/*********************************************************************************/ /* 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 DSSP 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 Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1n97.dssp 2. 1jpza tikempqpktfgelknlpllntdkpvqalmkiadelgeifkfeapgrvtrylssqrlikeacdesrfdknlsqalkfvrdfagdglftswtheknwkkah nillpsfsqqamkgyhammvdiavqlvqkwerlnadehievpedmtrltldtiglcgfnyrfnsfyrdqphpfitsmvraldeamnklqranpddpayde nkrqfqedikvmndlvdkiiadrkasqsddllthmlngkdpetgeplddeniryqiitfliaghettsgllsfalyflvknphvlqkaaeeaarvlvdpv psykqvkqlkyvgmvlnealrlwptapafslyakedtvlggeyplekgdelmvlipqlhrdktiwgddveefrperfenpsaipqhafkpfgngqracig qqfalheatlvlgmmlkhfdfedhtnyeldiketltlkpegfvvkakskkiplggi 456 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1jpz.dssp 3. 1dt6a ppgptpfpiignilqidakdisksltkfsecygpvftvylgmkptvvlhgyeavkealvdlgeefagrgsvpilekvskglgiafsnaktwkemrrfslm tlrnfgmgkrsiedriqeearclveelrktnaspcdptfilgcapcnvicsvifhnrfdykdeeflklmeslhenvellgtpldyfpgihktllknadyi knfimekvkehqklldvnnprdfidcflikmeqennleftleslviavsdlfgagtettsttlryslllllkhpevaarvqeeiervigrhrspcmqdrs rmpytdaviheiqrfidllptnlphavtrdvrfrnyfipkgtdiitsltsvlhdekafpnpkvfdpghfldesgnfkksdyfmpfsagkrmcvgeglarm elflfltsilqnfklqslvepkdlditavvngfvsvppsyqlcfipihh 449 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1dt6.dssp 4. 1gwia aripldpfvtdldgesarlraagplaavelpggvpvwavthhaeakalltdprlvkdinvwgawrrgeipadwpliglanpgrsmltvdgaehrrlrtlv aqaltvrrvehmrgriteltdrlldelpadggvvdlkaafayplpmyvvadlmgieearlprlkvlfekffstqtppeevvatltelasimtdtvaakra apgddltsaliqasengdhltdaeivstlqlmvaaghettislivnavvnlsthpeqralvlsgeaewsavveetlrfstptshvlirfaaedvpvgdrv ipagdalivsygalgrderahgptadrfdltrtsgnrhisfghgphvcpgaalsrmeagvalpalyarfphldlavpaaelrnkpvvtqndlfelpvrla hh 402 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1gwi.dssp 5. 1jipa ttvpdlesdsfhvdwyrtyaelretapvtpvrflgqdawlvtgydeakaalsdlrlssdpkkkypgvevefpaylgfpedvrnyfatnmgtsdppthtrl rklvsqeftvrrveamrprveqitaelldevgdsgvvdivdrfahplpikvicellgvdekyrgefgrwsseilvmdperaeqrgqaarevvnfildlve rrrtepgddllsalirvqddddgrlsadeltsialvlllagfessvsligigtylllthpdqlalvrrdpsalpnaveeilryiappetttrfaaeevei ggvaipqystvlvangaanrdpkqfpdphrfdvtrdtrghlsfgqgihfcmgrplaklegevalralfgrfpalslgidaddvvwrrslllrgidhlpvr ldg 403 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1jip.dssp 6. 1lfka dprplhirrqgldpadellaagaltrvtaethwmatahavvrqvmgdhqqfstrrrwdpelvgnlmdydppehtrlrrkltpgftlrkmqrmapyieqiv ndrldemeragspadliafvadkvpgavlcelvgvprddrdmfmklchghldaslsqkrraalgdkfsryllamiarerkepgegmigavvaeygddatd eelrgfcvqvmlagddnisgmiglgvlamlrhpeqidafrgdeqsaqravdeliryltvpysptpriaredltlagqeikkgdsvicslpaanrdpalap dvdrldvtrepiphvafghgvhhclgaalarlelrtvftelwrrfpalrladpaqdtefrlttpaygltelmvaw 375 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1lfk.dssp 7. 1jfba apsfpfsrasgpeppaefaklratnpvsqvklfdgslawlvtkhkdvcfvatseklskvrtrqgfpelsasgkqaakakptfvdmdppehmhqrsmvept ftpeavknlqpyiqrtvddlleqmkqkgcangpvdlvkefalpvpsyiiytllgvpfndleyltqqnairtngsstareasaanqelldylailveqrlv epkddiisklcteqvkpgnidksdavqiaflllvagnatmvnmialgvatlaqhpdqlaqlkanpslapqfveelcryhtasalaikrtakedvmigdkl vranegiiasnqsanrdeevfenpdefnmnrkwppqdplgfgfgdhrciaehlakaelttvfstlyqkfpdlkvavplgkinytplnrdvgivdlpvif 399 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1jfb.dssp 8. 1io7a mydwfsemrkkdpvyydgniwqvfsyrytkevlnnfskfssdltgyherledlrngkirfdiptrytmltsdpplhdelrsmsadifspqklqtletfir ettrslldsidpreddivkklavplpiiviskilglpiedkekfkewsdlvafrlgkpgeifelgkkyleligyvkdhlnsgtevvsrvvnsnlsdiekl gyiillliagnetttnlisnsvidftrfnlwqrireenlylkaieealrysppvmrtvrktkervklgdqtieegeyvrvwiasanrdeevfhdgekfip drnpnphlsfgsgihlclgaplarleariaieefskrfrhieildtekvpnevlngykrlvvrlks 366 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1io7.dssp 9. 1cpt mdaratipehiartvilpqgyaddeviypafkwlrdeqplamahiegydpmwiatkhadvmqigkqpglfsnaegseilydqnneafmrsisggcphvid sltsmdppthtayrgltlnwfqpasirkleenirriaqasvqrlldfdgecdfmtdcalyyplhvvmtalgvpeddeplmlkltqdffgveaarrfheti atfydyfngftvdrrscpkddvmsllanskldgnyiddkyinayyvaiataghdttssssggaiiglsrnpeqlalaksdpaliprlvdeavrwtapvks fmrtaladtevrgqnikrgdrimlsypsanrdeevfsnpdefditrfpnrhlgfgwgahmclgqhlaklemkiffeellpklksvelsgpprlvatnfvg gpknvpirftka 412 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1cpt.dssp 10. 1n40a atvllevpfsargdripdavaelrtrepirkvrtitgaeawlvssyalctqvledrrfsmketaaagaprlnaltvppevvnnmgniadaglrkavmkai tpkapgleqflrdtanslldnlitegapadlrndfadplatalhckvlgipqedgpklfrslsiafmssadpipaakinwdrdieymagilenpnittgl mgelsrlrkdpayshvsdelfatigvtffgagvistgsflttalisliqrpqlrnllhekpelipagveellrinlsfadglprlatadiqvgdvlvrkg elvlvlleganfdpehfpnpgsieldrpnptshlafgrgqhfcpgsalgrrhaqigieallkkmpgvdlavpidqlvwrtrfqrriperlpvlw 394 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1n40.dssp 11. 1qmqa anlaplpphvpehlvfdfdmynpsnlsagvqeawavlqesnvpdlvwtrcngghwiatrgqlireayedyrhfssecpfipreageaydfiptsmdppeq rqfralanqvvgmpvvdklenriqelacslieslrpqgqcnftedyaepfpirifmllaglpeediphlkyltdqmtrpdgsmtfaeakealydylipii eqrrqkpgtdaisivangqvngrpitsdeakrmcglllvggldtvvnflsfsmeflakspehrqelierperipaaceellrrfslvadgriltsdyefh gvqlkkgdqillpqmlsglderenaapmhvdfsrqkvshttfghgshlclgqhlarreiivtlkewltripdfsiapgaqiqhksgivsgvqalplvwdp attkav 406 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1qmq.dssp 12. 1e9xa msavalprvsgghdehghleefrtdpiglmqrvrdecgdvgtfqlagkqvvllsgshanefffragdddldqakaypfmtpifgegvvfdasperrkeml hnaalrgeqmkghaatiedqvrrmiadwgeageidlldffaeltiytssacligkkfrdqldgrfaklyhelergtdplayvdpylpiesfrrrdearng lvalvadimngrianpptdksdrdmldvliavkaetgtprfsadeitgmfismmfaghhtssgtaswtlielmrhrdayaavideldelygdgrsvsfha lrqipqlenvlketlrlhppliilmrvakgefevqghrihegdlvaaspaisnripedfpdphdfvparyeqprqedllnrwtwipfgagrhrcvgaafa imqikaifsvllreyefemaqppesyrndhskmvvqlaqpacvryrrrt 449 amino acids Reading /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/1e9x.dssp Running PSI-BLAST (e-value threshold: 0.010000) for sequence [1] 1n97a Filtering PSI-BLAST alignment file /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/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/7dc3f8864fc64711afb1c7eee5b976df/1e9xa-p450_psiali.fasta Removed 20 redundant sequences from 101 hits. [0s] 1n97a #MKR-LSLREA-----WPYL-----KDLQQD-PLAVLLAWGRAHP-RL--- [0ssp] # ee hhhh hhhh hhhhh hhhhhhhhhhh ee [0s] 1jpza #--TIKEMPQPKTFGELKNL-----PLLNTDKPVQALMKIADELGEIF--- [0ssp] # hhh h hhh hhhhhhhhhhhh ee [0s] 1e9xa #MSAVALPRVSGGHDEHGHL-----EEFRTD-PIGLMQRVRDECGDVG--- [0ssp] # e e e h hhhhh hhhhhhhhhhhh ee [0s] 1dt6a #------PPGPTPFPIIGNI-----LQIDAKDISKSLTKFSECYGPVF--- [0ssp] # hhh hhhhhhhhhhhh ee [0s] 1gwia #--------ARI-PL----------DPFVTD-LDGESARLRAAGPLAA--- [0ssp] # e e hhhhhhhhhh eee [0s] 1jipa #-----TTVPDL-ES----------DSFHVD-WYRTYAELRETAPVTP--- [0ssp] # e hhh hhhhhhhhhhh eee [0s] 1jfba #-------APSFPFS----------RASGPE-PPAEFAKLRATNPVSQ--- [0ssp] # e hhhhhhhh eee [0s] 1n40a #----ATVLLEVPF-----------SARGDR-IPDAVAELRTREPIRK--- [0ssp] # e hhhhhhhhh eee [0s] 1lfka #-----------------------------D-PRPLHIRRQGLDPADELLA [0ssp] # hhh ee ee hhhh [0s] 1cpt #MDARATIPEHIARTVILPQG----YADDEV-IYPAFKWLRDEQPLAM--- [0ssp] # hhhhhhhh hh hh hhh hhhhhhhhhhh eee [0s] 1qmqa #-ANLAPLPPHVPEHLVFDFDMYNPSNLSAG-VQEAWAVLQESNVPDL--- [0ssp] # hhhe hhh hhhhhhhhh e [0s] 1io7a #-------------------------------MYDWFSEMRKKDPVYY--- [0ssp] # hhhhhhhhhh eee [0c] Conservation #00001112222111000010000022222404234444564425333000 [0s] 1n97a #---FLPLPRFPLALIFDPEGVEGALLA---EGTTKAT-----------FQ [0ssp] # ee eeee hhhhhhhhh ee hh [0s] 1jpza #---KFEAPGRVTRYLSSQRLIKEACDE--SRFDKNLS-----------QA [0ssp] # eeee eeeeee hhhhhhh eeee hh [0s] 1e9xa #---TFQLAGKQVVLLSGSHANEFFFRA--GDDDLDQA-----------KA [0ssp] # eeee eeeeee hhhhhhhhhh ee [0s] 1dt6a #---TVYLGMKPTVVLHGYEAVKEALVD--LGEEFAGR-----------GS [0ssp] # eee eeeee hhhhhhhh [0s] 1gwia #---VELPGGVPVWAVTHHAEAKALLTDPRLVKDINVWGAWRRG--EIPAD [0ssp] # eee eeeeee hhhhhhhh ee hhh hhhh [0s] 1jipa #---VRFL-GQDAWLVTGYDEAKAALSDLRLSSDPKKKYPGVEVEFPAYLG [0ssp] # eee eeeeee hhhhhhhhh ee hhh [0s] 1jfba #---VKLFDGSLAWLVTKHKDVCFVATSEKLSKVRTRQGFPE-------LS [0ssp] # ee eeeee hhhhhhhhh ee [0s] 1n40a #---VRTITGAEAWLVSSYALCTQVLEDRRFSMKETAAAGAP--------- [0ssp] # ee eeeee hhhhhhhh ee hhhh [0s] 1lfka #AGALTRVTAETHWMATAHAVVRQVMGDHQQFSTRRR-------------- [0ssp] # eeee eeee hhhhhhhhh eee [0s] 1cpt #---AHIEGYDPMWIATKHADVMQIGKQPGLFSNAEGSEILYDQNNEAFMR [0ssp] # e eeee hhhhhhhhh ee hhhhhhhh [0s] 1qmqa #---VWTRCNGGHWIATRGQLIREAYEDYRHFSSECPF----IPREAGEA- [0ssp] # eee hhh eeee hhhhhhhhh ee hhhh [0s] 1io7a #--------DGNIWQVFSYRYTKEVLNNFSKFSSDLTGYH---ERLEDLRN [0ssp] # eee hhhhhhhhh ee hh hhhhhh [0c] Conservation #00042232433455654443554643512334433320000000000022 [0s] 1n97a #YRALSRLT-GRGLLT--DWGESWKEARKALKDPF-LPKNVR-GYREAMEE [0ssp] #hhhhhhhh hhhhhhhhhhh hhh hhhhh hhhhhh [0s] 1jpza #LKFVRDFA-GDGLFTSWTHEKNWKKAHNILLPSF-SQQAMK-GYHAMMVD [0ssp] #hhhhhhhh hhhhhhhhhhhhhh hhhhh hhhhhhhh [0s] 1e9xa #YPFMTPIF-GEGVVF---DASPERRKEMLHNAAL-RGEQMK-GHAATIED [0ssp] # hhhhhhh hhhhhhhhh hhhhh hhhhhhhh [0s] 1dt6a #VPILEKVSKGLGIAF--SNAKTWKEMRRFSLMTLRNFGMGKRSIEDRIQE [0ssp] # hhhhhhhhhhh hhhhhhh [0s] 1gwia #WPLIGLANPGRSMLT--VDGAEHRRLRTLVAQAL-TVRRVE-HMRGRITE [0ssp] # hhhh hhh hhhhhhhhhhh hhhhh hhhhhh [0s] 1jipa #FPEDVRNYFATNMGT--SDPPTHTRLRKLVSQEF-TVRRVE-AMRPRVEQ [0ssp] # hhhhhhh hhh hhhhhhhhhh hhhhh hhhhhh [0s] 1jfba #ASGKQAAKAKPTFVD--MDPPEHMHQRSMVEPTF-TPEAVK-NLQPYIQR [0ssp] #hhhhhh hhh hhhhhh hhhh hhhhh hhhhhhhh [0s] 1n40a #-RLNALTVPPEVVNN--MGNIADAGLRKAVMKAI-TPK-AP-GLEQFLRD [0ssp] # hhhhhh hhhhhh hhhhhhh hhhhhhh [0s] 1lfka #----WDPELVGNLMD--YDPPEHTRLRRKLTPGF-TLRKMQ-RMAPYIEQ [0ssp] # hhh hhhhhhhhhhhhh hhhhh hhhhhhhh [0s] 1cpt #SISGGCPHVIDSLTS--MDPPTHTAYRGLTLNWF-QPASIR-KLEENIRR [0ssp] #hh hhh hhhhhhhhhh hhhhh hhhhhhhh [0s] 1qmqa #--------YDFIPTS--MDPPEQRQFRALANQVV-GMPVVD-KLENRIQE [0ssp] # hhhhhhhhhhhhh hhhhh hhhhhhhh [0s] 1io7a #GKIRFDIPTRYTMLT--SDPPLHDELRSMSADIF-SPQKLQ-TLETFIRE [0ssp] # hhh hhh hhhhhhhhh hhhhh hhhhhhhh [0c] Conservation #12222222132454400354444444845434360434365045533856 [0s] 1n97a #EARAFFGEWR----GE-ERDLDHEMLA-LSLRLLGRALFGKPLSPSLA-- [0ssp] #hhhhhhh eehhhhhhh hhhhhhhhhhh hhhh [0s] 1jpza #IAVQLVQKWERLNADE-HIEVPEDMTR-LTLDTIGLCGFNYRFNSFYRDQ [0ssp] #hhhhhhhhhh eehhhhhhh hhhhhhhhhhh hhh [0s] 1e9xa #QVRRMIADWGE---AG-EIDLLDFFAE-LTIYTSSACLIGK--KFRDQ-L [0ssp] #hhhhhh ee eeehhhhhhh hhhhhhhhhh h hhh [0s] 1dt6a #EARCLVEELRK-TNAS-PCDPTFILGC-APCNVICSVIFHNRFDYK---- [0ssp] #hhhhhhhhhh hhhh hhhhhhhhhh [0s] 1gwia #LTDRLLDELPADGG---VVDLKAAFAYPLPMYVVADLMGIEEARL----- [0ssp] #hhhhhhh eehhhh hhhhhhhhhhh hhhh [0s] 1jipa #ITAELLDEVGDSGV----VDIVDRFAHPLPIKVICELLGVDEKYR----- [0ssp] #hhhhhhh e eehhhh hhhhhhhhhhh [0s] 1jfba #TVDDLLEQMKQKGCANGPVDLVKEFALPVPSYIIYTLLGVPFNDL----- [0ssp] #hhhhhhhhhhhh eehhhh hhhhhhhhhhh hhhh [0s] 1n40a #TANSLLDNLITEGA---PADLRNDFADPLATALHCKVLGIPQEDG----- [0ssp] #hhhhhhhhhhhh ee hhhhhhhhhhhhh hhhh [0s] 1lfka #IVNDRLDEMERAGS---PADLIAFVADKVPGAVLCELVGVPRDDR----- [0ssp] #hhhhhhhhhhhh eehhhh hhhhhhhhhh hhhh [0s] 1cpt #IAQASVQRLLDFDG---ECDFMTDCALYYPLHVVMTALGVPEDDE----- [0ssp] #hhhhhhhhhh eeehhhh hhhhhhhhhh hhhh [0s] 1qmqa #LACSLIESLRP-QG---QCNFTEDYAEPFPIRIFMLLAGLPEEDI----- [0ssp] #hhhhhhhhhhh h eeehhhh hhhhhhhhhhh hhhh [0s] 1io7a #TTRSLLDSIDPRE-----DDIVKKLAVPLPIIVISKILGLPIEDK----- [0ssp] #hhhhhhh eehhhh hhhhhhhhhhh hhhh [0c] Conservation #46346755533132000348633357226643753456544325200000 [0s] 1n97a #-EHALKALDRIMA---------------------QTRSPLALLDLAAEAR [0ssp] # hhhhhhhhhhhh hhh hhhhh hhhhhh [0s] 1jpza #PHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKI [0ssp] # hhhhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhhhhhh [0s] 1e9xa #DGRFAKLYHELERGTDPL---AYVDPYLPIESFRRRDEARNGLVALVADI [0ssp] # hhhhhhhhhhhh hh hh hhhhhhhhhhhhhhhhhhhh [0s] 1dt6a #DEEFLKLMESLHENVEL----LGTPLDYFPGIHKTLLKNADYIKNFIMEK [0ssp] # hhhhhhhhhhhhhhh hhhhhhhhhhhhhhhhhhhh [0s] 1gwia #-PRLKVLFEKFFS--------------T-QTPPEEVVATLTELASIMTDT [0ssp] # hhhhhhhhhhh hhhhhhhhhhhhhhhhhh [0s] 1jipa #-GEFGRWSSEILV--------------MDPERAEQRGQAAREVVNFILDL [0ssp] # hhhhhhhhhh hhhhhhhhhhhhhhhhhhhhh [0s] 1jfba #-EYLTQQNAIRTN--------------G-SSTAREASAANQELLDYLAIL [0ssp] # hhhhhhhhhhh hhhhhhhhhhhhhhhhhh [0s] 1n40a #-PKLFRSLSIAFM--------------SSADPIPAAKINWDRDIEYMAGI [0ssp] # hhhhh hhhh e hhhhhhhhhhhhhhhhh [0s] 1lfka #-DMFMKLCHGHLD--------------A-SLSQKRRAALGDKFSRYLLAM [0ssp] # hhhhhhhhh hhhhhhhhhhhhhhhhhh [0s] 1cpt #-PLMLKLTQDFFG----------------VEAARRFHETIATFYDYFNGF [0ssp] # hhhhhhhh hhhhhhhhhhhhhhhhhhh [0s] 1qmqa #-PHLKYLTDQMTR----------------PDGSMTFAEAKEALYDYLIPI [0ssp] # hhhhhhhhhhh hhhhhhhhhhhhhhh [0s] 1io7a #-EKFKEWSDLVAF--------------R-LGKPGEIFELGKKYLELIGYV [0ssp] # hhhhhhhhh hhhhhhhhhhhhhhh [0c] Conservation #04363543434330000000000000010332235335334353456335 [0s] 1n97a #FRKDRGA--------LYREAEALIVH-PPLSH-LPRERALSEAVTLLVAG [0ssp] #hhhhhhh hhhhhhhh hhh hhhhhhhhhhhhhhh [0s] 1jpza #IADRKASQ-----SDDLLTHMLNGKDPETGEP-LDDENIRYQIITFLIAG [0ssp] #hhhhh hhhhhhh e e hhhhhhhhhhhhhh [0s] 1e9xa #MNGRIANPPTDKSDRDMLDVLIAVKA-ETGTPRFSADEITGMFISMMFAG [0ssp] #hhhhhh hhhhhhh e e hhhhhhhhhhhhhhh [0s] 1dt6a #VKEHQKLL-DVNNPRDFIDCFLI-KMEQENNLEFTLESLVIAVSDLFGAG [0ssp] #hhhhh hhhhhh hhhhhhhhhhhhhhh [0s] 1gwia #VAAKRAAP-----GDDLTSALIQASE-NG-DH-LTDAEIVSTLQLMVAAG [0ssp] #hhhhhh hhhhhhh e e hhhhhhhhhhhhhhh [0s] 1jipa #VERRRTEP-----GDDLLSALIRVQD-DDDGR-LSADELTSIALVLLLAG [0ssp] #hhhhhh hhhhhhh ee ee hhhhhhhhhhhhhhh [0s] 1jfba #VEQRLVEP-----KDDIISKLCTEQV-KP-GN-IDKSDAVQIAFLLLVAG [0ssp] #hhhhhh hhhhhhhh hhhhhhhhhhhhhhh [0s] 1n40a #LENPN--I-----TTGLMGELSRLRKDPAYSH-VSDELFATIGVTFFGAG [0ssp] #hh hhhhhhhhhh hhh hhhhhhhhhhhhhhh [0s] 1lfka #IARERKEP-----GEGMIGAVVAEYG----DD-ATDEELRGFCVQVMLAG [0ssp] #hhhhhh hhhhhhhhhh hh hhhhhhhhhhhhhh [0s] 1cpt #TVDRRSCP-----KDDVMSLLANSKL--DGNY-IDDKYINAYYVAIATAG [0ssp] #hhhh hhhhhhh e e hhhhhhhhhhhhhhh [0s] 1qmqa #IEQRRQKP-----GTDAISIVANGQV--NGRP-ITSDEAKRMCGLLLVGG [0ssp] #hhhhhh hhhhhh ee ee hhhhhhhhhhhhh [0s] 1io7a #KDHLN--S-----GTEVVSRVVNSN--------LSDIEKLGYIILLLIAG [0ssp] #hhh hhhhhhh hhhhhhhhhhhhh [0c] Conservation #5444532400000345565365434201213206545454333446649* [0s] 1n97a #HETVASALTWSFLLLSHRPDWQKRVAESEEAAL----------------- [0ssp] # hhhhhhhhhhhhhh hhhhhhhhh hhhhh [0s] 1jpza #HETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPV-PSYKQVKQLKYV [0ssp] # hhhhhhhhhhhhhhhh hhhhhhhhhhhhhh hhhhh hhh [0s] 1e9xa #HHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQL [0ssp] #hhhhhhhhhhhhhhhhh hhhhhhhhhhhhhhhhh hhhh hhh [0s] 1dt6a #TETTSTTLRYSLLLLLKHPEVAARVQEEIERVIGRHRSPCMQDRSRMPYT [0ssp] #hhhhhhhhhhhhhhhhh hhhhhhhhhhhhhh hhhh hhh [0s] 1gwia #HETTISLIVNAVVNLSTHPEQRALVLSGEAEW------------------ [0ssp] #hhhhhhhhhhhhhhhhh hhhhhhhh h [0s] 1jipa #FESSVSLIGIGTYLLLTHPDQLALVRRDPSAL------------------ [0ssp] #hhhhhhhhhhhhhhhh hhhhhhhhh hhhh [0s] 1jfba #NATMVNMIALGVATLAQHPDQLAQLKANPSLA------------------ [0ssp] #hhhhhhhhhhhhhhhhh hhhhhhhhh hhhh [0s] 1n40a #VISTGSFLTTALISLIQRPQLRNLLHEKPELI------------------ [0ssp] #hhhhhhhhhhhhhhhh hhhhhhhhh hhhh [0s] 1lfka #DDNISGMIGLGVLAMLRHPEQIDAFRGDEQSA------------------ [0ssp] # hhhhhhhhhhhhhhhh hhhhhhh hhhh [0s] 1cpt #HDTTSSSSGGAIIGLSRNPEQLALAKSDPALI------------------ [0ssp] #hhhhhhhhhhhhhhhhh hhhhhhhhh hhhh [0s] 1qmqa #LDTVVNFLSFSMEFLAKSPEHRQELIERPERI------------------ [0ssp] # hhhhhhhhhhhhhhhh hhhhhhhhh hhhh [0s] 1io7a #NETTTNLISNSVIDFTRFNLWQRIRE--ENLY------------------ [0ssp] #hhhhhhhhhhhhhhhhh hhhhhh h h [0c] Conservation #35755546436653855575345453444545000000000000000000 [0s] 1n97a #-AAFQEALRLYPPAW-ILTRRLERPLLL-GEDRLPPGTTLVLSPYVTQRL [0ssp] # hhhhhhhhh eeeee eee eee eeee hhhhhhh [0s] 1jpza #GMVLNEALRLWPTAP-AFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRD [0ssp] #hhhhhhhhhh eeeeee eee eee eeeeehhhh [0s] 1e9xa #ENVLKETLRLHPPLI-ILMRVAKGEFEV-QGHRIHEGDLVAASPAISNRI [0ssp] #hhhhhhhhhh eeeee eee eee eeee hhhh [0s] 1dt6a #DAVIHEIQRFIDLLPTNLPHAVTRDVRF-RNYFIPKGTDIITSLTSVLHD [0ssp] #hhhhhhhhhhh e ee e e eeeeehhhhh [0s] 1gwia #SAVVEETLRFSTPTSHVLIRFAAEDVPV-GDRVIPAGDALIVSYGALGRD [0ssp] #hhhhhhhhhh e eeeeee eee eee eeee hhhh [0s] 1jipa #PNAVEEILRYIAPPE-TTTRFAAEEVEI-GGVAIPQYSTVLVANGAANRD [0ssp] #hhhhhhhhhh eeeee eee eee eeee hhhh [0s] 1jfba #PQFVEELCRYHTASALAIKRTAKEDVMI-GDKLVRANEGIIASNQSANRD [0ssp] #hhhhhhhhhh eeee eee eee eeee hhhh [0s] 1n40a #PAGVEELLRINLSFADGLPRLATADIQV-GDVLVRKGELVLVLLEGANFD [0ssp] #hhhhhhhhh e eeeee eee eee eeee hhhhh [0s] 1lfka #QRAVDELIRYLTVPYSPTPRIAREDLTL-AGQEIKKGDSVICSLPAANRD [0ssp] #hhhhhhhhhhh e eee eee eee eeee hhhh [0s] 1cpt #PRLVDEAVRWTAPVK-SFMRTALADTEV-RGQNIKRGDRIMLSYPSANRD [0ssp] #hhhhhhhhhhh e eeee eee eee eeee hhhh [0s] 1qmqa #PAACEELLRRFSLVA--DGRILTSDYEF-HGVQLKKGDQILLPQMLSGLD [0ssp] #hhhhhhhhhh e eeeee eee eee eeee hhhh [0s] 1io7a #LKAIEEALRYSPPVM-RTVRKTKERVKL-GDQTIEEGEYVRVWIASANRD [0ssp] #hhhhhhhhhh e eeeee eee eee eeee hhhh [0c] Conservation #34566*56*43444302437364565460553384576386553346567 [0s] 1n97a #H--F-PDG-EAFRPERFLE---ERGTPSGRYFPFGLGQRLCLGRDFALLE [0ssp] # hhhh e e hhhhhhh [0s] 1jpza #KTIW-GDDVEEFRPERFEN---PSAIPQHAFKPFGNGQRACIGQQFALHE [0ssp] #hhhh hhhh hhh hhh hhhhhhh [0s] 1e9xa #PEDF-PDP-HDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQ [0ssp] # hhhh hhhh hhh hhhhhhh [0s] 1dt6a #EKAF-PNP-KVFDPGHFLDES-GNFKKSDYFMPFSAGKRMCVGEGLARME [0ssp] # hhhh hhhhhhh [0s] 1gwia #ERAHGPTA-DRFDLTRTS---------GNRHISFGHGPHVCPGAALSRME [0ssp] #hhhh hhh h hhhhhhh [0s] 1jipa #PKQF-PDP-HRFDVTRDT----------RGHLSFGQGIHFCMGRPLAKLE [0ssp] # hhhhhhh [0s] 1jfba #EEVF-ENP-DEFNMNRKWP--------PQDPLGFGFGDHRCIAEHLAKAE [0ssp] # hhh hhhhhhh [0s] 1n40a #PEHF-PNP-GSIELDRPN---------PTSHLAFGRGQHFCPGSALGRRH [0ssp] # hhh hhhhhhh [0s] 1lfka #PALA-PDV-DRLDVTREP----------IPHVAFGHGVHHCLGAALARLE [0ssp] # hhhhhhh [0s] 1cpt #EEVF-SNP-DEFDITRFP----------NRHLGFGWGAHMCLGQHLAKLE [0ssp] # hhhhhhh [0s] 1qmqa #EREN-AAP-MHVDFSRQK----------VSHTTFGHGSHLCLGQHLARRE [0ssp] # hhhhhhh [0s] 1io7a #EEVF-HDG-EKFIPDRNP----------NPHLSFGSGIHLCLGAPLARLE [0ssp] # hhh hhhhhhh [0c] Conservation #543505540447444833000000000133554*93*374*595378558 [0s] 1n97a #GPIVLRAFFRRF-RL-DP-LPFPRVLAQ---VTLRPEGGLPARPRE---- [0ssp] #hhhhhhhhh e eee eee ee e [0s] 1jpza #ATLVLGMMLKHF-DF-ED-HTNYELDIKE-TLTLKPEGF-VVKAKSKKIP [0ssp] #hhhhhhhhhhhe ee e eee eee eeeeee [0s] 1e9xa #IKAIFSVLLREY-EFEMA-QPPESYRNDHSKMVVQLAQPACVRYRRRT-- [0ssp] #hhhhhhhhhhhe eeee hhh ee ee eeeeee [0s] 1dt6a #LFLFLTSILQNF-KLQSLVEPKDLDITAVVNGFVSVPPSYQLCFIPIHH- [0ssp] #hhhhhhhhhhhe eee hhh e e eeee [0s] 1gwia #AGVALPALYARFPHLDLAVPAAELRNKPV-VTQNDLF---ELPVRLAHH- [0ssp] #hhhhhhhhhhh ee hhh e e e eee [0s] 1jipa #GEVALRALFGRFPALSLGIDADDVVWRRS-LLLRGID---HLPVRLDG-- [0ssp] #hhhhhhhhh ee hhh e e eee [0s] 1jfba #LTTVFSTLYQKFPDLKVAVPLGKINYTPL-NRDVGIV---DLPVIF---- [0ssp] #hhhhhhhhhhh ee hhh ee ee e eee [0s] 1n40a #AQIGIEALLKKMPGVDLAVPIDQLVWRTR-FQRRIPE---RLPVLW---- [0ssp] #hhhhhhhhhhh ee hhh e e e e eee [0s] 1lfka #LRTVFTELWRRFPALRLADPAQDTEFRLT-TPAYGLT---ELMVAW---- [0ssp] #hhhhhhhhhhh ee eee e eee e eee [0s] 1cpt #MKIFFEELLPKLKSVELS---GPPRLVAT-NFVGGPK---NVPIRFTKA- [0ssp] #hhhhhhhhhhheeeeee ee e ee e eeeeee [0s] 1qmqa #IIVTLKEWLTRIPDFSIA--PGAQIQHKS-GIVSGVQ---ALPLVWDPAT [0ssp] #hhhhhhhhhhh ee ee e ee eee hhh [0s] 1io7a #ARIAIEEFSKRFRHIEI----LDTEKVPN-EVLNGYK---RLVVRLKS-- [0ssp] #hhhhhhhhh eeee eeeee e ee eeeeeee [0c] Conservation #43646456546723635412324332333023334430003745421100 [0s] 1n97a #---- [0ssp] # [0s] 1jpza #LGGI [0ssp] # [0s] 1e9xa #---- [0ssp] # [0s] 1dt6a #---- [0ssp] # [0s] 1gwia #---- [0ssp] # [0s] 1jipa #---- [0ssp] # [0s] 1jfba #---- [0ssp] # [0s] 1n40a #---- [0ssp] # [0s] 1lfka #---- [0ssp] # [0s] 1cpt #---- [0ssp] # [0s] 1qmqa #TKAV [0ssp] # [0s] 1io7a #---- [0ssp] # [0c] Conservation #0000 Iteration 0 SP= 220922.00 AvSP= 8.900 SId= 4991 AvSId= 0.201 Nseq= 12 Len= 504 Naa= 4896 Ngaps= 1152 [tr0] ------------------------------------------- 1 1n97a [tr0] ------------------------------+ 5259.8 [tr0] | | -------- 2 1jpza [tr0] | -----------------------------------+ 6172.9 [tr0] | -------- 12 1e9xa [tr0]-----------------------------------+ 4470.5 [tr0]| ------------------------------------------------------------------------- 3 1dt6a [tr0]+ 3544.9 [tr0]| ---------------------------------------- 4 1gwia [tr0]| -----+ 5354.0 [tr0]| | ---------------------------------------- 5 1jipa [tr0]| -----+ 5207.6 [tr0]| | --------------------------------------------- 7 1jfba [tr0]| --------+ 5094.3 [tr0]| | -------------------------------------------------- 10 1n40a [tr0]| --+ 4881.9 [tr0]| | ---------------------------------------------------------- 6 1lfka [tr0]| ---------------+ 4815.1 [tr0]| | | ------------------------------------------------ 9 1cpt [tr0]| | ------------+ 5145.3 [tr0]| | ------------------------------------------------ 11 1qmqa [tr0]---------------------------------+ 4430.5 [tr0] --------------------------------------------------------------------------- 8 1io7a Alignment written to file /data01/scratch/jobs/7dc3f8864fc64711afb1c7eee5b976df/p450.msf PRALINE computation time has been: 3294.000 seconds (54 mins 54 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 dssp tree msf 1> results.out 2> errors.out