;; pepper version 3.20 run on phycomt.all ;; ;; First non-blank line of input file: ;; 62,082 nt, circular mapping; assembly provided by Jane Grimwood, jane@paxil.stanford.edu ;; ;; Genetic code used: 1 ;; ;; ;; Protein(s) reported: ;; atp6 atp8 atp9 cob cox1 ;; cox2 cox3 nad1 nad2 nad3 ;; nad4 nad4L nad5 nad6 orf138 ;; orf150 orf168 orf178 orf190 orf223 ;; orf246 orf271 orf291 orf303 orf318 ;; orf331 orf361 orf378 orf380 orf408 ;; orf511 ;; ;; The switch '-m' was not used. ;; >Phycomyces blakesleeanus atp6 ; 259 aa on 'Phycomyces' MSTLATTFLVNNPLEQFEIIDFVFILAPILGFTKLSLTNIGFYLILVVVITISMNILSLN NGNVIPSRWAIHSESIYGSILNMVREQIGSANEIYVPLIFTLFNFVLFSNLIGLVPYSFT ATSHLILTLSLSTAILIGVTIIGFQRHGLGFFAFFIPAGTPLGLVFLLVAIELISYLARA VSLGVRLGANMIAGHSLLKIISTFTWKMVVAGPVLLLVSVLPLLFLTALAGLEFGIAMLQ AYVFTILTCSYLKDAIDLH* >Phycomyces blakesleeanus atp8 ; 48 aa on 'Phycomyces' MPQLVPFYFLNQVSFAFLLLMVLLYVVSKYILPNFMLVQSARMFLASK* >Phycomyces blakesleeanus atp9 ; 74 aa on 'Phycomyces' MVAAAKILGAGLATIGLAGAGVGVGLVFAALINSTSRNPSLRPQLFSYTILGFALTEAIG LFALMMAFLLLYAA* >Phycomyces blakesleeanus cob ; 386 aa on 'Phycomyces' MKLLKSHSLLSLANSYVIDSPQPSNLNYAWNFGSLLALCLGIQIVTGVTLAMHYTPNIDL AFISVEHIMRDVNYGWMIRYLHANTASFFFLFVYLHIGRGLYYGSYKSPRALPWSIGVII LILMMATAFLGYVLPWGQMSLWGATVITNLLSAIPWIGKDLVEFIWGGFSVDNATLNRFF SLHYLLPFILAALAVMHLITLHEHGSSNPLGITANADRLYMHPYYTFKDLVTIFLFFLVL GLFLFYAPNKLGHPDNYIPANPMQTPASIVPEWYLLPFYAILRSIPDKLGGVIAMFGSLL ILLAMPVLDTSRVRGSAFRPLMKLAFWLLVVDFLILLWCGGQHVEEPFITLGQFATGFYF AWFLILLPAIGIIENTLMDLAPENND* >Phycomyces blakesleeanus cox1 ; 528 aa on 'Phycomyces' MVRWLFSTNAKDIGTLYIIFSIFAGMIGTAFSMLIRLELAGPGVQYLQGDHQLYNVIVTA HAFVMIFFLVMPAMIGGFGNWFVPLMIGAPDMAFPRLNNISFWLLPPSLFLLVASAFVEN GAGTGWTVYPPLSGVASHSGGSVDLAIFSLHLSGISSMLGAMNFITTILNMRAPGMSFHK MPLFVWAVLITAVLLLLSLPVLAGGITMLLTDRNFNTSFYEPAGGGDPLLYQHLFWFFGH PEVYILIIPGFGIVSHVVSTFCGKPIFGYLGMVYAMLSIGVLGFIVWSHHMYTVGLDVDT RAYFTAATMIIAVPTGIKIFSWLATLYGGSIRFTTPMLFALGFLALFTIGGLTGVMLANA SMDVALHDTYYVVAHFHYVLSMGAVFALFAAFYYWIGKITGKTYNELLGQIHFWTLFIGV NLTFFPQHMLGLAGMPRRIPDYPDAYAGWNLVSSFGSIISIVASLVFLYALYDLLAKQEY NLANNYWFVPQFFSSSRVIGATSTATTLEWSLTSPPSFHTVNSLPVQS* >Phycomyces blakesleeanus cox2 ; 255 aa on 'Phycomyces' MLNMLKSLNIITPVWNDAPEPWQLSFQDGASPSFEGIVELHDQIMFYLVIILFGVSWMLS SVIFNFGSNQNKIVYKYHNHGTLIELIWTITPALVLIAIAFPSFKLLYLMDEVIDPAMTI KALGHQWYWSYEYSDFVNEDGESIEFDSYLVPTDELEEGQLRLLEVDNRVVVPVGTHIRF IVTGADVIHSFAVPSLGLKIDAIPGRLNQTSVLVEREGVYYGQCSEICGVHHGFMPIAVE AVSLEKYLAWLNEQA* >Phycomyces blakesleeanus cox3 ; 270 aa on 'Phycomyces' MTTKLINRSVQAHPFHLVEASPWPIAVSFSLLVTTLSGVMTFHGYSNGLFLLTLGLISTI ATMTLWFKDITREGTFQGHHTFAVQKGLSLGFVLFVISEVFFFISIFWAFFHSSLAPTVE LGAHWPPAGIETLNPWEVPLLNTVILLSSGATVTYAHHSLIQGNRAGVIYGLIATVVLAT IFTGFQGFEYYNAPFTFSDGVYGSTFYMATGFHGIHVVIGTIFLTVGLFRVLSYHLTDHH HLGFEQAILYWHFVDVVWLFLFISVYWWGG* >Phycomyces blakesleeanus nad1 ; 325 aa on 'Phycomyces' MLLSLIEVLIVIVPLLLSVAFMTIAERKAMGSMQRRLGPNRVGYYGLLQPFADALKLFVK ESVLPAHSNKALFLFAPVISLITSLLSWGVVPFGAGLTLSDLSLGILYLLAVSSLGVYGV IFAGWAANSKYAFLGGLRSTAQMVSYEVVLGLIIITVVLLVGSLNVTEIIQAQISVWYII PLLPLSLMFLISAIAETNRAPFDLPEAESELVAGFFTEHSSVPFVMFFLAEYASIILMST LVSILFLGGYLIPFVSFENPTFLSLEGLSLGLKTCLILFIYIWVRASFPRLRYDQLMSFT WTGMLPLALGFIILVPCILVAFEIA* >Phycomyces blakesleeanus nad2 ; 501 aa on 'Phycomyces' MVLFSVLTMILAIALFSLRIPAIYFNRITIIILLYSALLSYNTLYTDLVSSGVGLFGGLF QVTAITQSIDVFIYLLGALVLLLGENSTLVSKGKKLSVLAEYPLIALLSVLGMSSLISSS DLVSMFLSIELQSFAVYILATIYRESESATAAGLKYFLLGSLSSALILLGSSLLYGFTGL TSFEGLYMLCSTTTTNHAAIEISVLLMVVGLLFKVSAAPFHNWAPDVYDGVPTVVTTWLT TMPKISFLVFILEFQGFTQLGNWSSWTYLLLISSLLSLVVGTVGGLAQYRIKRLLTFSTI SHVGFLLLALAINSEESVESFLFYLIQYSLTNVNVFFILIAFGYLLQTKGLSPYSPIQYI NQLKGQFQANPLLGLSLAICLFSMAGIPPLVGFFGKQMVLYAATHNGNFFLALVAVVVSV VSAAYYLRVIKVIHFDPLNVTETVETNNGSSNNIGGSVSGVLTTSSSLVIATITLLLIFF ILNPSPLLNSVHLLTLNLFYW* >Phycomyces blakesleeanus nad3 ; 120 aa on 'Phycomyces' MSTLTFFVLFIPVLTLVLLVVNQLLAVNKPYSEKVSPYECGFTPLGDARQKFSVQFYLVA ILFIVFDLEVLFLFPFAVSLYEVSSMGFWIVIIFLIILTIGFVYEWSKGALKFTKDPREA * >Phycomyces blakesleeanus nad4 ; 475 aa on 'Phycomyces' MILSLLITPILGVIGVILSGENSSLQKRVALASSLLTFVLSLVLWAGFDSNYNGFQFVSS FPTVTTKEVVGVDGISLFFVLLTTFIIPICILSSWDSIKTGIKYFLIAFLILETLLIAVF VVLDLLLFYICFESVLIPMFLIIGIWGARERKIHAAYQFFLYTLLGSLFMLLAILVIYFE VGSTDYQVLAVADISETRQRILWLGFFLSFAVKVPMIPFHIWLPEAHVEASLAGSIILAG ILLKLAGYGFLRYSIGILPDASAFFTPLVYSLAVISIIYSSFTTLRQIDLKKIIAYSSVG HMNITLLGLFSNTIQGIEGSLILMLAHGVVSPALFICVVILYDRYHTRLLKYYRGLTQHM PVWSVMFFLFTLGNIAVPLSANFVGEFMTFTGAYQQNPVLTVLGGLGMILSAAYGIWLYN RTAFGAQSRYLAPLGDINRREFMTLLPLLVLMFVMGLFPNLFLEPMHLAVSNLLY* >Phycomyces blakesleeanus nad4L ; 88 aa on 'Phycomyces' MNLSMVLFLIGILGFILNRKNIILMLISIEIMLLAVTLLIILSSFSFDDILGQTYGIYII AIAGAESAIGLGILVAYYRLRGSIAIKS* >Phycomyces blakesleeanus nad5 ; 658 aa on 'Phycomyces' MYLAILTLPLLSATVAGFLGRKVGRTGSHLITCSSLVLTALLALVAFYEVGLCQSPVSIK LMSWIDSEFLLVSWGFIYDSLTVSMLLPVLIVSALVHIYSVGYMSEDPHNQRFFSYLSMF TFFMLMLVTGDNYLLMFIGWEGVGISSYLLINFWFTRLQANKAAIKALVMNRVGDWGFSI GLWAIFWTFGNLDFTTVFSLAPFISEEVITIISICLLVAAMGKSAQIGLHTWLPDAMEGP TPVSALIHAATMVTAGVYLLLRSSPILEYGSTPLILITWVGALTAFFAATTGLLQNDLKR VIAYSTCSQLGLLFLVCGLSQYNVALFHLVNHAWFKALLFLSAGSVIHAMNDEQDLRKFG GLANLLPFTYSMMVIGSLSLMALPFLTGFYSKDLIIELAYGHYSFSGNLVYWLASVAAVF TAMYSIRSLYLTFLGYPNGPKINYQSIHEAPLIMAIPLVVLAVFSIFFGYVTKDLFVGMG TDFWNNSLFVHPNHSILVDTEFGLPTSIKLLPLIGSLLGTLGVFAIYWIFDTLPNQFISS SLGRGIYRFFNQKYFFDNIYNNLILNKLLDFGYTTNKILDRGAIELVGPYGLVNVFRTAS NKITSLDSGFIPSYAMYIFSGLILFITLIFFIEDPRVFLLLLWAVLLLPNNTNLKNQK* >Phycomyces blakesleeanus nad6 ; 197 aa on 'Phycomyces' MNAILLDLLAFGSVLSGILVITSRNPVISVLFLIAVFVNVACYLILLGINFIGLTYLIVY VGAIAILFLFVVMMLNIKLVELQDSAEDNSNPYPLAFVLGTLFVSGLGLTNTNLDKIDLP AIFDSINFLSFKSDKLETLFVSHSNWDNVFVSLDQINSIGQVLYTSHALFLIIASMILLL AMVGPITLCLKPTKRIG* >Phycomyces blakesleeanus orf138 ; 138 aa on 'Phycomyces' MVPIEGASGVDPLTWKKESFLSKFYVPRELRSRGPCPPRLSRGGNENYMLPDWVEMSTAS SFSYDKLSKWLTLCKPASKKQTRAVHGNVPSHWESPPGALLGRVKAWVVFIISPGVIIGF TPPPLTQPFIYHSRVIPV* >Phycomyces blakesleeanus orf150 ; 150 aa on 'Phycomyces' MRRYLGPPEESSDSGSDSGDEDISNYISNYTHDDSSPRRFLGLIRYRYTQDTGQTEGNLG VEALNERAILHHLDNDHPLIGDGPLFERRLILNPPRDPHGFNLDVDQDSLSNTGSEDSNS SDPDSRGGSPPEGVEPPSSPRSGSFSTIID* >Phycomyces blakesleeanus orf168 ; 168 aa on 'Phycomyces' MFGQTSVEHKAYYESVFKLFEPYCTADIKSYLKTWTDKRNGKVYQSLFFATMALPCFNPF REYFYSDGKKIVPSNIDVLLTDIGLAHWIMDDGSKHGKGLHLNVYAFSEEDIKRLTDTLS NKFGLKCSVHTPNGKPRIYVWAESMIQLRAIVKHYMHPTMHYKIDEIN* >Phycomyces blakesleeanus orf178 ; 178 aa on 'Phycomyces' MIYSVNKQVELKREEMKLQRDIKLSEDKLKWERLELDKFDRGLSSKFDTPQKPLEKIDTP ISDYLNHKFEAPELQDSKILNHIPDVSKKFKESINSPVEDDLFIFSLNNLNSSSDDYLMN FVSVNVVHYAGLTILGCLITITSAFLVLYLNQLYTKYGDENIHKAPFFKHCIIFLNIL* >Phycomyces blakesleeanus orf190 ; 190 aa on 'Phycomyces' MMLGDGNIRMNGKHALLSVQQKNKEFVDHLWIICNRFDIVVNPVKKLIRVDKRFNNTTIA YGFQTLTLPYFTDLYKRWYQKVGKTTVKIIPVDIEKFLTPLAIAYWVAGDGTFDKSKSRV IICTDNFTKEECDVLQDVLLKKYNIKTYLKLSGVKTKDQYRIVIPKKELEKFQTLVVDYL HSSIYYRIGL* >Phycomyces blakesleeanus orf223 ; 223 aa on 'Phycomyces' MGSFRIRGRKQLANTIFPIFDQYPLLTTKYFNYAKFKSAYAILEDKELTKSQRNAQIETL LSTKPDESYISPAWNKITLPIADANEAGIVISKSWLIGFVEAEGSFYLTSKDVSRIVHGF GITQKLDRVVLEGIRHILHISTKVVYKEKYNHHMIDTTNSRAISNVSEYFFNTMKGMKGV EYRIWSRSFNKHKGDYSQLVKIQKVLRGLRKVRADNTLWTSKF* >Phycomyces blakesleeanus orf246 ; 246 aa on 'Phycomyces' MKNFKTISEYSLKRYFNKSLKLDSYKTDYRLNNLPSYLHETLTGVLLSDGSLERPSLSGG SRLSVNLGEKSLPYILHLHNLFEPFIDTDVSMVTVKLEEKIHTTVRFKTISTPFFSNYYE AFYPIIHKNKKIVPKNISDNFTEVSLAHLIMGDGNFFKERNMIRIYTNAFTHEDVLKLSS VIKNNFDVNNDVFKDRENQYIIRIQSPDLDKTRNLVLPYLHPSMYYRVGLKTNNENFDYK KILDRV* >Phycomyces blakesleeanus orf271 ; 271 aa on 'Phycomyces' ; Warning ! Unusual start codon AAT for orf271 NKKQTTNGLNFNQKRNYNSSRTIEDFRFISKKYYNIEESKYTIYRELKEKAGVYMLINRI TGDTYVGSSVDLRNRMKRYIHETKSTKTTTIIIHRALRKYGLWNFSLIILTFCKSDVKTC LKLEQIALNLFKPVYNILTIAGSSQGFKHSAETIAKLKELSGENHPKSGTFHSEDSKKAI SKSVKTYLDTFGHHNKGKTGELAPQYGIGGSLVYIYNADTIEFVKSFPSINAAQKFLRVR FDTVKSNLDTKIPIKGKYITEKWILTSKPLD* >Phycomyces blakesleeanus orf291 ; 291 aa on 'Phycomyces' ; Warning ! Unusual start codon GAG for orf291 EPLENGFIYSNIVELSLLPVIGTVNSKAANKIKLRTEEEKLEALKISKSFLAMLVGLIDG DGYIAITKTPKDYIRIDLVISLDLRDLDLLNYIHSVLKVGRINKYPKLNLVKLTISRTDL QTILFPLFIYHNLYFLTETRRAQYDKVLFILQSNLKKYSNLPGEFLVYNNLPVTASGYSE LDFFKNWTVGFTMTEGSFLMKNNKDICFSLKQRTHELLFEAFRILFDTKVKINNFDGYSQ FMVSSIKDIQTVVNFFSFSDLHPLVGYKLTQYEVWLNQIQEHPRYKNINLP* >Phycomyces blakesleeanus orf303 ; 303 aa on 'Phycomyces' ; Warning ! Unusual start codon ACA for orf303 TPFITTSVLTHKKQLNTLVFPEDKSELFDFSFFYKKYNEYFNNSKPLPEYEFLTWFIGFS EGDGSFVINNRNELSFVITQSTEDEQVLKLILDKLNFGRVIKQGKRTSRYIVEDKKGLEL INYLFNGNIVLPSKQQSFNKFLQVFNQKAIKGKILLDEIKPINSNKLPSLSNNWLVGFTD SEGCFTVSFLSNSNAFRLRFLVSQKGDINVPVLSHFILLFKTGAIEAHSKKSNYSYVITG TKACFNVYDYFDNYPLKTKKLRSYLLWKEIHKHIMNKDHLNPELRQNLVKMATEVNSTKR KSK* >Phycomyces blakesleeanus orf318 ; 318 aa on 'Phycomyces' ; Warning ! Unusual start codon AAA for orf318 KYMLPHYLNSDDKFPLYTGNSLNSIVLAFFPVTINRFGQSVGNLQSLDQTLIESSETKYG LSEQWSNWLTGLIEADGSFPNEKDKTLSFYISQSTKNAPLIYAIKFWLGFGKVRWQHSEK MVHFVIEDIPNLLNLANLINGRLRTESKYETYVKWVNRLNKKTFVKNKVIIKPLNSEINF NWLAGFTEGDGSFFIGQGNTPRSKLGIQITLNISWTQKSRKTLELISQHFRGAWSYNKSH KFWVYTIKRQSEVKKLLFSVFVNNPLYGIKRYDYLDLKQACELFNTKRHLTESGLELLLE IKSNMNSRRTSISDPRVD* >Phycomyces blakesleeanus orf331 ; 331 aa on 'Phycomyces' MDLIPSLQVFNLTSFWLDKNQIMEFFLKFFRVFIVSFTLLVLYYFVAHTELNWNTDFIST VYCEEGDPSPSSTSLETNKLNQTLESINNLSERGVTHNVNVSVQPEIVNVLHKMFGVLNS SISVYAGAQAASYIPHPYGKAAVFVGTFGLVYGAQQMISAATQGPRLFRSAVDSNVNTSL ASTAGPSEGLLIGGKESDKVYEDLKVPSTPQTQNPVDPDIVAKSVLEKGDSSYFVNSVIE TTETFNQLLIGMNILTVTGLYVLAALGVALFSQELKLEEKEFIKTRPLLLKFVTLKKQPN RVVLFLLYVLTFLCFLGVFFGLCWINVQLPT* >Phycomyces blakesleeanus orf361 ; 361 aa on 'Phycomyces' ; Warning ! Unusual start codon AAT for orf361 NSLFLFSNLTNLSENSSNISKLSSKVNLNTGIQKFLYLTIGNSVRRYSTNNSLDNKLGEN PPAAAPPGDFSPRSAGENPPHPFVKVVIDDPYENRDLITVAKNKVGVYIFEVLGTKDVYV GHSINLYSRICSYFMPSILNTKARYVLSYFNKYGFKNVRLTILILKSDATVVEAVEMEQY FINTLKPNLNIDLVASGSGTHTPMSEETKQRLRSQRGTPVSIYNMKSLELIYRFESKQHL YNTLNIHHVTLHNCLENGTLWLKVFLLSLEPIDEITSENLINQDKMIKLTKYYRSINSTL HPESKRILAENILNPELTKEYHSLSLLAKDLKGDRTTIRAYLNGTKPGLFRKQWRFIKLD D* >Phycomyces blakesleeanus orf378 ; 378 aa on 'Phycomyces' ; Warning ! Unusual start codon AAA for orf378 KLILPALNSAICWELFDNYTLCQTQSAGNPLDLNLLGIFRDYTPELICCTILPVSQLKPN KVNKDWPARSAGLSEGALRAPSDLRFFDESNLNLTDYNLTNSNFNSYFAGLIEGDGTIIV PKTERSPKGRINYPSVQIVFHLKDLPLALVIQKQLRNGSLSRKKGVNAYILTINNYEGLL LVATLLNGNMRTPKIKALHKLIDCLNLKFKNLNMINKPLDTSPLDSNAWLSGFIEADGHF SVRTTVSPKYSKVECKFELTQGQKDHNSEDKLLLMNVLAEFLLTTVKSIREDKPKPEYRV RTTNLKGNLVLENYLDQFPLFGTKFIDYRDWVKILDYFKPGKFNHKENIDNIIDMKSCMN DKRTIFTWDHLQNFYNLD* >Phycomyces blakesleeanus orf380 ; 380 aa on 'Phycomyces' MKNIVNKNFSSAYLSGFTQADGNFHVGFQKISNYSIGVRVTPKFSLTQHIRAKPLFEELK FNLGVGHVVTHRSDVNYVVNSLPHIKDKLLPLFDAYPLRAGKLESYMRFKYVIDMMDNKQ HLNKEGLANIVNNSYLMNTASSRTEDKKQELLKLIGYEGNLKIEELILPKLPPINSDFVS GLTDGDGSFFIGFRGNGRITASYTVIQESSCKSVLEELVDYFNCGKVYDLKSKSSRFQVE NLDDICNKIIPNFKNNELLTDKNTHFHLFSRACELIQNKAHKTQEGLVEIIDLAYNMNKE GKGRKLTKEEYTNLMLSKFKSSPKLIGLEELDVDLTSEVDDYTDSTSMEGNPYYHMTKDL DNFGNSEILTNLDLLDKKKS* >Phycomyces blakesleeanus orf408 ; 408 aa on 'Phycomyces' ; Warning ! Unusual start codon TGC for orf408 CLLGGRYGTTINKMLMGLAHKLQLTIYEHLVRFNSTHHNSKSNNPIINDVDLFSENSKGP NKDKSSWLTYMSKEMKKKFELARDFMLTNEKANVDIINKLLDSNISEKDLQNMLNGPKIL FTNLSDKKFLMKTITKTGKDFGSLAGIYIWTHIPSNQKYVGSAIHLPTRLRSYFLKTSNI GKLLPILNNSPKGAASRPLRDPGPATRGPSPLSEFSLEVKFTPYSNDFRNELVVEQYYLL DKSFNLNTIRVSNNPSGSNAKSLFMYNRDCSILYYSSLKQIDFVRKLGIHHTTFTKHLNN KTFYLGKYLFLKEFIDTAQKVDLSMFDLLNMLEKDRVKFNINKPVNSLSTSVVLIDASTQ EKYFFLSLGSALKFIRDKGYRADQRTLVKRLDTNIQYYNYYCKKAPVK* >Phycomyces blakesleeanus orf511 ; 511 aa on 'Phycomyces' MWNLMIHYYANPRINANQHGHRAGKGSVTCWKQILTEVIDSKFIYEFDYKKFHDLISRAG MAGALLRFGFPEEVARTLVHICSPYVRGADDNDPLRLKLAHMGEYHHYYRGVVQGNNVAA LLGMIVLEDLGVYDLKHGQLVGYADDGILYGDDPRMVEEWLSKLDPKMGVFPKPAATKWV RFSGEWKSELKFVGLAYDGSTDTLRANTRSGKTEVFKWDREEGITPDVEEFLRLSRTGES SQSGHNSAPYQRTLTHRNGVPYLGFLLAKIWSNDPRSRYEPGETAKLKYKPESLLGKWNK FGDWPFSMNAINASSQAYGYLGKWIKLYEPASLRQPVAHRLRRGTGIFKGVPRTEARALS EMMEPWKFSGPAGSLITEGNEVLGDVTSLPVGMDMLPSFQSIPTPRWLRAGEVPFNWAEG FLVAQRPRESNRISSSTKREIRPIQARPDDTPPSYDELRFERALAKRVKAVWTKGIGVVL KKRVENLRNRAMKRAGSVMANTKVVKSCKSG*