------------------------------------------------------------ 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 24 sequences from file XYLOSE_ISOMERASE_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 24 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 XYLOSE_ISOMERASE_1.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: XYLA_ACTMI 393 XYLA_AMPSP 394 XYLA_ARTS7 394 XYLA_BACSU 440 XYLA_CLOTS 439 XYLA_ECOLI 440 XYLA_HAEIN 439 XYLA_KLEAE 440 XYLA_LACBR 449 XYLA_LACPE 449 XYLA_STAXY 439 XYLA_STRAL 390 XYLA_STRMR 388 XYLA_STROL 386 XYLA_STRRO 393 XYLA_STRRU 387 XYLA_STRSQ 9 XYLA_STRVN 12 XYLA_STRVO 388 XYLA_THEET 438 XYLA_THENE 444 XYLA_THESA 439 XYLA_THETH 387 XYLA_THETU 439 Pratt run started at Thu Feb 6 21:35:55 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 40( 24) T-F 2: 7.3401 166( 24) G-x(1,3)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 8.3401 40( 24) T-F B 2: 7.3401 166( 24) G-x(1,3)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 8.3401 40( 24) T-F Occurences: 40(24) XYLA_ACTMI : 51- 52: gaygi TF hdddl XYLA_AMPSP : 52- 53: gaygv TF hdddl XYLA_ARTS7 : 11- 12: padhf TF glwtv XYLA_ARTS7 : 51- 52: gaygi TF hdndl XYLA_ARTS7 : 132- 133: emgae TF vmwgg XYLA_BACSU : 58- 59: iaywh TF tadgt XYLA_BACSU : 284- 285: tlagh TF ehelr XYLA_CLOTS : 51- 52: iaywh TF tadgt XYLA_ECOLI : 51- 52: acywh TF cwnga XYLA_HAEIN : 51- 52: vcywh TF cwngn XYLA_HAEIN : 278- 279: tlagh TF qheia XYLA_KLEAE : 51- 52: acywh TF cwnga XYLA_LACBR : 53- 54: vaywh TF dqrlv XYLA_LACPE : 53- 54: vaywh TF dqrlv XYLA_LACPE : 365- 366: ivgid TF aaglr XYLA_STAXY : 49- 50: vaywh TF tadls XYLA_STAXY : 208- 209: ldnla TF fkmak XYLA_STAXY : 275- 276: tlagh TF qhelr XYLA_STAXY : 358- 359: iagmd TF alglr XYLA_STRAL : 11- 12: pedrf TF glwtv XYLA_STRAL : 51- 52: gahgv TF hdddl XYLA_STRMR : 12- 13: pedrf TF glwtv XYLA_STRMR : 52- 53: gaygv TF hdddl XYLA_STROL : 11- 12: pedrf TF glwtv XYLA_STROL : 51- 52: gahgv TF hdddl XYLA_STRRO : 11- 12: pedkf TF glwtv XYLA_STRRO : 51- 52: gaygv TF hdddl XYLA_STRRU : 11- 12: pedrf TF glwtv XYLA_STRRU : 51- 52: gahgv TF hdddl XYLA_STRSQ : 8- 9: agsah TF XYLA_STRVN : 3- 4: gv TF hdddl XYLA_STRVO : 11- 12: pedkf TF glwtv XYLA_STRVO : 51- 52: gaygv TF hdddl XYLA_THEET : 50- 51: vaywh TF tangt XYLA_THENE : 51- 52: vafwh TF vnegr XYLA_THENE : 278- 279: tlagh TF qhelr XYLA_THENE : 362- 363: iagmd TF algfk XYLA_THESA : 51- 52: iaywh TF tadgt XYLA_THETH : 11- 12: pehrf TF glwtv XYLA_THETU : 51- 52: iaywh TF tadgt B 2: 7.3401 166( 24) G-x(1,3)-T Occurences: 166(24) XYLA_ACTMI : 13- 16: dkfsf Glw-T vgwqa XYLA_ACTMI : 26- 29: ardaf Gda-T rtald XYLA_ACTMI : 49- 51: eigay Gi--T fhddd XYLA_ACTMI : 101- 104: pvfkd Ggf-T sndrs XYLA_ACTMI : 102- 104: vfkdg Gf--T sndrs XYLA_ACTMI : 129- 132: lgael Gak-T lvlwg XYLA_AMPSP : 14- 17: dkfsf Glw-T vgwqa XYLA_AMPSP : 27- 30: ardaf Gda-T rpvld XYLA_AMPSP : 50- 52: eigay Gv--T fhddd XYLA_AMPSP : 102- 105: pvfkd Ggf-T sndrs XYLA_AMPSP : 103- 105: vfkdg Gf--T sndrs XYLA_AMPSP : 130- 133: lgael Gak-T lvlwg XYLA_AMPSP : 351- 353: ptlnp Ge--T yadll XYLA_ARTS7 : 13- 16: dhftf Glw-T vgwtg XYLA_ARTS7 : 18- 20: glwtv Gw--T gadpf XYLA_ARTS7 : 26- 29: gadpf Gva-T rknld XYLA_ARTS7 : 49- 51: elgay Gi--T fhdnd XYLA_ARTS7 : 101- 104: pvfkd Ggf-T sndrs XYLA_ARTS7 : 102- 104: vfkdg Gf--T sndrs XYLA_ARTS7 : 129- 132: laaem Gae-T fvmwg XYLA_ARTS7 : 160- 163: drmre Gvd-T aagyi XYLA_ARTS7 : 224- 228: heqma GlnfT hgiaq XYLA_ARTS7 : 262- 265: lvfgh Gdl-T safft XYLA_ARTS7 : 282- 286: gfpng GpkyT gprhf XYLA_ARTS7 : 344- 346: gvfel Ge--T tlnag XYLA_ARTS7 : 344- 347: gvfel Get-T lnage XYLA_BACSU : 22- 26: kvvfe GkasT nplaf XYLA_BACSU : 41- 44: pqevi Ggk-T mkehl XYLA_BACSU : 42- 44: qevig Gk--T mkehl XYLA_BACSU : 68- 71: gtdvf Gaa-T mqrpw XYLA_BACSU : 115- 117: diape Gs--T lketn XYLA_BACSU : 159- 162: prfvh Gaa-T scnad XYLA_BACSU : 179- 182: aqvkk Gle-T akelg XYLA_BACSU : 199- 202: wggre Gye-T llntd XYLA_BACSU : 282- 284: hatla Gh--T fehel XYLA_BACSU : 311- 314: ghpll Gwd-T defpt XYLA_BACSU : 401- 405: ftegi GleiT egran XYLA_CLOTS : 35- 37: eevid Gk--T meehl XYLA_CLOTS : 61- 64: gtdqf Gka-T mqrpw XYLA_CLOTS : 109- 111: diape Gd--T lretn XYLA_CLOTS : 153- 156: prfvh Gas-T scnad XYLA_CLOTS : 193- 196: wggre Gye-T llntd XYLA_CLOTS : 305- 308: gdmll Gwd-T dqfpt XYLA_ECOLI : 153- 156: pryga Gaa-T npdpe XYLA_ECOLI : 193- 196: wggre Gye-T llntd XYLA_ECOLI : 224- 228: hkhki GfqgT lliep XYLA_ECOLI : 305- 308: gdaql Gwd-T dqfpn XYLA_ECOLI : 329- 332: eilka Ggf-T tggln XYLA_ECOLI : 329- 333: eilka GgftT gglnf XYLA_ECOLI : 330- 332: ilkag Gf--T tggln XYLA_ECOLI : 330- 333: ilkag Gft-T gglnf XYLA_ECOLI : 358- 362: fyghi GamdT malal XYLA_HAEIN : 15- 19: kisfe GeksT npfaf XYLA_HAEIN : 35- 37: nqvil Gk--T maehl XYLA_HAEIN : 153- 156: pryms Gaa-T npnpe XYLA_HAEIN : 193- 196: wggre Gye-T llntd XYLA_HAEIN : 224- 228: hkhki GfkgT lliep XYLA_HAEIN : 276- 278: hatla Gh--T fqhei XYLA_HAEIN : 305- 308: gdpql Gwd-T dqfpn XYLA_HAEIN : 329- 332: eilkh Ggf-T tggfn XYLA_HAEIN : 329- 333: eilkh GgftT ggfnf XYLA_HAEIN : 330- 332: ilkhg Gf--T tggfn XYLA_HAEIN : 330- 333: ilkhg Gft-T ggfnf XYLA_HAEIN : 401- 403: qhilq Gk--T sletl XYLA_KLEAE : 15- 19: rvrye GpksT nplaf XYLA_KLEAE : 153- 156: pryga Gaa-T npdpe XYLA_KLEAE : 193- 196: wggre Gye-T llntd XYLA_KLEAE : 224- 228: hkhki GfkgT lliep XYLA_KLEAE : 305- 308: gdpql Gwd-T dqfpn XYLA_KLEAE : 329- 332: eifka Ggf-T tggln XYLA_KLEAE : 329- 333: eifka GgftT gglnf XYLA_KLEAE : 330- 332: ifkag Gf--T tggln XYLA_KLEAE : 330- 333: ifkag Gft-T gglnf XYLA_KLEAE : 358- 362: fyghi GamdT mavsl XYLA_KLEAE : 401- 404: qqiln Gqm-T lsdia XYLA_LACBR : 63- 66: lvdpf Gdg-T aqrpy XYLA_LACBR : 111- 113: dlape Gd--T lretn XYLA_LACBR : 155- 158: prfve Gaa-T spyad XYLA_LACBR : 278- 280: hanla Gh--T yqhei XYLA_LACPE : 63- 66: lvdpf Gdg-T aqrpy XYLA_LACPE : 111- 113: dlape Gd--T lretn XYLA_LACPE : 155- 158: prfva Gaa-T spdad XYLA_LACPE : 278- 280: hanla Gh--T yqhei XYLA_LACPE : 362- 365: yghiv Gid-T faagl XYLA_STAXY : 150- 153: erfvh Gaa-T ssnae XYLA_STAXY : 221- 223: yadei Gy--T gqfli XYLA_STAXY : 273- 275: hatla Gh--T fqhel XYLA_STAXY : 302- 305: ghpll Gwd-T destd XYLA_STAXY : 355- 358: lthia Gmd-T falgl XYLA_STAXY : 397- 399: kkive Ge--T slkel XYLA_STRAL : 13- 16: drftf Glw-T vgweg XYLA_STRAL : 26- 29: grdpf Gda-T rtald XYLA_STRAL : 49- 51: elgah Gv--T fhddd XYLA_STRAL : 101- 104: pvfkd Ggf-T andrd XYLA_STRAL : 102- 104: vfkdg Gf--T andrd XYLA_STRAL : 129- 132: lavel Gae-T yvawg XYLA_STRAL : 165- 169: afdll GeyvT sqgyd XYLA_STRMR : 14- 17: drftf Glw-T vgwqg XYLA_STRMR : 27- 30: grdpf Gda-T rpald XYLA_STRMR : 50- 52: elgay Gv--T fhddd XYLA_STRMR : 62- 66: dlipf GssdT eresh XYLA_STRMR : 83- 85: aldat Gm--T vpmat XYLA_STRMR : 102- 105: pvfkd Ggf-T andrd XYLA_STRMR : 103- 105: vfkdg Gf--T andrd XYLA_STRMR : 130- 133: laael Gak-T yvawg XYLA_STRMR : 166- 170: afdll GeyvT aqgyd XYLA_STROL : 13- 16: drftf Glw-T vgwqg XYLA_STROL : 26- 29: grdpf Gda-T rpald XYLA_STROL : 49- 51: elgah Gv--T fhddd XYLA_STROL : 61- 65: dlipf GssdT eresh XYLA_STROL : 82- 84: aldat Gm--T vpmat XYLA_STROL : 101- 104: pvfkd Ggf-T andrd XYLA_STROL : 102- 104: vfkdg Gf--T andrd XYLA_STROL : 129- 132: lavel Gak-T yvawg XYLA_STROL : 165- 169: afdll GeyvT sqgyd XYLA_STROL : 172- 175: yvtsq Gyd-T rfaie XYLA_STRRO : 13- 16: dkftf Glw-T vgwqg XYLA_STRRO : 26- 29: grdpf Gda-T rpgld XYLA_STRRO : 49- 51: elgay Gv--T fhddd XYLA_STRRO : 61- 65: dlnpf GssdT eresh XYLA_STRRO : 82- 84: aldat Gm--T vpmat XYLA_STRRO : 128- 131: laael Gak-T yvawg XYLA_STRRO : 164- 168: afdll GeyvT aqgyd XYLA_STRRO : 367- 371: aaaar GmvrT prpag XYLA_STRRU : 13- 16: drftf Glw-T vgwqg XYLA_STRRU : 26- 29: grdpf Gda-T rrald XYLA_STRRU : 49- 51: elgah Gv--T fhddd XYLA_STRRU : 101- 104: pvfkd Ggf-T andrd XYLA_STRRU : 102- 104: vfkdg Gf--T andrd XYLA_STRRU : 129- 132: lavel Gae-T yvawg XYLA_STRRU : 165- 169: afdll GeyvT sqgyd XYLA_STRSQ : 4- 8: rha GsahT f XYLA_STRVN : 1- 3: Gv--T fhddd XYLA_STRVO : 13- 16: dkftf Glw-T vgwqg XYLA_STRVO : 26- 29: grdpf Gda-T rpald XYLA_STRVO : 49- 51: elgay Gv--T fhddd XYLA_STRVO : 61- 65: dlipf GssdT eresh XYLA_STRVO : 82- 84: aldat Gm--T vpmat XYLA_STRVO : 101- 104: pvfkd Ggf-T andrd XYLA_STRVO : 102- 104: vfkdg Gf--T andrd XYLA_STRVO : 129- 132: laael Gak-T yvawg XYLA_STRVO : 165- 169: afdll GeyvT aqgyd XYLA_THEET : 60- 63: gtdpf Gap-T mqrpw XYLA_THEET : 108- 110: diape Ge--T lretn XYLA_THEET : 152- 155: prfvh Gaa-T scnad XYLA_THEET : 192- 195: wggre Gye-T llntd XYLA_THEET : 304- 307: gdmll Gwd-T dqypt XYLA_THENE : 15- 19: kvqfe GkesT nplaf XYLA_THENE : 61- 64: grdpf Gdp-T adrpw XYLA_THENE : 109- 111: diape Gk--T lretn XYLA_THENE : 153- 156: prymh Gaa-T tcsad XYLA_THENE : 153- 157: prymh GaatT csadv XYLA_THENE : 193- 196: wggre Gye-T llntd XYLA_THENE : 224- 226: yakri Gf--T gqfli XYLA_THENE : 276- 278: hatla Gh--T fqhel XYLA_THENE : 305- 308: gdlll Gwd-T dqfpt XYLA_THENE : 329- 332: evika Ggf-T kggln XYLA_THENE : 330- 332: vikag Gf--T kggln XYLA_THENE : 359- 362: ighia Gmd-T falgf XYLA_THESA : 35- 37: eevid Gk--T meehl XYLA_THESA : 61- 64: gtdqf Gka-T mqrpw XYLA_THESA : 109- 111: diape Gd--T lretn XYLA_THESA : 153- 156: prfvh Gas-T scnad XYLA_THESA : 193- 196: wggre Gye-T llntd XYLA_THESA : 305- 308: gdmll Gwd-T dqfpt XYLA_THETH : 13- 16: hrftf Glw-T vgnvg XYLA_THETH : 101- 104: pafkd Gaf-T spdpw XYLA_THETH : 304- 308: wafar GcmrT ylilk XYLA_THETU : 35- 37: eevid Gk--T meehl XYLA_THETU : 61- 64: gtdqf Gka-T mqrpw XYLA_THETU : 109- 111: diape Gd--T lretn XYLA_THETU : 153- 156: prfvh Gas-T scnad XYLA_THETU : 193- 196: wggre Gye-T llntd XYLA_THETU : 305- 308: gdmll Gwd-T dqfpt Number of patterns evaluated by Pratt:2 Total running time: 1 seconds