------------------------------------------------------------ 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 GLC_GALNAC_ISOMERASE 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 GLC_GALNAC_ISOMERASE.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: AGAI_ECOLI 251 NAG1_CANAL 248 NAG1_HUMAN 289 NAGB_ECOLI 266 YIEK_ECOLI 213 Pratt run started at Thu Feb 6 19:34:24 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 29.1904 5( 5) G-x(3)-L-x(3)-G-x-G-x(2)-G-H-x(3)-N 2: 28.6904 8( 5) G-x(2,3)-L-x(3)-G-x-G-x(2)-G-H-x(3)-N 3: 25.0203 5( 5) L-x(3)-G-x-G-x(2)-G-H-x(3)-N 4: 24.0203 5( 5) L-x(1,2)-T-x(0,1)-G-x(2)-P-x(3)-Y-x(2)-L 5: 23.5203 6( 5) L-x(0,2)-G-x(1,2)-G-x(2)-G-H-x(3)-N 6: 20.8503 5( 5) G-x-G-x(2)-G-H-x(3)-N 7: 20.3503 5( 5) T-x(0,1)-G-x(2)-P-x(3)-Y-x(2)-L 8: 16.6802 5( 5) G-x(2)-G-H-x(3)-N 9: 16.6802 5( 5) G-x(2)-P-x(3)-Y-x(2)-L 10: 15.6802 6( 5) L-x(3)-G-x(3,4)-G-x(3,4)-N 11: 15.6802 5( 5) L-G-L-x(0,2)-G 12: 15.6802 5( 5) D-x(3,4)-G-L-x(3,4)-H 13: 15.6802 9( 5) G-x(1,2)-G-x(1,2)-G-x(4)-N 14: 15.1802 5( 5) L-x(1,3)-V-x(5)-A-x(4,5)-L 15: 15.1802 6( 5) L-x(3,4)-G-x-G-x(3,5)-A 16: 15.1802 8( 5) L-x(0,2)-G-x(2)-G-x(2,3)-G 17: 15.1802 6( 5) L-x-V-x(0,1)-G-x(3,5)-D 18: 15.1802 8( 5) G-x(1,3)-L-x(5)-G-x(1,2)-G 19: 15.1802 5( 5) L-x(2)-G-x(1,2)-P-x(1,3)-Y 20: 14.6802 5( 5) I-x(3)-G-x(1,3)-L-x(1,3)-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 63.3937 5( 5) G-x-[IL]-[DEH]-L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] B 2: 57.0026 8( 5) G-x(2,3)-L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] C 3: 53.4124 8( 5) G-x(1,3)-L-x-[LMV]-[GL]-G-[ILV]-G-x(1,2)-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] D 4: 53.3325 5( 5) L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] E 5: 43.1631 6( 5) L-x(0,2)-G-x(1,2)-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] F 6: 43.1549 5( 5) G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] G 7: 39.2855 6( 5) L-x(3,4)-G-x-G-x(3,5)-A-x(2)-[ENR]-x-[AGL]-[QST]-[AGS]-x-[ANV]-[ST]-x-[ADT]-x(3)-[EST]-[FLV] H 8: 38.5375 5( 5) L-x(1,2)-T-x(0,1)-G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] I 9: 36.9029 8( 5) G-x(1,2)-G-x(1,2)-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] J 10: 36.3231 5( 5) G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] K 11: 34.8674 5( 5) T-x(0,1)-G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] L 12: 33.3451 5( 5) L-x-[LMV]-[GL]-G-x(3,4)-G-x(3,4)-N-x-[AP]-[AGN]-[EST]-[ST] M 13: 31.1974 5( 5) G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] N 14: 29.4703 5( 5) I-x(3)-G-x(1,3)-L-x(1,3)-G-x(4)-[DGV]-x(4)-[NV]-[ET]-x-[AG]-[EPS] O 15: 25.5443 8( 5) L-x(0,2)-G-x(2)-G-x(2,3)-G-x(4)-[GNT]-[ET]-x(3)-[EPS]-x-[ACNTV] P 16: 22.6643 5( 5) L-x(1,3)-V-[CGST]-[DET]-x(2)-[ADP]-A-x(4,5)-L Q 17: 21.1053 5( 5) L-G-L-x(0,2)-G-x-[DNST]-[GP] R 18: 17.8421 6( 5) L-x-V-x(0,1)-G-x(3,5)-D-[AGN] S 19: 17.8007 5( 5) L-[APV]-x-G-x(1,2)-P-x(1,3)-Y T 20: 15.6802 5( 5) D-x(3,4)-G-L-x(3,4)-H Best patterns with alignements: fitness hits(seqs) Pattern A 1: 63.3937 5( 5) G-x-[IL]-[DEH]-L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 5(5) AGAI_ECOLI : 142- 165: liark GgLDLcVLGLGkNGHLGlNePGES lqpac NAG1_CANAL : 125- 148: kikqy GrIDLfLGGLGpEGHLAfNeAGSS rnskt NAG1_HUMAN : 129- 152: kikaa GgIELfVGGIGpDGHIAfNePGSS lvsrt NAGB_ECOLI : 129- 152: kirsy GkIHLfMGGVGnDGHIAfNePASS lasrt YIEK_ECOLI : 94- 117: klare GgLDLvVLGLGaDGHFCgNlPNTT hfheq B 2: 57.0026 8( 5) G-x(2,3)-L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 8(5) AGAI_ECOLI : 142- 165: liark GgldLcVLGLGkNGHLGlNePGES lqpac AGAI_ECOLI : 143- 165: iarkg Gld-LcVLGLGkNGHLGlNePGES lqpac NAG1_CANAL : 125- 148: kikqy GridLfLGGLGpEGHLAfNeAGSS rnskt NAG1_HUMAN : 129- 152: kikaa GgieLfVGGIGpDGHIAfNePGSS lvsrt NAG1_HUMAN : 130- 152: ikaag Gie-LfVGGIGpDGHIAfNePGSS lvsrt NAGB_ECOLI : 129- 152: kirsy GkihLfMGGVGnDGHIAfNePASS lasrt YIEK_ECOLI : 94- 117: klare GgldLvVLGLGaDGHFCgNlPNTT hfheq YIEK_ECOLI : 95- 117: lareg Gld-LvVLGLGaDGHFCgNlPNTT hfheq C 3: 53.4124 8( 5) G-x(1,3)-L-x-[LMV]-[GL]-G-[ILV]-G-x(1,2)-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 8(5) AGAI_ECOLI : 142- 165: liark GgldLcVLGLGknGHLGlNePGES lqpac AGAI_ECOLI : 143- 165: iarkg Gld-LcVLGLGknGHLGlNePGES lqpac NAG1_CANAL : 125- 148: kikqy GridLfLGGLGpeGHLAfNeAGSS rnskt NAG1_HUMAN : 129- 152: kikaa GgieLfVGGIGpdGHIAfNePGSS lvsrt NAG1_HUMAN : 130- 152: ikaag Gie-LfVGGIGpdGHIAfNePGSS lvsrt NAGB_ECOLI : 129- 152: kirsy GkihLfMGGVGndGHIAfNePASS lasrt YIEK_ECOLI : 94- 117: klare GgldLvVLGLGadGHFCgNlPNTT hfheq YIEK_ECOLI : 95- 117: lareg Gld-LvVLGLGadGHFCgNlPNTT hfheq D 4: 53.3325 5( 5) L-x-[LMV]-[GL]-G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 5(5) AGAI_ECOLI : 146- 165: kggld LcVLGLGkNGHLGlNePGES lqpac NAG1_CANAL : 129- 148: ygrid LfLGGLGpEGHLAfNeAGSS rnskt NAG1_HUMAN : 133- 152: aggie LfVGGIGpDGHIAfNePGSS lvsrt NAGB_ECOLI : 133- 152: ygkih LfMGGVGnDGHIAfNePASS lasrt YIEK_ECOLI : 98- 117: eggld LvVLGLGaDGHFCgNlPNTT hfheq E 5: 43.1631 6( 5) L-x(0,2)-G-x(1,2)-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 6(5) AGAI_ECOLI : 149- 165: ldlcv L--Gl-GkNGHLGlNePGES lqpac NAG1_CANAL : 129- 148: ygrid LflGglGpEGHLAfNeAGSS rnskt NAG1_CANAL : 131- 148: ridlf Lg-Gl-GpEGHLAfNeAGSS rnskt NAG1_CANAL : 131- 148: ridlf L--GglGpEGHLAfNeAGSS rnskt NAG1_HUMAN : 133- 152: aggie LfvGgiGpDGHIAfNePGSS lvsrt NAGB_ECOLI : 133- 152: ygkih LfmGgvGnDGHIAfNePASS lasrt YIEK_ECOLI : 101- 117: ldlvv L--Gl-GaDGHFCgNlPNTT hfheq F 6: 43.1549 5( 5) G-[ILV]-G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 5(5) AGAI_ECOLI : 150- 165: dlcvl GLGkNGHLGlNePGES lqpac NAG1_CANAL : 133- 148: dlflg GLGpEGHLAfNeAGSS rnskt NAG1_HUMAN : 137- 152: elfvg GIGpDGHIAfNePGSS lvsrt NAGB_ECOLI : 137- 152: hlfmg GVGnDGHIAfNePASS lasrt YIEK_ECOLI : 102- 117: dlvvl GLGaDGHFCgNlPNTT hfheq G 7: 39.2855 6( 5) L-x(3,4)-G-x-G-x(3,5)-A-x(2)-[ENR]-x-[AGL]-[QST]-[AGS]-x-[ANV]-[ST]-x-[ADT]-x(3)-[EST]-[FLV] Occurences: 6(5) AGAI_ECOLI : 210- 238: narev LllvtGeGkqd--AtdRfLTAkVStAipaSF lwlhs AGAI_ECOLI : 211- 238: arevl Llvt-GeGkqd--AtdRfLTAkVStAipaSF lwlhs NAG1_CANAL : 129- 158: ygrid Lflg-GlGpeghlAfnEaGSSrNSkTrkvEL vesti NAG1_HUMAN : 133- 162: aggie Lfvg-GiGpdghiAfnEpGSSlVSrTrvkTL amdti NAGB_ECOLI : 133- 162: ygkih Lfmg-GvGndghiAfnEpASSlASrTrikTL thdtr YIEK_ECOLI : 167- 195: aaknl LiivsGaGkaq--AlkNvLQGpVTeDvpaSV lqlhp H 8: 38.5375 5( 5) L-x(1,2)-T-x(0,1)-G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] Occurences: 5(5) AGAI_ECOLI : 53- 72: navic La-T-GATPlltYhyLvEkiHQ qqvdv NAG1_CANAL : 35- 54: tfvlg Lp-T-GSSPegiYakLiEanKQ grvsf NAG1_HUMAN : 39- 58: yftlg Lp-T-GSTPlgcYkkLiEyyKN gdlsf NAGB_ECOLI : 39- 58: pfvlg Lp-T-GGTPmttYkaLvEmhKA gqvsf YIEK_ECOLI : 9- 30: trrvn LaiTaGSTPkgmYeyLtTlvKG kpwyd I 9: 36.9029 8( 5) G-x(1,2)-G-x(1,2)-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 8(5) AGAI_ECOLI : 150- 165: dlcvl Gl-GknGHLGlNePGES lqpac NAG1_CANAL : 132- 148: idlfl GglGpeGHLAfNeAGSS rnskt NAG1_CANAL : 133- 148: dlflg Gl-GpeGHLAfNeAGSS rnskt NAG1_HUMAN : 136- 152: ielfv GgiGpdGHIAfNePGSS lvsrt NAG1_HUMAN : 137- 152: elfvg Gi-GpdGHIAfNePGSS lvsrt NAGB_ECOLI : 136- 152: ihlfm GgvGndGHIAfNePASS lasrt NAGB_ECOLI : 137- 152: hlfmg Gv-GndGHIAfNePASS lasrt YIEK_ECOLI : 102- 117: dlvvl Gl-GadGHFCgNlPNTT hfheq J 10: 36.3231 5( 5) G-x-[DEN]-G-H-[FIL]-[ACG]-x-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 5(5) AGAI_ECOLI : 152- 165: cvlgl GkNGHLGlNePGES lqpac NAG1_CANAL : 135- 148: flggl GpEGHLAfNeAGSS rnskt NAG1_HUMAN : 139- 152: fvggi GpDGHIAfNePGSS lvsrt NAGB_ECOLI : 139- 152: fmggv GnDGHIAfNePASS lasrt YIEK_ECOLI : 104- 117: vvlgl GaDGHFCgNlPNTT hfheq K 11: 34.8674 5( 5) T-x(0,1)-G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] Occurences: 5(5) AGAI_ECOLI : 55- 72: vicla T-GATPlltYhyLvEkiHQ qqvdv NAG1_CANAL : 37- 54: vlglp T-GSSPegiYakLiEanKQ grvsf NAG1_HUMAN : 41- 58: tlglp T-GSTPlgcYkkLiEyyKN gdlsf NAGB_ECOLI : 41- 58: vlglp T-GGTPmttYkaLvEmhKA gqvsf YIEK_ECOLI : 12- 30: vnlai TaGSTPkgmYeyLtTlvKG kpwyd L 12: 33.3451 5( 5) L-x-[LMV]-[GL]-G-x(3,4)-G-x(3,4)-N-x-[AP]-[AGN]-[EST]-[ST] Occurences: 5(5) AGAI_ECOLI : 146- 165: kggld LcVLGlgknGhlglNePGES lqpac NAG1_CANAL : 129- 148: ygrid LfLGGlgpeGhlafNeAGSS rnskt NAG1_HUMAN : 133- 152: aggie LfVGGigpdGhiafNePGSS lvsrt NAGB_ECOLI : 133- 152: ygkih LfMGGvgndGhiafNePASS lasrt YIEK_ECOLI : 98- 117: eggld LvVLGlgadGhfcgNlPNTT hfheq M 13: 31.1974 5( 5) G-[AGS]-[ST]-P-x(3)-Y-x(2)-L-x-[ET]-x(2)-[HK]-[AGNQ] Occurences: 5(5) AGAI_ECOLI : 56- 72: iclat GATPlltYhyLvEkiHQ qqvdv NAG1_CANAL : 38- 54: lglpt GSSPegiYakLiEanKQ grvsf NAG1_HUMAN : 42- 58: lglpt GSTPlgcYkkLiEyyKN gdlsf NAGB_ECOLI : 42- 58: lglpt GGTPmttYkaLvEmhKA gqvsf YIEK_ECOLI : 14- 30: laita GSTPkgmYeyLtTlvKG kpwyd N 14: 29.4703 5( 5) I-x(3)-G-x(1,3)-L-x(1,3)-G-x(4)-[DGV]-x(4)-[NV]-[ET]-x-[AG]-[EPS] Occurences: 5(5) AGAI_ECOLI : 138- 164: rvtnl IarkGgldLcvlGlgknGhlglNEpGE slqpa NAG1_CANAL : 121- 147: nyekk IkqyGridLflgGlgpeGhlafNEaGS srnsk NAG1_HUMAN : 125- 151: afeek IkaaGgieLfvgGigpdGhiafNEpGS slvsr NAGB_ECOLI : 125- 151: qyeek IrsyGkihLfmgGvgndGhiafNEpAS slasr YIEK_ECOLI : 135- 157: gemvd IvahGe--Lg--GdfslVpdsyVTmGP ksima O 15: 25.5443 8( 5) L-x(0,2)-G-x(2)-G-x(2,3)-G-x(4)-[GNT]-[ET]-x(3)-[EPS]-x-[ACNTV] Occurences: 8(5) AGAI_ECOLI : 149- 170: ldlcv LglGknGhl-GlnepGEslqPaC hisql AGAI_ECOLI : 151- 170: lcvlg L--GknGhl-GlnepGEslqPaC hisql NAG1_CANAL : 129- 150: ygrid LflGglGpe-GhlafNEagsSrN sktrk NAG1_CANAL : 131- 150: ridlf L--GglGpe-GhlafNEagsSrN sktrk NAG1_HUMAN : 133- 154: aggie LfvGgiGpd-GhiafNEpgsSlV srtrv NAGB_ECOLI : 133- 154: ygkih LfmGgvGnd-GhiafNEpasSlA srtri YIEK_ECOLI : 101- 123: ldlvv LglGadGhfcGnlpnTThfhEqT vefpi YIEK_ECOLI : 103- 123: lvvlg L--GadGhfcGnlpnTThfhEqT vefpi P 16: 22.6643 5( 5) L-x(1,3)-V-[CGST]-[DET]-x(2)-[ADP]-A-x(4,5)-L Occurences: 5(5) AGAI_ECOLI : 226- 241: atdrf LtakVSTaiPAsflw-L hsnfi NAG1_CANAL : 234- 248: dhanv Li--VCDnaAAglkskL NAG1_HUMAN : 186- 202: vptma LtvgVGTvmDArevmiL itgah NAGB_ECOLI : 186- 202: vpkya LtvgVGTllDAeevmiL vlgsq YIEK_ECOLI : 183- 198: alknv LqgpVTEdvPAsvlq-L hpslm Q 17: 21.1053 5( 5) L-G-L-x(0,2)-G-x-[DNST]-[GP] Occurences: 5(5) AGAI_ECOLI : 149- 155: ldlcv LGL--GkNG hlgln NAG1_CANAL : 33- 41: prtfv LGLptGsSP egiya NAG1_HUMAN : 37- 45: ekyft LGLptGsTP lgcyk NAGB_ECOLI : 37- 45: drpfv LGLptGgTP mttyk YIEK_ECOLI : 101- 107: ldlvv LGL--GaDG hfcgn R 18: 17.8421 6( 5) L-x-V-x(0,1)-G-x(3,5)-D-[AGN] Occurences: 6(5) AGAI_ECOLI : 211- 221: arevl LlVtGegkq-DA tdrfl NAG1_CANAL : 182- 192: vpkya LsV-GistilDN sdeia NAG1_HUMAN : 133- 142: aggie LfVgGigp--DG hiafn NAG1_HUMAN : 133- 142: aggie LfV-Ggigp-DG hiafn NAG1_HUMAN : 186- 196: vptma LtV-GvgtvmDA revmi NAGB_ECOLI : 186- 196: vpkya LtV-GvgtllDA eevmi YIEK_ECOLI : 98- 107: eggld LvVlGlga--DG hfcgn S 19: 17.8007 5( 5) L-[APV]-x-G-x(1,2)-P-x(1,3)-Y Occurences: 5(5) AGAI_ECOLI : 53- 63: navic LAtGatPlltY hylve NAG1_CANAL : 35- 45: tfvlg LPtGssPegiY aklie NAG1_HUMAN : 39- 49: yftlg LPtGstPlgcY kklie NAGB_ECOLI : 39- 49: pfvlg LPtGgtPmttY kalve YIEK_ECOLI : 27- 34: eyltt LVkGk-Pw--Y dncyf T 20: 15.6802 5( 5) D-x(3,4)-G-L-x(3,4)-H Occurences: 5(5) AGAI_ECOLI : 145- 156: rkggl DlcvlGLgkngH lglne NAG1_CANAL : 128- 139: qygri DlflgGLgpegH lafne NAG1_HUMAN : 72- 81: ktfnm Deyv-GLprd-H pesyh NAGB_ECOLI : 72- 81: vtfnm Deyv-GLpke-H pesyy YIEK_ECOLI : 97- 108: reggl DlvvlGLgadgH fcgnl Number of patterns evaluated by Pratt:3314 Total running time: 1 seconds