------------------------------------------------------------ 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 9 sequences from file DHPS_1 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 9 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 DHPS_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: DHP1_ECOLI 279 DHP2_ECOLI 271 DHPS_BACSU 285 DHPS_CLOAB 205 DHPS_ECOLI 282 DHPS_HAEIN 275 DHPS_MYCLE 291 DHPS_STRPN 316 FAS_PNECA 740 Pratt run started at Thu Feb 6 19:18:14 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 29.1904 9( 9) I-x-N-x-T-x-D-S-F-x-D 2: 25.0203 9( 9) N-x-T-x-D-S-F-x-D 3: 20.8503 9( 9) T-x-D-S-F-x-D 4: 16.6802 9( 9) G-x(4)-D-x-G-x(5)-P 5: 16.6802 9( 9) D-S-F-x-D 6: 15.6802 11( 9) I-x(0,1)-N-x(3)-D-x(3,4)-D 7: 15.6802 10( 9) I-x(5)-D-x(0,1)-F-x(0,1)-D 8: 15.6802 9( 9) D-x(0,1)-G-x(0,1)-G-x(4)-P 9: 15.6802 10( 9) I-x-N-x(2,3)-D-x(2,3)-D 10: 15.1802 10( 9) N-x(3)-D-x(1,3)-F-x(1,2)-D 11: 15.1802 12( 9) A-x(2,3)-I-x(0,2)-D-x-G 12: 12.5102 11( 9) N-x(3)-D-x(3)-D 13: 12.5102 9( 9) G-x(4)-N-D 14: 12.5102 13( 9) A-x(3)-G-A 15: 12.5102 10( 9) E-x(2)-R-x(2)-P 16: 12.5102 9( 9) S-F-x-D 17: 12.0102 15( 9) D-x-G-x(0,1)-G 18: 12.0102 15( 9) A-x(2,3)-G-x(4)-N 19: 12.0102 12( 9) N-x(3)-D-x(3,4)-D 20: 12.0102 12( 9) A-G-x(0,1)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 37.6362 9( 9) I-[ILV]-N-x-T-[EPS]-D-S-F-x-D-x-[GS] B 2: 36.4835 9( 9) G-[AS]-x-[IMV]-[ILV]-D-[ILV]-G-[GP]-x(2)-[AST]-x-P-[DGN] C 3: 32.4662 9( 9) I-[ILV]-N-x-T-[EPS]-D-x(0,1)-F-x(0,1)-D-x-[GS] D 4: 30.8043 9( 9) N-x-T-[EPS]-D-S-F-x-D-x-[GS] E 5: 28.6812 9( 9) E-[ILM]-x-R-[ILV]-[AIV]-P-x-[ILV]-[DEK]-x-[ILV] F 6: 26.6343 9( 9) T-[EPS]-D-S-F-x-D-x-[GS] G 7: 26.6343 9( 9) N-x-T-[EPS]-D-x-F-x-D-x-[GS] H 8: 26.1343 10( 9) I-x(0,1)-N-x-T-[EPS]-D-x(3)-D-x-[GS] I 9: 25.2202 9( 9) A-[AILV]-x(2)-G-A-x(2)-[ILV]-[DNR]-[DTV]-x(2)-[GPV] J 10: 24.0801 10( 9) A-x(2,3)-G-x(3)-[ILV]-N-D-x(2)-[AGS]-x(3)-[ADP] K 11: 22.4642 9( 9) N-x-T-[EPS]-D-x(3)-D-x-[GS] L 12: 21.5226 9( 9) I-[ILV]-N-x(2,3)-D-x(2,3)-D-x-[GS] M 13: 20.4101 9( 9) G-x(3)-[ILV]-N-D-x(2)-[AGS]-x(3)-[ADP] N 14: 19.9180 9( 9) D-[IPV]-G-x(0,1)-G-x(4)-[ALP]-[AGN] O 15: 19.8607 9( 9) D-S-F-x-D-x-[GS] P 16: 17.9347 9( 9) D-x(0,1)-G-x(0,1)-G-x(4)-P-[ADGN] Q 17: 17.4160 11( 9) A-x(2,3)-I-x(0,2)-D-[ILPV]-G R 18: 15.6907 9( 9) S-F-x-D-x-[GS] S 19: 14.6756 10( 9) A-G-x(0,1)-A-x(2)-[AIV] T 20: 12.5102 11( 9) N-x(3)-D-x(3)-D Best patterns with alignements: fitness hits(seqs) Pattern A 1: 37.6362 9( 9) I-[ILV]-N-x-T-[EPS]-D-S-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 7- 19: vtvfg ILNlTEDSFfDeS rrldp DHP2_ECOLI : 10- 22: liifg IVNiTSDSFsDgG rylap DHPS_BACSU : 30- 42: tlvmg ILNvTPDSFsDgG kydsl DHPS_CLOAB : 19- 31: tyimg ILNfTPDSFsDgG kfndi DHPS_ECOLI : 20- 32: phvmg ILNvTPDSFsDgG thnsl DHPS_HAEIN : 20- 32: pqimg ILNfTPDSFsDsG qffsl DHPS_MYCLE : 20- 32: qlima IVNrTPDSFyDrG atfsd DHPS_STRPN : 15- 27: tvicg IINvTPDSFsDgG qffal FAS_PNECA : 476- 488: tyima ILNlTPDSFfDgG ihsyd B 2: 36.4835 9( 9) G-[AS]-x-[IMV]-[ILV]-D-[ILV]-G-[GP]-x(2)-[AST]-x-P-[DGN] Occurences: 9(9) DHP1_ECOLI : 38- 52: emlrv GSdVVDVGPaaShPD arpvs DHP2_ECOLI : 41- 55: klmae GAdVIDLGPasSnPD aapvs DHPS_BACSU : 61- 75: emidd GAhIIDIGGesTrPG aecvs DHPS_CLOAB : 50- 64: emidn GAdIIDVGGesTrPG yeivs DHPS_ECOLI : 51- 65: lmina GAtIIDVGGesTrPG aaevs DHPS_HAEIN : 51- 65: kmlee GAtIIDIGGesTrPN adevs DHPS_MYCLE : 51- 65: ravae GAdVIDVGGvkAgPG qgvdv DHPS_STRPN : 46- 60: kliae GAsMLDIGGesTrPG ssyve FAS_PNECA : 506- 520: kfina GAtIIDIGGqsTrPG syiip C 3: 32.4662 9( 9) I-[ILV]-N-x-T-[EPS]-D-x(0,1)-F-x(0,1)-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 7- 19: vtvfg ILNlTEDsFfDeS rrldp DHP2_ECOLI : 10- 22: liifg IVNiTSDsFsDgG rylap DHPS_BACSU : 30- 42: tlvmg ILNvTPDsFsDgG kydsl DHPS_CLOAB : 19- 31: tyimg ILNfTPDsFsDgG kfndi DHPS_ECOLI : 20- 32: phvmg ILNvTPDsFsDgG thnsl DHPS_HAEIN : 20- 32: pqimg ILNfTPDsFsDsG qffsl DHPS_MYCLE : 20- 32: qlima IVNrTPDsFyDrG atfsd DHPS_STRPN : 15- 27: tvicg IINvTPDsFsDgG qffal FAS_PNECA : 476- 488: tyima ILNlTPDsFfDgG ihsyd D 4: 30.8043 9( 9) N-x-T-[EPS]-D-S-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 9- 19: vfgil NlTEDSFfDeS rrldp DHP2_ECOLI : 12- 22: ifgiv NiTSDSFsDgG rylap DHPS_BACSU : 32- 42: vmgil NvTPDSFsDgG kydsl DHPS_CLOAB : 21- 31: imgil NfTPDSFsDgG kfndi DHPS_ECOLI : 22- 32: vmgil NvTPDSFsDgG thnsl DHPS_HAEIN : 22- 32: imgil NfTPDSFsDsG qffsl DHPS_MYCLE : 22- 32: imaiv NrTPDSFyDrG atfsd DHPS_STRPN : 17- 27: icgii NvTPDSFsDgG qffal FAS_PNECA : 478- 488: imail NlTPDSFfDgG ihsyd E 5: 28.6812 9( 9) E-[ILM]-x-R-[ILV]-[AIV]-P-x-[ILV]-[DEK]-x-[ILV] Occurences: 9(9) DHP1_ECOLI : 61- 72: vspad EIrRIAPlLDaL sdqmh DHP2_ECOLI : 64- 75: vssdt EIaRIAPvLDaL kadgi DHPS_BACSU : 84- 95: vsede EMsRVIPvIErI tkelg DHPS_CLOAB : 73- 84: vseee EIsRVVPiIKaI kedfd DHPS_ECOLI : 74- 85: vsvee ELqRVIPvVEaI aqrfe DHPS_HAEIN : 74- 85: vseqe ELhRVVPvVEaV rnrfd DHPS_MYCLE : 73- 84: vdvdt EIaRLVPfIEwL rsayt DHPS_STRPN : 71- 82: ieiee EIqRVVPvIKaI rkesd FAS_PNECA : 529- 540: iplee EIfRVIPaIKyL qktyp F 6: 26.6343 9( 9) T-[EPS]-D-S-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 11- 19: gilnl TEDSFfDeS rrldp DHP2_ECOLI : 14- 22: givni TSDSFsDgG rylap DHPS_BACSU : 34- 42: gilnv TPDSFsDgG kydsl DHPS_CLOAB : 23- 31: gilnf TPDSFsDgG kfndi DHPS_ECOLI : 24- 32: gilnv TPDSFsDgG thnsl DHPS_HAEIN : 24- 32: gilnf TPDSFsDsG qffsl DHPS_MYCLE : 24- 32: aivnr TPDSFyDrG atfsd DHPS_STRPN : 19- 27: giinv TPDSFsDgG qffal FAS_PNECA : 480- 488: ailnl TPDSFfDgG ihsyd G 7: 26.6343 9( 9) N-x-T-[EPS]-D-x-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 9- 19: vfgil NlTEDsFfDeS rrldp DHP2_ECOLI : 12- 22: ifgiv NiTSDsFsDgG rylap DHPS_BACSU : 32- 42: vmgil NvTPDsFsDgG kydsl DHPS_CLOAB : 21- 31: imgil NfTPDsFsDgG kfndi DHPS_ECOLI : 22- 32: vmgil NvTPDsFsDgG thnsl DHPS_HAEIN : 22- 32: imgil NfTPDsFsDsG qffsl DHPS_MYCLE : 22- 32: imaiv NrTPDsFyDrG atfsd DHPS_STRPN : 17- 27: icgii NvTPDsFsDgG qffal FAS_PNECA : 478- 488: imail NlTPDsFfDgG ihsyd H 8: 26.1343 10( 9) I-x(0,1)-N-x-T-[EPS]-D-x(3)-D-x-[GS] Occurences: 10(9) DHP1_ECOLI : 7- 19: vtvfg IlNlTEDsffDeS rrldp DHP2_ECOLI : 10- 22: liifg IvNiTSDsfsDgG rylap DHPS_BACSU : 30- 42: tlvmg IlNvTPDsfsDgG kydsl DHPS_CLOAB : 19- 31: tyimg IlNfTPDsfsDgG kfndi DHPS_ECOLI : 20- 32: phvmg IlNvTPDsfsDgG thnsl DHPS_HAEIN : 20- 32: pqimg IlNfTPDsfsDsG qffsl DHPS_MYCLE : 20- 32: qlima IvNrTPDsfyDrG atfsd DHPS_STRPN : 15- 27: tvicg IiNvTPDsfsDgG qffal DHPS_STRPN : 16- 27: vicgi I-NvTPDsfsDgG qffal FAS_PNECA : 476- 488: tyima IlNlTPDsffDgG ihsyd I 9: 25.2202 9( 9) A-[AILV]-x(2)-G-A-x(2)-[ILV]-[DNR]-[DTV]-x(2)-[GPV] Occurences: 9(9) DHP1_ECOLI : 237- 250: aaelh AIgnGAdyVRThaP gdlrs DHP2_ECOLI : 238- 251: aaela AAagGAdfIRTheP rplrd DHPS_BACSU : 116- 129: svade AVkaGAsiINDiwG akhdp DHPS_CLOAB : 105- 118: kvaeq AIeaGAnlINDiwG fkkdk DHPS_ECOLI : 246- 259: acavi AAmqGAhiIRVhdV ketve DHPS_HAEIN : 246- 259: agali AVqkGAkiLRVhdV aatsd DHPS_MYCLE : 47- 60: aaahr AVaeGAdvIDVggV kagpg DHPS_STRPN : 103- 116: qvaea ALaaGAdlVNDitG lmgde FAS_PNECA : 562- 575: evaeq AVkaGAslVNDisG grydp J 10: 24.0801 10( 9) A-x(2,3)-G-x(3)-[ILV]-N-D-x(2)-[AGS]-x(3)-[ADP] Occurences: 10(9) DHP1_ECOLI : 92- 109: etqry AlkrGvgyLNDiqGfpdP alypd DHP2_ECOLI : 95- 112: atqay AlsrGvayLNDirGfpdA afypq DHPS_BACSU : 116- 133: svade AvkaGasiINDiwGakhD pkmas DHPS_CLOAB : 105- 122: kvaeq AieaGanlINDiwGfkkD kdmak DHPS_ECOLI : 107- 123: vires Akv-GahiINDirSlseP galea DHPS_HAEIN : 106- 123: vvmre AanvGmdlINDirAlqeP nalet DHPS_HAEIN : 107- 123: vmrea Anv-GmdlINDirAlqeP nalet DHPS_MYCLE : 106- 123: evarl ActaGadlINDswGgadP amhev DHPS_STRPN : 103- 120: qvaea AlaaGadlVNDitGlmgD ekmph FAS_PNECA : 562- 579: evaeq AvkaGaslVNDisGgryD pkmfn K 11: 22.4642 9( 9) N-x-T-[EPS]-D-x(3)-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 9- 19: vfgil NlTEDsffDeS rrldp DHP2_ECOLI : 12- 22: ifgiv NiTSDsfsDgG rylap DHPS_BACSU : 32- 42: vmgil NvTPDsfsDgG kydsl DHPS_CLOAB : 21- 31: imgil NfTPDsfsDgG kfndi DHPS_ECOLI : 22- 32: vmgil NvTPDsfsDgG thnsl DHPS_HAEIN : 22- 32: imgil NfTPDsfsDsG qffsl DHPS_MYCLE : 22- 32: imaiv NrTPDsfyDrG atfsd DHPS_STRPN : 17- 27: icgii NvTPDsfsDgG qffal FAS_PNECA : 478- 488: imail NlTPDsffDgG ihsyd L 12: 21.5226 9( 9) I-[ILV]-N-x(2,3)-D-x(2,3)-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 7- 19: vtvfg ILNlteDsffDeS rrldp DHP2_ECOLI : 10- 22: liifg IVNitsDsfsDgG rylap DHPS_BACSU : 30- 42: tlvmg ILNvtpDsfsDgG kydsl DHPS_CLOAB : 19- 31: tyimg ILNftpDsfsDgG kfndi DHPS_ECOLI : 20- 32: phvmg ILNvtpDsfsDgG thnsl DHPS_HAEIN : 20- 32: pqimg ILNftpDsfsDsG qffsl DHPS_MYCLE : 20- 32: qlima IVNrtpDsfyDrG atfsd DHPS_STRPN : 15- 27: tvicg IINvtpDsfsDgG qffal FAS_PNECA : 476- 488: tyima ILNltpDsffDgG ihsyd M 13: 20.4101 9( 9) G-x(3)-[ILV]-N-D-x(2)-[AGS]-x(3)-[ADP] Occurences: 9(9) DHP1_ECOLI : 96- 109: yalkr GvgyLNDiqGfpdP alypd DHP2_ECOLI : 99- 112: yalsr GvayLNDirGfpdA afypq DHPS_BACSU : 120- 133: eavka GasiINDiwGakhD pkmas DHPS_CLOAB : 109- 122: qaiea GanlINDiwGfkkD kdmak DHPS_ECOLI : 110- 123: esakv GahiINDirSlseP galea DHPS_HAEIN : 110- 123: eaanv GmdlINDirAlqeP nalet DHPS_MYCLE : 110- 123: lacta GadlINDswGgadP amhev DHPS_STRPN : 107- 120: aalaa GadlVNDitGlmgD ekmph FAS_PNECA : 566- 579: qavka GaslVNDisGgryD pkmfn N 14: 19.9180 9( 9) D-[IPV]-G-x(0,1)-G-x(4)-[ALP]-[AGN] Occurences: 9(9) DHP1_ECOLI : 173- 183: drlil DPGmGfflsPA petsl DHP2_ECOLI : 174- 184: nrlvl DPGmGfflgAA petsl DHPS_BACSU : 66- 75: gahii DIG-GestrPG aecvs DHPS_CLOAB : 55- 64: gadii DVG-GestrPG yeivs DHPS_ECOLI : 56- 65: gatii DVG-GestrPG aaevs DHPS_HAEIN : 56- 65: gatii DIG-GestrPN adevs DHPS_MYCLE : 56- 65: gadvi DVG-GvkagPG qgvdv DHPS_STRPN : 51- 60: gasml DIG-GestrPG ssyve FAS_PNECA : 511- 520: gatii DIG-GqstrPG syiip O 15: 19.8607 9( 9) D-S-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 13- 19: lnlte DSFfDeS rrldp DHP2_ECOLI : 16- 22: vnits DSFsDgG rylap DHPS_BACSU : 36- 42: lnvtp DSFsDgG kydsl DHPS_CLOAB : 25- 31: lnftp DSFsDgG kfndi DHPS_ECOLI : 26- 32: lnvtp DSFsDgG thnsl DHPS_HAEIN : 26- 32: lnftp DSFsDsG qffsl DHPS_MYCLE : 26- 32: vnrtp DSFyDrG atfsd DHPS_STRPN : 21- 27: invtp DSFsDgG qffal FAS_PNECA : 482- 488: lnltp DSFfDgG ihsyd P 16: 17.9347 9( 9) D-x(0,1)-G-x(0,1)-G-x(4)-P-[ADGN] Occurences: 9(9) DHP1_ECOLI : 173- 183: drlil DpGmGfflsPA petsl DHP2_ECOLI : 20- 28: sdsfs D-G-GrylaPD aaiaq DHPS_BACSU : 66- 75: gahii DiG-GestrPG aecvs DHPS_CLOAB : 55- 64: gadii DvG-GestrPG yeivs DHPS_ECOLI : 56- 65: gatii DvG-GestrPG aaevs DHPS_HAEIN : 56- 65: gatii DiG-GestrPN adevs DHPS_MYCLE : 56- 65: gadvi DvG-GvkagPG qgvdv DHPS_STRPN : 51- 60: gasml DiG-GestrPG ssyve FAS_PNECA : 511- 520: gatii DiG-GqstrPG syiip Q 17: 17.4160 11( 9) A-x(2,3)-I-x(0,2)-D-[ILPV]-G Occurences: 11(9) DHP1_ECOLI : 167- 175: rsgva AdrlIl-DPG mgffl DHP2_ECOLI : 42- 48: lmaeg Adv-I--DLG passn DHPS_BACSU : 62- 68: middg Ahi-I--DIG gestr DHPS_CLOAB : 51- 57: midng Adi-I--DVG gestr DHPS_ECOLI : 50- 58: nlmin AgatIi-DVG gestr DHPS_ECOLI : 52- 58: minag Ati-I--DVG gestr DHPS_HAEIN : 52- 58: mleeg Ati-I--DIG gestr DHPS_MYCLE : 52- 58: avaeg Adv-I--DVG gvkag DHPS_STRPN : 196- 205: aeagi ApenIllDPG igfgl FAS_PNECA : 505- 513: ekfin AgatIi-DIG gqstr FAS_PNECA : 507- 513: finag Ati-I--DIG gqstr R 18: 15.6907 9( 9) S-F-x-D-x-[GS] Occurences: 9(9) DHP1_ECOLI : 14- 19: nlted SFfDeS rrldp DHP2_ECOLI : 17- 22: nitsd SFsDgG rylap DHPS_BACSU : 37- 42: nvtpd SFsDgG kydsl DHPS_CLOAB : 26- 31: nftpd SFsDgG kfndi DHPS_ECOLI : 27- 32: nvtpd SFsDgG thnsl DHPS_HAEIN : 27- 32: nftpd SFsDsG qffsl DHPS_MYCLE : 27- 32: nrtpd SFyDrG atfsd DHPS_STRPN : 22- 27: nvtpd SFsDgG qffal FAS_PNECA : 483- 488: nltpd SFfDgG ihsyd S 19: 14.6756 10( 9) A-G-x(0,1)-A-x(2)-[AIV] Occurences: 10(9) DHP1_ECOLI : 25- 30: rrldp AG-AvtA aieml DHP2_ECOLI : 240- 246: elaaa AGgAdfI rthep DHPS_BACSU : 119- 124: deavk AG-AsiI ndiwg DHPS_CLOAB : 108- 113: eqaie AG-AnlI ndiwg DHPS_ECOLI : 50- 55: nlmin AG-AtiI dvgge DHPS_HAEIN : 241- 246: iigsa AG-AliA vqkga DHPS_MYCLE : 109- 114: rlact AG-AdlI ndswg DHPS_STRPN : 106- 111: eaala AG-AdlV nditg FAS_PNECA : 505- 510: ekfin AG-AtiI diggq FAS_PNECA : 565- 570: eqavk AG-AslV ndisg T 20: 12.5102 11( 9) N-x(3)-D-x(3)-D Occurences: 11(9) DHP1_ECOLI : 9- 17: vfgil NlteDsffD esrrl DHP2_ECOLI : 12- 20: ifgiv NitsDsfsD ggryl DHPS_BACSU : 32- 40: vmgil NvtpDsfsD ggkyd DHPS_CLOAB : 21- 29: imgil NftpDsfsD ggkfn DHPS_CLOAB : 149- 157: nteyk NlmeDilnD lkeci DHPS_ECOLI : 22- 30: vmgil NvtpDsfsD ggthn DHPS_HAEIN : 22- 30: imgil NftpDsfsD sgqff DHPS_HAEIN : 108- 116: mreaa NvgmDlinD iralq DHPS_MYCLE : 22- 30: imaiv NrtpDsfyD rgatf DHPS_STRPN : 17- 25: icgii NvtpDsfsD ggqff FAS_PNECA : 478- 486: imail NltpDsffD ggihs Number of patterns evaluated by Pratt:2329 Total running time: 2 seconds