------------------------------------------------------------ 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 41 sequences from file NEUROHYPOPHYS_HORM PATTERN CONSERVATION: CM: min Nr of Seqs to Match 41 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 NEUROHYPOPHYS_HORM.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CONO_CONGE 9 CONO_CONST 9 CONO_LYMST 155 DNF1_LOCMI 9 ISOT_CYPCA 9 NEU1_BOVIN 125 NEU1_CATCO 154 NEU1_HORSE 105 NEU1_HUMAN 125 NEU1_MOUSE 125 NEU1_ONCKE 153 NEU1_PIG 125 NEU1_RAT 125 NEU1_SHEEP 125 NEU2_BALPH 107 NEU2_BOVIN 166 NEU2_CATCO 148 NEU2_CAVPO 144 NEU2_HUMAN 164 NEU2_MOUSE 168 NEU2_ONCKE 158 NEU2_PIG 166 NEU2_RAT 168 NEU2_SHEEP 147 NEU3_CATCO 152 NEU4_CATCO 155 NEUI_ONCMA 159 NEUM_BUFJA 125 NEUV_BUFJA 159 NEUV_BUFRE 27 NEUV_CHICK 161 NEUV_ONCMA 155 NEUV_RANES 141 OXYA_SCYCA 9 OXYA_SQUAC 9 OXYF_SCYCA 9 OXYT_CYPCA 9 OXYT_OCTVU 9 OXYT_RABIT 9 OXYT_RAJCL 9 OXYV_SQUAC 9 Pratt run started at Thu Feb 6 20:24:38 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.8503 41( 41) C-x(3)-N-C-P-x-G 2: 16.6802 41( 41) N-C-P-x-G 3: 12.5102 41( 41) C-P-x-G 4: 8.3401 107( 41) P-x-G Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 24.0213 41( 41) C-x-[FI]-x-N-C-P-x-G B 2: 16.6802 41( 41) N-C-P-x-G C 3: 12.5102 41( 41) C-P-x-G D 4: 8.3401 107( 41) P-x-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 24.0213 41( 41) C-x-[FI]-x-N-C-P-x-G Occurences: 41(41) CONO_CONGE : 1- 9: CfIrNCPkG CONO_CONST : 1- 9: CiIrNCPrG CONO_LYMST : 27- 35: sltda CfIrNCPkG gkrsl DNF1_LOCMI : 1- 9: ClItNCPrG ISOT_CYPCA : 1- 9: CyIsNCPiG NEU1_BOVIN : 20- 28: altsa CyIqNCPlG gkrav NEU1_CATCO : 21- 29: svcsa CyIsNCPiG gkrai NEU1_HORSE : 1- 9: CyIqNCPlG gkraa NEU1_HUMAN : 20- 28: altsa CyIqNCPlG gkraa NEU1_MOUSE : 20- 28: altsa CyIqNCPlG gkrav NEU1_ONCKE : 21- 29: alssa CyIqNCPrG gkrsf NEU1_PIG : 20- 28: altsa CyIqNCPlG gkrav NEU1_RAT : 20- 28: altsa CyIqNCPlG gkraa NEU1_SHEEP : 20- 28: altsa CyIqNCPlG gkrav NEU2_BALPH : 1- 9: CyFqNCPrG xxxam NEU2_BOVIN : 20- 28: aftsa CyFqNCPrG gkram NEU2_CATCO : 21- 29: svcsa CyIsNCPiG gkrav NEU2_CAVPO : 1- 9: CyFqNCPrG gkral NEU2_HUMAN : 20- 28: afssa CyFqNCPrG gkram NEU2_MOUSE : 24- 32: afssa CyFqNCPrG gkrai NEU2_ONCKE : 20- 28: afssa CyIqNCPrG gkral NEU2_PIG : 20- 28: altsa CyFqNCPkG gkram NEU2_RAT : 24- 32: altsa CyFqNCPrG gkrat NEU2_SHEEP : 1- 9: CyFqNCPrG xxxam NEU3_CATCO : 20- 28: alssa CyIqNCPrG gkrsq NEU4_CATCO : 21- 29: clssa CyIqNCPrG gkral NEUI_ONCMA : 23- 31: svcta CyIsNCPiG gkrsa NEUM_BUFJA : 20- 28: alssa CyIqNCPiG gkrsv NEUV_BUFJA : 18- 26: alssa CyIqNCPrG gkrsy NEUV_BUFRE : 1- 9: CyIqNCPrG gkrsy NEUV_CHICK : 20- 28: alssa CyIqNCPrG gkral NEUV_ONCMA : 21- 29: alssa CyIqNCPrG gkrsf NEUV_RANES : 1- 9: CyIqNCPrG gkrsy OXYA_SCYCA : 1- 9: CyInNCPvG OXYA_SQUAC : 1- 9: CyInNCPlG OXYF_SCYCA : 1- 9: CyFnNCPvG OXYT_CYPCA : 1- 9: CyIqNCPrG OXYT_OCTVU : 1- 9: CyFrNCPiG OXYT_RABIT : 1- 9: CyIqNCPlG OXYT_RAJCL : 1- 9: CyIsNCPqG OXYV_SQUAC : 1- 9: CyIqNCPvG B 2: 16.6802 41( 41) N-C-P-x-G Occurences: 41(41) CONO_CONGE : 5- 9: cfir NCPkG CONO_CONST : 5- 9: ciir NCPrG CONO_LYMST : 31- 35: acfir NCPkG gkrsl DNF1_LOCMI : 5- 9: clit NCPrG ISOT_CYPCA : 5- 9: cyis NCPiG NEU1_BOVIN : 24- 28: acyiq NCPlG gkrav NEU1_CATCO : 25- 29: acyis NCPiG gkrai NEU1_HORSE : 5- 9: cyiq NCPlG gkraa NEU1_HUMAN : 24- 28: acyiq NCPlG gkraa NEU1_MOUSE : 24- 28: acyiq NCPlG gkrav NEU1_ONCKE : 25- 29: acyiq NCPrG gkrsf NEU1_PIG : 24- 28: acyiq NCPlG gkrav NEU1_RAT : 24- 28: acyiq NCPlG gkraa NEU1_SHEEP : 24- 28: acyiq NCPlG gkrav NEU2_BALPH : 5- 9: cyfq NCPrG xxxam NEU2_BOVIN : 24- 28: acyfq NCPrG gkram NEU2_CATCO : 25- 29: acyis NCPiG gkrav NEU2_CAVPO : 5- 9: cyfq NCPrG gkral NEU2_HUMAN : 24- 28: acyfq NCPrG gkram NEU2_MOUSE : 28- 32: acyfq NCPrG gkrai NEU2_ONCKE : 24- 28: acyiq NCPrG gkral NEU2_PIG : 24- 28: acyfq NCPkG gkram NEU2_RAT : 28- 32: acyfq NCPrG gkrat NEU2_SHEEP : 5- 9: cyfq NCPrG xxxam NEU3_CATCO : 24- 28: acyiq NCPrG gkrsq NEU4_CATCO : 25- 29: acyiq NCPrG gkral NEUI_ONCMA : 27- 31: acyis NCPiG gkrsa NEUM_BUFJA : 24- 28: acyiq NCPiG gkrsv NEUV_BUFJA : 22- 26: acyiq NCPrG gkrsy NEUV_BUFRE : 5- 9: cyiq NCPrG gkrsy NEUV_CHICK : 24- 28: acyiq NCPrG gkral NEUV_ONCMA : 25- 29: acyiq NCPrG gkrsf NEUV_RANES : 5- 9: cyiq NCPrG gkrsy OXYA_SCYCA : 5- 9: cyin NCPvG OXYA_SQUAC : 5- 9: cyin NCPlG OXYF_SCYCA : 5- 9: cyfn NCPvG OXYT_CYPCA : 5- 9: cyiq NCPrG OXYT_OCTVU : 5- 9: cyfr NCPiG OXYT_RABIT : 5- 9: cyiq NCPlG OXYT_RAJCL : 5- 9: cyis NCPqG OXYV_SQUAC : 5- 9: cyiq NCPvG C 3: 12.5102 41( 41) C-P-x-G Occurences: 41(41) CONO_CONGE : 6- 9: cfirn CPkG CONO_CONST : 6- 9: ciirn CPrG CONO_LYMST : 32- 35: cfirn CPkG gkrsl DNF1_LOCMI : 6- 9: clitn CPrG ISOT_CYPCA : 6- 9: cyisn CPiG NEU1_BOVIN : 25- 28: cyiqn CPlG gkrav NEU1_CATCO : 26- 29: cyisn CPiG gkrai NEU1_HORSE : 6- 9: cyiqn CPlG gkraa NEU1_HUMAN : 25- 28: cyiqn CPlG gkraa NEU1_MOUSE : 25- 28: cyiqn CPlG gkrav NEU1_ONCKE : 26- 29: cyiqn CPrG gkrsf NEU1_PIG : 25- 28: cyiqn CPlG gkrav NEU1_RAT : 25- 28: cyiqn CPlG gkraa NEU1_SHEEP : 25- 28: cyiqn CPlG gkrav NEU2_BALPH : 6- 9: cyfqn CPrG xxxam NEU2_BOVIN : 25- 28: cyfqn CPrG gkram NEU2_CATCO : 26- 29: cyisn CPiG gkrav NEU2_CAVPO : 6- 9: cyfqn CPrG gkral NEU2_HUMAN : 25- 28: cyfqn CPrG gkram NEU2_MOUSE : 29- 32: cyfqn CPrG gkrai NEU2_ONCKE : 25- 28: cyiqn CPrG gkral NEU2_PIG : 25- 28: cyfqn CPkG gkram NEU2_RAT : 29- 32: cyfqn CPrG gkrat NEU2_SHEEP : 6- 9: cyfqn CPrG xxxam NEU3_CATCO : 25- 28: cyiqn CPrG gkrsq NEU4_CATCO : 26- 29: cyiqn CPrG gkral NEUI_ONCMA : 28- 31: cyisn CPiG gkrsa NEUM_BUFJA : 25- 28: cyiqn CPiG gkrsv NEUV_BUFJA : 23- 26: cyiqn CPrG gkrsy NEUV_BUFRE : 6- 9: cyiqn CPrG gkrsy NEUV_CHICK : 25- 28: cyiqn CPrG gkral NEUV_ONCMA : 26- 29: cyiqn CPrG gkrsf NEUV_RANES : 6- 9: cyiqn CPrG gkrsy OXYA_SCYCA : 6- 9: cyinn CPvG OXYA_SQUAC : 6- 9: cyinn CPlG OXYF_SCYCA : 6- 9: cyfnn CPvG OXYT_CYPCA : 6- 9: cyiqn CPrG OXYT_OCTVU : 6- 9: cyfrn CPiG OXYT_RABIT : 6- 9: cyiqn CPlG OXYT_RAJCL : 6- 9: cyisn CPqG OXYV_SQUAC : 6- 9: cyiqn CPvG D 4: 8.3401 107( 41) P-x-G Occurences: 107(41) CONO_CONGE : 7- 9: firnc PkG CONO_CONST : 7- 9: iirnc PrG CONO_LYMST : 33- 35: firnc PkG gkrsl CONO_LYMST : 55- 57: cmkcg PgG tgqcv DNF1_LOCMI : 7- 9: litnc PrG ISOT_CYPCA : 7- 9: yisnc PiG NEU1_BOVIN : 26- 28: yiqnc PlG gkrav NEU1_BOVIN : 43- 45: vrtcl PcG pggkg NEU1_BOVIN : 46- 48: clpcg PgG kgrcf NEU1_BOVIN : 91- 93: qsgqk PcG sggrc NEU1_BOVIN : 107- 109: giccs PdG chedp NEU1_CATCO : 27- 29: yisnc PiG gkrai NEU1_HORSE : 7- 9: yiqnc PlG gkraa NEU1_HORSE : 24- 26: vrkcl PcG pggkg NEU1_HORSE : 27- 29: clpcg PgG kgrcf NEU1_HORSE : 72- 74: qsgqk PcG sggrc NEU1_HORSE : 88- 90: giccs PdG cladp NEU1_HUMAN : 26- 28: yiqnc PlG gkraa NEU1_HUMAN : 43- 45: vrkcl PcG pggkg NEU1_HUMAN : 46- 48: clpcg PgG kgrcf NEU1_HUMAN : 107- 109: glccs PdG chadp NEU1_MOUSE : 26- 28: yiqnc PlG gkrav NEU1_MOUSE : 43- 45: mrkcl PcG pggkg NEU1_MOUSE : 46- 48: clpcg PgG kgrcf NEU1_MOUSE : 91- 93: qsgqk PcG sggrc NEU1_MOUSE : 107- 109: giccs PdG crtdp NEU1_ONCKE : 27- 29: yiqnc PrG gkrsf NEU1_PIG : 26- 28: yiqnc PlG gkrav NEU1_PIG : 43- 45: vrkcl PcG pggkg NEU1_PIG : 46- 48: clpcg PgG kgrcf NEU1_PIG : 91- 93: qsgqk PcG segrc NEU1_PIG : 107- 109: giccn PdG crfdp NEU1_RAT : 26- 28: yiqnc PlG gkraa NEU1_RAT : 43- 45: mrkcl PcG pggkg NEU1_RAT : 46- 48: clpcg PgG kgrcf NEU1_RAT : 91- 93: qsgqk PcG sggrc NEU1_RAT : 107- 109: giccs PdG crtdp NEU1_SHEEP : 26- 28: yiqnc PlG gkrav NEU1_SHEEP : 43- 45: vrtcl PcG pgakg NEU1_SHEEP : 91- 93: qsgqk PcG sggrc NEU1_SHEEP : 107- 109: giccs PdG shadp NEU2_BALPH : 7- 9: yfqnc PrG xxxam NEU2_BALPH : 24- 26: lrqcl PcG pggkg NEU2_BALPH : 27- 29: clpcg PgG kgrcf NEU2_BALPH : 72- 74: qsgqk PcG sggrc NEU2_BOVIN : 26- 28: yfqnc PrG gkram NEU2_BOVIN : 43- 45: lrqcl PcG pggkg NEU2_BOVIN : 46- 48: clpcg PgG kgrcf NEU2_BOVIN : 91- 93: qsgqk PcG sggrc NEU2_BOVIN : 140- 142: tlldg PsG alllr NEU2_CATCO : 27- 29: yisnc PiG gkrav NEU2_CAVPO : 7- 9: yfqnc PrG gkral NEU2_CAVPO : 24- 26: lrqcl PcG pggqg NEU2_CAVPO : 27- 29: clpcg PgG qgrcf NEU2_CAVPO : 72- 74: qsgqk PcG sggrc NEU2_CAVPO : 119- 121: tqldg PaG alllr NEU2_CAVPO : 141- 143: pqpaa PgG y NEU2_HUMAN : 26- 28: yfqnc PrG gkram NEU2_HUMAN : 43- 45: lrqcl PcG pggkg NEU2_HUMAN : 46- 48: clpcg PgG kgrcf NEU2_HUMAN : 138- 140: tqldg PaG alllr NEU2_MOUSE : 30- 32: yfqnc PrG gkrai NEU2_MOUSE : 47- 49: lrqcl PcG pggkg NEU2_MOUSE : 50- 52: clpcg PgG kgrcf NEU2_MOUSE : 95- 97: qsgqk PcG sggrc NEU2_ONCKE : 26- 28: yiqnc PrG gkral NEU2_ONCKE : 91- 93: qtggr PcG sdagr NEU2_PIG : 26- 28: yfqnc PkG gkram NEU2_PIG : 43- 45: lrqcl PcG pggkg NEU2_PIG : 46- 48: clpcg PgG kgrcf NEU2_PIG : 91- 93: qsgqk PcG sggrc NEU2_PIG : 140- 142: tlldg PsG alllr NEU2_RAT : 30- 32: yfqnc PrG gkrat NEU2_RAT : 47- 49: lrqcl PcG pggkg NEU2_RAT : 50- 52: clpcg PgG kgrcf NEU2_RAT : 95- 97: qsgqk PcG sggrc NEU2_SHEEP : 7- 9: yfqnc PrG xxxam NEU2_SHEEP : 24- 26: lrqcl PcG pggkg NEU2_SHEEP : 27- 29: clpcg PgG kgrcf NEU2_SHEEP : 72- 74: qsgqk PcG sggrc NEU2_SHEEP : 121- 123: tlldg PsG alllr NEU3_CATCO : 26- 28: yiqnc PrG gkrsq NEU3_CATCO : 90- 92: etggr PcG degrc NEU4_CATCO : 27- 29: yiqnc PrG gkral NEUI_ONCMA : 29- 31: yisnc PiG gkrsa NEUM_BUFJA : 26- 28: yiqnc PiG gkrsv NEUM_BUFJA : 44- 46: vrkci PcG prnkg NEUM_BUFJA : 92- 94: esgrk PcG nnggn NEUV_BUFJA : 24- 26: yiqnc PrG gkrsy NEUV_BUFJA : 41- 43: vrqci PcG pgnrg NEUV_BUFRE : 7- 9: yiqnc PrG gkrsy NEUV_BUFRE : 24- 26: vpqci PcG p NEUV_CHICK : 26- 28: yiqnc PrG gkral NEUV_CHICK : 43- 45: lrqcl PcG pgnrg NEUV_CHICK : 91- 93: qaggq PcG sdgrc NEUV_ONCMA : 27- 29: yiqnc PrG gkrsf NEUV_RANES : 7- 9: yiqnc PrG gkrsy NEUV_RANES : 24- 26: vrqci PcG pgnrg NEUV_RANES : 72- 74: eaggk PcG aggrc OXYA_SCYCA : 7- 9: yinnc PvG OXYA_SQUAC : 7- 9: yinnc PlG OXYF_SCYCA : 7- 9: yfnnc PvG OXYT_CYPCA : 7- 9: yiqnc PrG OXYT_OCTVU : 7- 9: yfrnc PiG OXYT_RABIT : 7- 9: yiqnc PlG OXYT_RAJCL : 7- 9: yisnc PqG OXYV_SQUAC : 7- 9: yiqnc PvG Number of patterns evaluated by Pratt:10 Total running time: 0 seconds