/*********************************************************************************/ /* PRALINE: A PROGRAM FOR MULTIPLE ALIGNMENT OF PROTEIN SEQUENCES */ /* */ /* copyright (c) 1998-2004 Jaap Heringa NIMR, London NW7 1AA, U.K. */ /* copyright (c) 2001-2004 Victor A. Simossis NIMR, London NW7 1AA, U.K. */ /* copyright (c) 2004- Jaap Heringa VU University, Amsterdam, NL */ /* copyright (c) 2004-2005 Victor A. Simossis VU University, Amsterdam, NL */ /* copyright (c) 2005-2009 Walter Pirovano VU University, Amsterdam, NL */ /* */ /* AUTHORS : Walter Pirovano, Victor A. Simossis, and Jaap Heringa */ /* ONLINE SERVER : http://www.ibi.vu.nl/programs/pralinewww */ /*********************************************************************************/ Set paths for webserver: Homedir /home/ibivu Expanded to /home/ibivu Expanded DATA_DIR from /data01/ibivu/data () Expanded APPS_DIR from /home/ibivu/apps (/home/ibivu) Expanded PRALINE_DIR from /home/ibivu/apps/praline-b (/home/ibivu/apps) Expanded BLAST_DIR from /home/ibivu/apps/blast (/home/ibivu/apps) Expanded PRED_DIR from /home/ibivu/tools (/home/ibivu) Expanded MAT_DIR from /home/ibivu/apps/praline-b/mat (/home/ibivu/apps/praline-b) When using PRALINE please cite: SECONDARY STRUCTURE INTEGRATION: Pirovano W., Simossis V.A. and Heringa J. (2009) submitted. TRANSMEMBRANE STRUCTURE INTEGRATION: Pirovano W., Feenstra K.A. and Heringa J. (2008) Bioinformatics 24(4), 492-497. HOMOLOGY-EXTENDED ALIGNMENT STRATEGY: Simossis V.A., Kleinjung J. and Heringa J. (2005) Nucleic Acids Res. 33(3), 812-824. ORIGINAL ALIGNMENT METHOD: Heringa J. (1999) Computers and Chemistry, 23, 341-364. SERVER USAGE: Simossis V.A. and Heringa J. (2003) Comp. Biol. Chem. 27(4-5), 511-519. Simossis V.A. and Heringa J. (2005) Nucleic Acids Res. 33, W289-W294. ...reading substitution values from file: /home/ibivu/apps/praline/mat/blosum62.mat The gap-open penalty is set to 12.00 The gap-extension penalty is set to 1.00 Option PSIDB is set ON with value: PSIDB=nr Option PSIHITS is set ON with value: 100 Option PSIITER is set ON with value: 3 Option PSIPREPRO is set ON with value: 0.010000 Option TREE is set ON Option MSF is set ON Input file p450.fasta contains 12 sequences 1. 1n97a mkrlslreawpylkdlqqdplavllawgrahprlflplprfplalifdpegvegallaegttkatfqyralsrltgrglltdwgeswkearkalkdpflp knvrgyreameeearaffgewrgeerdldhemlalslrllgralfgkplspslaehalkaldrimaqtrsplalldlaaearfrkdrgalyreaealivh pplshlpreralseavtllvaghetvasaltwsflllshrpdwqkrvaeseeaalaafqealrlyppawiltrrlerplllgedrlppgttlvlspyvtq rlhfpdgeafrperfleergtpsgryfpfglgqrlclgrdfallegpivlraffrrfrldplpfprvlaqvtlrpegglparpre 385 amino acids 2. 1jpza tikempqpktfgelknlpllntdkpvqalmkiadelgeifkfeapgrvtrylssqrlikeacdesrfdknlsqalkfvrdfagdglftswtheknwkkah nillpsfsqqamkgyhammvdiavqlvqkwerlnadehievpedmtrltldtiglcgfnyrfnsfyrdqphpfitsmvraldeamnklqranpddpayde nkrqfqedikvmndlvdkiiadrkasqsddllthmlngkdpetgeplddeniryqiitfliaghettsgllsfalyflvknphvlqkaaeeaarvlvdpv psykqvkqlkyvgmvlnealrlwptapafslyakedtvlggeyplekgdelmvlipqlhrdktiwgddveefrperfenpsaipqhafkpfgngqracig qqfalheatlvlgmmlkhfdfedhtnyeldiketltlkpegfvvkakskkiplggi 456 amino acids 3. 1dt6a ppgptpfpiignilqidakdisksltkfsecygpvftvylgmkptvvlhgyeavkealvdlgeefagrgsvpilekvskglgiafsnaktwkemrrfslm tlrnfgmgkrsiedriqeearclveelrktnaspcdptfilgcapcnvicsvifhnrfdykdeeflklmeslhenvellgtpldyfpgihktllknadyi knfimekvkehqklldvnnprdfidcflikmeqennleftleslviavsdlfgagtettsttlryslllllkhpevaarvqeeiervigrhrspcmqdrs rmpytdaviheiqrfidllptnlphavtrdvrfrnyfipkgtdiitsltsvlhdekafpnpkvfdpghfldesgnfkksdyfmpfsagkrmcvgeglarm elflfltsilqnfklqslvepkdlditavvngfvsvppsyqlcfipihh 449 amino acids 4. 1gwia aripldpfvtdldgesarlraagplaavelpggvpvwavthhaeakalltdprlvkdinvwgawrrgeipadwpliglanpgrsmltvdgaehrrlrtlv aqaltvrrvehmrgriteltdrlldelpadggvvdlkaafayplpmyvvadlmgieearlprlkvlfekffstqtppeevvatltelasimtdtvaakra apgddltsaliqasengdhltdaeivstlqlmvaaghettislivnavvnlsthpeqralvlsgeaewsavveetlrfstptshvlirfaaedvpvgdrv ipagdalivsygalgrderahgptadrfdltrtsgnrhisfghgphvcpgaalsrmeagvalpalyarfphldlavpaaelrnkpvvtqndlfelpvrla hh 402 amino acids 5. 1jipa ttvpdlesdsfhvdwyrtyaelretapvtpvrflgqdawlvtgydeakaalsdlrlssdpkkkypgvevefpaylgfpedvrnyfatnmgtsdppthtrl rklvsqeftvrrveamrprveqitaelldevgdsgvvdivdrfahplpikvicellgvdekyrgefgrwsseilvmdperaeqrgqaarevvnfildlve rrrtepgddllsalirvqddddgrlsadeltsialvlllagfessvsligigtylllthpdqlalvrrdpsalpnaveeilryiappetttrfaaeevei ggvaipqystvlvangaanrdpkqfpdphrfdvtrdtrghlsfgqgihfcmgrplaklegevalralfgrfpalslgidaddvvwrrslllrgidhlpvr ldg 403 amino acids 6. 1lfka dprplhirrqgldpadellaagaltrvtaethwmatahavvrqvmgdhqqfstrrrwdpelvgnlmdydppehtrlrrkltpgftlrkmqrmapyieqiv ndrldemeragspadliafvadkvpgavlcelvgvprddrdmfmklchghldaslsqkrraalgdkfsryllamiarerkepgegmigavvaeygddatd eelrgfcvqvmlagddnisgmiglgvlamlrhpeqidafrgdeqsaqravdeliryltvpysptpriaredltlagqeikkgdsvicslpaanrdpalap dvdrldvtrepiphvafghgvhhclgaalarlelrtvftelwrrfpalrladpaqdtefrlttpaygltelmvaw 375 amino acids 7. 1jfba apsfpfsrasgpeppaefaklratnpvsqvklfdgslawlvtkhkdvcfvatseklskvrtrqgfpelsasgkqaakakptfvdmdppehmhqrsmvept ftpeavknlqpyiqrtvddlleqmkqkgcangpvdlvkefalpvpsyiiytllgvpfndleyltqqnairtngsstareasaanqelldylailveqrlv epkddiisklcteqvkpgnidksdavqiaflllvagnatmvnmialgvatlaqhpdqlaqlkanpslapqfveelcryhtasalaikrtakedvmigdkl vranegiiasnqsanrdeevfenpdefnmnrkwppqdplgfgfgdhrciaehlakaelttvfstlyqkfpdlkvavplgkinytplnrdvgivdlpvif 399 amino acids 8. 1io7a mydwfsemrkkdpvyydgniwqvfsyrytkevlnnfskfssdltgyherledlrngkirfdiptrytmltsdpplhdelrsmsadifspqklqtletfir ettrslldsidpreddivkklavplpiiviskilglpiedkekfkewsdlvafrlgkpgeifelgkkyleligyvkdhlnsgtevvsrvvnsnlsdiekl gyiillliagnetttnlisnsvidftrfnlwqrireenlylkaieealrysppvmrtvrktkervklgdqtieegeyvrvwiasanrdeevfhdgekfip drnpnphlsfgsgihlclgaplarleariaieefskrfrhieildtekvpnevlngykrlvvrlks 366 amino acids 9. 1cpt mdaratipehiartvilpqgyaddeviypafkwlrdeqplamahiegydpmwiatkhadvmqigkqpglfsnaegseilydqnneafmrsisggcphvid sltsmdppthtayrgltlnwfqpasirkleenirriaqasvqrlldfdgecdfmtdcalyyplhvvmtalgvpeddeplmlkltqdffgveaarrfheti atfydyfngftvdrrscpkddvmsllanskldgnyiddkyinayyvaiataghdttssssggaiiglsrnpeqlalaksdpaliprlvdeavrwtapvks fmrtaladtevrgqnikrgdrimlsypsanrdeevfsnpdefditrfpnrhlgfgwgahmclgqhlaklemkiffeellpklksvelsgpprlvatnfvg gpknvpirftka 412 amino acids 10. 1n40a atvllevpfsargdripdavaelrtrepirkvrtitgaeawlvssyalctqvledrrfsmketaaagaprlnaltvppevvnnmgniadaglrkavmkai tpkapgleqflrdtanslldnlitegapadlrndfadplatalhckvlgipqedgpklfrslsiafmssadpipaakinwdrdieymagilenpnittgl mgelsrlrkdpayshvsdelfatigvtffgagvistgsflttalisliqrpqlrnllhekpelipagveellrinlsfadglprlatadiqvgdvlvrkg elvlvlleganfdpehfpnpgsieldrpnptshlafgrgqhfcpgsalgrrhaqigieallkkmpgvdlavpidqlvwrtrfqrriperlpvlw 394 amino acids 11. 1qmqa anlaplpphvpehlvfdfdmynpsnlsagvqeawavlqesnvpdlvwtrcngghwiatrgqlireayedyrhfssecpfipreageaydfiptsmdppeq rqfralanqvvgmpvvdklenriqelacslieslrpqgqcnftedyaepfpirifmllaglpeediphlkyltdqmtrpdgsmtfaeakealydylipii eqrrqkpgtdaisivangqvngrpitsdeakrmcglllvggldtvvnflsfsmeflakspehrqelierperipaaceellrrfslvadgriltsdyefh gvqlkkgdqillpqmlsglderenaapmhvdfsrqkvshttfghgshlclgqhlarreiivtlkewltripdfsiapgaqiqhksgivsgvqalplvwdp attkav 406 amino acids 12. 1e9xa msavalprvsgghdehghleefrtdpiglmqrvrdecgdvgtfqlagkqvvllsgshanefffragdddldqakaypfmtpifgegvvfdasperrkeml hnaalrgeqmkghaatiedqvrrmiadwgeageidlldffaeltiytssacligkkfrdqldgrfaklyhelergtdplayvdpylpiesfrrrdearng lvalvadimngrianpptdksdrdmldvliavkaetgtprfsadeitgmfismmfaghhtssgtaswtlielmrhrdayaavideldelygdgrsvsfha lrqipqlenvlketlrlhppliilmrvakgefevqghrihegdlvaaspaisnripedfpdphdfvparyeqprqedllnrwtwipfgagrhrcvgaafa imqikaifsvllreyefemaqppesyrndhskmvvqlaqpacvryrrrt 449 amino acids Running PSI-BLAST (e-value threshold: 0.010000) for sequence [1] 1n97a Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1n97a-p450_psiali.fasta Removed 14 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [2] 1jpza Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1jpza-p450_psiali.fasta Removed 14 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [3] 1dt6a Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1dt6a-p450_psiali.fasta Removed 17 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [4] 1gwia Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1gwia-p450_psiali.fasta Removed 11 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [5] 1jipa Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1jipa-p450_psiali.fasta Removed 8 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [6] 1lfka Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1lfka-p450_psiali.fasta Removed 6 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [7] 1jfba Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1jfba-p450_psiali.fasta Removed 17 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [8] 1io7a Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1io7a-p450_psiali.fasta Removed 5 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [9] 1cpt Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1cpt-p450_psiali.fasta Removed 6 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [10] 1n40a Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1n40a-p450_psiali.fasta Removed 12 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [11] 1qmqa Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1qmqa-p450_psiali.fasta Removed 11 redundant sequences from 101 hits. Running PSI-BLAST (e-value threshold: 0.010000) for sequence [12] 1e9xa Filtering PSI-BLAST alignment file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/1e9xa-p450_psiali.fasta Removed 20 redundant sequences from 101 hits. [0s] 1n97a #--MKR-LSLREA-----WPYLKDLQQD-PLAVLLAWGRAHPRLFL----- [0s] 1jpza #----TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFK----- [0s] 1e9xa #--MSAVALPRVSGGHDEHGHLEEFRTD-PIGLMQRVRDECGDVGT----- [0s] 1dt6a #--------PPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVFT----- [0s] 1gwia #------------------ARIPLDPFVTDLDGESARLRAAGPLAA----- [0s] 1jipa #---------------TTVPDLESDSFHVDWYRTYAELRETAPVTP----- [0s] 1n40a #--------------ATVLLEVPFSARGDRIPDAVAELRTREPIRK----- [0s] 1jfba #--------------APSFP--FSRASGPEPPAEFAKLRATNPVSQ----- [0s] 1cpt #---MDARATIPEHIARTVILPQGYADDEVIYPAFKWLRDEQPLAM----- [0s] 1qmqa #ANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDL----- [0s] 1lfka #----------------------------DPRPLHIRRQGLDPADELLAAG [0s] 1io7a #-----------------------------MYDWFSEMRKKDPVYY----- [0c] Conservation #00000000000100111221322222212433435346434563300000 [0s] 1n97a #--PL-PRFPLALIFDPEGVEGALL-AEGTTKATFQYRALSRLT-GRGLLT [0s] 1jpza #--FEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFA-GDGLFT [0s] 1e9xa #--FQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKAYPFMTPIF-GEGVVF [0s] 1dt6a #--VYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGSVPILEKVSKGLGIAF [0s] 1gwia #-VELPGGVPVWAVTHHAEAKALLTDPRLVKDINVWGAWRRGEIP--ADWP [0s] 1jipa #-VRFL-GQDAWLVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLGFP [0s] 1n40a #-VRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAPR---------- [0s] 1jfba #-VKLFDGSLAWLVTKHKDVCFVATSEKLSKVRTRQGFPEL-------SAS [0s] 1cpt #-AHIEGYDPMWIATKHADVMQIGKQPGLFSNAEGSEILYDQNNEAFMRSI [0s] 1qmqa #-VWTRCNGGHWIATRGQLIREAYEDYRHFSSECPF-------------IP [0s] 1lfka #ALTRVTAETHWMATAHAVVRQVMGDHQQFSTRRRW--------------- [0s] 1io7a #------DGNIWQVFSYRYTKEVLNNFSKFSSDLTGYHERLEDL---RNGK [0c] Conservation #02232243345565444355464342433443333211221110101122 [0s] 1n97a #--DWGESWKEARKA-LKDPFLPKNVRGYRE-AMEEEARAFFGEWR----G [0s] 1jpza #SWTHEKNWKKAHNI-LLPSFSQQAMKGYHA-MMVDIAVQLVQKWERLNAD [0s] 1e9xa #---DASPERRKEML-HNAALRGEQMKGHAA-TIEDQVRRMIADWGE---A [0s] 1dt6a #--SNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEARCLVEELRK-TNA [0s] 1gwia #--LIGLANPGRSMLTVDGAEHRRLRTLVAQALTVRRVEHMRGRITELT-D [0s] 1jipa #--EDVRNYFATNMGTSDPPTHTRLRKLVSQEFTVRRVEAMRPRVEQIT-A [0s] 1n40a #--LNALTVPPEVVNNMGNIADAGLRKAVMKAITPK-APGLEQFLRDTA-N [0s] 1jfba #--GKQAAKAKPTFVDMDPPEHMHQRSMVEPTFTPEAVKNLQPYIQRTV-D [0s] 1cpt #--SGGCPHVIDSLTSMDPPTHTAYRGLTLNWFQPASIRKLEENIRRIA-Q [0s] 1qmqa #--REAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELA-C [0s] 1lfka #-----DPELVGNLMDYDPPEHTRLRRKLTPGFTLRKMQRMAPYIEQIV-N [0s] 1io7a #--IRFDIPTRYTMLTSDPPLHDELRSMSADIFSPQKLQTLETFIRETT-R [0c] Conservation #00223332332344344553434455343414444364374335553303 [0s] 1n97a #EERDLDHEMLAL--SLRLLGRALFGKPLSPS---LAEHALKALDRIMA-- [0s] 1jpza #EHIEVPEDMTRL--TLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEA [0s] 1e9xa #GEIDLLDFFAEL--TIYTSSACLIGKKFRDQ---LDGRFAKLYHELERGT [0s] 1dt6a #SPCDPTFILGCA--PCNVICSVIFHNRFDY----KDEEFLKLMESLHENV [0s] 1gwia #RLLDELPADGG---VVDLKAAFAYPLPMYV-----VADLMGIEEARLPRL [0s] 1jipa #ELLDEVGDSGV----VDIVDRFAHPLPIKV-----ICELLGVDEKYRGEF [0s] 1n40a #SLLDNLITEGA---PADLRNDFADPLATAL-----HCKVLGIPQEDGPKL [0s] 1jfba #DLLEQMKQKGCANGPVDLVKEFALPVPSYI-----IYTLLGVPFNDLEYL [0s] 1cpt #ASVQRLLDFDG---ECDFMTDCALYYPLHV-----VMTALGVPEDDEPLM [0s] 1qmqa #SLIES-LRPQG---QCNFTEDYAEPFPIRI-----FMLLAGLPEEDIPHL [0s] 1lfka #DRLDEMERAGS---PADLIAFVADKVPGAV-----LCELVGVPRDDRDMF [0s] 1io7a #SLLDSIDPRE-----DDIVKKLAVPLPIIV-----ISKILGLPIEDKEKF [0c] Conservation #54673423342000246553346344543400000323575644533424 [0s] 1n97a #-------------------QTRSPLALLDLAAEARFRKDR--------GA [0s] 1jpza #MNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKAS-----QSD [0s] 1e9xa #D---PLAYVDPYLPIESFRRRDEARNGLVALVADIMNGRIANPPTDKSDR [0s] 1dt6a #E----LLGTPLDYFPGIHKTLLKNADYIKNFIMEKVKEHQKLL-DVNNPR [0s] 1gwia #K---VLFEKFFST-QTPPEEVVATLTELASIMTDTVAAKRAA-----PGD [0s] 1jipa #G---RWSSEILVMDPERAEQRGQAAREVVNFILDLVERRRTE-----PGD [0s] 1n40a #F---RSLSIAFMSSADPIPAAKINWDRDIEYMAGILENPN-------ITT [0s] 1jfba #T---QQNAIRTNG-SSTAREASAANQELLDYLAILVEQRLVE-----PKD [0s] 1cpt #L---KLTQDFFG--VEAARRFHETIATFYDYFNGFTVDRRSC-----PKD [0s] 1qmqa #K---YLTDQMTR--PDGSMTFAEAKEALYDYLIPIIEQRRQK-----PGT [0s] 1lfka #M---KLCHGHLDA-SLSQKRRAALGDKFSRYLLAMIARERKE-----PGE [0s] 1io7a #K---EWSDLVAFR-LGKPGEIFELGKKYLELIGYV--KDHLN-----SGT [0c] Conservation #20002333223210332235335334353456335534553200000444 [0s] 1n97a #LYREAEALIVH-PPLSH-LPRERALSEAVTLLVAGHETVASALTWSFLLL [0s] 1jpza #DLLTHMLNGKDPETGEP-LDDENIRYQIITFLIAGHETTSGLLSFALYFL [0s] 1e9xa #DMLDVLIAVKA-ETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIEL [0s] 1dt6a #DFIDCFLIKMEQENNLE-FTLESLVIAVSDLFGAGTETTSTTLRYSLLLL [0s] 1gwia #DLTSALIQASE-NG--DHLTDAEIVSTLQLMVAAGHETTISLIVNAVVNL [0s] 1jipa #DLLSALIRVQD-DD-DGRLSADELTSIALVLLLAGFESSVSLIGIGTYLL [0s] 1n40a #GLMGELSRLRK-DPAYSHVSDELFATIGVTFFGAGVISTGSFLTTALISL [0s] 1jfba #DIISKLCTEQV-KP--GNIDKSDAVQIAFLLLVAGNATMVNMIALGVATL [0s] 1cpt #DVMSLLANSKL-DG--NYIDDKYINAYYVAIATAGHDTTSSSSGGAIIGL [0s] 1qmqa #DAISIVANGQV-NG--RPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFL [0s] 1lfka #GMIGAVVAEYG-D----DATDEELRGFCVQVMLAGDDNISGMIGLGVLAM [0s] 1io7a #EVVSRVVNSN--------LSDIEKLGYIILLLIAGNETTTNLISNSVIDF [0c] Conservation #5565365434204200216545454333446649*357555464366538 [0s] 1n97a #SHRPDWQKRVAESEEAAL------------------AAFQEALRLYPPAW [0s] 1jpza #VKNPHVLQKAAEEAARVLVDPVP-SYKQVKQLKYVGMVLNEALRLWPTAP [0s] 1e9xa #MRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLKETLRLHPPLI [0s] 1dt6a #LKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDAVIHEIQRFIDLLP [0s] 1gwia #STHPEQRALVLSGEAEW------------------SAVVEETLRFSTPTS [0s] 1jipa #LTHPDQLALVRRDPSAL------------------PNAVEEILRYIAPPE [0s] 1n40a #IQRPQLRNLLHEKPELI------------------PAGVEELLRINLSFA [0s] 1jfba #AQHPDQLAQLKANPSLA------------------PQFVEELCRYHTASA [0s] 1cpt #SRNPEQLALAKSDPALI------------------PRLVDEAVRWTAPVK [0s] 1qmqa #AKSPEHRQELIERPERI------------------PAACEELLRRFSLV- [0s] 1lfka #LRHPEQIDAFRGDEQSA------------------QRAVDELIRYLTVPY [0s] 1io7a #TRFNLW--QRIREENLY------------------LKAIEEALRYSPPVM [0c] Conservation #5557533445355454500000000000000000034566*56*434442 [0s] 1n97a #-ILTRRLERPLLL-GEDRLPPGTTLVLSPYVTQRLH--FPDG-EAFRPER [0s] 1jpza #-AFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPER [0s] 1e9xa #-ILMRVAKGEFEV-QGHRIHEGDLVAASPAISNRIPEDFPDP-HDFVPAR [0s] 1dt6a #TNLPHAVTRDVRF-RNYFIPKGTDIITSLTSVLHDEKAFPNP-KVFDPGH [0s] 1gwia #HVLIRFAAEDVPV-GDRVIPAGDALIVSYGALGRDERAHGPTADRFDLTR [0s] 1jipa #TTT-RFAAEEVEI-GGVAIPQYSTVLVANGAANRDPKQF-PDPHRFDVTR [0s] 1n40a #DGLPRLATADIQV-GDVLVRKGELVLVLLEGANFDPEHF-PNPGSIELDR [0s] 1jfba #LAIKRTAKEDVMI-GDKLVRANEGIIASNQSANRDEEVF-ENPDEFNMNR [0s] 1cpt #SFM-RTALADTEV-RGQNIKRGDRIMLSYPSANRDEEVF-SNPDEFDITR [0s] 1qmqa #ADG-RILTSDYEF-HGVQLKKGDQILLPQMLSGLDEREN-AAPMHVDFSR [0s] 1lfka #SPTPRIAREDLTL-AGQEIKKGDSVICSLPAANRDPALA-PDVDRLDVTR [0s] 1io7a #RTV-RKTKERVKL-GDQTIEEGEYVRVWIASANRDEEVF-HDGEKFIPDR [0c] Conservation #23517364565460553384576386553346567543504424474448 [0s] 1n97a #FLEERG---TPSGRYFPFGLGQRLCLGRDFALLEGPIVLRAFFRRFRL-- [0s] 1jpza #FENPSA---IPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDF-- [0s] 1e9xa #YEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKAIFSVLLREYEFEM [0s] 1dt6a #FLDESGNFKKSDY-FMPFSAGKRMCVGEGLARMELFLFLTSILQNFKL-- [0s] 1gwia #TS-GNR--------HISFGHGPHVCPGAALSRMEAGVALPALYARFPHLD [0s] 1jipa #DT--RG--------HLSFGQGIHFCMGRPLAKLEGEVALRALFGRFPALS [0s] 1n40a #PN-PTS--------HLAFGRGQHFCPGSALGRRHAQIGIEALLKKMPGVD [0s] 1jfba #KWPPQD--------PLGFGFGDHRCIAEHLAKAELTTVFSTLYQKFPDLK [0s] 1cpt #FP--NR--------HLGFGWGAHMCLGQHLAKLEMKIFFEELLPKLKSVE [0s] 1qmqa #QK--VS--------HTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFS [0s] 1lfka #EP--IP--------HVAFGHGVHHCLGAALARLELRTVFTELWRRFPALR [0s] 1io7a #NP--NP--------HLSFGSGIHLCLGAPLARLEARIAIEEFSKRFRHIE [0c] Conservation #33014300000000554*93*374*5953785584364645654674332 [0s] 1n97a #--DPLPFPRVLAQVTLRPEGGLPARPRE-------- [0s] 1jpza #EDHTNYELDIKETLTLKPEGF-VVKAKSKKIPLGGI [0s] 1e9xa #AQPPESYRNDHSKMVVQLAQPACVRYRRRT------ [0s] 1dt6a #-QSLVEPKDLDITAVVNGFVSVPPSYQLCFIPIHH- [0s] 1gwia #LAVPAAELRNKPVVTQNDLFELPVRLAHH------- [0s] 1jipa #LGIDADDVVWRRSLLLRGIDHLPVRLDG-------- [0s] 1n40a #LAVPIDQLVWRTRFQRRIPERLPVLW---------- [0s] 1jfba #VAVPLGKINYTPLNRDVGIVDLPVIF---------- [0s] 1cpt #LS---GPPRLVATNFVGGPKNVPIRFTKA------- [0s] 1qmqa #IA--PGAQIQHKSGIVSGVQALPLVWDPATTKAV-- [0s] 1lfka #LADPAQDTEFRLTTPAYGLTELMVAW---------- [0s] 1io7a #IL----DTEKVPNEVLNGYKRLVVRLKS-------- [0c] Conservation #441323333233434444333657432100000000 Iteration 0 SP= 218516.00 AvSP= 8.732 SId= 4852 AvSId= 0.194 Nseq= 12 Len= 486 Naa= 4896 Ngaps= 936 [tr0] ------------------------------------------- 1 1n97a [tr0] -------------------------------------+ 4382.5 [tr0] | | -------- 2 1jpza [tr0] | -----------------------------------+ 5118.7 [tr0] | -------- 12 1e9xa [tr0]----------------------------+ 3603.2 [tr0]| -------------------------------------------------------------------------------- 3 1dt6a [tr0]+ 2984.8 [tr0]| -------------------------------------- 4 1gwia [tr0]| ----+ 4484.2 [tr0]| | -------------------------------------- 5 1jipa [tr0]| -+ 4406.0 [tr0]| |------------------------------------------ 10 1n40a [tr0]| -------+ 4391.1 [tr0]| | ------------------------------------------- 7 1jfba [tr0]| ----+ 4234.2 [tr0]| | | ----------------------------------------------- 9 1cpt [tr0]| | ---+ 4307.9 [tr0]| | ----------------------------------------------- 11 1qmqa [tr0]| --------------+ 4155.0 [tr0]| | ------------------------------------------------------ 6 1lfka [tr0]----------------------------------------+ 3841.1 [tr0] -------------------------------------------------------------------- 8 1io7a Alignment written to file /data01/scratch/jobs/2ccd627f7c0d5b0bc36691498132a164/p450.msf PRALINE computation time has been: 3273.000 seconds (54 mins 33 secs) Command line used: /home/ibivu/apps/praline-b/praline p450.fasta /home/ibivu/apps/praline/mat/blosum62.mat 12 1 psidb=nr psihits=100 psiiter=3 psiprepro=0.010000 tree msf 1> results.out 2> errors.out