------------------------------------------------------------ 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 250 sequences from file CYTOCHROME_C PATTERN CONSERVATION: CM: min Nr of Seqs to Match 250 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 21 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 CYTOCHROME_C.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: BFCC_BACSU 255 C550_AQUIT 111 C550_BACHA 35 C550_BACSU 120 C550_MICAE 135 C550_NITWI 109 C550_PARDE 155 C550_PSEST 104 C550_THINO 107 C550_THIPA 134 C550_THIVE 154 C551_AZOVI 82 C551_CHLVI 206 C551_ECTHA 78 C551_ECTHL 79 C551_ERYSP 119 C551_PSEAE 104 C551_PSEDE 82 C551_PSEFC 82 C551_PSEME 82 C551_PSEST 82 C552_BACAZ 53 C552_BRAJA 73 C552_HYDTH 98 C552_PSEST 291 C552_THETH 131 C553_BRAJA 104 C553_DESDN 80 C553_DESVH 103 C553_DESVM 79 C554_CHLAU 414 C554_PARSP 83 C554_THINE 91 C555_BACAZ 50 C555_CHLLT 86 C555_METCA 96 C555_PROAE 99 C556_AGRTA 125 C556_AGRTB 122 C556_AGRTC 122 C556_RHOPA 129 C55L_SYNY3 105 C55X_PSEST 113 CCPR_PSESP 302 CY11_SOLTU 320 CY12_SOLTU 260 CY1_BOVIN 241 CY1_HUMAN 325 CY1_NEUCR 332 CY1_PARDE 450 CY1_RHOCA 279 CY1_RHORU 272 CY1_RHOSH 285 CY1_YEAST 309 CY21_RHOFU 99 CY21_RHOMO 100 CY21_RHOPA 114 CY22_RHOFU 96 CY22_RHOMO 97 CY22_RHOPA 114 CY2_AGRTC 111 CY2_RHOAC 107 CY2_RHOCA 137 CY2_RHOGE 85 CY2_RHOGL 106 CY2_RHOPH 113 CY2_RHORU 135 CY2_RHOSH 145 CY2_RHOTE 92 CY2_RHOVA 104 CY2_RHOVI 127 CY31_DESDN 118 CY32_DESDN 111 CY4C_PSEPU 78 CYC1_DROME 104 CYC1_YEAST 108 CYC2_DROME 107 CYC2_MOUSE 104 CYC2_RAT 104 CYC3_DESAC 68 CYC3_DESDE 102 CYC3_DESGI 111 CYC3_DESSA 106 CYC3_DESVH 129 CYC3_DESVM 107 CYC4_AZOVI 190 CYC4_PSEAE 181 CYC5_AZOVI 83 CYC5_PSEME 87 CYC6_ALAES 86 CYC6_ANANI 85 CYC6_ANASP 111 CYC6_ANASQ 111 CYC6_ANAVA 86 CYC6_APHFL 87 CYC6_BRYMA 88 CYC6_BUMFI 86 CYC6_CHLRE 148 CYC6_EUGGR 87 CYC6_EUGVI 87 CYC6_MICAE 81 CYC6_MONBR 89 CYC6_MONLU 83 CYC6_PETFA 85 CYC6_PLEBO 85 CYC6_PORTE 85 CYC6_SPIMA 89 CYC6_SYNLI 87 CYC6_SYNP7 111 CYC6_SYNSP 87 CYC6_SYNY3 120 CYC7_YEAST 113 CYCA_ACEPO 468 CYCL_METEX 197 CYCL_PARDE 177 CYCM_BRAJA 184 CYCP_ALCSP 127 CYCP_CHRVI 131 CYCP_PARSP 132 CYCP_RHOCA 129 CYCP_RHOFU 128 CYCP_RHOGE 129 CYCP_RHOMO 128 CYCP_RHOPA 125 CYCP_RHOPH 125 CYCP_RHORU 126 CYCP_RHOSH 130 CYCP_RHOSP 128 CYCP_RHOTE 133 CYCR_ERYSP 187 CYCR_RHOVI 356 CYC_ABUTH 111 CYC_ACENE 112 CYC_ALLPO 111 CYC_ANAPL 104 CYC_APIME 107 CYC_APTPA 104 CYC_ARATH 112 CYC_ARUMA 111 CYC_ASTRU 103 CYC_ATESP 104 CYC_BOEPE 107 CYC_BOVIN 104 CYC_BRAOL 111 CYC_CAEEL 110 CYC_CANFA 104 CYC_CANGA 104 CYC_CANSA 111 CYC_CHESE 104 CYC_CHICK 104 CYC_CHLRE 111 CYC_COLLI 104 CYC_CRIFA 113 CYC_CRION 112 CYC_CROAT 104 CYC_CUCMA 111 CYC_CYPCA 103 CYC_DRONO 104 CYC_EISFO 108 CYC_EMENI 110 CYC_ENTIN 111 CYC_ENTTR 104 CYC_EQUAS 104 CYC_ESCGI 104 CYC_EUGGR 102 CYC_EUGVI 102 CYC_FAGES 111 CYC_GINBI 113 CYC_GOSBA 111 CYC_GUIAB 111 CYC_HAEIR 107 CYC_HANAN 109 CYC_HELAN 111 CYC_HELAS 104 CYC_HIPAM 104 CYC_HORSE 104 CYC_HUMAN 104 CYC_ISSOR 109 CYC_KATPE 103 CYC_KLULA 110 CYC_LUCCU 107 CYC_LYCES 111 CYC_MACGI 104 CYC_MACMA 104 CYC_MACMU 104 CYC_MAIZE 111 CYC_MANSE 107 CYC_MINSC 104 CYC_MIRLE 104 CYC_MOUSE 104 CYC_NEUCR 107 CYC_NIGDA 111 CYC_ORYSA 111 CYC_PASSA 111 CYC_PHAAU 111 CYC_RABIT 104 CYC_RANCA 104 CYC_RICCO 111 CYC_SAMCY 107 CYC_SAMNI 111 CYC_SCHGR 107 CYC_SCHOC 109 CYC_SCHPO 108 CYC_SESIN 111 CYC_SOLTU 111 CYC_SPIOL 111 CYC_SQUSU 104 CYC_STRCA 104 CYC_TETPY 109 CYC_THELA 111 CYC_TORHA 109 CYC_TROMA 111 CYC_TRYBB 93 CYC_USTSP 107 CYC_VARVA 104 CYC_WHEAT 112 CYF_BRARA 320 CYF_CHLRE 317 CYF_MAIZE 320 CYF_MARPO 320 CYF_NOSSP 333 CYF_OENHO 318 CYF_ORYSA 320 CYF_PEA 320 CYF_PINTH 319 CYF_SPIOL 320 CYF_SYNP2 325 CYF_SYNY3 328 CYF_TOBAC 320 CYF_VICFA 320 CYF_WHEAT 320 CYSD_CHLLT 87 CYSD_CHRVI 199 FRDA_SHEPU 596 HMWC_DESVH 545 NAPB_ALCEU 169 NAPB_ECOLI 169 NAPB_HAEIN 150 NAPC_ECOLI 200 NAPC_HAEIN 200 NIRS_PSEAE 568 NIRS_PSEST 560 NIRT_PSEST 201 NRFA_ECOLI 478 NRFA_HAEIN 538 NRFB_ECOLI 188 NRFB_HAEIN 226 TORC_ECOLI 390 Y644_HAEIN 368 YHJA_ECOLI 465 Pratt run started at Thu Feb 6 19:15:14 1997 No patterns found