------------------------------------------------------------ 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 2 sequences from file DNA_PHOTOLYASES_2_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 2 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 DNA_PHOTOLYASES_2_2.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PHR_CARAU 556 PHR_METTH 28 Pratt run started at Thu Feb 6 19:22:22 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 27.6904 2( 2) E-x(3)-S-L-x(2)-E-x(0,2)-R-x(2)-G-x(1,2)-V 2: 27.1904 2( 2) D-x(0,2)-E-x(3)-S-L-x(2)-E-x(0,2)-R-x(2)-G 3: 24.0203 2( 2) P-R-x(1,2)-D-x(2)-Y-x(2)-Y-x(1,2)-M 4: 24.0203 2( 2) E-x(2)-R-x(2)-G-x(1,2)-V-x(1,2)-W-x-Q 5: 23.5203 2( 2) T-x-K-x(3,5)-D-G-x(1,2)-Y-x(5)-Q 6: 23.5203 2( 2) S-L-x(2)-E-x(0,2)-R-x(2)-G-x(1,2)-V 7: 23.5203 2( 2) R-x(3)-L-x(1,2)-T-x-K-x(3,5)-D-G 8: 23.5203 2( 2) R-x(4)-N-x(3,5)-P-x(2)-D-x(5)-Y-x(0,1)-W 9: 23.5203 2( 2) I-x(3,4)-I-R-x(2)-N-x(2,4)-K-x(3)-D 10: 23.0203 2( 2) R-x(0,2)-R-x(0,2)-D-x(4)-I-Y-x(2)-Q 11: 23.0203 2( 2) R-x-L-x(0,2)-N-x(3,5)-P-x(2)-D-x(5)-Y 12: 20.3503 2( 2) D-x(4)-I-Y-x(2)-Q-x(0,1)-A 13: 20.3503 2( 2) K-x(3)-D-G-x(1,2)-Y-x(5)-Q 14: 20.3503 2( 2) L-x(0,1)-T-E-x-P-x(2)-D 15: 19.8503 2( 2) N-x(0,1)-E-x(2)-R-x(2,3)-G-x(2)-V 16: 19.8503 2( 2) R-x(0,1)-S-L-x(4)-P-x(3,4)-G 17: 19.8503 2( 2) R-x(0,1)-I-R-x(3)-T-x(0,1)-K 18: 19.8503 2( 2) R-x(1,2)-S-L-x(4)-P-x(3,4)-G 19: 19.8503 2( 2) D-x(0,1)-E-x(3)-S-x(0,1)-L-x(2)-E 20: 19.8503 2( 2) H-x(4)-R-x(1,2)-L-x-T-x(0,1)-E Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 61.5479 2( 2) D-x(0,1)-E-[ER]-[IV]-x-S-x(0,1)-L-[EN]-[TV]-E-[KR]-[PS]-x(2)-[DE]-[GV]-[DK]-[WY]-[AV]-x(4)-[QS]-[AG] B 2: 60.2553 2( 2) H-[AD]-[EK]-[DR]-x-R-x(1,2)-L-x-T-x(0,1)-E-x-[LP]-[ER]-[NR]-[AD]-x(2)-[HY]-[DV]-x(2)-W-x-[AQ]-A C 3: 59.3381 2( 2) D-x(0,2)-E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-[EK]-x-[DV]-x(4)-[GQ]-[AT] D 4: 56.6515 2( 2) E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-x(1,2)-V-x-[WY]-x(2)-[PQ]-[AG] E 5: 45.9756 2( 2) S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-x(1,2)-V-x-[WY]-x(2)-[PQ]-[AG] F 6: 44.1066 2( 2) I-x(3,4)-I-R-x-[LM]-N-x(2,4)-K-x-[KR]-x-D-[GV]-x(2)-[FV]-x(4)-[QT]-A G 7: 43.4422 2( 2) R-x(0,1)-I-R-[GS]-x(2)-T-x(0,1)-K-[LP]-x(2)-[DE]-x(4)-I-x(2)-[MV]-[DQ]-[AT] H 8: 42.4653 2( 2) R-[ES]-L-x(0,2)-N-x(3,5)-P-[RS]-x-D-[GN]-x(2)-[GV]-[AI]-Y-x(2)-[AQ] I 9: 39.6713 2( 2) R-x(2)-[AS]-x-N-x(3,5)-P-[RS]-x-D-[GN]-x(2)-[GV]-[AI]-Y-x(0,1)-W J 10: 36.8194 2( 2) E-x-[EP]-R-[RS]-[DV]-G-x(1,2)-V-x(1,2)-W-x-Q-[AP] K 11: 35.8755 2( 2) D-x(0,2)-E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R L 12: 34.1590 2( 2) R-[IL]-R-x-L-x(1,2)-T-[EQ]-K-x(3,5)-D-G M 13: 33.7054 1( 1) E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-R N 14: 32.6473 2( 2) R-x(0,2)-R-x(0,2)-D-[GN]-x(2)-[LV]-I-Y-x(2)-Q-[AL] O 15: 30.0607 2( 2) K-[PQ]-x-[RS]-D-G-x(1,2)-Y-x-[IM]-x(3)-Q P 16: 30.0093 2( 2) T-[EQ]-K-x(3,5)-D-G-x(1,2)-Y-x-[IM]-x(3)-Q Q 17: 29.4455 2( 2) R-x(0,1)-S-L-[DN]-[GT]-x-[DK]-P-x(3,4)-G R 18: 29.4455 2( 2) R-x(1,2)-S-L-[DN]-[GT]-x-[DK]-P-x(3,4)-G S 19: 29.4282 2( 2) E-x-[EP]-R-[RS]-[DV]-G-x(1,2)-V-x(1,2)-W T 20: 27.1904 2( 2) P-R-x(1,2)-D-[AG]-x-Y-x(2)-Y-x(1,2)-M Best patterns with alignements: fitness hits(seqs) Pattern A 1: 61.5479 2( 2) D-x(0,1)-E-[ER]-[IV]-x-S-x(0,1)-L-[EN]-[TV]-E-[KR]-[PS]-x(2)-[DE]-[GV]-[DK]-[WY]-[AV]-x(4)-[QS]-[AG] Occurences: 2(2) PHR_CARAU : 287- 313: aaepv DwEEVlSsLEVERSvgEVDWAqpgtSG gmnml PHR_METTH : 4- 28: mih D-ERIrS-LNTEKPrrDGKYViywmQA B 2: 60.2553 2( 2) H-[AD]-[EK]-[DR]-x-R-x(1,2)-L-x-T-x(0,1)-E-x-[LP]-[ER]-[NR]-[AD]-x(2)-[HY]-[DV]-x(2)-W-x-[AQ]-A Occurences: 2(2) PHR_CARAU : 413- 440: ktlqd HAKDsRqyLyTkEqLENAktHDqlWnAA qrqlv PHR_METTH : 3- 28: mi HDERiRs-LnT-EkPRRDgkYViyWmQA C 3: 59.3381 2( 2) D-x(0,2)-E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-[EK]-x-[DV]-x(4)-[GQ]-[AT] Occurences: 2(2) PHR_CARAU : 287- 311: aaepv DweEvLSSLEVE--RSVGEvDwaqpGT sggmn PHR_METTH : 4- 28: mih D--ErIRSLNTEkpRRDGKyViywmQA D 4: 56.6515 2( 2) E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-x(1,2)-V-x-[WY]-x(2)-[PQ]-[AG] Occurences: 2(2) PHR_CARAU : 290- 310: pvdwe EvLSSLEVE--RSVGe-VdWaqPG tsggm PHR_METTH : 5- 28: mihd ErIRSLNTEkpRRDGkyViYwmQA E 5: 45.9756 2( 2) S-L-[EN]-[TV]-E-x(0,2)-R-[RS]-[DV]-G-x(1,2)-V-x-[WY]-x(2)-[PQ]-[AG] Occurences: 2(2) PHR_CARAU : 294- 310: eevls SLEVE--RSVGe-VdWaqPG tsggm PHR_METTH : 9- 28: derir SLNTEkpRRDGkyViYwmQA F 6: 44.1066 2( 2) I-x(3,4)-I-R-x-[LM]-N-x(2,4)-K-x-[KR]-x-D-[GV]-x(2)-[FV]-x(4)-[QT]-A Occurences: 2(2) PHR_CARAU : 513- 540: waerp Ifgk-IRfMNyagcKrKfDVaqFerkyTA vkens PHR_METTH : 2- 28: m IhderIRsLNte--KpRrDGkyViywmQA G 7: 43.4422 2( 2) R-x(0,1)-I-R-[GS]-x(2)-T-x(0,1)-K-[LP]-x(2)-[DE]-x(4)-I-x(2)-[MV]-[DQ]-[AT] Occurences: 2(2) PHR_CARAU : 252- 274: leyga RtIRGkiT-KLlpEflteIplVDT hphsa PHR_METTH : 6- 28: mihde R-IRSlnTeKPrrDgkyvIywMQA H 8: 42.4653 2( 2) R-[ES]-L-x(0,2)-N-x(3,5)-P-[RS]-x-D-[GN]-x(2)-[GV]-[AI]-Y-x(2)-[AQ] Occurences: 2(2) PHR_CARAU : 383- 406: elvvr RELadNfcfynPSyDNisGAYdwA kktlq PHR_METTH : 8- 27: hderi RSL--Ntek--PRrDGkyVIYwmQ a I 9: 39.6713 2( 2) R-x(2)-[AS]-x-N-x(3,5)-P-[RS]-x-D-[GN]-x(2)-[GV]-[AI]-Y-x(0,1)-W Occurences: 2(2) PHR_CARAU : 383- 405: elvvr RelAdNfcfynPSyDNisGAYdW akktl PHR_METTH : 6- 25: mihde RirSlNtek--PRrDGkyVIY-W mqa J 10: 36.8194 2( 2) E-x-[EP]-R-[RS]-[DV]-G-x(1,2)-V-x(1,2)-W-x-Q-[AP] Occurences: 2(2) PHR_CARAU : 296- 309: vlssl EvERSVGe-Vd-WaQP gtsgg PHR_METTH : 13- 28: rslnt EkPRRDGkyViyWmQA K 11: 35.8755 2( 2) D-x(0,2)-E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-x(0,2)-R Occurences: 2(2) PHR_CARAU : 287- 299: aaepv DweEvLSSLEVE--R svgev PHR_METTH : 4- 16: mih D--ErIRSLNTEkpR rdgky L 12: 34.1590 2( 2) R-[IL]-R-x-L-x(1,2)-T-[EQ]-K-x(3,5)-D-G Occurences: 2(2) PHR_CARAU : 93- 109: evnkk RLRyLsdTQKikqgsDG flywm PHR_METTH : 6- 19: mihde RIRsLn-TEKprr--DG kyviy M 13: 33.7054 1( 1) E-x-[IL]-[RS]-S-L-[EN]-[TV]-E-R Occurences: 1(1) PHR_CARAU : 290- 299: pvdwe EvLSSLEVER svgev N 14: 32.6473 2( 2) R-x(0,2)-R-x(0,2)-D-[GN]-x(2)-[LV]-I-Y-x(2)-Q-[AL] Occurences: 2(2) PHR_CARAU : 116- 132: lywms RdqRvqDNwaLIYaqQL alaek PHR_METTH : 16- 28: ntekp R--R--DGkyVIYwmQA O 15: 30.0607 2( 2) K-[PQ]-x-[RS]-D-G-x(1,2)-Y-x-[IM]-x(3)-Q Occurences: 2(2) PHR_CARAU : 104- 118: dtqki KQgSDGflYwMsrdQ rvqdn PHR_METTH : 14- 27: slnte KPrRDGk-YvIywmQ a P 16: 30.0093 2( 2) T-[EQ]-K-x(3,5)-D-G-x(1,2)-Y-x-[IM]-x(3)-Q Occurences: 2(2) PHR_CARAU : 100- 118: rylsd TQKikqgsDGflYwMsrdQ rvqdn PHR_METTH : 12- 27: irsln TEKprr--DGk-YvIywmQ a Q 17: 29.4455 2( 2) R-x(0,1)-S-L-[DN]-[GT]-x-[DK]-P-x(3,4)-G Occurences: 2(2) PHR_CARAU : 482- 495: iylnd RlSLDGcDPngyvG cmwsi PHR_METTH : 8- 19: hderi R-SLNTeKPrrd-G kyviy R 18: 29.4455 2( 2) R-x(1,2)-S-L-[DN]-[GT]-x-[DK]-P-x(3,4)-G Occurences: 2(2) PHR_CARAU : 482- 495: iylnd Rl-SLDGcDPngyvG cmwsi PHR_METTH : 6- 19: mihde RirSLNTeKPrrd-G kyviy S 19: 29.4282 2( 2) E-x-[EP]-R-[RS]-[DV]-G-x(1,2)-V-x(1,2)-W Occurences: 2(2) PHR_CARAU : 296- 306: vlssl EvERSVGe-Vd-W aqpgt PHR_METTH : 13- 25: rslnt EkPRRDGkyViyW mqa T 20: 27.1904 2( 2) P-R-x(1,2)-D-[AG]-x-Y-x(2)-Y-x(1,2)-M Occurences: 2(2) PHR_CARAU : 148- 161: cfclv PRylDAtYrqYafM lkglq PHR_METTH : 15- 26: lntek PRr-DGkYviYw-M qa Number of patterns evaluated by Pratt:1285 Total running time: 1 seconds