------------------------------------------------------------ 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 17 sequences from file RIESKE_2 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 17 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 RIESKE_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: BFCA_BACSU 167 UCR1_TOBAC 228 UCR2_TOBAC 228 UCRI_BOVIN 269 UCRI_NEUCR 231 UCRI_NOSSP 179 UCRI_PARDE 190 UCRI_PEA 230 UCRI_RAT 256 UCRI_RHOCA 191 UCRI_RHORU 182 UCRI_RHOSH 187 UCRI_SOLTU 265 UCRI_SPIOL 247 UCRI_SYNP2 180 UCRI_SYNY3 192 UCRI_YEAST 215 Pratt run started at Thu Feb 6 21:06:40 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 36.5305 17( 17) C-P-C-H-x(0,1)-G-x(1,2)-Y-x(3)-G-x(4)-G-x(2)-P 2: 32.3604 17( 17) P-C-H-x(0,1)-G-x(1,2)-Y-x(3)-G-x(4)-G-x(2)-P 3: 28.1904 17( 17) C-H-x(0,1)-G-x(1,2)-Y-x(3)-G-x(4)-G-x(2)-P 4: 27.1904 24( 17) F-x(2,4)-C-x(0,2)-H-x(3)-Y-x(3)-G-x(4)-G-x(2)-P 5: 20.8503 17( 17) C-x-H-L-G-C 6: 19.8503 17( 17) H-x(3)-Y-x(3)-G-x(3,5)-P-x(4)-L 7: 19.3503 17( 17) G-x(1,2)-Y-x(3)-G-x(3,5)-P-x(4)-L 8: 19.3503 17( 17) H-x(3)-Y-x(3)-G-x(3,5)-P-x(1,2)-P 9: 19.3503 17( 17) H-x(2,3)-Y-x(3)-G-x(3,5)-P-x(4)-L 10: 19.3503 17( 17) Y-x(3)-G-x(2,4)-G-x(1,2)-A-x(3)-L 11: 16.6802 17( 17) H-L-G-C 12: 16.1802 17( 17) G-x(4)-G-x-A-x(0,1)-P 13: 15.6802 17( 17) G-x(4)-G-x(1,2)-P-x(1,2)-L 14: 15.6802 17( 17) Y-x(3)-G-x(3,5)-P-x(4)-L 15: 15.1802 17( 17) P-x(0,1)-A-P-x(0,2)-L 16: 15.1802 17( 17) G-x(0,1)-P-x(0,2)-A-P 17: 15.1802 17( 17) Y-x(3)-G-x(3,5)-P-x(1,2)-P 18: 15.1802 37( 17) G-x(2,4)-G-x(1,2)-A-x(3)-L 19: 14.6802 17( 17) G-x(2)-Y-x(1,3)-G-x(3,5)-P 20: 14.6802 18( 17) P-x(0,2)-A-P-x(0,2)-L Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 53.0222 17( 17) C-P-C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] B 2: 48.8522 17( 17) P-C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] C 3: 46.8626 24( 17) F-x(2,4)-C-x(0,2)-H-x-[GS]-x-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] D 4: 44.6821 17( 17) C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] E 5: 37.4832 17( 17) H-x(3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] F 6: 36.9832 17( 17) G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] G 7: 36.9832 17( 17) H-x(2,3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] H 8: 32.5918 17( 17) H-x-[GS]-x-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-x(1,2)-P-x(2)-[AL]-x-[ILV] I 9: 29.3126 17( 17) Y-[DNT]-x-[AEQST]-G-x(2,4)-G-x(1,2)-A-[AP]-x(2)-L-x-[ILPV] J 10: 29.0841 17( 17) Y-x(3)-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] K 11: 28.1684 17( 17) C-x-H-L-G-C-x-[PV]-x(2)-[DEGNQ]-x-[ADGS] L 12: 25.2412 17( 17) Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-x(1,2)-P-x(2)-[AL]-x-[ILV] M 13: 24.0203 17( 17) C-P-C-H-x(0,1)-G-x(1,2)-Y N 14: 23.9984 17( 17) H-L-G-C-x-[PV]-x(2)-[DEGNQ]-x-[ADGS] O 15: 21.4950 17( 17) G-x-[ILV]-x(2)-G-x-A-x(0,1)-P-x-[GNS] P 16: 20.6371 18( 17) G-x(2,4)-G-x(1,2)-A-[AP]-x(2)-L-x-[ILPV] Q 17: 20.5574 17( 17) G-x(2)-Y-x(1,3)-G-x(3,5)-P-x-[GP]-x-[GNS] R 18: 20.1190 17( 17) G-x(4)-G-x(1,2)-P-x(1,2)-L-x-[ILPV]-[ALPV] S 19: 19.9092 17( 17) H-x(3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P T 20: 19.8503 17( 17) P-C-H-x(0,1)-G-x(1,2)-Y Best patterns with alignements: fitness hits(seqs) Pattern A 1: 53.0222 17( 17) C-P-C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] Occurences: 17(17) BFCA_BACSU : 121- 143: pnkff CPCHyGl-YEkDGtnvpGTPPlAP ldhye UCR1_TOBAC : 175- 197: enkfi CPCH-GsqYNnQGrvvrGPAPlSL alaha UCR2_TOBAC : 175- 197: enkfi CPCH-GsqYNnQGrvvrGPAPlSL alaha UCRI_BOVIN : 231- 253: fggyy CPCH-GshYDaSGrirkGPAPlNL evpsy UCRI_NEUCR : 193- 215: yggwf CPCH-GshYDiSGrirkGPAPlNL eiply UCRI_NOSSP : 126- 148: enkfk CPCH-GsqYDeTGkvvrGPAPlSL alaha UCRI_PARDE : 152- 174: fggwf CPCH-GshYDtSGrirrGPAPqNL hipva UCRI_PEA : 175- 197: enkfi CPCH-GsqYNdQGrvvrGPAPlSL alahc UCRI_RAT : 218- 240: fggyy CPCH-GshYDaSGrirkGPAPlNL evpty UCRI_RHOCA : 153- 175: fggwf CPCH-GshYDsAGrirkGPAPrNL dipva UCRI_RHORU : 144- 166: fdgwf CPCH-GshYDsAGrirkGPAPlNL pvppy UCRI_RHOSH : 149- 171: fggwf CPCH-GshYDsAGrirkGPAPeNL pipla UCRI_SOLTU : 227- 249: fggwf CPCH-GshYDiSGrirkGPAPyNL evpty UCRI_SPIOL : 193- 215: enkfi CPCH-GsqYNnQGrvvrGPAPlSL alahc UCRI_SYNP2 : 126- 148: enkfm CPCH-GsqYDeTGkvvrGPAPlSL alvha UCRI_SYNY3 : 138- 160: enkfm CPCH-GsqYNaEGkvvrGPAPlSL alaha UCRI_YEAST : 178- 200: fggwf CPCH-GshYDiSGrirkGPAPlNL eipay B 2: 48.8522 17( 17) P-C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] Occurences: 17(17) BFCA_BACSU : 122- 143: nkffc PCHyGl-YEkDGtnvpGTPPlAP ldhye UCR1_TOBAC : 176- 197: nkfic PCH-GsqYNnQGrvvrGPAPlSL alaha UCR2_TOBAC : 176- 197: nkfic PCH-GsqYNnQGrvvrGPAPlSL alaha UCRI_BOVIN : 232- 253: ggyyc PCH-GshYDaSGrirkGPAPlNL evpsy UCRI_NEUCR : 194- 215: ggwfc PCH-GshYDiSGrirkGPAPlNL eiply UCRI_NOSSP : 127- 148: nkfkc PCH-GsqYDeTGkvvrGPAPlSL alaha UCRI_PARDE : 153- 174: ggwfc PCH-GshYDtSGrirrGPAPqNL hipva UCRI_PEA : 176- 197: nkfic PCH-GsqYNdQGrvvrGPAPlSL alahc UCRI_RAT : 219- 240: ggyyc PCH-GshYDaSGrirkGPAPlNL evpty UCRI_RHOCA : 154- 175: ggwfc PCH-GshYDsAGrirkGPAPrNL dipva UCRI_RHORU : 145- 166: dgwfc PCH-GshYDsAGrirkGPAPlNL pvppy UCRI_RHOSH : 150- 171: ggwfc PCH-GshYDsAGrirkGPAPeNL pipla UCRI_SOLTU : 228- 249: ggwfc PCH-GshYDiSGrirkGPAPyNL evpty UCRI_SPIOL : 194- 215: nkfic PCH-GsqYNnQGrvvrGPAPlSL alahc UCRI_SYNP2 : 127- 148: nkfmc PCH-GsqYDeTGkvvrGPAPlSL alvha UCRI_SYNY3 : 139- 160: nkfmc PCH-GsqYNaEGkvvrGPAPlSL alaha UCRI_YEAST : 179- 200: ggwfc PCH-GshYDiSGrirkGPAPlNL eipay C 3: 46.8626 24( 17) F-x(2,4)-C-x(0,2)-H-x-[GS]-x-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] Occurences: 24(17) BFCA_BACSU : 119- 143: knpnk Ffcp-C--HyGlYEkDGtnvpGTPPlAP ldhye BFCA_BACSU : 120- 143: npnkf Fcp--C--HyGlYEkDGtnvpGTPPlAP ldhye UCR1_TOBAC : 173- 197: aaenk Ficp-C--HgSqYNnQGrvvrGPAPlSL alaha UCR2_TOBAC : 173- 197: aaenk Ficp-C--HgSqYNnQGrvvrGPAPlSL alaha UCRI_BOVIN : 226- 253: anagd FggyyCpcHgShYDaSGrirkGPAPlNL evpsy UCRI_NEUCR : 192- 215: dyggw Fcp--C--HgShYDiSGrirkGPAPlNL eiply UCRI_NOSSP : 124- 148: vaenk Fkcp-C--HgSqYDeTGkvvrGPAPlSL alaha UCRI_PARDE : 147- 174: dgagd FggwfCpcHgShYDtSGrirrGPAPqNL hipva UCRI_PARDE : 151- 174: dfggw Fcp--C--HgShYDtSGrirrGPAPqNL hipva UCRI_PEA : 173- 197: qaenk Ficp-C--HgSqYNdQGrvvrGPAPlSL alahc UCRI_RAT : 213- 240: anagd FggyyCpcHgShYDaSGrirkGPAPlNL evpty UCRI_RHOCA : 148- 175: dksgd FggwfCpcHgShYDsAGrirkGPAPrNL dipva UCRI_RHOCA : 152- 175: dfggw Fcp--C--HgShYDsAGrirkGPAPrNL dipva UCRI_RHORU : 139- 166: dpkgd FdgwfCpcHgShYDsAGrirkGPAPlNL pvppy UCRI_RHORU : 143- 166: dfdgw Fcp--C--HgShYDsAGrirkGPAPlNL pvppy UCRI_RHOSH : 144- 171: gvsgd FggwfCpcHgShYDsAGrirkGPAPeNL pipla UCRI_RHOSH : 148- 171: dfggw Fcp--C--HgShYDsAGrirkGPAPeNL pipla UCRI_SOLTU : 222- 249: pnagd FggwfCpcHgShYDiSGrirkGPAPyNL evpty UCRI_SOLTU : 226- 249: dfggw Fcp--C--HgShYDiSGrirkGPAPyNL evpty UCRI_SPIOL : 191- 215: aaenk Ficp-C--HgSqYNnQGrvvrGPAPlSL alahc UCRI_SYNP2 : 124- 148: taenk Fmcp-C--HgSqYDeTGkvvrGPAPlSL alvha UCRI_SYNY3 : 136- 160: asenk Fmcp-C--HgSqYNaEGkvvrGPAPlSL alaha UCRI_YEAST : 173- 200: geagd FggwfCpcHgShYDiSGrirkGPAPlNL eipay UCRI_YEAST : 177- 200: dfggw Fcp--C--HgShYDiSGrirkGPAPlNL eipay D 4: 44.6821 17( 17) C-H-x(0,1)-G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(4)-G-[PT]-[AP]-P-x-[ANS]-[LP] Occurences: 17(17) BFCA_BACSU : 123- 143: kffcp CHyGl-YEkDGtnvpGTPPlAP ldhye UCR1_TOBAC : 177- 197: kficp CH-GsqYNnQGrvvrGPAPlSL alaha UCR2_TOBAC : 177- 197: kficp CH-GsqYNnQGrvvrGPAPlSL alaha UCRI_BOVIN : 233- 253: gyycp CH-GshYDaSGrirkGPAPlNL evpsy UCRI_NEUCR : 195- 215: gwfcp CH-GshYDiSGrirkGPAPlNL eiply UCRI_NOSSP : 128- 148: kfkcp CH-GsqYDeTGkvvrGPAPlSL alaha UCRI_PARDE : 154- 174: gwfcp CH-GshYDtSGrirrGPAPqNL hipva UCRI_PEA : 177- 197: kficp CH-GsqYNdQGrvvrGPAPlSL alahc UCRI_RAT : 220- 240: gyycp CH-GshYDaSGrirkGPAPlNL evpty UCRI_RHOCA : 155- 175: gwfcp CH-GshYDsAGrirkGPAPrNL dipva UCRI_RHORU : 146- 166: gwfcp CH-GshYDsAGrirkGPAPlNL pvppy UCRI_RHOSH : 151- 171: gwfcp CH-GshYDsAGrirkGPAPeNL pipla UCRI_SOLTU : 229- 249: gwfcp CH-GshYDiSGrirkGPAPyNL evpty UCRI_SPIOL : 195- 215: kficp CH-GsqYNnQGrvvrGPAPlSL alahc UCRI_SYNP2 : 128- 148: kfmcp CH-GsqYDeTGkvvrGPAPlSL alvha UCRI_SYNY3 : 140- 160: kfmcp CH-GsqYNaEGkvvrGPAPlSL alaha UCRI_YEAST : 180- 200: gwfcp CH-GshYDiSGrirkGPAPlNL eipay E 5: 37.4832 17( 17) H-x(3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] Occurences: 17(17) BFCA_BACSU : 124- 144: ffcpc HyglYEkDGtnv--PGTpPLaPL dhyeq UCR1_TOBAC : 178- 200: ficpc HgsqYNnQGrvvrgPAPlSLaLA hadid UCR2_TOBAC : 178- 200: ficpc HgsqYNnQGrvvrgPAPlSLaLA hadid UCRI_BOVIN : 234- 256: yycpc HgshYDaSGrirkgPAPlNLeVP syeft UCRI_NEUCR : 196- 218: wfcpc HgshYDiSGrirkgPAPlNLeIP lyefp UCRI_NOSSP : 129- 151: fkcpc HgsqYDeTGkvvrgPAPlSLaLA hantv UCRI_PARDE : 155- 177: wfcpc HgshYDtSGrirrgPAPqNLhIP vaefl UCRI_PEA : 178- 200: ficpc HgsqYNdQGrvvrgPAPlSLaLA hcdvg UCRI_RAT : 221- 243: yycpc HgshYDaSGrirkgPAPlNLeVP tyeft UCRI_RHOCA : 156- 178: wfcpc HgshYDsAGrirkgPAPrNLdIP vaafv UCRI_RHORU : 147- 169: wfcpc HgshYDsAGrirkgPAPlNLpVP pyaft UCRI_RHOSH : 152- 174: wfcpc HgshYDsAGrirkgPAPeNLpIP lakfi UCRI_SOLTU : 230- 252: wfcpc HgshYDiSGrirkgPAPyNLeVP tysfl UCRI_SPIOL : 196- 218: ficpc HgsqYNnQGrvvrgPAPlSLaLA hcdvd UCRI_SYNP2 : 129- 151: fmcpc HgsqYDeTGkvvrgPAPlSLaLV haevt UCRI_SYNY3 : 141- 163: fmcpc HgsqYNaEGkvvrgPAPlSLaLA hatvt UCRI_YEAST : 181- 203: wfcpc HgshYDiSGrirkgPAPlNLeIP ayefd F 6: 36.9832 17( 17) G-x(1,2)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] Occurences: 17(17) BFCA_BACSU : 126- 144: cpchy Gl-YEkDGtnv--PGTpPLaPL dhyeq UCR1_TOBAC : 179- 200: icpch GsqYNnQGrvvrgPAPlSLaLA hadid UCR2_TOBAC : 179- 200: icpch GsqYNnQGrvvrgPAPlSLaLA hadid UCRI_BOVIN : 235- 256: ycpch GshYDaSGrirkgPAPlNLeVP syeft UCRI_NEUCR : 197- 218: fcpch GshYDiSGrirkgPAPlNLeIP lyefp UCRI_NOSSP : 130- 151: kcpch GsqYDeTGkvvrgPAPlSLaLA hantv UCRI_PARDE : 156- 177: fcpch GshYDtSGrirrgPAPqNLhIP vaefl UCRI_PEA : 179- 200: icpch GsqYNdQGrvvrgPAPlSLaLA hcdvg UCRI_RAT : 222- 243: ycpch GshYDaSGrirkgPAPlNLeVP tyeft UCRI_RHOCA : 157- 178: fcpch GshYDsAGrirkgPAPrNLdIP vaafv UCRI_RHORU : 148- 169: fcpch GshYDsAGrirkgPAPlNLpVP pyaft UCRI_RHOSH : 153- 174: fcpch GshYDsAGrirkgPAPeNLpIP lakfi UCRI_SOLTU : 231- 252: fcpch GshYDiSGrirkgPAPyNLeVP tysfl UCRI_SPIOL : 197- 218: icpch GsqYNnQGrvvrgPAPlSLaLA hcdvd UCRI_SYNP2 : 130- 151: mcpch GsqYDeTGkvvrgPAPlSLaLV haevt UCRI_SYNY3 : 142- 163: mcpch GsqYNaEGkvvrgPAPlSLaLA hatvt UCRI_YEAST : 182- 203: fcpch GshYDiSGrirkgPAPlNLeIP ayefd G 7: 36.9832 17( 17) H-x(2,3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] Occurences: 17(17) BFCA_BACSU : 124- 144: ffcpc HyglYEkDGtnv--PGTpPLaPL dhyeq UCR1_TOBAC : 178- 200: ficpc HgsqYNnQGrvvrgPAPlSLaLA hadid UCR2_TOBAC : 178- 200: ficpc HgsqYNnQGrvvrgPAPlSLaLA hadid UCRI_BOVIN : 234- 256: yycpc HgshYDaSGrirkgPAPlNLeVP syeft UCRI_NEUCR : 196- 218: wfcpc HgshYDiSGrirkgPAPlNLeIP lyefp UCRI_NOSSP : 129- 151: fkcpc HgsqYDeTGkvvrgPAPlSLaLA hantv UCRI_PARDE : 155- 177: wfcpc HgshYDtSGrirrgPAPqNLhIP vaefl UCRI_PEA : 178- 200: ficpc HgsqYNdQGrvvrgPAPlSLaLA hcdvg UCRI_RAT : 221- 243: yycpc HgshYDaSGrirkgPAPlNLeVP tyeft UCRI_RHOCA : 156- 178: wfcpc HgshYDsAGrirkgPAPrNLdIP vaafv UCRI_RHORU : 147- 169: wfcpc HgshYDsAGrirkgPAPlNLpVP pyaft UCRI_RHOSH : 152- 174: wfcpc HgshYDsAGrirkgPAPeNLpIP lakfi UCRI_SOLTU : 230- 252: wfcpc HgshYDiSGrirkgPAPyNLeVP tysfl UCRI_SPIOL : 196- 218: ficpc HgsqYNnQGrvvrgPAPlSLaLA hcdvd UCRI_SYNP2 : 129- 151: fmcpc HgsqYDeTGkvvrgPAPlSLaLV haevt UCRI_SYNY3 : 141- 163: fmcpc HgsqYNaEGkvvrgPAPlSLaLA hatvt UCRI_YEAST : 181- 203: wfcpc HgshYDiSGrirkgPAPlNLeIP ayefd H 8: 32.5918 17( 17) H-x-[GS]-x-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-x(1,2)-P-x(2)-[AL]-x-[ILV] Occurences: 17(17) BFCA_BACSU : 124- 144: ffcpc HyGlYEkDGtnv--PgtPplApL dhyeq UCR1_TOBAC : 178- 199: ficpc HgSqYNnQGrvvrgPa-PlsLaL ahadi UCR2_TOBAC : 178- 199: ficpc HgSqYNnQGrvvrgPa-PlsLaL ahadi UCRI_BOVIN : 234- 255: yycpc HgShYDaSGrirkgPa-PlnLeV psyef UCRI_NEUCR : 196- 217: wfcpc HgShYDiSGrirkgPa-PlnLeI plyef UCRI_NOSSP : 129- 150: fkcpc HgSqYDeTGkvvrgPa-PlsLaL ahant UCRI_PARDE : 155- 176: wfcpc HgShYDtSGrirrgPa-PqnLhI pvaef UCRI_PEA : 178- 199: ficpc HgSqYNdQGrvvrgPa-PlsLaL ahcdv UCRI_RAT : 221- 242: yycpc HgShYDaSGrirkgPa-PlnLeV ptyef UCRI_RHOCA : 156- 177: wfcpc HgShYDsAGrirkgPa-PrnLdI pvaaf UCRI_RHORU : 147- 168: wfcpc HgShYDsAGrirkgPa-PlnLpV ppyaf UCRI_RHOSH : 152- 173: wfcpc HgShYDsAGrirkgPa-PenLpI plakf UCRI_SOLTU : 230- 251: wfcpc HgShYDiSGrirkgPa-PynLeV ptysf UCRI_SPIOL : 196- 217: ficpc HgSqYNnQGrvvrgPa-PlsLaL ahcdv UCRI_SYNP2 : 129- 150: fmcpc HgSqYDeTGkvvrgPa-PlsLaL vhaev UCRI_SYNY3 : 141- 162: fmcpc HgSqYNaEGkvvrgPa-PlsLaL ahatv UCRI_YEAST : 181- 202: wfcpc HgShYDiSGrirkgPa-PlnLeI payef I 9: 29.3126 17( 17) Y-[DNT]-x-[AEQST]-G-x(2,4)-G-x(1,2)-A-[AP]-x(2)-L-x-[ILPV] Occurences: 17(17) BFCA_BACSU : 15- 31: rqfln YTlTGvg--GfmAAsmLmP mvrfa UCR1_TOBAC : 182- 199: chgsq YNnQGrvvrGp-APlsLaL ahadi UCR2_TOBAC : 182- 199: chgsq YNnQGrvvrGp-APlsLaL ahadi UCRI_BOVIN : 238- 255: chgsh YDaSGrirkGp-APlnLeV psyef UCRI_NEUCR : 200- 217: chgsh YDiSGrirkGp-APlnLeI plyef UCRI_NOSSP : 133- 150: chgsq YDeTGkvvrGp-APlsLaL ahant UCRI_PARDE : 159- 176: chgsh YDtSGrirrGp-APqnLhI pvaef UCRI_PEA : 182- 199: chgsq YNdQGrvvrGp-APlsLaL ahcdv UCRI_RAT : 225- 242: chgsh YDaSGrirkGp-APlnLeV ptyef UCRI_RHOCA : 160- 177: chgsh YDsAGrirkGp-APrnLdI pvaaf UCRI_RHORU : 151- 168: chgsh YDsAGrirkGp-APlnLpV ppyaf UCRI_RHOSH : 156- 173: chgsh YDsAGrirkGp-APenLpI plakf UCRI_SOLTU : 234- 251: chgsh YDiSGrirkGp-APynLeV ptysf UCRI_SPIOL : 200- 217: chgsq YNnQGrvvrGp-APlsLaL ahcdv UCRI_SYNP2 : 133- 150: chgsq YDeTGkvvrGp-APlsLaL vhaev UCRI_SYNY3 : 145- 162: chgsq YNaEGkvvrGp-APlsLaL ahatv UCRI_YEAST : 185- 202: chgsh YDiSGrirkGp-APlnLeI payef J 10: 29.0841 17( 17) Y-x(3)-G-x(3,5)-P-[AG]-[PT]-x-[NPS]-L-x-[ILPV]-[ALPV] Occurences: 17(17) BFCA_BACSU : 128- 144: chygl YekdGtnv--PGTpPLaPL dhyeq UCR1_TOBAC : 182- 200: chgsq YnnqGrvvrgPAPlSLaLA hadid UCR2_TOBAC : 182- 200: chgsq YnnqGrvvrgPAPlSLaLA hadid UCRI_BOVIN : 238- 256: chgsh YdasGrirkgPAPlNLeVP syeft UCRI_NEUCR : 200- 218: chgsh YdisGrirkgPAPlNLeIP lyefp UCRI_NOSSP : 133- 151: chgsq YdetGkvvrgPAPlSLaLA hantv UCRI_PARDE : 159- 177: chgsh YdtsGrirrgPAPqNLhIP vaefl UCRI_PEA : 182- 200: chgsq YndqGrvvrgPAPlSLaLA hcdvg UCRI_RAT : 225- 243: chgsh YdasGrirkgPAPlNLeVP tyeft UCRI_RHOCA : 160- 178: chgsh YdsaGrirkgPAPrNLdIP vaafv UCRI_RHORU : 151- 169: chgsh YdsaGrirkgPAPlNLpVP pyaft UCRI_RHOSH : 156- 174: chgsh YdsaGrirkgPAPeNLpIP lakfi UCRI_SOLTU : 234- 252: chgsh YdisGrirkgPAPyNLeVP tysfl UCRI_SPIOL : 200- 218: chgsq YnnqGrvvrgPAPlSLaLA hcdvd UCRI_SYNP2 : 133- 151: chgsq YdetGkvvrgPAPlSLaLV haevt UCRI_SYNY3 : 145- 163: chgsq YnaeGkvvrgPAPlSLaLA hatvt UCRI_YEAST : 185- 203: chgsh YdisGrirkgPAPlNLeIP ayefd K 11: 28.1684 17( 17) C-x-H-L-G-C-x-[PV]-x(2)-[DEGNQ]-x-[ADGS] Occurences: 17(17) BFCA_BACSU : 100- 112: alspi CkHLGCtVnwNsD pknpn UCR1_TOBAC : 157- 169: ginav CtHLGCvVpfNaA enkfi UCR2_TOBAC : 157- 169: ginav CtHLGCvVpfNaA enkfi UCRI_BOVIN : 212- 224: iligv CtHLGCvPiaNaG dfggy UCRI_NEUCR : 174- 186: vmlgv CtHLGCvPigEaG dyggw UCRI_NOSSP : 108- 120: ginai CtHLGCvVpwNvA enkfk UCRI_PARDE : 132- 144: vmigv CtHLGCvPigDgA gdfgg UCRI_PEA : 157- 169: ainav CtHLGCvVpfNqA enkfi UCRI_RAT : 199- 211: iligv CtHLGCvPiaNaG dfggy UCRI_RHOCA : 133- 145: vmlgv CtHLGCvPmgDkS gdfgg UCRI_RHORU : 120- 132: vmvgv CtHLGCiPlgQkA gdpkg UCRI_RHOSH : 129- 141: vmwgv CtHLGCvPigGvS gdfgg UCRI_SOLTU : 208- 220: vvvgv CtHLGCiPlpNaG dfggw UCRI_SPIOL : 175- 187: ginav CtHLGCvVpfNaA enkfi UCRI_SYNP2 : 108- 120: ginai CtHLGCvVpwNtA enkfm UCRI_SYNY3 : 120- 132: ginav CtHLGCvVpwNaS enkfm UCRI_YEAST : 159- 171: imlgi CtHLGCvPigEaG dfggw L 12: 25.2412 17( 17) Y-[DEN]-x-[ADEQST]-G-x(3,5)-P-x(1,2)-P-x(2)-[AL]-x-[ILV] Occurences: 17(17) BFCA_BACSU : 128- 144: chygl YEkDGtnv--PgtPplApL dhyeq UCR1_TOBAC : 182- 199: chgsq YNnQGrvvrgPa-PlsLaL ahadi UCR2_TOBAC : 182- 199: chgsq YNnQGrvvrgPa-PlsLaL ahadi UCRI_BOVIN : 238- 255: chgsh YDaSGrirkgPa-PlnLeV psyef UCRI_NEUCR : 200- 217: chgsh YDiSGrirkgPa-PlnLeI plyef UCRI_NOSSP : 133- 150: chgsq YDeTGkvvrgPa-PlsLaL ahant UCRI_PARDE : 159- 176: chgsh YDtSGrirrgPa-PqnLhI pvaef UCRI_PEA : 182- 199: chgsq YNdQGrvvrgPa-PlsLaL ahcdv UCRI_RAT : 225- 242: chgsh YDaSGrirkgPa-PlnLeV ptyef UCRI_RHOCA : 160- 177: chgsh YDsAGrirkgPa-PrnLdI pvaaf UCRI_RHORU : 151- 168: chgsh YDsAGrirkgPa-PlnLpV ppyaf UCRI_RHOSH : 156- 173: chgsh YDsAGrirkgPa-PenLpI plakf UCRI_SOLTU : 234- 251: chgsh YDiSGrirkgPa-PynLeV ptysf UCRI_SPIOL : 200- 217: chgsq YNnQGrvvrgPa-PlsLaL ahcdv UCRI_SYNP2 : 133- 150: chgsq YDeTGkvvrgPa-PlsLaL vhaev UCRI_SYNY3 : 145- 162: chgsq YNaEGkvvrgPa-PlsLaL ahatv UCRI_YEAST : 185- 202: chgsh YDiSGrirkgPa-PlnLeI payef M 13: 24.0203 17( 17) C-P-C-H-x(0,1)-G-x(1,2)-Y Occurences: 17(17) BFCA_BACSU : 121- 128: pnkff CPCHyGl-Y ekdgt UCR1_TOBAC : 175- 182: enkfi CPCH-GsqY nnqgr UCR2_TOBAC : 175- 182: enkfi CPCH-GsqY nnqgr UCRI_BOVIN : 231- 238: fggyy CPCH-GshY dasgr UCRI_NEUCR : 193- 200: yggwf CPCH-GshY disgr UCRI_NOSSP : 126- 133: enkfk CPCH-GsqY detgk UCRI_PARDE : 152- 159: fggwf CPCH-GshY dtsgr UCRI_PEA : 175- 182: enkfi CPCH-GsqY ndqgr UCRI_RAT : 218- 225: fggyy CPCH-GshY dasgr UCRI_RHOCA : 153- 160: fggwf CPCH-GshY dsagr UCRI_RHORU : 144- 151: fdgwf CPCH-GshY dsagr UCRI_RHOSH : 149- 156: fggwf CPCH-GshY dsagr UCRI_SOLTU : 227- 234: fggwf CPCH-GshY disgr UCRI_SPIOL : 193- 200: enkfi CPCH-GsqY nnqgr UCRI_SYNP2 : 126- 133: enkfm CPCH-GsqY detgk UCRI_SYNY3 : 138- 145: enkfm CPCH-GsqY naegk UCRI_YEAST : 178- 185: fggwf CPCH-GshY disgr N 14: 23.9984 17( 17) H-L-G-C-x-[PV]-x(2)-[DEGNQ]-x-[ADGS] Occurences: 17(17) BFCA_BACSU : 102- 112: spick HLGCtVnwNsD pknpn UCR1_TOBAC : 159- 169: navct HLGCvVpfNaA enkfi UCR2_TOBAC : 159- 169: navct HLGCvVpfNaA enkfi UCRI_BOVIN : 214- 224: igvct HLGCvPiaNaG dfggy UCRI_NEUCR : 176- 186: lgvct HLGCvPigEaG dyggw UCRI_NOSSP : 110- 120: naict HLGCvVpwNvA enkfk UCRI_PARDE : 134- 144: igvct HLGCvPigDgA gdfgg UCRI_PEA : 159- 169: navct HLGCvVpfNqA enkfi UCRI_RAT : 201- 211: igvct HLGCvPiaNaG dfggy UCRI_RHOCA : 135- 145: lgvct HLGCvPmgDkS gdfgg UCRI_RHORU : 122- 132: vgvct HLGCiPlgQkA gdpkg UCRI_RHOSH : 131- 141: wgvct HLGCvPigGvS gdfgg UCRI_SOLTU : 210- 220: vgvct HLGCiPlpNaG dfggw UCRI_SPIOL : 177- 187: navct HLGCvVpfNaA enkfi UCRI_SYNP2 : 110- 120: naict HLGCvVpwNtA enkfm UCRI_SYNY3 : 122- 132: navct HLGCvVpwNaS enkfm UCRI_YEAST : 161- 171: lgict HLGCvPigEaG dfggw O 15: 21.4950 17( 17) G-x-[ILV]-x(2)-G-x-A-x(0,1)-P-x-[GNS] Occurences: 17(17) BFCA_BACSU : 154- 165: qevkd GfLylGkAkPkG eg UCR1_TOBAC : 186- 196: qynnq GrVvrGpA-PlS lalah UCR2_TOBAC : 186- 196: qynnq GrVvrGpA-PlS lalah UCRI_BOVIN : 242- 252: hydas GrIrkGpA-PlN levps UCRI_NEUCR : 204- 214: hydis GrIrkGpA-PlN leipl UCRI_NOSSP : 137- 147: qydet GkVvrGpA-PlS lalah UCRI_PARDE : 163- 173: hydts GrIrrGpA-PqN lhipv UCRI_PEA : 186- 196: qyndq GrVvrGpA-PlS lalah UCRI_RAT : 229- 239: hydas GrIrkGpA-PlN levpt UCRI_RHOCA : 164- 174: hydsa GrIrkGpA-PrN ldipv UCRI_RHORU : 155- 165: hydsa GrIrkGpA-PlN lpvpp UCRI_RHOSH : 160- 170: hydsa GrIrkGpA-PeN lpipl UCRI_SOLTU : 238- 248: hydis GrIrkGpA-PyN levpt UCRI_SPIOL : 204- 214: qynnq GrVvrGpA-PlS lalah UCRI_SYNP2 : 137- 147: qydet GkVvrGpA-PlS lalvh UCRI_SYNY3 : 149- 159: qynae GkVvrGpA-PlS lalah UCRI_YEAST : 189- 199: hydis GrIrkGpA-PlN leipa P 16: 20.6371 18( 17) G-x(2,4)-G-x(1,2)-A-[AP]-x(2)-L-x-[ILPV] Occurences: 18(17) BFCA_BACSU : 19- 31: nytlt Gvg--GfmAAsmLmP mvrfa UCR1_TOBAC : 186- 199: qynnq GrvvrGp-APlsLaL ahadi UCR2_TOBAC : 186- 199: qynnq GrvvrGp-APlsLaL ahadi UCRI_BOVIN : 242- 255: hydas GrirkGp-APlnLeV psyef UCRI_NEUCR : 204- 217: hydis GrirkGp-APlnLeI plyef UCRI_NOSSP : 137- 150: qydet GkvvrGp-APlsLaL ahant UCRI_PARDE : 163- 176: hydts GrirrGp-APqnLhI pvaef UCRI_PEA : 186- 199: qyndq GrvvrGp-APlsLaL ahcdv UCRI_RAT : 229- 242: hydas GrirkGp-APlnLeV ptyef UCRI_RHOCA : 164- 177: hydsa GrirkGp-APrnLdI pvaaf UCRI_RHORU : 155- 168: hydsa GrirkGp-APlnLpV ppyaf UCRI_RHOSH : 160- 173: hydsa GrirkGp-APenLpI plakf UCRI_SOLTU : 238- 251: hydis GrirkGp-APynLeV ptysf UCRI_SPIOL : 204- 217: qynnq GrvvrGp-APlsLaL ahcdv UCRI_SYNP2 : 137- 150: qydet GkvvrGp-APlsLaL vhaev UCRI_SYNY3 : 37- 49: nlltf Gtit-Gv-AAgaLyP avkyl UCRI_SYNY3 : 149- 162: qynae GkvvrGp-APlsLaL ahatv UCRI_YEAST : 189- 202: hydis GrirkGp-APlnLeI payef Q 17: 20.5574 17( 17) G-x(2)-Y-x(1,3)-G-x(3,5)-P-x-[GP]-x-[GNS] Occurences: 17(17) BFCA_BACSU : 154- 167: qevkd GflYl--Gkak--PkGeG UCR1_TOBAC : 179- 196: icpch GsqYnnqGrvvrgPaPlS lalah UCR2_TOBAC : 179- 196: icpch GsqYnnqGrvvrgPaPlS lalah UCRI_BOVIN : 235- 252: ycpch GshYdasGrirkgPaPlN levps UCRI_NEUCR : 197- 214: fcpch GshYdisGrirkgPaPlN leipl UCRI_NOSSP : 130- 147: kcpch GsqYdetGkvvrgPaPlS lalah UCRI_PARDE : 156- 173: fcpch GshYdtsGrirrgPaPqN lhipv UCRI_PEA : 179- 196: icpch GsqYndqGrvvrgPaPlS lalah UCRI_RAT : 222- 239: ycpch GshYdasGrirkgPaPlN levpt UCRI_RHOCA : 157- 174: fcpch GshYdsaGrirkgPaPrN ldipv UCRI_RHORU : 148- 165: fcpch GshYdsaGrirkgPaPlN lpvpp UCRI_RHOSH : 153- 170: fcpch GshYdsaGrirkgPaPeN lpipl UCRI_SOLTU : 231- 248: fcpch GshYdisGrirkgPaPyN levpt UCRI_SPIOL : 197- 214: icpch GsqYnnqGrvvrgPaPlS lalah UCRI_SYNP2 : 130- 147: mcpch GsqYdetGkvvrgPaPlS lalvh UCRI_SYNY3 : 142- 159: mcpch GsqYnaeGkvvrgPaPlS lalah UCRI_YEAST : 182- 199: fcpch GshYdisGrirkgPaPlN leipa R 18: 20.1190 17( 17) G-x(4)-G-x(1,2)-P-x(1,2)-L-x-[ILPV]-[ALPV] Occurences: 17(17) BFCA_BACSU : 132- 144: lyekd GtnvpGt-Pp-LaPL dhyeq UCR1_TOBAC : 186- 200: qynnq GrvvrGpaPlsLaLA hadid UCR2_TOBAC : 186- 200: qynnq GrvvrGpaPlsLaLA hadid UCRI_BOVIN : 242- 256: hydas GrirkGpaPlnLeVP syeft UCRI_NEUCR : 204- 218: hydis GrirkGpaPlnLeIP lyefp UCRI_NOSSP : 137- 151: qydet GkvvrGpaPlsLaLA hantv UCRI_PARDE : 163- 177: hydts GrirrGpaPqnLhIP vaefl UCRI_PEA : 186- 200: qyndq GrvvrGpaPlsLaLA hcdvg UCRI_RAT : 229- 243: hydas GrirkGpaPlnLeVP tyeft UCRI_RHOCA : 164- 178: hydsa GrirkGpaPrnLdIP vaafv UCRI_RHORU : 155- 169: hydsa GrirkGpaPlnLpVP pyaft UCRI_RHOSH : 160- 174: hydsa GrirkGpaPenLpIP lakfi UCRI_SOLTU : 238- 252: hydis GrirkGpaPynLeVP tysfl UCRI_SPIOL : 204- 218: qynnq GrvvrGpaPlsLaLA hcdvd UCRI_SYNP2 : 137- 151: qydet GkvvrGpaPlsLaLV haevt UCRI_SYNY3 : 149- 163: qynae GkvvrGpaPlsLaLA hatvt UCRI_YEAST : 189- 203: hydis GrirkGpaPlnLeIP ayefd S 19: 19.9092 17( 17) H-x(3)-Y-[DEN]-x-[ADEQST]-G-x(3,5)-P Occurences: 17(17) BFCA_BACSU : 124- 136: ffcpc HyglYEkDGtnv--P gtppl UCR1_TOBAC : 178- 192: ficpc HgsqYNnQGrvvrgP aplsl UCR2_TOBAC : 178- 192: ficpc HgsqYNnQGrvvrgP aplsl UCRI_BOVIN : 234- 248: yycpc HgshYDaSGrirkgP aplnl UCRI_NEUCR : 196- 210: wfcpc HgshYDiSGrirkgP aplnl UCRI_NOSSP : 129- 143: fkcpc HgsqYDeTGkvvrgP aplsl UCRI_PARDE : 155- 169: wfcpc HgshYDtSGrirrgP apqnl UCRI_PEA : 178- 192: ficpc HgsqYNdQGrvvrgP aplsl UCRI_RAT : 221- 235: yycpc HgshYDaSGrirkgP aplnl UCRI_RHOCA : 156- 170: wfcpc HgshYDsAGrirkgP aprnl UCRI_RHORU : 147- 161: wfcpc HgshYDsAGrirkgP aplnl UCRI_RHOSH : 152- 166: wfcpc HgshYDsAGrirkgP apenl UCRI_SOLTU : 230- 244: wfcpc HgshYDiSGrirkgP apynl UCRI_SPIOL : 196- 210: ficpc HgsqYNnQGrvvrgP aplsl UCRI_SYNP2 : 129- 143: fmcpc HgsqYDeTGkvvrgP aplsl UCRI_SYNY3 : 141- 155: fmcpc HgsqYNaEGkvvrgP aplsl UCRI_YEAST : 181- 195: wfcpc HgshYDiSGrirkgP aplnl T 20: 19.8503 17( 17) P-C-H-x(0,1)-G-x(1,2)-Y Occurences: 17(17) BFCA_BACSU : 122- 128: nkffc PCHyGl-Y ekdgt UCR1_TOBAC : 176- 182: nkfic PCH-GsqY nnqgr UCR2_TOBAC : 176- 182: nkfic PCH-GsqY nnqgr UCRI_BOVIN : 232- 238: ggyyc PCH-GshY dasgr UCRI_NEUCR : 194- 200: ggwfc PCH-GshY disgr UCRI_NOSSP : 127- 133: nkfkc PCH-GsqY detgk UCRI_PARDE : 153- 159: ggwfc PCH-GshY dtsgr UCRI_PEA : 176- 182: nkfic PCH-GsqY ndqgr UCRI_RAT : 219- 225: ggyyc PCH-GshY dasgr UCRI_RHOCA : 154- 160: ggwfc PCH-GshY dsagr UCRI_RHORU : 145- 151: dgwfc PCH-GshY dsagr UCRI_RHOSH : 150- 156: ggwfc PCH-GshY dsagr UCRI_SOLTU : 228- 234: ggwfc PCH-GshY disgr UCRI_SPIOL : 194- 200: nkfic PCH-GsqY nnqgr UCRI_SYNP2 : 127- 133: nkfmc PCH-GsqY detgk UCRI_SYNY3 : 139- 145: nkfmc PCH-GsqY naegk UCRI_YEAST : 179- 185: ggwfc PCH-GshY disgr Number of patterns evaluated by Pratt:909 Total running time: 1 seconds