------------------------------------------------------------ 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 61 sequences from file SOD_CU_ZN_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 61 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 SOD_CU_ZN_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: SOD1_ORYSA 151 SOD2_ORYSA 151 SOD2_PICAB 21 SOD4_MAIZE 151 SOD5_MAIZE 151 SODC_ACTPL 11 SODC_ARATH 151 SODC_BOVIN 151 SODC_BRAOC 151 SODC_BRUAB 154 SODC_BRUPA 158 SODC_CAEEL 158 SODC_CARCR 166 SODC_CAUCR 174 SODC_CAVPO 152 SODC_CERCA 152 SODC_CHYAM 152 SODC_DROME 152 SODC_DROVI 152 SODC_DROWI 152 SODC_HAEIN 187 SODC_HAEPA 187 SODC_HORSE 153 SODC_HUMAN 153 SODC_IPOBA 151 SODC_LYCES 151 SODC_MAIZE 150 SODC_MOUSE 153 SODC_NEUCR 153 SODC_NICPL 151 SODC_NPVAC 151 SODC_ONCVO 158 SODC_PEA 151 SODC_PHOLE 173 SODC_PIG 152 SODC_PINSY 154 SODC_PRIGL 152 SODC_RABIT 152 SODC_RANCA 24 SODC_RAT 153 SODC_SCHMA 153 SODC_SCHPO 154 SODC_SHEEP 151 SODC_SPIOL 152 SODC_XENLA 150 SODC_XIPGL 151 SODC_YEAST 153 SODD_XENLA 150 SODE_BRUPA 199 SODE_HUMAN 240 SODE_ONCVO 201 SODE_RAT 244 SODE_SCHMA 184 SODP_LYCES 217 SODP_PEA 202 SODP_PETHY 219 SODP_PICAB 23 SODP_PINSY 141 SODP_POPTM 201 SODP_SPIOL 222 YMF1_CAEEL 184 Pratt run started at Thu Feb 6 21:14:18 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 221( 61) G-x(0,1)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.8401 221( 61) G-x(0,1)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.8401 221( 61) G-x(0,1)-V Occurences: 221(61) SOD1_ORYSA : 31- 33: pttvt GsV sglkp SOD1_ORYSA : 83- 85: hagdl GnV taged SOD1_ORYSA : 91- 92: taged G-V anihv SOD1_ORYSA : 140- 142: tgnag GrV acgii SOD2_ORYSA : 12- 13: lasse G-V kgtif SOD2_ORYSA : 31- 33: ptsvt GsV sglkp SOD2_ORYSA : 91- 92: tagad G-V anvnv SOD2_ORYSA : 140- 142: tgnag GrV acgii SOD2_PICAB : 16- 17: gadvk G-V vqft SOD2_PICAB : 16- 18: gadvk GvV qft SOD4_MAIZE : 12- 13: lgsse G-V kgtif SOD4_MAIZE : 31- 33: pttvt GsV sglkp SOD4_MAIZE : 83- 85: hagdl GnV tagad SOD4_MAIZE : 91- 92: tagad G-V aninv SOD4_MAIZE : 140- 142: tgnag GrV acgii SOD5_MAIZE : 12- 13: lgssd G-V kgtif SOD5_MAIZE : 31- 33: ptavt GsV sglkp SOD5_MAIZE : 83- 85: hagdl GnV tagad SOD5_MAIZE : 91- 92: tagad G-V aninv SOD5_MAIZE : 140- 142: tgnag GrV acgii SODC_ACTPL : 8- 9: prmac G-V ik SODC_ARATH : 3- 4: ak G-V avlns SODC_ARATH : 12- 13: lnsse G-V tgtif SODC_ARATH : 25- 26: tqegd G-V ttvsg SODC_ARATH : 31- 33: vttvs GtV sglkp SODC_ARATH : 140- 142: tgnag GrV acgii SODC_BOVIN : 12- 14: vlkgd GpV qgtih SODC_BOVIN : 83- 85: hvgdl GnV tadkn SODC_BOVIN : 91- 92: tadkn G-V aivdi SODC_BOVIN : 145- 146: srlac G-V igiak SODC_BRAOC : 3- 4: ak G-V avlns SODC_BRAOC : 12- 13: lnsse G-V kgtif SODC_BRAOC : 31- 33: attvt GtV sglrp SODC_BRAOC : 140- 142: tgnag GrV acgii SODC_BRUAB : 20- 22: pgkev GtV visea SODC_BRUAB : 103- 105: sanad GkV setvv SODC_BRUAB : 151- 152: arfac G-V ie SODC_BRUPA : 129- 130: ddlgk G-V gdkkd SODC_BRUPA : 150- 152: arvac GiV avsaa SODC_CAEEL : 85- 87: hvgdl GnV eagad SODC_CAEEL : 93- 94: eagad G-V akikl SODC_CAEEL : 129- 130: ddlge G-V gdkae SODC_CAEEL : 150- 151: araac G-V ialaa SODC_CARCR : 21- 23: kepvk GpV kepvk SODC_CARCR : 39- 41: eqqgn GpV tlsgs SODC_CARCR : 97- 99: hvgdl GnV ianke SODC_CARCR : 105- 106: ianke G-V aevci SODC_CARCR : 159- 160: srlac G-V vgiak SODC_CARCR : 159- 161: srlac GvV giakl SODC_CAUCR : 40- 42: dgkda GaV tvtea SODC_CAUCR : 50- 51: teaph G-V llkle SODC_CAUCR : 171- 172: arvac G-V ik SODC_CAVPO : 12- 14: vlkgd GpV qgiih SODC_CAVPO : 26- 28: eqkan GpV vvkgr SODC_CAVPO : 36- 38: kgrit GlV egkhg SODC_CAVPO : 84- 86: hvgdl GnV tagad SODC_CAVPO : 92- 93: tagad G-V anvsi SODC_CAVPO : 146- 147: srlac G-V igiaq SODC_CERCA : 10- 12: vcvin GdV kgtvh SODC_CERCA : 14- 16: ngdvk GtV hfeqq SODC_CERCA : 31- 33: pvlvt GeV nglak SODC_CERCA : 145- 146: arlgc G-V igick SODC_CHYAM : 14- 16: ngdak GtV yfeqe SODC_CHYAM : 145- 146: arigc G-V igick SODC_DROME : 14- 16: ngdak GtV ffeqe SODC_DROME : 31- 33: pvkvs GeV cglak SODC_DROME : 145- 146: arigc G-V igiak SODC_DROVI : 14- 16: ngdak GtV ffeqe SODC_DROVI : 31- 33: pvkvt GeV tglak SODC_DROVI : 145- 146: arigc G-V igiak SODC_DROWI : 14- 16: ngdak GtV ffeqe SODC_DROWI : 31- 33: pvkvt GeV tglgk SODC_DROWI : 145- 146: arigc G-V igiak SODC_HAEIN : 19- 20: gicaa G-V anahd SODC_HAEIN : 52- 54: gnkdv GtV tites SODC_HAEIN : 62- 64: tesny GlV ftpnl SODC_HAEIN : 184- 185: prmac G-V ik SODC_HAEPA : 19- 20: gicaa G-V anahd SODC_HAEPA : 52- 54: gnkdv GtV tites SODC_HAEPA : 62- 64: tesny GlV ftpnl SODC_HAEPA : 184- 185: prmac G-V ik SODC_HORSE : 12- 14: vlkgd GpV hgvih SODC_HORSE : 16- 17: dgpvh G-V ihfeq SODC_HORSE : 27- 29: qqqeg GpV vlkgf SODC_HORSE : 85- 87: hvgdl GnV taden SODC_HORSE : 147- 148: srlac G-V igiap SODC_HUMAN : 12- 14: vlkgd GpV qgiin SODC_HUMAN : 27- 29: qkesn GpV kvwgs SODC_HUMAN : 85- 87: hvgdl GnV tadkd SODC_HUMAN : 93- 94: tadkd G-V advsi SODC_HUMAN : 147- 148: srlac G-V igiaq SODC_IPOBA : 12- 13: lssse G-V sgtif SODC_IPOBA : 31- 33: pttvt GnV sglkp SODC_IPOBA : 140- 142: tgnag GrV acgii SODC_LYCES : 12- 13: lnsse G-V sgtyl SODC_LYCES : 23- 24: lftqv G-V apttv SODC_MAIZE : 82- 84: hagdl GnV taged SODC_MAIZE : 90- 91: taged G-V vnvni SODC_MAIZE : 90- 92: taged GvV nvnit SODC_MAIZE : 139- 141: tgnag GrV acgii SODC_MOUSE : 12- 14: vlkgd GpV qgtih SODC_MOUSE : 85- 87: hvgdl GnV tagkd SODC_MOUSE : 93- 94: tagkd G-V anvsi SODC_MOUSE : 147- 148: srlac G-V igiaq SODC_NEUCR : 15- 17: dsnvk GtV ifeqe SODC_NEUCR : 97- 99: qgnak GtV tdnlv SODC_NEUCR : 147- 148: prpac G-V igisq SODC_NICPL : 12- 13: lssse G-V sgtif SODC_NICPL : 31- 33: pttvt GnV sglkp SODC_NICPL : 140- 142: tgnag GrV acgii SODC_NPVAC : 9- 11: iciis GdV hgkiy SODC_ONCVO : 33- 35: pttvt GeV kgltp SODC_ONCVO : 129- 130: ddlgk G-V gakkd SODC_ONCVO : 150- 152: arvac GiV aigaa SODC_PEA : 91- 93: nvgdd GtV sftit SODC_PEA : 140- 142: tgnag GrV acgii SODC_PHOLE : 49- 50: sqnky G-V vftpe SODC_PHOLE : 49- 51: sqnky GvV ftpel SODC_PHOLE : 81- 83: ssekd GkV vlgga SODC_PHOLE : 170- 171: arvac G-V iq SODC_PIG : 12- 14: vlkgd GpV qgtiy SODC_PIG : 84- 86: hvgdl GnV tagkd SODC_PIG : 92- 93: tagkd G-V atvyi SODC_PIG : 146- 147: srlac G-V igitq SODC_PINSY : 18- 19: aadvk G-V vqftq SODC_PINSY : 18- 20: aadvk GvV qftqe SODC_PINSY : 86- 88: hagdl GnV tvgtd SODC_PINSY : 94- 96: tvgtd GtV efsit SODC_PINSY : 148- 149: grlac G-V vglqg SODC_PINSY : 148- 150: grlac GvV glqg SODC_PRIGL : 11- 13: vlkgt GeV tgtvl SODC_PRIGL : 15- 17: tgevt GtV lfeqa SODC_PRIGL : 25- 27: eqaad GpV tlkgs SODC_PRIGL : 83- 85: hvgdl GnV eangn SODC_PRIGL : 91- 92: eangn G-V aefei SODC_PRIGL : 145- 146: srlac G-V igiak SODC_RABIT : 12- 14: vlkgd GpV eatih SODC_RABIT : 26- 28: eqkgt GpV vvkgr SODC_RABIT : 84- 86: hvgdl GnV tagsn SODC_RABIT : 92- 93: tagsn G-V advli SODC_RABIT : 146- 147: srlac G-V igisp SODC_RANCA : 15- 16: xsevt G-V vrfeq SODC_RANCA : 15- 17: xsevt GvV rfeqq SODC_RAT : 12- 14: vlkgd GpV qgvih SODC_RAT : 16- 17: dgpvq G-V ihfeq SODC_RAT : 85- 87: hvgdl GnV aagkd SODC_RAT : 93- 94: aagkd G-V anvsi SODC_RAT : 147- 148: srlac G-V igiaq SODC_SCHMA : 12- 13: mtgta G-V kgvvk SODC_SCHMA : 15- 16: tagvk G-V vkftq SODC_SCHMA : 15- 17: tagvk GvV kftqe SODC_SCHMA : 26- 28: qetdn GpV hvhae SODC_SCHMA : 84- 86: hvgdl GnV vagad SODC_SCHMA : 146- 147: grlac G-V iglaa SODC_SCHPO : 16- 17: dskvs G-V vtfeq SODC_SCHPO : 16- 18: dskvs GvV tfeqv SODC_SCHPO : 148- 149: arnac G-V igiav SODC_SHEEP : 12- 14: vlkgd GpV qgtir SODC_SHEEP : 83- 85: hvgdl GnV kadkn SODC_SHEEP : 91- 92: kadkn G-V aivdi SODC_SHEEP : 145- 146: grlac G-V igiap SODC_SPIOL : 13- 14: lssse G-V sgtvy SODC_SPIOL : 16- 18: segvs GtV yfaqe SODC_SPIOL : 32- 34: pttvt GnV sglkp SODC_SPIOL : 141- 143: tgnag GrV acgii SODC_XENLA : 11- 13: vlags GdV kgvvr SODC_XENLA : 15- 16: sgdvk G-V vrfeq SODC_XENLA : 15- 17: sgdvk GvV rfeqq SODC_XENLA : 25- 27: eqqdd GdV tvegk SODC_XENLA : 83- 85: hvgdl GnV taegg SODC_XENLA : 89- 91: nvtae GgV aqfkf SODC_XENLA : 90- 91: vtaeg G-V aqfkf SODC_XENLA : 144- 145: grlac G-V igfcp SODC_XIPGL : 16- 18: agett GtV yfeqe SODC_XIPGL : 85- 87: hvgdl GnV tadan SODC_XIPGL : 93- 94: tadan G-V akidi SODC_XIPGL : 146- 147: srlac G-V igte SODC_YEAST : 12- 13: lkgda G-V sgvvk SODC_YEAST : 15- 16: dagvs G-V vkfeq SODC_YEAST : 15- 17: dagvs GvV kfeqa SODC_YEAST : 56- 58: gdatn GcV sagph SODC_YEAST : 85- 87: hvgdm GnV ktden SODC_YEAST : 93- 94: ktden G-V akgsf SODC_YEAST : 147- 148: prpac G-V igltn SODD_XENLA : 11- 13: vlags GdV kgvvh SODD_XENLA : 15- 16: sgdvk G-V vhfeq SODD_XENLA : 15- 17: sgdvk GvV hfeqq SODD_XENLA : 25- 27: eqqde GaV svegk SODD_XENLA : 83- 85: hvgdl GnV taegg SODD_XENLA : 89- 91: nvtae GgV aqfki SODD_XENLA : 90- 91: vtaeg G-V aqfki SODD_XENLA : 144- 145: grlac G-V igysp SODE_BRUPA : 172- 173: ddlgk G-V gdkkd SODE_BRUPA : 188- 190: tgnag GrV acgiv SODE_BRUPA : 193- 195: grvac GiV aisa SODE_HUMAN : 80- 81: qprvt G-V vlfrq SODE_HUMAN : 80- 82: qprvt GvV lfrql SODE_HUMAN : 211- 212: accvv G-V cgpgl SODE_ONCVO : 56- 57: lrgda G-V sgiiy SODE_ONCVO : 76- 78: ittis GsV sgltp SODE_ONCVO : 136- 137: vagan G-V aevyi SODE_ONCVO : 193- 194: srlac G-V igiaa SODE_RAT : 15- 17: llvac GsV twtms SODE_RAT : 28- 29: dtges G-V dladr SODE_RAT : 87- 89: qpqit GlV lfrql SODE_RAT : 143- 144: hynpl G-V phpqh SODE_SCHMA : 47- 49: kepyi GaV wftqh SODE_SCHMA : 62- 64: ymyvn GsV aglpp SODE_SCHMA : 122- 124: irvgr GgV akfdf SODE_SCHMA : 123- 124: rvgrg G-V akfdf SODP_LYCES : 35- 36: nssfl G-V slnvn SODP_LYCES : 80- 81: nsnve G-V vtlsq SODP_LYCES : 80- 82: nsnve GvV tlsqd SODP_LYCES : 156- 157: vanad G-V aevtl SODP_LYCES : 210- 211: grlac G-V vgltp SODP_LYCES : 210- 212: grlac GvV gltpi SODP_PEA : 24- 25: rtsfs G-V svkla SODP_PEA : 65- 66: tsave G-V vtltq SODP_PEA : 65- 67: tsave GvV tltqd SODP_PEA : 141- 142: vanae G-V aeati SODP_PEA : 195- 196: grlac G-V vgltp SODP_PEA : 195- 197: grlac GvV gltpv SODP_PETHY : 37- 38: sssfh G-V slkvk SODP_PETHY : 82- 83: tsnve G-V vtltq SODP_PETHY : 82- 84: tsnve GvV tltqd SODP_PETHY : 158- 159: eanas G-V aeatl SODP_PETHY : 212- 213: grlac G-V vgltp SODP_PETHY : 212- 214: grlac GvV gltpi SODP_PICAB : 16- 17: isqve G-V vnllq SODP_PICAB : 16- 18: isqve GvV nllqe SODP_PINSY : 4- 5: qve G-V vtlsq SODP_PINSY : 4- 6: qve GvV tlsqe SODP_PINSY : 80- 81: vagsd G-V aeati SODP_PINSY : 134- 135: grlac G-V vgltp SODP_PINSY : 134- 136: grlac GvV gltpi SODP_POPTM : 24- 25: rtsfs G-V svkla SODP_POPTM : 103- 104: vipqm G-V sqqdh SODP_POPTM : 139- 140: vanae G-V aecrq SODP_POPTM : 194- 195: grlac G-V vgltp SODP_POPTM : 194- 196: grlac GvV gltpv SODP_SPIOL : 85- 86: tsnve G-V vtltq SODP_SPIOL : 85- 87: tsnve GvV tltqe SODP_SPIOL : 161- 162: vantd G-V aeati SODP_SPIOL : 215- 216: grlac G-V vgltp SODP_SPIOL : 215- 217: grlac GvV gltpv YMF1_CAEEL : 57- 59: flkln GsV sglaa Number of patterns evaluated by Pratt:1 Total running time: 1 seconds