------------------------------------------------------------ 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 4 sequences from file RNA_POL_L_13KD PATTERN CONSERVATION: CM: min Nr of Seqs to Match 4 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 RNA_POL_L_13KD.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RPBY_YEAST 120 RPC9_CAEEL 144 RPC9_YEAST 142 RPOL_SULAC 90 Pratt run started at Thu Feb 6 21:08:41 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 24.0203 4( 4) E-x(0,1)-E-x(0,1)-H-T-x-G-N 2: 23.5203 4( 4) I-x(2,3)-E-x(1,3)-H-T-x-G-N 3: 20.8503 4( 4) V-x-F-x(2)-Y-x(3)-H-P 4: 20.3503 4( 4) V-x(0,1)-F-x(2)-Y-x(3)-H-P 5: 20.3503 5( 4) E-x(0,1)-H-T-x-G-N 6: 16.6802 4( 4) F-x(2)-Y-x(3)-H-P 7: 16.6802 4( 4) H-T-x-G-N 8: 16.1802 4( 4) F-x(1,2)-Y-x(3)-H-P 9: 15.6802 4( 4) V-x-F-x(2)-Y-x(2,4)-P 10: 14.6802 4( 4) G-x(0,2)-I-x(2,4)-E-x-L 11: 12.5102 4( 4) Y-x(3)-H-P 12: 12.5102 4( 4) T-x-G-N 13: 12.0102 4( 4) K-x(1,2)-I-x(3)-E 14: 12.0102 4( 4) K-x(1,2)-L-x(5)-V 15: 12.0102 5( 4) I-x(2)-E-x(0,1)-E 16: 12.0102 5( 4) E-x(5)-E-x(0,1)-E 17: 12.0102 6( 4) L-x(1,2)-L-x(4)-E 18: 12.0102 4( 4) K-x(3)-E-x(0,1)-E 19: 11.5102 5( 4) E-x-K-x(0,2)-I 20: 11.5102 4( 4) N-L-x(0,2)-I Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 90.0863 4( 4) V-x(0,1)-F-[AC]-[AG]-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] B 2: 87.3747 4( 4) V-x-F-[AC]-[AG]-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST] C 3: 79.9281 4( 4) F-x(2)-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] D 4: 79.4281 4( 4) F-x(1,2)-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] E 5: 75.7581 4( 4) Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] F 6: 37.1283 4( 4) E-x(0,1)-E-x(0,1)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] G 7: 36.6283 4( 4) I-x(2,3)-E-x(1,3)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] H 8: 33.4583 5( 4) E-x(0,1)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] I 9: 29.7882 4( 4) H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] J 10: 25.6182 4( 4) T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] K 11: 25.3434 4( 4) V-x-F-[AC]-[AG]-Y-x(2,4)-P-[FH] L 12: 23.6664 4( 4) K-x(3)-E-x(0,1)-E-x(4)-[DET]-x(3)-[DV]-[DEG]-[AE] M 13: 19.1700 4( 4) I-x(2)-E-x(0,1)-E-[DEHK]-x(2)-[GILV]-[DGN] N 14: 17.8407 4( 4) K-x(1,2)-I-[ENQ]-x(2)-E-x(2)-[AD] O 15: 17.4933 4( 4) L-x(1,2)-L-x(4)-E-[DEST]-[HK] P 16: 17.4168 4( 4) K-x(1,2)-L-x(5)-V-x(4)-[FY]-[ANST] Q 17: 14.6802 4( 4) G-x(0,2)-I-x(2,4)-E-x-L R 18: 14.2135 4( 4) E-x(5)-E-x(0,1)-E-[EQST] S 19: 14.0998 4( 4) E-x-K-x(0,2)-I-x(2)-[DER] T 20: 12.0102 4( 4) K-x(1,2)-L-x(5)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 90.0863 4( 4) V-x(0,1)-F-[AC]-[AG]-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] Occurences: 4(4) RPBY_YEAST : 56- 105: lndrk VlFAAYkVEHPffArFkLRIqTtEGyDPkDALknAcnsIiNklGaLkTnF etewn RPC9_CAEEL : 86- 135: srmde VeFCGYnVPHPleDkIlFRVqTkDGiNAlEVLakAfesVeQifStIrGkF eesye RPC9_YEAST : 86- 135: mknpd VeFCGYsIPHPseNlLnIRIqTyGEtTAvDALqkGlkdLmDlcDvVeSkF tekik RPOL_SULAC : 38- 87: lkvpg VkFAAYsLPHPliTsItIKIlTdGSiSArEALikAielAeNyaNlFiDeV kki B 2: 87.3747 4( 4) V-x-F-[AC]-[AG]-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST] Occurences: 4(4) RPBY_YEAST : 56- 103: lndrk VlFAAYkVEHPffArFkLRIqTtEGyDPkDALknAcnsIiNklGaLkT nfete RPC9_CAEEL : 86- 133: srmde VeFCGYnVPHPleDkIlFRVqTkDGiNAlEVLakAfesVeQifStIrG kfees RPC9_YEAST : 86- 133: mknpd VeFCGYsIPHPseNlLnIRIqTyGEtTAvDALqkGlkdLmDlcDvVeS kftek RPOL_SULAC : 38- 85: lkvpg VkFAAYsLPHPliTsItIKIlTdGSiSArEALikAielAeNyaNlFiD evkki C 3: 79.9281 4( 4) F-x(2)-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] Occurences: 4(4) RPBY_YEAST : 58- 105: drkvl FaaYkVEHPffArFkLRIqTtEGyDPkDALknAcnsIiNklGaLkTnF etewn RPC9_CAEEL : 88- 135: mdeve FcgYnVPHPleDkIlFRVqTkDGiNAlEVLakAfesVeQifStIrGkF eesye RPC9_YEAST : 88- 135: npdve FcgYsIPHPseNlLnIRIqTyGEtTAvDALqkGlkdLmDlcDvVeSkF tekik RPOL_SULAC : 40- 87: vpgvk FaaYsLPHPliTsItIKIlTdGSiSArEALikAielAeNyaNlFiDeV kki D 4: 79.4281 4( 4) F-x(1,2)-Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] Occurences: 4(4) RPBY_YEAST : 58- 105: drkvl FaaYkVEHPffArFkLRIqTtEGyDPkDALknAcnsIiNklGaLkTnF etewn RPC9_CAEEL : 88- 135: mdeve FcgYnVPHPleDkIlFRVqTkDGiNAlEVLakAfesVeQifStIrGkF eesye RPC9_YEAST : 88- 135: npdve FcgYsIPHPseNlLnIRIqTyGEtTAvDALqkGlkdLmDlcDvVeSkF tekik RPOL_SULAC : 40- 87: vpgvk FaaYsLPHPliTsItIKIlTdGSiSArEALikAielAeNyaNlFiDeV kki E 5: 75.7581 4( 4) Y-x-[ILV]-[EP]-H-P-x(2)-[ADNT]-x-[FIL]-x-[FIL]-[KR]-[IV]-x-T-x-[DEG]-[EGS]-x-[DNST]-[AP]-x-[DE]-[AV]-L-x(2)-[AG]-x(3)-[AILV]-x-[DNQ]-x(2)-[DGNS]-x-[FILV]-x-[DGST]-x-[FV] Occurences: 4(4) RPBY_YEAST : 61- 105: vlfaa YkVEHPffArFkLRIqTtEGyDPkDALknAcnsIiNklGaLkTnF etewn RPC9_CAEEL : 91- 135: vefcg YnVPHPleDkIlFRVqTkDGiNAlEVLakAfesVeQifStIrGkF eesye RPC9_YEAST : 91- 135: vefcg YsIPHPseNlLnIRIqTyGEtTAvDALqkGlkdLmDlcDvVeSkF tekik RPOL_SULAC : 43- 87: vkfaa YsLPHPliTsItIKIlTdGSiSArEALikAielAeNyaNlFiDeV kki F 6: 37.1283 4( 4) E-x(0,1)-E-x(0,1)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] Occurences: 4(4) RPBY_YEAST : 36- 50: vvitf EkEdHTLGNlIRaeL lndrk RPC9_CAEEL : 67- 80: tlimy E-EdHTIGNsIKhiL srmde RPC9_YEAST : 67- 80: sfqiv E-EdHTLGNaLRyvI mknpd RPOL_SULAC : 20- 32: lqidg E-E-HTIGNlLKgmL lkvpg G 7: 36.6283 4( 4) I-x(2,3)-E-x(1,3)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] Occurences: 4(4) RPBY_YEAST : 33- 50: pnavv Itf-EkedHTLGNlIRaeL lndrk RPC9_CAEEL : 64- 80: snltl ImyeEd--HTIGNsIKhiL srmde RPC9_CAEEL : 64- 80: snltl Imy-Eed-HTIGNsIKhiL srmde RPC9_YEAST : 65- 80: sasfq Ive-Ed--HTLGNaLRyvI mknpd RPOL_SULAC : 17- 32: ylelq Idg-Ee--HTIGNlLKgmL lkvpg H 8: 33.4583 5( 4) E-x(0,1)-H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] Occurences: 5(4) RPBY_YEAST : 38- 50: itfek EdHTLGNlIRaeL lndrk RPC9_CAEEL : 68- 80: limye EdHTIGNsIKhiL srmde RPC9_YEAST : 68- 80: fqive EdHTLGNaLRyvI mknpd RPOL_SULAC : 20- 32: lqidg EeHTIGNlLKgmL lkvpg RPOL_SULAC : 21- 32: qidge E-HTIGNlLKgmL lkvpg I 9: 29.7882 4( 4) H-T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] Occurences: 4(4) RPBY_YEAST : 40- 50: feked HTLGNlIRaeL lndrk RPC9_CAEEL : 70- 80: myeed HTIGNsIKhiL srmde RPC9_YEAST : 70- 80: iveed HTLGNaLRyvI mknpd RPOL_SULAC : 22- 32: idgee HTIGNlLKgmL lkvpg J 10: 25.6182 4( 4) T-[IL]-G-N-x-[IL]-[KR]-x(2)-[IL] Occurences: 4(4) RPBY_YEAST : 41- 50: ekedh TLGNlIRaeL lndrk RPC9_CAEEL : 71- 80: yeedh TIGNsIKhiL srmde RPC9_YEAST : 71- 80: veedh TLGNaLRyvI mknpd RPOL_SULAC : 23- 32: dgeeh TIGNlLKgmL lkvpg K 11: 25.3434 4( 4) V-x-F-[AC]-[AG]-Y-x(2,4)-P-[FH] Occurences: 4(4) RPBY_YEAST : 56- 67: lndrk VlFAAYkvehPF farfk RPC9_CAEEL : 86- 95: srmde VeFCGYnv--PH pledk RPC9_YEAST : 86- 95: mknpd VeFCGYsi--PH psenl RPOL_SULAC : 38- 47: lkvpg VkFAAYsl--PH plits L 12: 23.6664 4( 4) K-x(3)-E-x(0,1)-E-x(4)-[DET]-x(3)-[DV]-[DEG]-[AE] Occurences: 4(4) RPBY_YEAST : 102- 119: klgal KtnfEtEwnlqTlaaDDA f RPC9_CAEEL : 7- 24: gkkne KiveEaEkveaEtmeVDE qpqet RPC9_YEAST : 20- 37: tpqep KhiqEeEeqdvDmtgDEE qeeep RPOL_SULAC : 4- 20: mei KvikE-EqnylElqiDGE ehtig M 13: 19.1700 4( 4) I-x(2)-E-x(0,1)-E-[DEHK]-x(2)-[GILV]-[DGN] Occurences: 4(4) RPBY_YEAST : 33- 43: pnavv ItfEkEDhtLG nlira RPC9_CAEEL : 64- 73: snltl ImyE-EDhtIG nsikh RPC9_YEAST : 22- 31: qepkh IqeE-EEqdVD mtgde RPOL_SULAC : 17- 26: ylelq IdgE-EHtiGN llkgm N 14: 17.8407 4( 4) K-x(1,2)-I-[ENQ]-x(2)-E-x(2)-[AD] Occurences: 4(4) RPBY_YEAST : 72- 82: ffarf KlrIQttEgyD pkdal RPC9_CAEEL : 108- 118: frvqt KdgINalEvlA kafes RPC9_YEAST : 20- 29: tpqep Kh-IQeeEeqD vdmtg RPOL_SULAC : 71- 80: reali Ka-IElaEnyA nlfid O 15: 17.4933 4( 4) L-x(1,2)-L-x(4)-E-[DEST]-[HK] Occurences: 4(4) RPBY_YEAST : 9- 18: pdrfe Lf-LlgegESK lkidp RPC9_CAEEL : 61- 70: qdpsn Lt-LimyeEDH tigns RPC9_YEAST : 124- 134: kglkd LmdLcdvvESK fteki RPOL_SULAC : 13- 22: eeqny Le-LqidgEEH tignl P 16: 17.4168 4( 4) K-x(1,2)-L-x(5)-V-x(4)-[FY]-[ANST] Occurences: 4(4) RPBY_YEAST : 55- 69: llndr Kv-LfaaykVehpfFA rfklr RPC9_CAEEL : 77- 92: ignsi KhiLsrmdeVefcgYN vphpl RPC9_YEAST : 122- 136: lqkgl Kd-LmdlcdVveskFT ekiks RPOL_SULAC : 29- 44: ignll KgmLlkvpgVkfaaYS lphpl Q 17: 14.6802 4( 4) G-x(0,2)-I-x(2,4)-E-x-L Occurences: 4(4) RPBY_YEAST : 43- 51: edhtl GnlIra--ElL ndrkv RPC9_CAEEL : 110- 117: vqtkd G--Inal-EvL akafe RPC9_YEAST : 90- 100: dvefc GysIphpsEnL lniri RPOL_SULAC : 61- 69: kiltd Gs-Isar-EaL ikaie R 18: 14.2135 4( 4) E-x(5)-E-x(0,1)-E-[EQST] Occurences: 4(4) RPBY_YEAST : 8- 17: apdrf ElfllgEgES klkid RPC9_CAEEL : 10- 19: nekiv EeaekvEaET mevde RPC9_YEAST : 18- 26: evtpq EpkhiqE-EE eqdvd RPC9_YEAST : 18- 27: evtpq EpkhiqEeEE qdvdm RPOL_SULAC : 2- 10: m EikvikE-EQ nylel S 19: 14.0998 4( 4) E-x-K-x(0,2)-I-x(2)-[DER] Occurences: 4(4) RPBY_YEAST : 16- 24: llgeg EsKlkIdpD tkapn RPC9_CAEEL : 98- 104: vphpl EdK--IlfR vqtkd RPC9_YEAST : 18- 25: evtpq EpKh-IqeE eeqdv RPOL_SULAC : 2- 9: m EiKv-IkeE qnyle T 20: 12.0102 4( 4) K-x(1,2)-L-x(5)-V Occurences: 4(4) RPBY_YEAST : 55- 63: llndr Kv-LfaaykV ehpff RPC9_CAEEL : 77- 86: ignsi KhiLsrmdeV efcgy RPC9_YEAST : 122- 130: lqkgl Kd-LmdlcdV veskf RPOL_SULAC : 29- 38: ignll KgmLlkvpgV kfaay Number of patterns evaluated by Pratt:868 Total running time: 1 seconds