------------------------------------------------------------ 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 13 sequences from file DHODEHASE_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 13 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 DHODEHASE_1.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PYRD_AGRAE 328 PYRD_ARATH 434 PYRD_BACCL 313 PYRD_BACSU 311 PYRD_DROME 389 PYRD_ECOLI 336 PYRD_HAEIN 339 PYRD_HUMAN 396 PYRD_MYCLE 309 PYRD_PLAFA 569 PYRD_SALTY 336 PYRD_SCHPO 443 PYRD_YEAST 314 Pratt run started at Thu Feb 6 19:18:05 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 19.3503 13( 13) T-x(5)-G-N-x(0,2)-P-x(2,3)-R 2: 16.6802 13( 13) N-x-S-x-P-N 3: 16.6802 13( 13) G-N-x(2)-P-R 4: 16.1802 19( 13) G-G-x(1,2)-S-G 5: 15.6802 13( 13) N-x(2)-G-x(1,2)-N-x(1,2)-G 6: 15.1802 13( 13) G-N-x(0,2)-P-x(2,3)-R 7: 12.5102 16( 13) I-x(2)-G-G 8: 12.5102 14( 13) T-x(5)-G-x(3)-P 9: 12.5102 18( 13) A-G-A 10: 12.5102 17( 13) A-x(5)-A-G 11: 12.5102 14( 13) P-x-I-x(3)-G 12: 12.5102 14( 13) P-x(3)-A-x-G 13: 12.5102 19( 13) N-x(2)-G-L 14: 12.5102 14( 13) S-x-P-N 15: 12.5102 13( 13) N-x(2)-P-R 16: 12.0102 23( 13) G-G-x(1,2)-S 17: 12.0102 17( 13) I-x(1,2)-G-G 18: 12.0102 18( 13) G-I-x(1,2)-G 19: 12.0102 33( 13) G-x(1,2)-S-G 20: 12.0102 28( 13) A-x(0,1)-G-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 31.1846 13( 13) T-x(3)-[QR]-x-G-N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] B 2: 25.9427 13( 13) I-x(2)-G-G-[IV]-x-[GST]-[AGLV]-x-[ADNT]-[AV] C 3: 25.7744 13( 13) N-[ILV]-S-[CS]-P-N-[TV] D 4: 25.4427 13( 13) I-x(1,2)-G-G-[IV]-x-[GST]-[AGLV]-x-[ADNT]-[AV] E 5: 24.4037 13( 13) T-x(3)-[QR]-x-G-N-x(0,2)-P-x(2,3)-R-x(2)-[DEQRS] F 6: 23.8437 13( 13) G-N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] G 7: 23.5507 13( 13) P-x-I-x(2)-[GIL]-G-x(2)-[GST]-[AGILV]-x-[ADGNST]-[AGPV] H 8: 21.4224 16( 13) G-G-x(1,2)-S-G-x-[ADP]-[ALV] I 9: 20.5546 13( 13) P-[FILV]-x(2)-A-[AS]-G-x(4)-[AGT] J 10: 19.6737 13( 13) N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] K 11: 18.9426 13( 13) S-[CS]-P-N-[TV] L 12: 17.2523 27( 13) G-x(1,2)-S-G-x-[ADP]-[ALV] M 13: 17.0628 13( 13) G-N-x(0,2)-P-x(2,3)-R-x(2)-[DEQRS] N 14: 16.6103 16( 13) N-[APST]-x-G-L-x-[ADNTV] O 15: 16.3201 15( 13) A-x(5)-A-G-x(4)-[AENQT]-x(2)-[GNSTV] P 16: 15.6802 13( 13) N-x(2)-G-x(1,2)-N-x(1,2)-G Q 17: 12.5102 18( 13) A-G-A R 18: 12.0102 19( 13) G-G-x(1,2)-S S 19: 12.0102 18( 13) G-I-x(1,2)-G T 20: 12.0102 33( 13) G-x(1,2)-S-G Best patterns with alignements: fitness hits(seqs) Pattern A 1: 31.1846 13( 13) T-x(3)-[QR]-x-G-N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] Occurences: 13(13) PYRD_AGRAE : 87- 105: eigti TprpQsGNPrPRifRlvdD kavin PYRD_ARATH : 167- 185: evgsv TpvpQeGNPkPRifRlsqE gaiin PYRD_BACCL : 48- 66: mikat TkepRfGNPtPRvaEtpgG mlnai PYRD_BACSU : 46- 64: mikat TkepRfGNPtPRvaEtgaG mlnai PYRD_DROME : 129- 147: evgtv TpaaQeGNPkPRvfRlteD kaiin PYRD_ECOLI : 88- 106: eigtv TprpQpGNDkPRlfRlvdA eglin PYRD_HAEIN : 90- 108: elgtv TpvaQdGNAkPRqfRlieA egiin PYRD_HUMAN : 122- 140: eigsv TpkpQeGNPrPRvfRlpeD qavin PYRD_MYCLE : 45- 63: evgtv TaypQpGNPaPRmfRlpaD ralln PYRD_PLAFA : 251- 269: eigti TprgQtGNAkPRifRdveS rsiin PYRD_SALTY : 88- 106: eigtv TprpQpGNDkPRlfRlvdA eglin PYRD_SCHPO : 148- 166: eigsv TpkpQpGNPkPRyfRlkpD lsvin PYRD_YEAST : 49- 67: itksa TtleReGNPePRyiSvplG sinsm B 2: 25.9427 13( 13) I-x(2)-G-G-[IV]-x-[GST]-[AGLV]-x-[ADNT]-[AV] Occurences: 13(13) PYRD_AGRAE : 291- 302: pdmpl IgvGGVdSAeTA ltkvk PYRD_ARATH : 396- 407: gkipl IgcGGVsSGeDA ykkir PYRD_BACCL : 240- 251: vsipi IgmGGIqTAeDV leffy PYRD_BACSU : 238- 249: vnipi IgmGGVqTAeDA lefll PYRD_DROME : 336- 347: gkipi IgvGGVaSGyDA yekie PYRD_ECOLI : 293- 304: grlpi IgvGGIdSViAA rekia PYRD_HAEIN : 295- 306: gqipi IgsGGIdGLqNA qekie PYRD_HUMAN : 331- 342: grvpi IgvGGVsSGqNA lekir PYRD_MYCLE : 242- 253: drlvl IsvGGIeTAdDA wdrit PYRD_PLAFA : 503- 514: kqipi IasGGIfSGlDA lekie PYRD_SALTY : 293- 304: gqlpi IgvGGIdSViAA rekia PYRD_SCHPO : 383- 394: sdipi IgcGGIsSGkDA ieyar PYRD_YEAST : 249- 260: peikv IgtGGIkSGkDA fehll C 3: 25.7744 13( 13) N-[ILV]-S-[CS]-P-N-[TV] Occurences: 13(13) PYRD_AGRAE : 170- 176: ryftv NISSPNT pglrn PYRD_ARATH : 274- 280: dylvi NVSSPNT aglrm PYRD_BACCL : 127- 133: halel NISCPNV kkggi PYRD_BACSU : 125- 131: halel NISCPNV ktggi PYRD_DROME : 215- 221: dylvi NVSSPNT kglrd PYRD_ECOLI : 172- 178: gyiai NISSPNT pglrt PYRD_HAEIN : 174- 180: gyitv NISSPNT pdlrq PYRD_HUMAN : 212- 218: dylvv NVSSPNT aglrs PYRD_MYCLE : 129- 135: sylvv NVSSPNT pglrd PYRD_PLAFA : 342- 348: dyiai NVSSPNT pglrd PYRD_SALTY : 172- 178: gyiai NISSPNT pglrt PYRD_SCHPO : 264- 270: dilvi NVSSPNT pglrn PYRD_YEAST : 130- 136: gitel NLSCPNV pgkpq D 4: 25.4427 13( 13) I-x(1,2)-G-G-[IV]-x-[GST]-[AGLV]-x-[ADNT]-[AV] Occurences: 13(13) PYRD_AGRAE : 291- 302: pdmpl IgvGGVdSAeTA ltkvk PYRD_ARATH : 396- 407: gkipl IgcGGVsSGeDA ykkir PYRD_BACCL : 240- 251: vsipi IgmGGIqTAeDV leffy PYRD_BACSU : 238- 249: vnipi IgmGGVqTAeDA lefll PYRD_DROME : 336- 347: gkipi IgvGGVaSGyDA yekie PYRD_ECOLI : 293- 304: grlpi IgvGGIdSViAA rekia PYRD_HAEIN : 295- 306: gqipi IgsGGIdGLqNA qekie PYRD_HUMAN : 331- 342: grvpi IgvGGVsSGqNA lekir PYRD_MYCLE : 242- 253: drlvl IsvGGIeTAdDA wdrit PYRD_PLAFA : 503- 514: kqipi IasGGIfSGlDA lekie PYRD_SALTY : 293- 304: gqlpi IgvGGIdSViAA rekia PYRD_SCHPO : 383- 394: sdipi IgcGGIsSGkDA ieyar PYRD_YEAST : 249- 260: peikv IgtGGIkSGkDA fehll E 5: 24.4037 13( 13) T-x(3)-[QR]-x-G-N-x(0,2)-P-x(2,3)-R-x(2)-[DEQRS] Occurences: 13(13) PYRD_AGRAE : 87- 101: eigti TprpQsGN--Prp-RifR lvddk PYRD_AGRAE : 87- 104: eigti TprpQsGNprPrifRlvD dkavi PYRD_ARATH : 167- 181: evgsv TpvpQeGN--Pkp-RifR lsqeg PYRD_ARATH : 167- 184: evgsv TpvpQeGNpkPrifRlsQ egaii PYRD_BACCL : 48- 62: mikat TkepRfGN--Ptp-RvaE tpggm PYRD_BACSU : 46- 60: mikat TkepRfGN--Ptp-RvaE tgagm PYRD_DROME : 129- 143: evgtv TpaaQeGN--Pkp-RvfR ltedk PYRD_DROME : 129- 146: evgtv TpaaQeGNpkPrvfRltE dkaii PYRD_ECOLI : 88- 105: eigtv TprpQpGNdkPrlfRlvD aegli PYRD_HAEIN : 90- 107: elgtv TpvaQdGNakPrqfRliE aegii PYRD_HUMAN : 122- 136: eigsv TpkpQeGN--Prp-RvfR lpedq PYRD_HUMAN : 122- 139: eigsv TpkpQeGNprPrvfRlpE dqavi PYRD_MYCLE : 45- 59: evgtv TaypQpGN--Pap-RmfR lpadr PYRD_PLAFA : 251- 268: eigti TprgQtGNakPrifRdvE srsii PYRD_SALTY : 88- 105: eigtv TprpQpGNdkPrlfRlvD aegli PYRD_SCHPO : 148- 162: eigsv TpkpQpGN--Pkp-RyfR lkpdl PYRD_YEAST : 49- 63: itksa TtleReGN--Pep-RyiS vplgs F 6: 23.8437 13( 13) G-N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] Occurences: 13(13) PYRD_AGRAE : 93- 105: prpqs GNPrPRifRlvdD kavin PYRD_ARATH : 173- 185: pvpqe GNPkPRifRlsqE gaiin PYRD_BACCL : 54- 66: keprf GNPtPRvaEtpgG mlnai PYRD_BACSU : 52- 64: keprf GNPtPRvaEtgaG mlnai PYRD_DROME : 135- 147: paaqe GNPkPRvfRlteD kaiin PYRD_ECOLI : 94- 106: prpqp GNDkPRlfRlvdA eglin PYRD_HAEIN : 96- 108: pvaqd GNAkPRqfRlieA egiin PYRD_HUMAN : 128- 140: pkpqe GNPrPRvfRlpeD qavin PYRD_MYCLE : 51- 63: aypqp GNPaPRmfRlpaD ralln PYRD_PLAFA : 257- 269: prgqt GNAkPRifRdveS rsiin PYRD_SALTY : 94- 106: prpqp GNDkPRlfRlvdA eglin PYRD_SCHPO : 154- 166: pkpqp GNPkPRyfRlkpD lsvin PYRD_YEAST : 55- 67: tlere GNPePRyiSvplG sinsm G 7: 23.5507 13( 13) P-x-I-x(2)-[GIL]-G-x(2)-[GST]-[AGILV]-x-[ADGNST]-[AGPV] Occurences: 13(13) PYRD_AGRAE : 289- 302: vgpdm PlIgvGGvdSAeTA ltkvk PYRD_ARATH : 394- 407: trgki PlIgcGGvsSGeDA ykkir PYRD_BACCL : 238- 251: qavsi PiIgmGGiqTAeDV leffy PYRD_BACSU : 236- 249: qmvni PiIgmGGvqTAeDA lefll PYRD_DROME : 334- 347: tdgki PiIgvGGvaSGyDA yekie PYRD_ECOLI : 291- 304: lngrl PiIgvGGidSViAA rekia PYRD_HAEIN : 293- 306: lkgqi PiIgsGGidGLqNA qekie PYRD_HUMAN : 329- 342: tqgrv PiIgvGGvsSGqNA lekir PYRD_MYCLE : 205- 218: dclvt PgIdaLGagGIsGP pvarr PYRD_PLAFA : 501- 514: tnkqi PiIasGGifSGlDA lekie PYRD_SALTY : 291- 304: lkgql PiIgvGGidSViAA rekia PYRD_SCHPO : 381- 394: lssdi PiIgcGGisSGkDA ieyar PYRD_YEAST : 244- 257: ytrlr PeIkvIGtgGIkSG kdafe H 8: 21.4224 16( 13) G-G-x(1,2)-S-G-x-[ADP]-[ALV] Occurences: 16(13) PYRD_AGRAE : 262- 269: grdet GGl-SGaPL fdrst PYRD_ARATH : 367- 374: vatet GGl-SGkPL falst PYRD_ARATH : 399- 407: pligc GGvsSGeDA ykkir PYRD_BACCL : 213- 220: langt GGl-SGpAV kpiai PYRD_BACSU : 211- 218: lankt GGl-SGpAV kpvai PYRD_DROME : 307- 314: laeet GGl-SGpPL karst PYRD_DROME : 339- 347: piigv GGvaSGyDA yekie PYRD_ECOLI : 264- 271: ncdqt GGl-SGrPL qlkst PYRD_HAEIN : 266- 273: naeqq GGl-SGkPL qhkst PYRD_HUMAN : 302- 309: lrset GGl-SGkPL rdlst PYRD_MYCLE : 213- 220: dalga GGi-SGpPV arrav PYRD_PLAFA : 506- 514: piias GGifSGlDA lekie PYRD_SALTY : 264- 271: ncqqt GGl-SGrPL qlkst PYRD_SCHPO : 354- 361: hveet GGl-SGpPL kpial PYRD_SCHPO : 386- 394: piigc GGisSGkDA ieyar PYRD_YEAST : 252- 260: kvigt GGikSGkDA fehll I 9: 20.5546 13( 13) P-[FILV]-x(2)-A-[AS]-G-x(4)-[AGT] Occurences: 13(13) PYRD_AGRAE : 56- 67: lqfpn PLgmAAGydknA evpda PYRD_ARATH : 136- 147: rkfsn PIglAAGfdknA eateg PYRD_BACCL : 16- 27: lslkn PImpASGcfgfG reyar PYRD_BACSU : 14- 25: ldlkn PIipASGcfgfG kefsr PYRD_DROME : 98- 109: rmlsn PIgiAAGfdknA eavdg PYRD_ECOLI : 57- 68: ltfkn PLglAAGldkdG ecida PYRD_HAEIN : 59- 70: vnfpn PIglAAGadknG daidg PYRD_HUMAN : 91- 102: hkfrn PVgiAAGfdkhG eavdg PYRD_MYCLE : 14- 25: vrfpg PLglAAGfdkdG mglla PYRD_PLAFA : 220- 231: ldfin PFgvAAGfdknG vcids PYRD_SALTY : 57- 68: ltfkn PLglAAGldkdG ecida PYRD_SCHPO : 117- 128: kkfcn PIglAAGfdkqA daisg PYRD_YEAST : 17- 28: ntyen PFmnASGvhcmT tqeld J 10: 19.6737 13( 13) N-[ADP]-x-P-R-x(2)-[ERS]-x(3)-[ADEGS] Occurences: 13(13) PYRD_AGRAE : 94- 105: rpqsg NPrPRifRlvdD kavin PYRD_ARATH : 174- 185: vpqeg NPkPRifRlsqE gaiin PYRD_BACCL : 55- 66: eprfg NPtPRvaEtpgG mlnai PYRD_BACSU : 53- 64: eprfg NPtPRvaEtgaG mlnai PYRD_DROME : 136- 147: aaqeg NPkPRvfRlteD kaiin PYRD_ECOLI : 95- 106: rpqpg NDkPRlfRlvdA eglin PYRD_HAEIN : 97- 108: vaqdg NAkPRqfRlieA egiin PYRD_HUMAN : 129- 140: kpqeg NPrPRvfRlpeD qavin PYRD_MYCLE : 52- 63: ypqpg NPaPRmfRlpaD ralln PYRD_PLAFA : 258- 269: rgqtg NAkPRifRdveS rsiin PYRD_SALTY : 95- 106: rpqpg NDkPRlfRlvdA eglin PYRD_SCHPO : 155- 166: kpqpg NPkPRyfRlkpD lsvin PYRD_YEAST : 56- 67: lereg NPePRyiSvplG sinsm K 11: 18.9426 13( 13) S-[CS]-P-N-[TV] Occurences: 13(13) PYRD_AGRAE : 172- 176: ftvni SSPNT pglrn PYRD_ARATH : 276- 280: lvinv SSPNT aglrm PYRD_BACCL : 129- 133: lelni SCPNV kkggi PYRD_BACSU : 127- 131: lelni SCPNV ktggi PYRD_DROME : 217- 221: lvinv SSPNT kglrd PYRD_ECOLI : 174- 178: iaini SSPNT pglrt PYRD_HAEIN : 176- 180: itvni SSPNT pdlrq PYRD_HUMAN : 214- 218: lvvnv SSPNT aglrs PYRD_MYCLE : 131- 135: lvvnv SSPNT pglrd PYRD_PLAFA : 344- 348: iainv SSPNT pglrd PYRD_SALTY : 174- 178: iaini SSPNT pglrt PYRD_SCHPO : 266- 270: lvinv SSPNT pglrn PYRD_YEAST : 132- 136: telnl SCPNV pgkpq L 12: 17.2523 27( 13) G-x(1,2)-S-G-x-[ADP]-[ALV] Occurences: 27(13) PYRD_AGRAE : 262- 269: grdet GglSGaPL fdrst PYRD_AGRAE : 263- 269: rdetg Gl-SGaPL fdrst PYRD_ARATH : 367- 374: vatet GglSGkPL falst PYRD_ARATH : 368- 374: atetg Gl-SGkPL falst PYRD_ARATH : 400- 407: ligcg GvsSGeDA ykkir PYRD_BACCL : 213- 220: langt GglSGpAV kpiai PYRD_BACCL : 214- 220: angtg Gl-SGpAV kpiai PYRD_BACSU : 211- 218: lankt GglSGpAV kpvai PYRD_BACSU : 212- 218: anktg Gl-SGpAV kpvai PYRD_DROME : 307- 314: laeet GglSGpPL karst PYRD_DROME : 308- 314: aeetg Gl-SGpPL karst PYRD_DROME : 340- 347: iigvg GvaSGyDA yekie PYRD_ECOLI : 264- 271: ncdqt GglSGrPL qlkst PYRD_ECOLI : 265- 271: cdqtg Gl-SGrPL qlkst PYRD_HAEIN : 266- 273: naeqq GglSGkPL qhkst PYRD_HAEIN : 267- 273: aeqqg Gl-SGkPL qhkst PYRD_HUMAN : 302- 309: lrset GglSGkPL rdlst PYRD_HUMAN : 303- 309: rsetg Gl-SGkPL rdlst PYRD_MYCLE : 213- 220: dalga GgiSGpPV arrav PYRD_MYCLE : 214- 220: algag Gi-SGpPV arrav PYRD_PLAFA : 507- 514: iiasg GifSGlDA lekie PYRD_SALTY : 264- 271: ncqqt GglSGrPL qlkst PYRD_SALTY : 265- 271: cqqtg Gl-SGrPL qlkst PYRD_SCHPO : 354- 361: hveet GglSGpPL kpial PYRD_SCHPO : 355- 361: veetg Gl-SGpPL kpial PYRD_SCHPO : 387- 394: iigcg GisSGkDA ieyar PYRD_YEAST : 253- 260: vigtg GikSGkDA fehll M 13: 17.0628 13( 13) G-N-x(0,2)-P-x(2,3)-R-x(2)-[DEQRS] Occurences: 13(13) PYRD_AGRAE : 93- 101: prpqs GN--Prp-RifR lvddk PYRD_AGRAE : 93- 104: prpqs GNprPrifRlvD dkavi PYRD_ARATH : 173- 181: pvpqe GN--Pkp-RifR lsqeg PYRD_ARATH : 173- 184: pvpqe GNpkPrifRlsQ egaii PYRD_BACCL : 54- 62: keprf GN--Ptp-RvaE tpggm PYRD_BACSU : 52- 60: keprf GN--Ptp-RvaE tgagm PYRD_DROME : 135- 143: paaqe GN--Pkp-RvfR ltedk PYRD_DROME : 135- 146: paaqe GNpkPrvfRltE dkaii PYRD_ECOLI : 94- 105: prpqp GNdkPrlfRlvD aegli PYRD_HAEIN : 96- 107: pvaqd GNakPrqfRliE aegii PYRD_HUMAN : 128- 136: pkpqe GN--Prp-RvfR lpedq PYRD_HUMAN : 128- 139: pkpqe GNprPrvfRlpE dqavi PYRD_MYCLE : 51- 59: aypqp GN--Pap-RmfR lpadr PYRD_PLAFA : 257- 268: prgqt GNakPrifRdvE srsii PYRD_SALTY : 94- 105: prpqp GNdkPrlfRlvD aegli PYRD_SCHPO : 154- 162: pkpqp GN--Pkp-RyfR lkpdl PYRD_YEAST : 55- 63: tlere GN--Pep-RyiS vplgs N 14: 16.6103 16( 13) N-[APST]-x-G-L-x-[ADNTV] Occurences: 16(13) PYRD_AGRAE : 175- 181: nissp NTpGLrN lqard PYRD_ARATH : 135- 141: grkfs NPiGLaA gfdkn PYRD_BACCL : 69- 75: pggml NAiGLqN pgldk PYRD_BACSU : 67- 73: gagml NAiGLqN pglds PYRD_DROME : 220- 226: nvssp NTkGLrD mqske PYRD_ECOLI : 56- 62: gltfk NPlGLaA gldkd PYRD_ECOLI : 177- 183: nissp NTpGLrT lqyge PYRD_HAEIN : 58- 64: gvnfp NPiGLaA gadkn PYRD_HUMAN : 150- 156: nrygf NShGLsV vehrl PYRD_MYCLE : 134- 140: nvssp NTpGLrD lqave PYRD_PLAFA : 347- 353: nvssp NTpGLrD nqeag PYRD_SALTY : 56- 62: gltfk NPlGLaA gldkd PYRD_SALTY : 177- 183: nissp NTpGLrT lqygd PYRD_SCHPO : 116- 122: gkkfc NPiGLaA gfdkq PYRD_SCHPO : 269- 275: nvssp NTpGLrN lqkks PYRD_YEAST : 70- 76: plgsi NSmGLpN egidy O 15: 16.3201 15( 13) A-x(5)-A-G-x(4)-[AENQT]-x(2)-[GNSTV] Occurences: 15(13) PYRD_AGRAE : 43- 58: apndl AlsvkvAGlqfpNplG maagy PYRD_ARATH : 407- 422: ssged AykkirAGatlvQlyT gfayg PYRD_BACCL : 177- 192: divam AkaieqAGadglTmiN tlvgm PYRD_BACSU : 175- 190: nitei AlaieeAGadglTmiN tligm PYRD_BACSU : 249- 264: qtaed AlefllAGasavAvgT anfvn PYRD_DROME : 347- 362: asgyd AyekieAGasyvQiyT alvye PYRD_ECOLI : 304- 319: dsvia ArekiaAGaslvQiyS gfifk PYRD_HAEIN : 306- 321: dglqn AqekieAGaellQvyS gliyh PYRD_HUMAN : 342- 357: ssgqn AlekirAGaslvQlyT alpfw PYRD_MYCLE : 182- 197: ditdl AvelrlAGivatNttV srdcl PYRD_MYCLE : 253- 268: etadd AwdritAGasllQgyT gfiyg PYRD_PLAFA : 514- 529: fsgld AlekieAGasvcQlyS clvfn PYRD_SALTY : 304- 319: dsvia ArekiaAGatlvQiyS gfifk PYRD_SCHPO : 394- 409: ssgkd AieyarAGatmvQvyT algyd PYRD_YEAST : 98- 113: ypdap AiffsvAGmsidEnlN llrki P 16: 15.6802 13( 13) N-x(2)-G-x(1,2)-N-x(1,2)-G Occurences: 13(13) PYRD_AGRAE : 110- 118: dkavi NrlGfnNe-G hdaaf PYRD_AGRAE : 110- 118: dkavi NrlGf-NneG hdaaf PYRD_ARATH : 190- 198: egaii NrcGf-NseG ivvva PYRD_BACCL : 69- 77: pggml NaiGlqNp-G ldkvl PYRD_BACSU : 67- 75: gagml NaiGlqNp-G ldsvl PYRD_DROME : 152- 160: dkaii NryGf-NsdG hqavl PYRD_ECOLI : 111- 119: aegli NrmGfnNl-G vdnlv PYRD_ECOLI : 111- 119: aegli NrmGf-NnlG vdnlv PYRD_HAEIN : 113- 121: aegii NrnGfnNn-G idyli PYRD_HAEIN : 113- 121: aegii NrnGf-NnnG idyli PYRD_HUMAN : 145- 153: dqavi NryGf-NshG lsvve PYRD_MYCLE : 68- 76: drall NrmGfnNn-G agala PYRD_MYCLE : 68- 76: drall NrmGf-NnnG agala PYRD_PLAFA : 274- 282: srsii NscGfnNm-G cdkvt PYRD_PLAFA : 274- 282: srsii NscGf-NnmG cdkvt PYRD_SALTY : 111- 119: aegli NrmGfnNl-G vdnlv PYRD_SALTY : 111- 119: aegli NrmGf-NnlG vdnlv PYRD_SCHPO : 171- 179: dlsvi NryGf-NsiG hdail PYRD_YEAST : 70- 78: plgsi NsmGlpNe-G idyyl Q 17: 12.5102 18( 13) A-G-A Occurences: 18(13) PYRD_AGRAE : 308- 310: ltkvk AGA rsrpa PYRD_ARATH : 413- 415: ykkir AGA tlvql PYRD_BACCL : 183- 185: kaieq AGA dgltm PYRD_BACCL : 257- 259: leffy AGA savav PYRD_BACSU : 181- 183: laiee AGA dgltm PYRD_BACSU : 255- 257: lefll AGA savav PYRD_DROME : 353- 355: yekie AGA syvqi PYRD_DROME : 377- 379: vedik AGA vgadh PYRD_ECOLI : 310- 312: rekia AGA slvqi PYRD_HAEIN : 64- 66: pigla AGA dkngd PYRD_HAEIN : 312- 314: qekie AGA ellqv PYRD_HUMAN : 348- 350: lekir AGA slvql PYRD_MYCLE : 77- 79: fnnng AGA laiql PYRD_MYCLE : 259- 261: wdrit AGA sllqg PYRD_PLAFA : 520- 522: lekie AGA svcql PYRD_SALTY : 310- 312: rekia AGA tlvqi PYRD_SCHPO : 400- 402: ieyar AGA tmvqv PYRD_YEAST : 40- 42: lansk AGA fitks R 18: 12.0102 19( 13) G-G-x(1,2)-S Occurences: 19(13) PYRD_AGRAE : 262- 265: grdet GGl-S gaplf PYRD_ARATH : 232- 235: ddvkp GGk-S gpgil PYRD_ARATH : 367- 370: vatet GGl-S gkplf PYRD_ARATH : 399- 403: pligc GGvsS geday PYRD_BACCL : 213- 216: langt GGl-S gpavk PYRD_BACSU : 211- 214: lankt GGl-S gpavk PYRD_DROME : 307- 310: laeet GGl-S gpplk PYRD_DROME : 339- 343: piigv GGvaS gyday PYRD_ECOLI : 264- 267: ncdqt GGl-S grplq PYRD_HAEIN : 266- 269: naeqq GGl-S gkplq PYRD_HUMAN : 302- 305: lrset GGl-S gkplr PYRD_HUMAN : 334- 338: piigv GGvsS gqnal PYRD_MYCLE : 213- 216: dalga GGi-S gppva PYRD_PLAFA : 474- 477: fenkk GGv-S gaklk PYRD_PLAFA : 506- 510: piias GGifS gldal PYRD_SALTY : 264- 267: ncqqt GGl-S grplq PYRD_SCHPO : 354- 357: hveet GGl-S gpplk PYRD_SCHPO : 386- 390: piigc GGisS gkdai PYRD_YEAST : 252- 256: kvigt GGikS gkdaf S 19: 12.0102 18( 13) G-I-x(1,2)-G Occurences: 18(13) PYRD_AGRAE : 134- 137: ragks GIv-G vniga PYRD_ARATH : 238- 241: gksgp GIl-G vnlgk PYRD_BACCL : 137- 141: nvkkg GIafG tvpdv PYRD_BACSU : 135- 139: nvktg GIafG tnpem PYRD_DROME : 100- 104: lsnpi GIaaG fdkna PYRD_ECOLI : 137- 141: ydgvl GIniG knkdt PYRD_HAEIN : 139- 143: ykgvi GIniG knkft PYRD_HAEIN : 299- 302: iigsg GId-G lqnaq PYRD_HUMAN : 93- 97: frnpv GIaaG fdkhg PYRD_HUMAN : 276- 279: vvkel GId-G livtn PYRD_MYCLE : 214- 217: algag GIs-G ppvar PYRD_PLAFA : 507- 511: iiasg GIfsG ldale PYRD_SALTY : 134- 137: kahfd GIl-G inigk PYRD_SALTY : 137- 141: fdgil GIniG knkdt PYRD_SCHPO : 232- 236: pnkfl GInlG knkng PYRD_SCHPO : 387- 391: iigcg GIssG kdaie PYRD_YEAST : 221- 224: kngfg GIg-G eyvkp PYRD_YEAST : 253- 257: vigtg GIksG kdafe T 20: 12.0102 33( 13) G-x(1,2)-S-G Occurences: 33(13) PYRD_AGRAE : 131- 134: lsqra Gk-SG ivgvn PYRD_AGRAE : 262- 266: grdet GglSG aplfd PYRD_AGRAE : 263- 266: rdetg Gl-SG aplfd PYRD_ARATH : 232- 236: ddvkp GgkSG pgilg PYRD_ARATH : 233- 236: dvkpg Gk-SG pgilg PYRD_ARATH : 367- 371: vatet GglSG kplfa PYRD_ARATH : 368- 371: atetg Gl-SG kplfa PYRD_ARATH : 400- 404: ligcg GvsSG edayk PYRD_BACCL : 213- 217: langt GglSG pavkp PYRD_BACCL : 214- 217: angtg Gl-SG pavkp PYRD_BACSU : 211- 215: lankt GglSG pavkp PYRD_BACSU : 212- 215: anktg Gl-SG pavkp PYRD_DROME : 307- 311: laeet GglSG pplka PYRD_DROME : 308- 311: aeetg Gl-SG pplka PYRD_DROME : 340- 344: iigvg GvaSG ydaye PYRD_ECOLI : 264- 268: ncdqt GglSG rplql PYRD_ECOLI : 265- 268: cdqtg Gl-SG rplql PYRD_HAEIN : 266- 270: naeqq GglSG kplqh PYRD_HAEIN : 267- 270: aeqqg Gl-SG kplqh PYRD_HUMAN : 302- 306: lrset GglSG kplrd PYRD_HUMAN : 303- 306: rsetg Gl-SG kplrd PYRD_HUMAN : 335- 339: iigvg GvsSG qnale PYRD_MYCLE : 213- 217: dalga GgiSG ppvar PYRD_MYCLE : 214- 217: algag Gi-SG ppvar PYRD_PLAFA : 474- 478: fenkk GgvSG aklkd PYRD_PLAFA : 475- 478: enkkg Gv-SG aklkd PYRD_PLAFA : 507- 511: iiasg GifSG ldale PYRD_SALTY : 264- 268: ncqqt GglSG rplql PYRD_SALTY : 265- 268: cqqtg Gl-SG rplql PYRD_SCHPO : 354- 358: hveet GglSG pplkp PYRD_SCHPO : 355- 358: veetg Gl-SG pplkp PYRD_SCHPO : 387- 391: iigcg GisSG kdaie PYRD_YEAST : 253- 257: vigtg GikSG kdafe Number of patterns evaluated by Pratt:4560 Total running time: 5 seconds