/*********************************************************************************/ /* 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 SSMAT is set ON with value: SSMAT=/home/ibivu/apps/praline/mat/luthy.mat Option H_GO is set ON with value: 13.000000 Option E_GO is set ON with value: 13.000000 Option C_GO is set ON with value: 6.000000 Option PSIPRED is set ON Option TREE is set ON Option MSF is set ON ...reading secondary structure substitution values from file: /home/ibivu/apps/praline/mat/luthy.mat matrix: H E C 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/e4f31c7d121924ca83863aa226cccdd0/1n97a-p450_psiali.fasta Removed 14 redundant sequences from 101 hits. Running PSIPRED on 1n97a Running PSI-BLAST (e-value threshold: 0.010000) for sequence [2] 1jpza Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1jpza-p450_psiali.fasta Removed 14 redundant sequences from 101 hits. Running PSIPRED on 1jpza Running PSI-BLAST (e-value threshold: 0.010000) for sequence [3] 1dt6a Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1dt6a-p450_psiali.fasta Removed 17 redundant sequences from 101 hits. Running PSIPRED on 1dt6a Running PSI-BLAST (e-value threshold: 0.010000) for sequence [4] 1gwia Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1gwia-p450_psiali.fasta Removed 11 redundant sequences from 101 hits. Running PSIPRED on 1gwia Running PSI-BLAST (e-value threshold: 0.010000) for sequence [5] 1jipa Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1jipa-p450_psiali.fasta Removed 8 redundant sequences from 101 hits. Running PSIPRED on 1jipa Running PSI-BLAST (e-value threshold: 0.010000) for sequence [6] 1lfka Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1lfka-p450_psiali.fasta Removed 6 redundant sequences from 101 hits. Running PSIPRED on 1lfka Running PSI-BLAST (e-value threshold: 0.010000) for sequence [7] 1jfba Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1jfba-p450_psiali.fasta Removed 17 redundant sequences from 101 hits. Running PSIPRED on 1jfba Running PSI-BLAST (e-value threshold: 0.010000) for sequence [8] 1io7a Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1io7a-p450_psiali.fasta Removed 5 redundant sequences from 101 hits. Running PSIPRED on 1io7a Running PSI-BLAST (e-value threshold: 0.010000) for sequence [9] 1cpt Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1cpt-p450_psiali.fasta Removed 6 redundant sequences from 101 hits. Running PSIPRED on 1cpt Running PSI-BLAST (e-value threshold: 0.010000) for sequence [10] 1n40a Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1n40a-p450_psiali.fasta Removed 12 redundant sequences from 101 hits. Running PSIPRED on 1n40a Running PSI-BLAST (e-value threshold: 0.010000) for sequence [11] 1qmqa Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1qmqa-p450_psiali.fasta Removed 11 redundant sequences from 101 hits. Running PSIPRED on 1qmqa Running PSI-BLAST (e-value threshold: 0.010000) for sequence [12] 1e9xa Filtering PSI-BLAST alignment file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/1e9xa-p450_psiali.fasta Removed 20 redundant sequences from 101 hits. Running PSIPRED on 1e9xa [0s] 1n97a #-----MK-RLSLRE---AWPYLKDLQQD-PLAVLLAWGRAHPRLF----- [0ssp] # hh hhhhhhhhhhh hhhhhhhhhhh ee [0s] 1jpza #----TIK-EMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIF----- [0ssp] # hhhh hhhhhhhhhhh ee [0s] 1e9xa #--MSAVA-LPRVSGGHDEHGHLEEFRTD-PIGLMQRVRDECGDVG----- [0ssp] # hh hhhhh hhhhhhhhhhhh ee [0s] 1dt6a #---------PPGPTPFPIIGNILQIDAKDISKSLTKFSECYGPVF----- [0ssp] # hhh hhhhhhhhhhhh ee [0s] 1gwia #-----------------ARI-PLDPFVTDLDGESARLRAAGPLAA----- [0ssp] # hhhhhhhhh eee [0s] 1jipa #--------------TTVPDL-ESDSFHVDWYRTYAELRETAPVTP----- [0ssp] # hhhhhhhhh eee [0s] 1jfba #----------------APSFPFSRASGPEPPAEFAKLRATNPVSQ----- [0ssp] # hhhhhhhhh eee [0s] 1n40a #-------------ATVLLEVPF-SARGDRIPDAVAELRTREPIRK----- [0ssp] # hhhhhhhh eee [0s] 1cpt #--MD-ARATIPEHIARTVILPQGYADDEVIYPAFKWLRDEQPLAM----- [0ssp] # hhhh hhhhhhhh eee [0s] 1qmqa #ANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDL----- [0ssp] # hhh hhh hhhhhhhh e [0s] 1lfka #----------------------------DPRPLHIRRQGLDPADELLAAG [0ssp] # hhhhhh hhhhhh [0s] 1io7a #-----------------------------MYDWFSEMRKKDPV------- [0ssp] # hhhhhhhh e [0c] Conservation #00000000001000111212121222222423444456442533200000 [0s] 1n97a #-LPL-PRFPLALIFDPEGVEGALLA-EGTTKATFQ-------------YR [0ssp] # eee eeeeee hhhhhhhh h hh [0s] 1jpza #-KFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQA-------------LK [0ssp] # eeee eeeeee hhhhhhhhh h hh [0s] 1e9xa #-TFQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKA-------------YP [0ssp] # eeee eeeeeee hhhhhhhhh hhh hh [0s] 1dt6a #-TVYLGMKPTVVLHGYEAVKEALVDLGEEFAGRGS-------------VP [0ssp] # eeee eeeeee hhhhhhhhhh hhhh h [0s] 1gwia #-VELPGGVPVWAVTHHAEAKALLTDPRLVKDINVWGAWRRGEIP--ADWP [0ssp] # ee eeeeee hhhhhhhh [0s] 1jipa #-VRFL-GQDAWLVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLGFP [0ssp] # ee eeee hhhhhhhh h [0s] 1jfba #-VKLFDGSLAWLVTKHKDVCFVATSEKLSKVRTRQGFPE-------LSAS [0ssp] # ee eeeee hhhhhhhh [0s] 1n40a #-VRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAP----------R [0ssp] # ee eeeee hhhhhhhh [0s] 1cpt #-AHIEGYDPMWIATKHADVMQIGKQPGLFSNAEGSEILYDQNNEAFMRSI [0ssp] # ee eeeeee hhhhhhhh [0s] 1qmqa #-VWTRCNGGHWIATRGQLIREAYEDYRHFSSECPF-------------IP [0ssp] # eee eeeee hhhhhhhh [0s] 1lfka #ALTRVTAETHWMATAHAVVRQVMGDHQQFST------------------R [0ssp] # eeee eeeee hhhhhhhh [0s] 1io7a #-YYD---GNIWQVFSYRYTKEVLNNFSKFSSDLTGYHERLEDL---RNGK [0ssp] # ee eeeee hhhhhhhh [0c] Conservation #05232233345565444355464352433442323000000000000024 [0s] 1n97a #ALSRLT-GRGLLTD--WGESWKEARKA-LKDPFLPKN-VRGYREAMEEEA [0ssp] #hhhhhh hhhhhhhhh hhh hhhhhhhhhhhh [0s] 1jpza #FVRDFA-GDGLFTSWTHEKNWKKAHNI-LLPSFSQQA-MKGYHAMMVDIA [0ssp] #hhhhhh eee hhhhhhhhh hhh hhhhhhhhhhhh [0s] 1e9xa #FMTPIF-GEGVVF---DASPERRKEML-HNAALRGEQ-MKGHAATIEDQV [0ssp] #hhhhh ee hhhhhhhhh h hhh hhhhhhhhhhhh [0s] 1dt6a #ILEKVSKGLGIAFS--NAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQEEA [0ssp] #hhhhhh eeee hhhhhhhhhhhhhhhh hhhhhhhhhhh [0s] 1gwia #LIGLANPGRSMLTV--DGAEHRRLRTL-VAQALTVRR-VEHMRGRITELT [0ssp] # hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1jipa #EDVRNYFATNMGTS--DPPTHTRLRKL-VSQEFTVRR-VEAMRPRVEQIT [0ssp] #hhhhhh hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1jfba #GKQAAKAKPTFVDM--DPPEHMHQRSM-VEPTFTPEA-VKNLQPYIQRTV [0ssp] # hhhh hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1n40a #LNALTVPPEVVNNM--GNIADAGLRKA-VMKAITPK--APGLEQFLRDTA [0ssp] # hhh hhhhhhhh hhhhh hh hhhhhhhhhhhh [0s] 1cpt #SGGCPHVIDSLTSM--DPPTHTAYRGL-TLNWFQPAS-IRKLEENIRRIA [0ssp] # hh hhh hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1qmqa #REAGEAYDFIPTSM--DPPEQRQFRAL-ANQVVGMPV-VDKLENRIQELA [0ssp] # hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1lfka #RRWDPELVGNLMDY--DPPEHTRLRRK-LTPGFTLRK-MQRMAPYIEQIV [0ssp] # hhh hhhhhhhh hhhh hhh hhhhhhhhhhhh [0s] 1io7a #IRFDIPTRYTMLTS--DPPLHDELRSM-SADIFSPQK-LQTLETFIRETT [0ssp] # hhhhhhhh hhhh hhh hhhhhhhhhhhh [0c] Conservation #33323313245443005444444484505343543430654553385646 [0s] 1n97a #RAFFGEWRGE-----ERD-LDHEMLALSLRLLGRALFG--KPLSPS-LAE [0ssp] #hhhhhhh hhhhhhhhhhhhhhhhh hh hhh [0s] 1jpza #VQLVQKWERLNADE-HIE-VPEDMTRLTLDTIGLCGFNYRFNSFYRDQPH [0ssp] #hhhhhhhhhh ee hhhhhhhhhhhhhhhhh [0s] 1e9xa #RRMIADWGEA---G-EID-LLDFFAELTIYTSSACLIG--KKFRDQ-LDG [0ssp] #hhhhhh eee hhhhhhhhhhhhhhhhh hh [0s] 1dt6a #RCLVEELRKTNA-S-PCDPTFI-LGCAPCNVICSVIFHNRFDY----KDE [0ssp] #hhhhhhhhhh hhh hhhhhhhhhhhhhh h [0s] 1gwia #DRLLDELPADGG---VVDLKAAFAYPLPMYVVADLMG----------IEE [0ssp] #hhhhhhhhh eehhhhhhhhhhhhhhhhhh h [0s] 1jipa #AELLDEVGDSG----VVDIVDRFAHPLPIKVICELLG----------VDE [0ssp] #hhhhhhhh hhhhhhhhhhhhhhhhhh h [0s] 1jfba #DDLLEQMKQKGCANGPVDLVKEFALPVPSYIIYTLLG----------VPF [0ssp] #hhhhhhhhhh eehhhhhhhhhhhhhhhhhh h [0s] 1n40a #NSLLDNLITEGA---PADLRNDFADPLATALHCKVLG----------IPQ [0ssp] #hhhhhhhhh eehhhhhhhhhhhhhhhhhh h [0s] 1cpt #QASVQRLLDFDG---ECDFMTDCALYYPLHVVMTALG----------VPE [0ssp] #hhhhhhhhh eehhhhhhhhhhhhhhhhhh h [0s] 1qmqa #CSLIESLRP-QG---QCNFTEDYAEPFPIRIFMLLAG----------LPE [0ssp] #hhhhhhhhh hhhhhhhhhhhhhhhhhh h [0s] 1lfka #NDRLDEMERAGS---PADLIAFVADKVPGAVLCELVG----------VPR [0ssp] #hhhhhhhhh eehhhhhhhhhhhhhhhhhh h [0s] 1io7a #RSLLDSIDPRE-----DDIVKKLAVPLPIIVISKILG----------LPI [0ssp] #hhhhhhh hhhhhhhhhhhhhhhhhh h [0c] Conservation #34675553333200034835333624664375345650000000000654 [0s] 1n97a #HALKALDRIMA---------------------QTRSPLALLDLAAEARFR [0ssp] #hhhhhhhhhhh hhhhhhhh hhhhhhh [0s] 1jpza #PFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIA [0ssp] #hhhhhhhhhhhhhhhhhhh hhhh hhhhhhhhhhhhhhhhhhhh [0s] 1e9xa #RFAKLYHELERGTDPLAY---VDPYLPIESFRRRDEARNGLVALVADIMN [0ssp] #hhhhhhhhhhhh hhh hhhhhhhhhhhhhhhhhhhhh [0s] 1dt6a #EFLKLMESLHENVELLGTP----LDYFPGIHKTLLKNADYIKNFIMEKVK [0ssp] #hhhhhhhhhhhhhhhhhhh hhh hhhhhhhhhhhhhhhhhhhhh [0s] 1gwia #ARLPRLKVLFEKFFST-QT----------PPEEVVATLTELASIMTDTVA [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1jipa #KYRGEFGRWSSEILVMDPE----------RAEQRGQAAREVVNFILDLVE [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1jfba #NDLEYLTQQNAIRTNG-SS----------TAREASAANQELLDYLAILVE [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1n40a #EDGPKLFRSLSIAFMSSAD----------PIPAAKINWDRDIEYMAGILE [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1cpt #DDEPLMLKLTQDFFG--VE----------AARRFHETIATFYDYFNGFTV [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1qmqa #EDIPHLKYLTDQMTR--PD----------GSMTFAEAKEALYDYLIPIIE [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1lfka #DDRDMFMKLCHGHLDA-SL----------SQKRRAALGDKFSRYLLAMIA [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1io7a #EDKEKFKEWSDLVAFR-LG----------KPGEIFELGKKYLELIGYVKD [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0c] Conservation #44343634434233220320000000000223533533435345633554 [0s] 1n97a #KDRGA--------LYREAEALIVH-PPLSH-LPRERALSEAVTLLVAGHE [0ssp] #hhhhh hhhhhhhhhhh hhhhhhhhhhhhhh hh [0s] 1jpza #DRKASQ-----SDDLLTHMLNGKDPETGEP-LDDENIRYQIITFLIAGHE [0ssp] #hhhh hhhhhhh hhhhhhhhhhhh hh [0s] 1e9xa #GRIANPPTDKSDRDMLDVLIAVKA-ETGTPRFSADEITGMFISMMFAGHH [0ssp] #hhhh hhhhhhh hhhhhhhhhhhhh h [0s] 1dt6a #EHQKLL-DVNNPRDFIDCFLIKMEQENNLE-FTLESLVIAVSDLFGAGTE [0ssp] #hhhh hhhhhhhhhhh hhhhhhhhhhhhh hh [0s] 1gwia #AKRAAP-----GDDLTSALIQASENG--DH-LTDAEIVSTLQLMVAAGHE [0ssp] #hhhh hhhhhhh hhhhhhhhhhhhhhhhh [0s] 1jipa #RRRTEP-----GDDLLSALIRVQDDD-DGR-LSADELTSIALVLLLAGFE [0ssp] #hhhh hhhhhhhhh hhhhhhhhhhhhhhhhh [0s] 1jfba #QRLVEP-----KDDIISKLCTEQVKP--GN-IDKSDAVQIAFLLLVAGNA [0ssp] #hhhh hhhhhhhhh hhhhhhhhhhhhhhhhh [0s] 1n40a #NPN--I-----TTGLMGELSRLRKDPAYSH-VSDELFATIGVTFFGAGVI [0ssp] #h hhhhhhhhhh hhhhhhhhhhhhhhhhh [0s] 1cpt #DRRSCP-----KDDVMSLLANSKLDG--NY-IDDKYINAYYVAIATAGHD [0ssp] #hhhh hhhhhhh hhhhhhhhhhhhhhhhh [0s] 1qmqa #QRRQKP-----GTDAISIVANGQVNG--RP-ITSDEAKRMCGLLLVGGLD [0ssp] #hhhh hhhhhhh hhhhhhhhhhhhhhhhh [0s] 1lfka #RERKEP-----GEGMIGAVVAEYGD----D-ATDEELRGFCVQVMLAGDD [0ssp] #hhhh hhhhhhhh hhhhhhhhhhhhhhhhh [0s] 1io7a #HLN--S-----GTEVVSRVVNSN--------LSDIEKLGYIILLLIAGNE [0ssp] # hhhhhh hhhhhhhhhhhhhhhhh [0c] Conservation #44532400000345565365434222002306545454333446649*35 [0s] 1n97a #TVASALTWSFLLLSHRPDWQKRVAESEEAAL------------------A [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhh h [0s] 1jpza #TTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVP-SYKQVKQLKYVGM [0ssp] #hhhhhhhhhhhhhh hhhhhhhhhhhhhhh hhhhh hhhhh [0s] 1e9xa #TSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLEN [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhhhhhhhh hhhhh hhhh [0s] 1dt6a #TTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYTDA [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhhhhhhh hhhh hhhh [0s] 1gwia #TTISLIVNAVVNLSTHPEQRALVLSGEAEW------------------SA [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1jipa #SSVSLIGIGTYLLLTHPDQLALVRRDPSAL------------------PN [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1jfba #TMVNMIALGVATLAQHPDQLAQLKANPSLA------------------PQ [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1n40a #STGSFLTTALISLIQRPQLRNLLHEKPELI------------------PA [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1cpt #TTSSSSGGAIIGLSRNPEQLALAKSDPALI------------------PR [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1qmqa #TVVNFLSFSMEFLAKSPEHRQELIERPERI------------------PA [0ssp] #hhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1lfka #NISGMIGLGVLAMLRHPEQIDAFRGDEQSA------------------QR [0ssp] #hhhhhhhhhhhhhhh hhhhhhhhh hhhh hh [0s] 1io7a #TTTNLISNSVIDFTRFNLWQRIRE--ENLY------------------LK [0ssp] #hhhhhhhhhhhhh hhhhhhh h hh [0c] Conservation #75554643665385557534545344454500000000000000000034 [0s] 1n97a #AFQEALRLYPPAW-ILTRRLERPLLL-GEDRLPPGTTLVLSPYVTQRLH- [0ssp] #hhhhhhh eeeee eee eee eeee hhhhh [0s] 1jpza #VLNEALRLWPTAP-AFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKT [0ssp] #hhhhhhh eeeeee eee eeee eeeeehhhh [0s] 1e9xa #VLKETLRLHPPLI-ILMRVAKGEFEV-QGHRIHEGDLVAASPAISNRIPE [0ssp] #hhhhhh eee eee eee eeee hhhh [0s] 1dt6a #VIHEIQRFIDLLPTNLPHAVTRDVRF-RNYFIPKGTDIITSLTSVLHDEK [0ssp] #hhhhhhhhh eee ee ee eeee hhhhh [0s] 1gwia #VVEETLRFSTPTSHVLIRFAAEDVPV-GDRVIPAGDALIVSYGALGRDER [0ssp] #hhhhhhhh eee eee eee eeee hhh hh [0s] 1jipa #AVEEILRYIAPPETTT-RFAAEEVEI-GGVAIPQYSTVLVANGAANRDPK [0ssp] #hhhhhhhh eee eee eee eeee hh [0s] 1jfba #FVEELCRYHTASALAIKRTAKEDVMI-GDKLVRANEGIIASNQSANRDEE [0ssp] #hhhhhhhh eee eee eee eeeee hh [0s] 1n40a #GVEELLRINLSFADGLPRLATADIQV-GDVLVRKGELVLVLLEGANFDPE [0ssp] #hhhhhhhh eee eee eee eeee hh [0s] 1cpt #LVDEAVRWTAPVKSFM-RTALADTEV-RGQNIKRGDRIMLSYPSANRDEE [0ssp] #hhhhhhhh hhh ee eee eee eee eeeee hh [0s] 1qmqa #ACEELLRRFSLVA-DG-RILTSDYEF-HGVQLKKGDQILLPQMLSGLDER [0ssp] #hhhhhhhh eee eee eee eeee hh hh [0s] 1lfka #AVDELIRYLTVPYSPTPRIAREDLTL-AGQEIKKGDSVICSLPAANRDPA [0ssp] #hhhhhhhh eee eee eee eeee hhh hh [0s] 1io7a #AIEEALRYSPPVMRTV-RKTKERVKL-GDQTIEEGEYVRVWIASANRDEE [0ssp] #hhhhhhhh hhh eee eee eee eeeeehh hh [0c] Conservation #566*56*4344431351736456546055338457638655334656754 [0s] 1n97a #-FPDG-EAFRPERFLEERG---TPSGRYFPFGLGQRLCLGRDFALLEGPI [0ssp] # ee hhhhhhhhhhhh [0s] 1jpza #IWGDDVEEFRPERFENPSA---IPQHAFKPFGNGQRACIGQQFALHEATL [0ssp] # hhh eee hhhhhhhhhhhhhhh [0s] 1e9xa #DFPDP-HDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKA [0ssp] # ee hhhhhhhhhhhh [0s] 1dt6a #AFPNP-KVFDPGHFLDESGNF-KKSDYFMPFSAGKRMCVGEGLARMELFL [0ssp] # hhhhhhhhhh [0s] 1gwia #AHGP-----TADRFDLTRT---S-GNRHISFGHGPHVCPGAALSRMEAGV [0ssp] #h hhhhhhhhhh [0s] 1jipa #QF-P-----DPHRFDVTRD---T--RGHLSFGQGIHFCMGRPLAKLEGEV [0ssp] #h hhhhhhhhhh [0s] 1jfba #VF-E-----NPDEFNMNRK---WPPQDPLGFGFGDHRCIAEHLAKAELTT [0ssp] #h hhhhhhhhhh [0s] 1n40a #HF-P-----NPGSIELDRP---N-PTSHLAFGRGQHFCPGSALGRRHAQI [0ssp] #h hhhhhhhhhh [0s] 1cpt #VF-S-----NPDEFDITRF---P--NRHLGFGWGAHMCLGQHLAKLEMKI [0ssp] #h hhhhhhhhhh [0s] 1qmqa #EN-A-----APMHVDFSRQ---K--VSHTTFGHGSHLCLGQHLARREIIV [0ssp] #h hhhhhhhhhh [0s] 1lfka #LA-P-----DVDRLDVTRE---P--IPHVAFGHGVHHCLGAALARLELRT [0ssp] #h hhhhhhhhhh [0s] 1io7a #VF-H-----DGEKFIPDRN---P--NPHLSFGSGIHLCLGAPLARLEARI [0ssp] #h hhhhhhhhhh [0c] Conservation #350400000464574348300030133554*93*374*595378558436 [0s] 1n97a #VLRAFFRRF-RLD-P-LPF---PRVLAQVTLRPEGGLPARPRE------- [0ssp] #hhhhhhhhe eee eeeee eeeee [0s] 1jpza #VLGMMLKHF-DFE-D-HTNY-ELDIKETLTLKPE-GFVVKAKSKKIPLGG [0ssp] #hhhhhhhhe eee e eeeeee eeeeee [0s] 1e9xa #IFSVLLREY-EFEMA-QPPESYRNDHSKMVVQLAQPACVRYRRRT----- [0ssp] #hhhhhhhh eee ee eeeeeee [0s] 1dt6a #FLTSILQNF-KLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPIHH---- [0ssp] #hhhhhhhhe eee eeeeee [0s] 1gwia #ALPALYARFPHLDLAVPAA--ELRNKPVVTQNDLFELPVRLAHH------ [0ssp] #hhhhhhhh ee hh h ee eeeeeee [0s] 1jipa #ALRALFGRFPALSLGIDAD--DVVWRRSLLLRGIDHLPVRLDG------- [0ssp] #hhhhhhhh ee ee eeeeeee [0s] 1jfba #VFSTLYQKFPDLKVAVPLG--KINYTPLNRDVGIVDLPVIF--------- [0ssp] #hhhhhhhh ee ee ee eee [0s] 1n40a #GIEALLKKMPGVDLAVPID--QLVWRTRFQRRIPERLPVLW--------- [0ssp] #hhhhhhhh ee hh h ee eeeeee [0s] 1cpt #FFEELLPKLKSVELS---G--PPRLVATNFVGGPKNVPIRFTKA------ [0ssp] #hhhhhhhh ee ee eeeeeeee [0s] 1qmqa #TLKEWLTRIPDFSIA--PG--AQIQHKSGIVSGVQALPLVWDPATTK--A [0ssp] #hhhhhhhh ee eee eeeeee [0s] 1lfka #VFTELWRRFPALRLADPAQ--DTEFRLTTPAYGLTELMVAW--------- [0ssp] #hhhhhhhh ee ee [0s] 1io7a #AIEEFSKRFRHIEI----L--DTEKVPNEVLNGYKRLVVRLKS------- [0ssp] #hhhhhhhh ee eeeeeee [0c] Conservation #46456546723654412320034323343344332364743220000000 [0s] 1n97a #- [0ssp] # [0s] 1jpza #I [0ssp] # [0s] 1e9xa #- [0ssp] # [0s] 1dt6a #- [0ssp] # [0s] 1gwia #- [0ssp] # [0s] 1jipa #- [0ssp] # [0s] 1jfba #- [0ssp] # [0s] 1n40a #- [0ssp] # [0s] 1cpt #- [0ssp] # [0s] 1qmqa #V [0ssp] # [0s] 1lfka #- [0ssp] # [0s] 1io7a #- [0ssp] # [0c] Conservation #0 Iteration 0 SP= 221556.00 AvSP= 8.890 SId= 4983 AvSId= 0.200 Nseq= 12 Len= 501 Naa= 4896 Ngaps= 1116 [tr0] ------------------------------------------- 1 1n97a [tr0] ------------------------------+ 5295.6 [tr0] | | --------- 2 1jpza [tr0] | ----------------------------------+ 6114.8 [tr0] | --------- 12 1e9xa [tr0]-----------------------------------+ 4568.9 [tr0]| ------------------------------------------------------------------------- 3 1dt6a [tr0]+ 3730.2 [tr0]| ---------------------------------------- 4 1gwia [tr0]| ---+ 5375.1 [tr0]| | ---------------------------------------- 5 1jipa [tr0]| ----+ 5280.0 [tr0]| | ------------------------------------------- 7 1jfba [tr0]| -----+ 5204.6 [tr0]| | ----------------------------------------------- 10 1n40a [tr0]| ------+ 5083.3 [tr0]| | | ------------------------------------------------ 9 1cpt [tr0]| | ----+ 5168.2 [tr0]| | ------------------------------------------------ 11 1qmqa [tr0]| --------------+ 4938.2 [tr0]| | ---------------------------------------------------------- 6 1lfka [tr0]------------------------------------+ 4589.2 [tr0] ------------------------------------------------------------------------ 8 1io7a Alignment written to file /data01/scratch/jobs/e4f31c7d121924ca83863aa226cccdd0/p450.msf PRALINE computation time has been: 3285.000 seconds (54 mins 45 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 ssmat=/home/ibivu/apps/praline/mat/luthy.mat H_GO=13.000000 E_GO=13.000000 C_GO=6.000000 psipred tree msf 1> results.out 2> errors.out