------------------------------------------------------------ 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 7 sequences from file RNA_POL_H_23KD PATTERN CONSERVATION: CM: min Nr of Seqs to Match 7 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 RNA_POL_H_23KD.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RPB5_HUMAN 210 RPB5_YEAST 215 RPOH_HALHA 75 RPOH_METVA 78 RPOH_SULAC 84 RPOH_THEAC 87 RPOH_THECE 82 Pratt run started at Thu Feb 6 21:06:58 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 20.3503 7( 7) G-x(4)-I-x-R-x-S-x(1,2)-T 2: 16.6802 7( 7) H-x(2)-V-P-x-H 3: 16.1802 7( 7) I-x-R-x-S-x(1,2)-T 4: 15.1802 7( 7) L-x(1,2)-I-x(1,3)-D-P 5: 14.6802 7( 7) P-x(1,3)-I-x(3)-D-x(0,2)-P 6: 12.5102 7( 7) V-P-x-H 7: 12.0102 7( 7) R-x-S-x(1,2)-T 8: 11.5102 9( 7) L-x(0,1)-V-x(0,1)-E 9: 11.5102 7( 7) E-x(1,2)-V-x(3,4)-I 10: 11.5102 7( 7) I-x(3)-D-x(0,2)-P 11: 11.5102 7( 7) I-x(1,3)-D-P 12: 11.5102 8( 7) I-x(2,3)-E-x(1,2)-P 13: 11.5102 10( 7) E-x(3,4)-L-x(1,2)-E 14: 11.5102 7( 7) E-x-V-x(0,2)-H 15: 11.5102 8( 7) E-x(1,3)-V-P 16: 11.0102 8( 7) G-x(1,2)-V-x(2,4)-R 17: 11.0102 9( 7) E-x(1,2)-P-x(1,3)-I 18: 11.0102 8( 7) T-x(0,2)-G-x(3,4)-Y 19: 10.5102 11( 7) E-x(1,3)-V-x(2,4)-I 20: 8.3401 14( 7) V-x-E Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 83.4898 7( 7) H-[EN]-[LM]-V-P-[EK]-H-x(2)-[ILMV]-[DPQST]-x-[DE]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR]-x(2)-[IL]-x(2)-[ENQST]-x-[FL]-P-x-[IL]-x(3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV] B 2: 75.2439 7( 7) V-P-[EK]-H-x(2)-[ILMV]-[DPQST]-x-[DE]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR]-x(2)-[IL]-x(2)-[ENQST]-x-[FL]-P-x-[IL]-x(3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] C 3: 34.8632 7( 7) G-[DEQT]-[IV]-[ILV]-[EK]-I-x-R-x-S-x(1,2)-T-x-[EG] D 4: 31.7799 7( 7) L-x(1,2)-I-x(1,3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] E 5: 28.2936 7( 7) E-x-V-x(0,2)-H-x(2)-[ILM]-x(2)-[DEG]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR] F 6: 28.1099 7( 7) I-x(1,3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] G 7: 19.5348 8( 7) E-x(1,3)-V-P-[EK]-[EH]-x(3)-[DNPQST] H 8: 19.4088 7( 7) I-x-R-x-S-x(1,2)-T-x-[EG] I 9: 18.9970 8( 7) G-x(1,2)-V-x(2,4)-R-x-[SV]-x-[ST]-[AEGNST] J 10: 16.9194 7( 7) P-x(1,3)-I-x(3)-D-x(0,2)-P-x-[AILV] K 11: 15.2387 7( 7) R-x-S-x(1,2)-T-x-[EG] L 12: 13.7494 7( 7) I-x(3)-D-x(0,2)-P-x-[AILV] M 13: 11.5102 9( 7) L-x(0,1)-V-x(0,1)-E N 14: 11.5102 7( 7) E-x(1,2)-V-x(3,4)-I O 15: 11.5102 8( 7) I-x(2,3)-E-x(1,2)-P P 16: 11.5102 10( 7) E-x(3,4)-L-x(1,2)-E Q 17: 11.0102 7( 7) L-x(1,2)-I-x(1,3)-D R 18: 11.0102 8( 7) G-x(1,2)-V-x(2,4)-R S 19: 11.0102 9( 7) E-x(1,2)-P-x(1,3)-I T 20: 11.0102 8( 7) T-x(0,2)-G-x(3,4)-Y Best patterns with alignements: fitness hits(seqs) Pattern A 1: 83.4898 7( 7) H-[EN]-[LM]-V-P-[EK]-H-x(2)-[ILMV]-[DPQST]-x-[DE]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR]-x(2)-[IL]-x(2)-[ENQST]-x-[FL]-P-x-[IL]-x(3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV] Occurences: 7(7) RPB5_HUMAN : 142- 190: inite HELVPEHvvMTkEEvteLLaRykLreNqLPrIqagDPVAryfGikrGqV vkiir RPB5_YEAST : 147- 195: vnith HELVPKHirLSsDEkreLLkRyrLkeSqLPrIqraDPVAlylGlkrGeV vkiir RPOH_HALHA : 7- 55: vdvsq HELVPEHtvLDeETldgVLaDydIdrTeLPkIkykDPALpdnAeigDvV eivrd RPOH_METVA : 6- 54: mkvss HEMVPEHeiIPgDEipfLLeKygIkiQqFPkLlisDPLVievGakvGdI vkitr RPOH_SULAC : 14- 62: idisn HELVPKHeiLQlEEaykLVkElgIkpEqLPwIrasDPVAksiGakpGdI ikitr RPOH_THEAC : 9- 57: fnvld HNLVPEHhiVPeEEeknILkElnIekEfLPkIspnDPAIkalEavhGkI kegti RPOH_THECE : 12- 60: fdifa HELVPEHriLSeEEtkeLLrRyrIqiSqLPqIkasDPAVvalGakpGdV leikr B 2: 75.2439 7( 7) V-P-[EK]-H-x(2)-[ILMV]-[DPQST]-x-[DE]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR]-x(2)-[IL]-x(2)-[ENQST]-x-[FL]-P-x-[IL]-x(3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] Occurences: 7(7) RPB5_HUMAN : 145- 193: tehel VPEHvvMTkEEvteLLaRykLreNqLPrIqagDPVAryfGikrGqVvkI irpse RPB5_YEAST : 150- 198: thhel VPKHirLSsDEkreLLkRyrLkeSqLPrIqraDPVAlylGlkrGeVvkI irkse RPOH_HALHA : 10- 58: sqhel VPEHtvLDeETldgVLaDydIdrTeLPkIkykDPALpdnAeigDvVeiV rdsrt RPOH_METVA : 9- 57: sshem VPEHeiIPgDEipfLLeKygIkiQqFPkLlisDPLVievGakvGdIvkI trksq RPOH_SULAC : 17- 65: snhel VPKHeiLQlEEaykLVkElgIkpEqLPwIrasDPVAksiGakpGdIikI trksp RPOH_THEAC : 12- 60: ldhnl VPEHhiVPeEEeknILkElnIekEfLPkIspnDPAIkalEavhGkIkeG tiiki RPOH_THECE : 15- 63: fahel VPEHriLSeEEtkeLLrRyrIqiSqLPqIkasDPAVvalGakpGdVleI krksr C 3: 34.8632 7( 7) G-[DEQT]-[IV]-[ILV]-[EK]-I-x-R-x-S-x(1,2)-T-x-[EG] Occurences: 7(7) RPB5_HUMAN : 188- 201: fgikr GQVVKIiRpSe-TaG ryity RPB5_YEAST : 193- 206: lglkr GEVVKIiRkSe-TsG ryasy RPOH_HALHA : 52- 66: dnaei GDVVEIvRdSrtTdE avvyr RPOH_METVA : 52- 65: vgakv GDIVKItRkSq-TaG etvyf RPOH_SULAC : 60- 74: igakp GDIIKItRkSpfTgE svtyr RPOH_THEAC : 60- 73: gkike GTIIKIvRkSp-TmG hsvyy RPOH_THECE : 58- 71: lgakp GDVLEIkRkSr-TaG yyyyy D 4: 31.7799 7( 7) L-x(1,2)-I-x(1,3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] Occurences: 7(7) RPB5_HUMAN : 170- 193: lrenq LprIqagDPVAryfGikrGqVvkI irpse RPB5_YEAST : 175- 198: lkesq LprIqraDPVAlylGlkrGeVvkI irkse RPOH_HALHA : 35- 58: idrte LpkIkykDPALpdnAeigDvVeiV rdsrt RPOH_METVA : 37- 57: qqfpk Ll-Is--DPLVievGakvGdIvkI trksq RPOH_SULAC : 42- 65: ikpeq LpwIrasDPVAksiGakpGdIikI trksp RPOH_THEAC : 37- 60: iekef LpkIspnDPAIkalEavhGkIkeG tiiki RPOH_THECE : 40- 63: iqisq LpqIkasDPAVvalGakpGdVleI krksr E 5: 28.2936 7( 7) E-x-V-x(0,2)-H-x(2)-[ILM]-x(2)-[DEG]-[ET]-x(3)-[ILV]-[LV]-x-[DEKR] Occurences: 7(7) RPB5_HUMAN : 143- 162: niteh ElVpeHvvMtkEEvteLLaR yklre RPB5_YEAST : 148- 167: nithh ElVpkHirLssDEkreLLkR yrlke RPOH_HALHA : 8- 27: dvsqh ElVpeHtvLdeETldgVLaD ydidr RPOH_METVA : 7- 26: kvssh EmVpeHeiIpgDEipfLLeK ygiki RPOH_SULAC : 15- 34: disnh ElVpkHeiLqlEEaykLVkE lgikp RPOH_THEAC : 51- 68: aikal EaV--HgkIkeGTiikIVrK sptmg RPOH_THECE : 13- 32: difah ElVpeHriLseEEtkeLLrR yriqi F 6: 28.1099 7( 7) I-x(1,3)-D-P-[ALV]-[AILV]-x(3)-[AEG]-x(3)-[DG]-x-[IV]-x(2)-[GIV] Occurences: 7(7) RPB5_HUMAN : 173- 193: nqlpr IqagDPVAryfGikrGqVvkI irpse RPB5_YEAST : 178- 198: sqlpr IqraDPVAlylGlkrGeVvkI irkse RPOH_HALHA : 38- 58: telpk IkykDPALpdnAeigDvVeiV rdsrt RPOH_METVA : 39- 57: fpkll Is--DPLVievGakvGdIvkI trksq RPOH_SULAC : 45- 65: eqlpw IrasDPVAksiGakpGdIikI trksp RPOH_THEAC : 40- 60: eflpk IspnDPAIkalEavhGkIkeG tiiki RPOH_THECE : 43- 63: sqlpq IkasDPAVvalGakpGdVleI krksr G 7: 19.5348 8( 7) E-x(1,3)-V-P-[EK]-[EH]-x(3)-[DNPQST] Occurences: 8(7) RPB5_HUMAN : 141- 152: linit EhelVPEHvvmT keevt RPB5_HUMAN : 143- 152: niteh El--VPEHvvmT keevt RPB5_YEAST : 148- 157: nithh El--VPKHirlS sdekr RPOH_HALHA : 8- 17: dvsqh El--VPEHtvlD eetld RPOH_METVA : 7- 16: kvssh Em--VPEHeiiP gdeip RPOH_SULAC : 15- 24: disnh El--VPKHeilQ leeay RPOH_THEAC : 14- 25: hnlvp EhhiVPEEeekN ilkel RPOH_THECE : 13- 22: difah El--VPEHrilS eeetk H 8: 19.4088 7( 7) I-x-R-x-S-x(1,2)-T-x-[EG] Occurences: 7(7) RPB5_HUMAN : 193- 201: gqvvk IiRpSe-TaG ryity RPB5_YEAST : 198- 206: gevvk IiRkSe-TsG ryasy RPOH_HALHA : 57- 66: gdvve IvRdSrtTdE avvyr RPOH_METVA : 57- 65: gdivk ItRkSq-TaG etvyf RPOH_SULAC : 65- 74: gdiik ItRkSpfTgE svtyr RPOH_THEAC : 65- 73: gtiik IvRkSp-TmG hsvyy RPOH_THECE : 63- 71: gdvle IkRkSr-TaG yyyyy I 9: 18.9970 8( 7) G-x(1,2)-V-x(2,4)-R-x-[SV]-x-[ST]-[AEGNST] Occurences: 8(7) RPB5_HUMAN : 188- 200: fgikr GqvVkii-RpSeTA gryit RPB5_HUMAN : 188- 200: fgikr Gq-VvkiiRpSeTA gryit RPB5_YEAST : 193- 205: lglkr GevVkii-RkSeTS gryas RPB5_YEAST : 193- 205: lglkr Ge-VvkiiRkSeTS gryas RPOH_HALHA : 52- 64: dnaei GdvVeiv-RdSrTT deavv RPOH_HALHA : 52- 64: dnaei Gd-VveivRdSrTT deavv RPOH_METVA : 52- 64: vgakv GdiVkit-RkSqTA getvy RPOH_METVA : 65- 76: ksqta GetVyf--RlVvSN sv RPOH_SULAC : 73- 84: kspft GesVty--RyViTG RPOH_THEAC : 73- 84: ksptm GhsVyy--RvVaSE vfk RPOH_THECE : 58- 70: lgakp Gd-VleikRkSrTA gyyyy J 10: 16.9194 7( 7) P-x(1,3)-I-x(3)-D-x(0,2)-P-x-[AILV] Occurences: 7(7) RPB5_HUMAN : 171- 180: renql Pr--IqagD--PvA ryfgi RPB5_YEAST : 176- 185: kesql Pr--IqraD--PvA lylgl RPOH_HALHA : 36- 45: drtel Pk--IkykD--PaL pdnae RPOH_METVA : 10- 23: shemv PeheIipgDeiPfL lekyg RPOH_SULAC : 43- 52: kpeql Pw--IrasD--PvA ksiga RPOH_THEAC : 38- 47: ekefl Pk--IspnD--PaI kalea RPOH_THECE : 41- 50: qisql Pq--IkasD--PaV valga K 11: 15.2387 7( 7) R-x-S-x(1,2)-T-x-[EG] Occurences: 7(7) RPB5_HUMAN : 195- 201: vvkii RpSe-TaG ryity RPB5_YEAST : 200- 206: vvkii RkSe-TsG ryasy RPOH_HALHA : 59- 66: vveiv RdSrtTdE avvyr RPOH_METVA : 59- 65: ivkit RkSq-TaG etvyf RPOH_SULAC : 67- 74: iikit RkSpfTgE svtyr RPOH_THEAC : 67- 73: iikiv RkSp-TmG hsvyy RPOH_THECE : 65- 71: vleik RkSr-TaG yyyyy L 12: 13.7494 7( 7) I-x(3)-D-x(0,2)-P-x-[AILV] Occurences: 7(7) RPB5_HUMAN : 173- 180: nqlpr IqagD--PvA ryfgi RPB5_YEAST : 178- 185: sqlpr IqraD--PvA lylgl RPOH_HALHA : 38- 45: telpk IkykD--PaL pdnae RPOH_METVA : 14- 23: vpehe IipgDeiPfL lekyg RPOH_SULAC : 45- 52: eqlpw IrasD--PvA ksiga RPOH_THEAC : 40- 47: eflpk IspnD--PaI kalea RPOH_THECE : 43- 50: sqlpq IkasD--PaV valga M 13: 11.5102 9( 7) L-x(0,1)-V-x(0,1)-E Occurences: 9(7) RPB5_HUMAN : 144- 147: itehe L-VpE hvvmt RPB5_YEAST : 78- 81: pdmgs LwV-E fcdep RPOH_HALHA : 9- 12: vsqhe L-VpE htvld RPOH_HALHA : 72- 75: avvyr L-ViE RPOH_METVA : 43- 46: lisdp L-ViE vgakv RPOH_SULAC : 31- 34: eeayk L-VkE lgikp RPOH_THEAC : 11- 14: vldhn L-VpE hhivp RPOH_THECE : 14- 17: ifahe L-VpE hrils RPOH_THECE : 78- 81: yyyyr LvV-E d RPOH_THECE : 78- 81: yyyyr L-VvE d N 14: 11.5102 7( 7) E-x(1,2)-V-x(3,4)-I Occurences: 7(7) RPB5_HUMAN : 79- 87: vffpe EpkVgiktI kvycq RPB5_YEAST : 148- 154: nithh El-Vpkh-I rlssd RPOH_HALHA : 66- 74: srttd EavVyrlvI e RPOH_METVA : 7- 14: kvssh Em-VpeheI ipgde RPOH_SULAC : 15- 22: disnh El-VpkheI lqlee RPOH_THEAC : 51- 57: aikal Ea-Vhgk-I kegti RPOH_THECE : 13- 20: difah El-VpehrI lseee O 15: 11.5102 8( 7) I-x(2,3)-E-x(1,2)-P Occurences: 8(7) RPB5_HUMAN : 139- 146: ellin ItehElvP ehvvm RPB5_YEAST : 144- 151: alvvn IthhElvP khirl RPOH_HALHA : 30- 36: ladyd IdrtEl-P kikyk RPOH_METVA : 15- 21: pehei IpgdEi-P fllek RPOH_SULAC : 11- 18: kkkid IsnhElvP kheil RPOH_SULAC : 37- 43: vkelg Ikp-EqlP wiras RPOH_THEAC : 32- 38: lkeln Iek-EflP kispn RPOH_THECE : 9- 16: kkefd IfahElvP ehril P 16: 11.5102 10( 7) E-x(3,4)-L-x(1,2)-E Occurences: 10(7) RPB5_HUMAN : 32- 39: lvtqd EldqtLe-E fkaqf RPB5_YEAST : 33- 40: yfitq Eeve-LplE dfkak RPOH_HALHA : 12- 18: helvp Ehtv-Ld-E etldg RPOH_HALHA : 12- 19: helvp Ehtv-LdeE tldgv RPOH_METVA : 19- 25: iipgd Eipf-Ll-E kygik RPOH_SULAC : 21- 27: lvpkh Eilq-Le-E ayklv RPOH_SULAC : 26- 34: eilql EeaykLvkE lgikp RPOH_SULAC : 27- 34: ilqle Eayk-LvkE lgikp RPOH_THEAC : 22- 29: ivpee EekniLk-E lniek RPOH_THEAC : 23- 29: vpeee Ekni-Lk-E lniek RPOH_THECE : 17- 23: helvp Ehri-Ls-E eetke RPOH_THECE : 17- 24: helvp Ehri-LseE etkel Q 17: 11.0102 7( 7) L-x(1,2)-I-x(1,3)-D Occurences: 7(7) RPB5_HUMAN : 170- 177: lrenq LprIqagD pvary RPB5_YEAST : 175- 182: lkesq LprIqraD pvaly RPOH_HALHA : 35- 42: idrte LpkIkykD palpd RPOH_METVA : 37- 41: qqfpk Ll-Is--D plvie RPOH_SULAC : 42- 49: ikpeq LpwIrasD pvaks RPOH_THEAC : 37- 44: iekef LpkIspnD paika RPOH_THECE : 40- 47: iqisq LpqIkasD pavva R 18: 11.0102 8( 7) G-x(1,2)-V-x(2,4)-R Occurences: 8(7) RPB5_HUMAN : 188- 195: fgikr GqvVkii-R pseta RPB5_HUMAN : 188- 195: fgikr Gq-VvkiiR pseta RPB5_YEAST : 193- 200: lglkr GevVkii-R ksets RPB5_YEAST : 193- 200: lglkr Ge-VvkiiR ksets RPOH_HALHA : 52- 59: dnaei GdvVeiv-R dsrtt RPOH_HALHA : 52- 59: dnaei Gd-VveivR dsrtt RPOH_METVA : 52- 59: vgakv GdiVkit-R ksqta RPOH_METVA : 65- 71: ksqta GetVyf--R lvvsn RPOH_SULAC : 73- 79: kspft GesVty--R yvitg RPOH_THEAC : 73- 79: ksptm GhsVyy--R vvase RPOH_THECE : 58- 65: lgakp Gd-VleikR ksrta S 19: 11.0102 9( 7) E-x(1,2)-P-x(1,3)-I Occurences: 9(7) RPB5_HUMAN : 78- 84: fvffp Ee-PkvgI ktikv RPB5_YEAST : 148- 154: nithh ElvPkh-I rlssd RPOH_HALHA : 34- 38: didrt El-Pk--I kykdp RPOH_METVA : 7- 14: kvssh EmvPeheI ipgde RPOH_METVA : 13- 20: mvpeh EiiPgdeI pflle RPOH_SULAC : 15- 22: disnh ElvPkheI lqlee RPOH_SULAC : 40- 45: lgikp EqlPw--I rasdp RPOH_THEAC : 35- 40: lniek EflPk--I spndp RPOH_THECE : 13- 20: difah ElvPehrI lseee T 20: 11.0102 8( 7) T-x(0,2)-G-x(3,4)-Y Occurences: 8(7) RPB5_HUMAN : 199- 206: irpse Ta-GryitY rlvq RPB5_YEAST : 107- 112: eknfq T--Gifv-Y qnnit RPB5_YEAST : 204- 211: irkse Ts-GryasY ricm RPOH_HALHA : 20- 28: vldee TldGvladY didrt RPOH_METVA : 63- 69: trksq Ta-Getv-Y frlvv RPOH_SULAC : 72- 78: rkspf T--GesvtY ryvit RPOH_THEAC : 71- 77: vrksp Tm-Ghsv-Y yrvva RPOH_THEAC : 71- 78: vrksp Tm-GhsvyY rvvas RPOH_THECE : 69- 75: krksr Ta-Gyyy-Y yrlvv RPOH_THECE : 69- 76: krksr Ta-GyyyyY rlvve Number of patterns evaluated by Pratt:266 Total running time: 1 seconds