQALEiADm--LirsGAL divvi RECA_MYCTU : 123- 139: sqpdt GeQALEiADm--LirsGAL divvi VATA_CANTR : 975- 993: vvqlv GkSALSdSDkitLdvaTLI kedfl VATA_YEAST : 958- 976: vvqlv GkSALSdSDkitLdvaTLI kedfl G 7: 34.3733 5( 5) E-x(3)-[DEK]-x-G-x(2,3)-V-x(2,3)-A-[DR]-x(2)-S-x(3)-[ER]-x-[ILM]-x(4)-[GNS] Occurences: 5(5) DPOL_THELI : 1068- 1095: emtir EieeKfGfk-Vly-ADsvSgesEiIirqnG kirfv RECA_MYCLE : 155- 184: lvpra ElegEmGdsyVglqARlmSqalRkMtgalS nsgtt RECA_MYCTU : 155- 184: lvpra ElegEmGdshVglqARlmSqalRkMtgalN nsgtt VATA_CANTR : 813- 841: gitla EyfrDqGkn-VsmiADssSrwaEaLreisG rlgem VATA_YEAST : 796- 824: gitla EyfrDqGkn-VsmiADssSrwaEaLreisG rlgem H 8: 31.3785 5( 5) A-x(5)-I-x(3)-I-x(1,3)-E-x(4,5)-G-x(2)-V-x(3)-[ADP]-x(2)-[DPS]-[GST] Occurences: 5(5) DPOL_THELI : 1056- 1085: aesvt AwgrhyIemtIr--EieekfGfkVlyaDsvSG eseii RECA_MYCLE : 679- 707: fllen AdvaneIekkIk--Eklgi-GavVtddDilPT pvdf RECA_MYCTU : 754- 782: flven AdvadeIekkIk--Eklgi-GavVtddPsnDG vlpap VATA_CANTR : 799- 830: snmpv AareasIytgItlaEyfrdqGknVsmiAdsSS rwaea VATA_YEAST : 782- 813: snmpv AareasIytgItlaEyfrdqGknVsmiAdsSS rwaea I 9: 30.9704 5( 5) A-x(0,1)-E-x(4)-I-x-[EGS]-[KR]-L-x(0,1)-G-x(3)-[ALV]-x(2)-[DEG] Occurences: 5(5) DPOL_THELI : 1491- 1511: likkk AkEflnyInSKLpGlleLeyE gfylr RECA_MYCLE : 682- 701: enadv AnEiekkIkEKL-GigaVvtD ddilp RECA_MYCTU : 757- 776: enadv AdEiekkIkEKL-GigaVvtD dpsnd VATA_CANTR : 833- 851: sssrw A-EalreIsGRL-GempAdqG fpayl VATA_YEAST : 816- 834: sssrw A-EalreIsGRL-GempAdqG fpayl J 10: 26.6471 5( 5) P-x(2)-Q-[AGP]-x(4)-L-x(1,2)-K-x(2)-S-x(1,2)-E Occurences: 5(5) DPOL_THELI : 32- 49: kield PhfQPyiyaLl-KddSaiE eikai RECA_MYCLE : 620- 637: nkvsp PfkQAefdiLygKgiSr-E gslid RECA_MYCTU : 695- 712: hncsp PfkQAefdiLygKgiSr-E gslid VATA_CANTR : 847- 865: rlgem PadQGfpayLgaKlaSfyE ragka VATA_YEAST : 830- 848: rlgem PadQGfpayLgaKlaSfyE ragka K 11: 25.6641 5( 5) E-x(2,3)-E-x(0,1)-A-x(2)-L-x-[DER]-x-[GP]-x-L Occurences: 5(5) DPOL_THELI : 1122- 1135: eycil Egv-E-AltLdDdGkL vwkpv RECA_MYCLE : 124- 139: qpdtg EqalEiAdmLiRsGaL divvi RECA_MYCTU : 124- 139: qpdtg EqalEiAdmLiRsGaL divvi VATA_CANTR : 757- 772: vhncg ErgnEmAevLmEfPeL fteis VATA_YEAST : 740- 755: vhncg ErgnEmAevLmEfPeL ytems L 12: 25.6517 5( 5) L-x(2,3)-S-[DQS]-x(2)-T-[GL]-x(2)-A-x(0,1)-L Occurences: 5(5) DPOL_THELI : 1686- 1700: yrked LryqSSkqTGldAwL kr RECA_MYCLE : 115- 127: vdtds Llv-SQpdTGeqA-L eiadm RECA_MYCTU : 115- 127: vdtds Llv-SQpdTGeqA-L eiadm VATA_CANTR : 979- 992: vgksa Lsd-SDkiTLdvAtL ikedf VATA_YEAST : 962- 975: vgksa Lsd-SDkiTLdvAtL ikedf M 13: 25.1667 7( 5) E-x(1,2)-E-x(2)-[DGV]-x(2)-V-x(2,3)-A-x(3)-S-[DGQ] Occurences: 7(5) DPOL_THELI : 1068- 1085: emtir EieEkfGfkVly-AdsvSG eseii RECA_MYCLE : 157- 174: prael Eg-EmgDsyVglqArlmSQ alrkm RECA_MYCTU : 157- 174: prael Eg-EmgDshVglqArlmSQ alrkm VATA_CANTR : 965- 983: ilsna EelEqvVqlVgksAlsdSD kitld VATA_CANTR : 966- 983: lsnae El-EqvVqlVgksAlsdSD kitld VATA_YEAST : 948- 966: ilsna EelEqvVqlVgksAlsdSD kitld VATA_YEAST : 949- 966: lsnae El-EqvVqlVgksAlsdSD kitld N 14: 25.1554 5( 5) V-x(2,3)-E-x(2)-G-x(2,3)-G-D-[GPS]-x(4)-[DGQ] Occurences: 5(5) DPOL_THELI : 1224- 1242: tseia VkfwElvGlivGDGnwggD srwae RECA_MYCLE : 151- 168: svaal VpraEleGem-GDSyvglQ arlms RECA_MYCTU : 151- 168: svaal VpraEleGem-GDShvglQ arlms VATA_CANTR : 73- 90: katiq Vye-EtaGvtvGDPvlrtG kplsv VATA_YEAST : 73- 90: katiq Vye-EtaGltvGDPvlrtG kplsv O 15: 25.1157 5( 5) L-G-I-[GST]-[AQS]-V-x(2,4)-D Occurences: 5(5) DPOL_THELI : 907- 917: fllns LGISSVkigfD sgvyr RECA_MYCLE : 693- 701: kikek LGIGAVvt--D ddilp RECA_MYCLE : 693- 702: kikek LGIGAVvtd-D dilpt RECA_MYCLE : 693- 703: kikek LGIGAVvtddD ilptp RECA_MYCTU : 768- 776: kikek LGIGAVvt--D dpsnd RECA_MYCTU : 768- 777: kikek LGIGAVvtd-D psndg VATA_CANTR : 904- 914: vttst LGITQVfwglD kklaq VATA_YEAST : 887- 897: vttat LGITQVfwglD kklaq P 16: 23.0308 5( 5) L-x(5)-D-x-[GS]-x(2)-A-x(3,4)-A-x(1,2)-L Occurences: 5(5) DPOL_THELI : 1539- 1558: ittrg LevvrrDwSeiAketqAkvL eailk RECA_MYCLE : 115- 133: vdtds LlvsqpDtGeqAlei-AdmL irsga RECA_MYCTU : 115- 133: vdtds LlvsqpDtGeqAlei-AdmL irsga VATA_CANTR : 843- 860: eisgr LgempaDqGfpAylg-Ak-L asfye VATA_YEAST : 826- 843: eisgr LgempaDqGfpAylg-Ak-L asfye Q 17: 22.4771 5( 5) Q-[AGP]-x(4)-L-x(1,2)-K-x(2)-S-x(1,2)-E Occurences: 5(5) DPOL_THELI : 35- 49: ldphf QPyiyaLl-KddSaiE eikai RECA_MYCLE : 623- 637: sppfk QAefdiLygKgiSr-E gslid RECA_MYCTU : 698- 712: sppfk QAefdiLygKgiSr-E gslid VATA_CANTR : 850- 865: empad QGfpayLgaKlaSfyE ragka VATA_YEAST : 833- 848: empad QGfpayLgaKlaSfyE ragka R 18: 20.3503 5( 5) A-x-E-x(2,3)-K-x-I-K Occurences: 5(5) DPOL_THELI : 47- 55: lkdds AiEei-KaIK gerhg RECA_MYCLE : 682- 690: enadv AnEie-KkIK eklgi RECA_MYCTU : 757- 765: enadv AdEie-KkIK eklgi VATA_CANTR : 4- 13: mag AlEnarKeIK rlsld VATA_YEAST : 4- 13: mag AiEnarKeIK risle S 19: 19.8503 5( 5) A-x(0,1)-E-x(2,3)-K-x-I-K Occurences: 5(5) DPOL_THELI : 47- 55: lkdds AiEei-KaIK gerhg RECA_MYCLE : 682- 690: enadv AnEie-KkIK eklgi RECA_MYCTU : 757- 765: enadv AdEie-KkIK eklgi VATA_CANTR : 4- 13: mag AlEnarKeIK rlsld VATA_YEAST : 4- 13: mag AiEnarKeIK risle T 20: 19.8503 5( 5) V-x(2,3)-E-x(2)-G-x(2,3)-G-D Occurences: 5(5) DPOL_THELI : 1224- 1236: tseia VkfwElvGlivGD gnwgg RECA_MYCLE : 151- 162: svaal VpraEleGem-GD syvgl RECA_MYCTU : 151- 162: svaal VpraEleGem-GD shvgl VATA_CANTR : 73- 84: katiq Vye-EtaGvtvGD pvlrt VATA_YEAST : 73- 84: katiq Vye-EtaGltvGD pvlrt Number of patterns evaluated by Pratt:99918 Total running time: 93 seconds