------------------------------------------------------------ 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 22 sequences from file CALRETICULIN_REPEAT PATTERN CONSERVATION: CM: min Nr of Seqs to Match 22 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 CALRETICULIN_REPEAT.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: CALX_ARATH 530 CALX_CAEEL 619 CALX_CANFA 593 CALX_HUMAN 592 CALX_MOUSE 591 CALX_RAT 591 CALX_SCHPO 560 CALX_YEAST 502 CRTC_BOVIN 13 CRTC_CAEEL 395 CRTC_CANFA 24 CRTC_DROME 406 CRTC_HUMAN 417 CRTC_MOUSE 416 CRTC_PIG 15 CRTC_RABIT 418 CRTC_RANES 13 CRTC_RAT 416 CRTC_SCHMA 393 CRTC_SPIOL 20 CRTD_BOVIN 421 RAL1_ONCVO 388 Pratt run started at Thu Feb 6 19:04:00 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.8401 58( 22) F-x(2,3)-G 2: 7.8401 53( 22) K-x(2,3)-F 3: 7.8401 56( 22) F-x(2,3)-F Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.8401 58( 22) F-x(2,3)-G B 2: 7.8401 53( 22) K-x(2,3)-F C 3: 7.8401 56( 22) F-x(2,3)-F Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.8401 58( 22) F-x(2,3)-G Occurences: 58(22) CALX_ARATH : 102- 105: qyevr Fqe-G lecgg CALX_CAEEL : 65- 68: nffdy Fpv-G skigl CALX_CAEEL : 146- 149: qydik Fee-G qecgg CALX_CAEEL : 499- 502: vaigv Fcf-G kqskp CALX_CANFA : 76- 79: yfads Fdr-G tlsgw CALX_CANFA : 155- 158: qyevn Fqn-G iecgg CALX_CANFA : 420- 424: fkmtp FsaiG lelws CALX_CANFA : 439- 443: iffdn FivcG drrvv CALX_CANFA : 502- 506: flvil FccsG kkqss CALX_HUMAN : 75- 78: yfads Fdr-G tlsgw CALX_HUMAN : 154- 157: qyevn Fqn-G iecgg CALX_HUMAN : 419- 423: frmtp FsaiG lelws CALX_HUMAN : 501- 505: flvil FccsG kkqts CALX_MOUSE : 76- 79: yfads Fdr-G slsgw CALX_MOUSE : 155- 158: qyevn Fqn-G iecgg CALX_MOUSE : 420- 424: fkmtp FsaiG lelws CALX_MOUSE : 439- 443: iffdn FiisG drrvv CALX_MOUSE : 502- 506: flvil FccsG kkqsn CALX_RAT : 76- 79: yfads Fdr-G slsgw CALX_RAT : 155- 158: qyevn Fqn-G iecgg CALX_RAT : 420- 424: frmtp FsaiG lelws CALX_RAT : 439- 443: iffdn FiisG drrvv CALX_RAT : 502- 506: flvil FccsG kkqsn CALX_SCHPO : 62- 65: shakr Fvn-G ieems CALX_YEAST : 399- 402: gvile Fws-G spnml CRTC_BOVIN : 10- 13: yfkeq Fld-G CRTC_CAEEL : 80- 84: kfdkd FsnkG ktlvi CRTC_CANFA : 10- 13: yfkeq Fld-G xgftd CRTC_DROME : 148- 152: kvhvi FsykG knhli CRTC_HUMAN : 27- 30: yfkeq Fld-G dgwts CRTC_HUMAN : 84- 88: asfep FsnkG qtlvv CRTC_HUMAN : 148- 152: kvhvi FnykG knvli CRTC_HUMAN : 311- 315: yaydn FgvlG ldlwq CRTC_MOUSE : 27- 30: yfkeq Fld-G dawtn CRTC_MOUSE : 84- 88: akfep FsnkG qtlvv CRTC_MOUSE : 113- 116: gyvkl Fps-G ldqkd CRTC_MOUSE : 148- 152: kvhvi FnykG knvli CRTC_MOUSE : 311- 315: yayds FavlG ldlwq CRTC_PIG : 10- 13: yfkeq Fld-G dg CRTC_RABIT : 27- 30: yfkeq Fld-G dgwte CRTC_RABIT : 84- 88: arfep FsnkG qplvv CRTC_RABIT : 113- 116: gyvkl Fpa-G ldqkd CRTC_RABIT : 148- 152: kvhvi FnykG knvli CRTC_RABIT : 311- 315: yayds FavlG ldlwq CRTC_RANES : 10- 13: ffkxx Fxx-G CRTC_RAT : 27- 30: yfkeq Fld-G dawtn CRTC_RAT : 84- 88: arfep FsnkG qtlvv CRTC_RAT : 113- 116: gyvkl Fpg-G ldqkd CRTC_RAT : 148- 152: kvhvi FnykG knvli CRTC_RAT : 311- 315: yayds FavlG ldlwq CRTC_SCHMA : 82- 86: kisep FsnrG ktmvl CRTC_SCHMA : 146- 150: kvhvi FnykG knhsi CRTC_SPIOL : 8- 11: ffeer Fed-G wenrw CRTD_BOVIN : 117- 120: gyvnv Fpa-G ldqtd CRTD_BOVIN : 152- 156: kvhvi FnykG knvli CRTD_BOVIN : 315- 319: yayen FavlG ldlwq RAL1_ONCVO : 71- 75: tqdak FysiG akfdk RAL1_ONCVO : 82- 86: kfdks FsnkG kslvi B 2: 7.8401 53( 22) K-x(2,3)-F Occurences: 53(22) CALX_ARATH : 148- 151: cggtn Kvh-F ilkhk CALX_ARATH : 402- 405: rqttw Kpk-F dveke CALX_ARATH : 430- 433: lksyq Kvv-F dllnk CALX_ARATH : 483- 486: fslfl Kli-F ggkka CALX_CAEEL : 40- 43: kgsdd Kee-F vpslf CALX_CAEEL : 266- 269: altpp Kqi-F detdl CALX_CAEEL : 444- 447: ssdva Kqt-F yvkqk CALX_CANFA : 138- 142: sakln KpflF dtkpl CALX_CANFA : 200- 203: cgedy Klh-F ifrhk CALX_CANFA : 228- 231: pdadl Kty-F tdkkt CALX_CANFA : 416- 420: dlepf KmtpF saigl CALX_HUMAN : 137- 141: sakln KpflF dtkpl CALX_HUMAN : 199- 202: cgedy Klh-F ifrhk CALX_HUMAN : 227- 230: pdadl Kty-F tdkkt CALX_MOUSE : 138- 142: sakln KpflF dtkpl CALX_MOUSE : 200- 203: cgedy Klh-F ifrhk CALX_MOUSE : 228- 231: pdadl Kty-F tdkkt CALX_MOUSE : 416- 420: dlepf KmtpF saigl CALX_RAT : 138- 142: sakln KpflF dtkpl CALX_RAT : 200- 203: cgedy Klh-F ifrhk CALX_RAT : 228- 231: pdadl Kty-F tdkkt CALX_SCHPO : 5- 8: mkyg Kvs-F lallc CALX_YEAST : 234- 238: hiedk KkvnF eppit CALX_YEAST : 235- 238: iedkk Kvn-F eppit CRTC_BOVIN : 7- 10: paiyf Keq-F ldg CRTC_CAEEL : 20- 23: aevyf Kee-F ndasw CRTC_CAEEL : 38- 41: vqskh Kdd-F gafkl CRTC_CANFA : 7- 10: paiyf Keq-F ldgxg CRTC_DROME : 24- 27: aevyl Ken-F dnenw CRTC_DROME : 80- 84: yaasr KfdgF snedk CRTC_HUMAN : 24- 27: pavyf Keq-F ldgdg CRTC_HUMAN : 43- 46: ieskh Ksd-F gkfvl CRTC_HUMAN : 164- 168: kdirc KddeF thlyt CRTC_MOUSE : 24- 27: paiyf Keq-F ldgda CRTC_MOUSE : 43- 46: veskh Ksd-F gkfvl CRTC_MOUSE : 80- 84: yalsa KfepF snkgq CRTC_MOUSE : 164- 168: kdirc KddeF thlyt CRTC_PIG : 7- 10: ptiyf Keq-F ldgdg CRTC_RABIT : 24- 27: pvvyf Keq-F ldgdg CRTC_RABIT : 43- 46: ieskh Ksd-F gkfvl CRTC_RABIT : 164- 168: kdirc KddeF thlyt CRTC_RANES : 7- 10: plvff Kxx-F xxg CRTC_RAT : 24- 27: paiyf Keq-F ldgda CRTC_RAT : 43- 46: veskh Ksd-F gkfvl CRTC_RAT : 164- 168: kdirc KddeF thlyt CRTC_SCHMA : 42- 46: tynae KqgeF kveag CRTC_SCHMA : 127- 130: gespy Kim-F gpdic CRTC_SPIOL : 1- 4: Kvf-F eerfe CRTD_BOVIN : 168- 172: kdirc KddeF thlyt RAL1_ONCVO : 18- 21: saina Kiy-F kedfs RAL1_ONCVO : 22- 25: akiyf Ked-F sdddw RAL1_ONCVO : 40- 43: ikskh Kdd-F gkwei RAL1_ONCVO : 162- 166: kdirc KddvF thlyt C 3: 7.8401 56( 22) F-x(2,3)-F Occurences: 56(22) CALX_ARATH : 7- 10: rqrql Fsv-F lllla CALX_ARATH : 16- 19: lllla Fvs-F qklcy CALX_ARATH : 35- 39: vlyes FdepF dgrwi CALX_ARATH : 477- 481: aivvv FfslF lklif CALX_ARATH : 478- 481: ivvvf Fsl-F lklif CALX_CAEEL : 10- 13: kwmyi Fiq-F llvss CALX_CAEEL : 61- 65: kstpn FfdyF pvgsk CALX_CAEEL : 62- 65: stpnf Fdy-F pvgsk CALX_CANFA : 72- 76: sgevy FadsF drgtl CALX_CANFA : 435- 439: mtsdi FfdnF ivcgd CALX_CANFA : 436- 439: tsdif Fdn-F ivcgd CALX_HUMAN : 71- 75: tgevy FadsF drgtl CALX_HUMAN : 434- 438: mtsdi FfdnF iicad CALX_HUMAN : 435- 438: tsdif Fdn-F iicad CALX_MOUSE : 72- 76: tgevy FadsF drgsl CALX_MOUSE : 435- 439: mtsdi FfdnF iisgd CALX_MOUSE : 436- 439: tsdif Fdn-F iisgd CALX_RAT : 72- 76: tgevy FadsF drgsl CALX_RAT : 435- 439: mtsdi FfdnF iisgd CALX_RAT : 436- 439: tsdif Fdn-F iisgd CALX_SCHPO : 229- 232: rqgsl Fyd-F ippvl CALX_SCHPO : 508- 511: iltcy Fyf-F asssp CALX_YEAST : 33- 37: laeds FwehF qaytn CRTC_BOVIN : 6- 10: epaiy FkeqF ldg CRTC_CAEEL : 19- 23: saevy FkeeF ndasw CRTC_CAEEL : 41- 44: khkdd Fga-F klsag CRTC_CAEEL : 76- 80: sraak FdkdF snkgk CRTC_CANFA : 6- 10: epaiy FkeqF ldgxg CRTC_DROME : 46- 49: hpgke Fgk-F vltpg CRTC_DROME : 81- 84: aasrk Fdg-F snedk CRTC_HUMAN : 23- 27: epavy FkeqF ldgdg CRTC_HUMAN : 46- 49: khksd Fgk-F vlssg CRTC_HUMAN : 81- 84: alsas Fep-F snkgq CRTC_HUMAN : 327- 330: ksgti Fdn-F litnd CRTC_MOUSE : 23- 27: dpaiy FkeqF ldgda CRTC_MOUSE : 46- 49: khksd Fgk-F vlssg CRTC_MOUSE : 81- 84: alsak Fep-F snkgq CRTC_MOUSE : 327- 330: ksgti Fdn-F litnd CRTC_PIG : 6- 10: eptiy FkeqF ldgdg CRTC_RABIT : 23- 27: epvvy FkeqF ldgdg CRTC_RABIT : 46- 49: khksd Fgk-F vlssg CRTC_RABIT : 81- 84: alsar Fep-F snkgq CRTC_RABIT : 327- 330: ksgti Fdn-F litnd CRTC_RANES : 6- 10: dplvf FkxxF xxg CRTC_RAT : 23- 27: dpaiy FkeqF ldgda CRTC_RAT : 46- 49: khksd Fgk-F vlssg CRTC_RAT : 81- 84: alsar Fep-F snkgq CRTC_RAT : 327- 330: ksgti Fdn-F litnd CRTC_SCHMA : 21- 25: ghevw FsetF pnesi CRTC_SCHMA : 93- 97: tmvlq FtvkF dktvs CRTC_SPIOL : 4- 8: kvf FeerF edgwe CRTD_BOVIN : 18- 22: sivll FhfvF yiclh CRTD_BOVIN : 40- 44: eetvf FseqF ltldl CRTD_BOVIN : 331- 334: ksgti Fdn-F litnd RAL1_ONCVO : 21- 25: nakiy FkedF sdddw RAL1_ONCVO : 78- 82: sigak FdksF snkgk Number of patterns evaluated by Pratt:7 Total running time: 0 seconds