#NEXUS 
begin paup;
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	log start file=tempfile.txt append;	
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	[!
Information on this file:	
	
	NOTE!  Any use made of these data or of this sequence alignment should cite: Kohler, S., C.F. Delwiche, L.G. Tilney, P. Webster, R.J.M. Wilson, J.D. Palmer, and D.S. Roos. 1997. A plastid of probable green algal origin in apicomplexan plastids. Science 275:1485-1489.
	
	Please do not redistribute these data or replicate this file without including this header information including the citation above.
	
	tufA; inferred amino acid sequences. 
	Derived from alignment used in Mol. Phylog. Evol. 1995 paper,
		this alignment is primarily intended for analysis of Plasmodium 
		"chloroplast" tufA sequence.
	Alignment has had some minor modifications from MPE'95.
		Astasia had an erroneous deletion of 'D' at #147: DQIDDN is correct.
		Euglena had an erroneous deletion of 'D' at #174: GDDIP is correct.
		Nitella had an erroneous deletion of 'D' at #177: PGDEDPV is correct.
		Plasmodium had KYD (wrong) instead of KIND (right) in IIIPTRKINDYFL at #230
		Derbesia had YHfMD (wrong) instead of YHLMD (right) at #210.
		Derbesia had GEnVEL (wrong) instead of GEtVEL (right) at #268.
		Pandorina had GLEMFqKTL at #290.  Should probably be GLEMFkKTL,
			but is coded here as ?.
	New bacterial sequences (mostly from W. Ludwig) have been added.
	Additional tufM seqs. are from P. Kuhlman.
		]
endblock;

BEGIN DATA;
DIMENSIONS  NTAX=68 NCHAR=450;
FORMAT MISSING=X GAP=.  DATATYPE=PROTEIN  SYMBOLS = " 1 2 3 4" ;

MATRIX
[                        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450]
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Thermotoga      MAKEKFVRTKPHVNVGTIGHIDHGKSTLTAAITKYL...SLKVLAQYIPYDQIDKAPEEKARGITINITHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHVLLARQVEVPY..MIVFINKTDMVDDP..ELIDLVEMEVRDLLSQYGYPGDEVPVIRGSALKAVE.APNDPNHEA......YKPIQELLDAMDN.......YIPDPQRDVDKPFLMPI.EDVFSITGRGTVVTGRIERGRIRPGDEVEIIGLSYEI.KKTVVT.SVEMFRKELDEGIAGDNVGCLLRGIDKDEVERGQVLAAPGSIKPHKRFKAQI..YVLKKEEGGRHTPFTKGYKPQFYIRTADVTGEIVGLPEGVE..............MVMPGDHVEMEIELIYPVAIEKGQRFAVREGGRTVGAGVVTEVIE..........   [400]
ChlamydiaA      MSKETFQRNKPHINIGTIGHVDHGKTTLTAAITRAL...SGDGLADFRDYSSIDNTPEEKARGITINASHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGAMPQTKEHILLARQVGVPY..IVVFLNKIDMISEEDAELVDLVEMELAELLEEKGYKG..CPIIRGSALKALE.GDAAYIEKVR..........ELMQAVDD.......NIPTPEREIDKPFLMPI.EDVFSISGRGTVVTGRIERGIVKVSDKVQLVGLRDT..KETIVT.GVEMFRKELPEGRAGENVGLLLRGIGKNDVERGMVVCLPNSVKPHTQFKCAV..YVLQKEEGGRHKPFFTGYRPQFFFRTTDVTGVV.TLPEGVE..............MVMPGDNVEFEVQLISPVALEEGMRFAIREGGRTIGAGTISKIIA..........   [394]
ChlamydiaB      MSKETFQRNKPHINIGAIGHVDHGRTTLTAAITRTL...SGDGLADFRDYSSIDNTPEEKARGIPINASHVEYETANRHYAHVDCPCHADYVKNMITGAAQMDGAILVVSATDGAMPQTKEHILLARQVGVPY..IVVFLNKIDMISEEDAELVDLVEMELAELLEEKGYKG..CPIIRGSALKALE......IEKVR..........ELMQAGDAAYVDD..NIPTPEREIDKPFLMPI.EDVFSISGRGTVVTGRIERGIVKVSDKVQLVGLRDT..KETLLL.GLEMFRKNSQKVRAGENVGLLLRGIGKNDVERGMVVCLPNSVKPHTRFKCAV..YVLQKEEGGRHKPFFTGYRPQFFFLTTDVTGVV.TLPEGVE..............MVMPGDNVEFEVQLISPVALEEGMRFAIREGGRTIGAGTISKIIA..........   [394]
Thermus_aq      MAKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVA..AAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPY..IVVFMNKVDMVDDP..ELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALE.EMHKNPKTKRGENEWVDKIWELLDAIDE.......YIPTPVRDVDKPFLMPV.EDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPET.RKTVVT.GVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASV..YILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVV.RLPQGVE..............MVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE..........   [406]
Thermus_th      MAKGEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVA..AAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPY..IVVFMNKVDMVDDP..ELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALE.QMHRNPKTRRGENEWVDKIWELLDAIDE.......YIPTPVRDVDKPFLMPV.EDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPET.RRTVVT.GVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASV..YVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVV.QLPPGVE..............MVMPGDNVTFTVELIKPVGLEEGLRFAIREGGRTVGAGVVTKIL...........   [405]
Deinonema       MAKGTFERTKPHVNVGTIGHVDHGKTTLTAAITFTA..AASDPTIEKLAYDQIDKAPEEKARGITINTAHVEYNTPTRHYSHVDCPGHADYVKNMITGAAQMDGAILVVSSADGPMPQTREHILLARQVGVPY..IVVFMNKVDMVDDE..ELLELVEMEVRELLSKYEFPGDDLPVIKGSALQALE.ALQANPKTARGEDKWVDRIWELLDAVDS.......YIPTPERATDKTFLMPV.EDVFTITGRGTVATGRVERGVVKVQDEVEIIGLRDT..KKTTVT.GIEMHRKLLDSGMAGDNVGVLLRGVARDDVERGQVLAKPGSIKPHTKFEASV..YVLSKDEGGRHSAFFGGYRPQFYFRTTDVTGVV.ELPEGVE..............MVMPGDNITFVVELIKPIAMEEGLRFAIREGGRTVGAGVVAKVLE..........   [405]
Chloroflexus    ...................HVDHGKTTLTAAITKVM...SLKGAAQFMAYDQIDNAPEERARGITIAIRHVEYQTDKRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSAPDGPMPQTREHILLARQVQVPA..IVVFLNKVDMMDDP..ELLELVELELRELLSKYGFPGDEIPIVRGTARNALE.SPSKDIN....APEY.KCILELMNAVDE.......YIPTPQRAVDQPFLMPI.EDVFGIKGRGTVVTGRIERGKVKVGDTVEIVGMTNDAPRRTVVT.GVEMFQKTLDEGIAGDNVGCLLRGIERTDVERGQVLCAPGSIKPHKKFEAQV..YVLKKEEGGRHTPFFSGYRPQFYIRTTDVTGAI.GLPAGME..............MVMPGDNVVMTIELIVPVAIEEGLRFAIREGGRTVGAGVVTKILD..........   [382]
Flexistipe      MSKQKYERKKPHVNVGTIGHVDHGKTTLTAAMTHVL...SLKGYADYIEFGNIDKAPEEKERGITIATAHVEYESDKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPS..IVVFMNKCDMVDDE..ELLELVELEIRDLLNTYEFPGDDIPIIKGSALQALE.....NAE....DEEKTKCIWELLQAMDD.......YIPAPERDIDKPFLMPI.EDVFSISGRGTVVTGRVERGKVRVQDEIEIVGLTDT..RKTVVT.GVEMFRKILDEGEAGDNVGVLLRGIKKDDVERGQVLAKPGSITPHRKFKCEA..YILTKEEGGRHTPFFSGYRPQFYFRTTDVTGVI.TLAEGVE..............MVMPGDNISCDVDLIQPIAMEQGLRFAIREGGRTVGAGVVTEIVE..........   [396]
Borrelia_b      MAKEVFQRTKPHMNVGTIGHVDHGKTTLTAAISIYC..SKLNKDAKALKYEDIDNAPEEKARGITINARHIEYETANRHYAHVDCPGHADYIKNMITGAAQMDAAILLVAADSGAEPQTKEHLLLAQRMGIKK..IIVFLNKLDLA.DP..ELVELVEVEVLELVEKYGFSAD.TPIIKGSAFGAMS.....NPE....DPESTKCVKELLESMDN.......YFDLPERDIDKPFLLAV.EDVFSISGRGTVATGRIERGIIKVGQEVEIVGIKET..RKTTVT.GVEMFQKILEQGQAGDNVGLLLRGVDKKDIERGQVLSAPGTITPHKKFKASI..YCLTKEEGGRHKPFFPGYRPQFFFRTTDVTGVV.AL.EGKE..............MVMPGDNVDIIVELISSIAMDKNVEFAVREGGRTVASGRILEILE..........   [394]
Spirochaeta     VAKQNFVRSKPHINVGAIGHVDHGKTTLTAALTMYG...AKKHGGKVMNYDDIDNAPEEKERGITINTRHVEYESAARHYAHVDCPGHADYVKNMITGAAQMDGAILLVAADSGPEPQTREHILLAKQVGVAN..LVIFLNKMDLA.DP..ELVELVEMEVRDLLNLYGFDGEKTPFIRGSAFAAMS.....KPD....DPAATKCLDELLDTMDK.......YFVIPERALDKPFLMPI.EDVFSISGRGTVVTGAIAQGKVKVGDTVEIVGIKPT..QTTVVT.GVEMFNKLLDAGQAGDNIGALLRGIEKNQVERGQVLAAPKSITPHTNFKATI..YCLSKEEGGRHNPFFSGYRPQFYFRTTDVTGTV.TLPEGKQ..............MVMPGDNTELVVELITPMDKGSRFA..............................   [375]
Chlorobium      MAKESYKRDKPHVNIGTIGHVDHGKTTLTAAITSVL...AKSGKAAAREFGDIDKAPEERERGITISTAHVEYQTDKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAGTDGPMPQTREHILLARQVNVPA..LVVFLNKVDIA.DP..ELLELVEMELRELLTEYGFPGDDIPIIKGSALNALN...........GDPEGEKAIMELMDAVDD.......YIPEPVRDVDKPFLMPV.EDVFSISGRGTVGTGRIERGIIKVGNEVEIVGIKPT..TKSVVT.GIEMFQKTLDEGQAGDNAGLLLRGVDKEALERGMVIAKPGSITPHTKFKAEV..YILKKEEGGRHTPFFNGYRPQFYFRTTDVTGSV.TLPEGVE..............MVMPGDNLSVDVELIAPIAMEESLRFAIREGGRTVGAGSVTKIVE..........   [393]
Fibrobacter     ...................HVDHGKTTLTAAICTTL...AAKGLAAAKRFDEIDNAPEEKARGITINTSHVEYTTANRHYAHVDCPGHADYVKNMVTGAAQMDGAILVVAATDGPMPQTREHILLAHQVGVPK..IVVFMNKCDMVDDA..EILDLVEMEVRELLSKYDFDGDNTPIIRGSALKALE...........GDPEYQDKVMELMNACDE.......YIPLPQRDTDKPFLMPI.EDVFTITGRGTVATGRIERGVVRLNDKVERIGLGET..TEYVIT.GVEMFRKLLDDAQAGDNVGLLLRGAEKKDIVRGMVLAAPKSVTPHTEFKAEI..YVLTKDEGGRHTPFMNGYRPQFYFRTTDVTGTI.QLPEGVE..............MVTPGDTVTIHVNLIAPIAMEKQLRFAIREGGRTVGAGSVTEIIK..........   [375]
Thiobacillus    MAKSKFERTKPHVNVGTIGHVDHGKTTLTAAITTVL...SSKFGGEAKAYDQIDAAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPY..IIVFLNKCDMVDDA..ELLELVEMEVRELLSKYDFPGDDTPIIKGSAKLALE.GDKGEL....GEGA....ILKLAEALDT.......YIPTPERAVDGAFLMPV.EDVFSISGRGTVVTGRVERGIIKVGEEIEIVGLKPT..LKTTCT.GVEMFRKLLDQGQAGDNVGILLRGTKREEVERGQVLCKPGSIKPHTHFTAEV..YVLSKDEGGRHTPFFNNYRPQFYFRTTDVTGAI.ELPKDKE..............MVMPGDNVSITVKLIAPIAMEEGLRFAIREGGRTVGAGVVAKIIE..........   [396]
yeast_tufM      SYAAAFDRSKPHVNIGTIGHVDHGKTTLTAAITKTL...AAKGGANFLDYAAIDKAPEERARGITISTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAIIVVAATDGQMPQTREHLLLARQVGVQH..IVVFVNKVDTIDDP..EMLELVEMEMRELLNEYGFDGDNAPIIMGSALCALE.GRQPEI....GEQA....IMKLLDAVDE.......YIPTPERDLNKPFLMPV.EDIFSISGRGTVVTGRVERGNLKKGEELEIVGHNSTP.LKTTVT.GIEMFRKELDSAMAGDNAGVLLRGIRRDQLKRGMVLAKPGTVKAHTKILASL..YILSKEEGGRHSGFGENYRPQMFIRTADVTVVM.RFPKEVE..........DHSMQVMPGDNVEMECDLIHPTPLEVGQRFNIREGGRTVGTGLITRIIE..........   [401]
arab_tufM       RSMATFTRNKPHVNVGTIGHVDHGKTTLTAAITKVL...AEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSGPDGPMPQTKEHILLARQVGVPS..LVCFLNKVDVVDDP..ELLELVEMELRELLSFYKFPGDDIPIIRGSALSALQ.GTNDEI....GRQA....ILKLMDAVDE.......YIPDPVRVLDKPFLMPI.EDVFSIQGRGTVATGRIEQGVIKVGEEVEILGLREGGCSTKSTVTGVEMFKKILDNGQAGDNVGLLLRGLKREDIQRGMVIAKPGSCKTYKKFEAEI..YVLTKDEGGRHTAFFSNYRPQFYLRTADITGKV.ELPENVK..............MVMPGDNVTAVFELIMPVPLETGQRFALREGGRTVGAGVVSKVMT..........   [399]
homo_tufM       EAKKTYVRDKPHVNVGTIGHVDHGKTTLTAAITKIL...AEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEH..VVVYVNKADAVQDS..EMVELVELEIRELLTEFGYKGEETPVIVGSALCALE.GRDPEL....GLKS....VQKLLDAVDT.......YIPVPARDLEKPFLLPV.EAVYSVPGRGTVVTGTLERGILKKGDECELLGHSKN..IRTVVT.GIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIKPHQKVEAQV..YILSKEEGGRHKPFVSHFMPVMFSLTWNMACRI.ILPPEKE..............LAMPGEDLKFNLILRQPMILEKGQRFTLRDGNRTIGTGLVTNTLAMTEEEKNIKW   [406]
caeno_tufM      GGKAVFKRDKPHLNVGTIGHVDHGKTTLTSAITKIL...ATSKGAKYRKYEDIDNAPEEKARGITINAFHLEYETAKRHYAHIDCPGHADYIKNMITGAAQMEGAILVVAATDGPMPQTREHLLLARQVGVPLDNIVVFMNKVDEVPDA..ETCELVEMDIREQLNEFGYPGDTCPVIFGSALCALE.GKQPEI....GEEA....VKQLLEVLDN.......KFVIPERKVNEEPMFAA.EHVYSIVGRGTVITGKLERGILKRGDKIEIVGGTKDGTTVKSVISGLESFRKTVDQAEPGDQLGVLLRGLGPKDVRRGCVL.LPQGHKHKVTDKVKAQLYVLKESEGGAKTPIANYFSEHVFSLTWDSGASV.RIIGKDF...............VMPGESAEVELSLNSQMFIEPQQRFTIRKGAKTIGTGVFTDVLPPLTNDEKDPK   [411]
Pseudomona      MAKGKFERTKPHVNVGTIGHVDHGKTTLTAAITTVL...TKKFGGEAKAYDQIDAAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY..IIVFLNKCDSVDDA..ELLELVEMEVRELLSKYDFPGDDTPIVKGSAKLALE.GDTGEL....GEVA....IMSLADALDT.......YIPTPERAVDGAFLMPV.EDVFSISGRGTVVTGRVERGIVKVGEEIEIVGIKPT..VKTTCT.GVEMFRKLLDQGQAGDNVGILLRGTKREDVERGQVLAKPGSITPHTHFTAEV..YVLSKDEGGRHTPFFNNYRPQFYFRTTDVTGSI.ELPKDKE..............MVMPGDNVSITVKLIAPIAMEEGLRFAIREGGRTVGAGVVAKILD..........   [396]
Bacteroide      MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVL...AKKGLSELRSFDSIDNAPEEKERGITINTSHVEYETANRHYAHVDCPGHADYVKNMVTGAAQMDGAIIVVAATDGPMPQTREHILLARQVNVPK..LVVFMNKCDMVEDA..EMLELVEMEMRELLSFYDFDGDNTPIIQGSALGALN...........GVEKWEDKVMELMEAVDT.......WIPLPPRDVDKPFLMPV.EDVFSITGRGTVATGRIETGVIHVGDEIEILGLGED..KKSVVT.GVEMFRKLLDQGEAGDNVGLLLRGVDKNEIKRGMVLCKPGQIKPHSKFKAEV..YILKKEEGGRHTPFHNKYRPQFYLRTMDCTGEI.TLPEGTE..............MVMPGDNVTITVELIYPVALNIGLRFAIREGGRTVGAGQITEIID..........   [394]
Ecoli           MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVL...AKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPY..IIVFLNKCDMVDDE..ELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE...........GDAEWEAKILELAGFLDS.......YIPEPERAIDKPFLLPI.EDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKET..QKSTCT.GVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEV..YILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTI.ELPEGVE..............MVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG..........   [394]
Shewanella      VAKAKFERIKPHVNVGTIGHVDHGKTTLTAAISHVL...AKTYGGEAKDFSQIDNAPEERERGITINTSHIEYDTPSRHYAHVDCPGHADYVKNMITGAAQMDGAILVVASTDGPMPQTREHILLSRQVGVPF..IIVFMNKCDMVDDE..ELLELVEMEVRELLSEYDFPGDDLPVIQGSALKALE...........GEPEWEAKILELAAALDS.......YIPEPQRDIDKPFLLPI.EDVFSISGRGTVVTGRVERGIVRVGDEVEIVGVRAT..TKTTCT.GVEMFRKLLDEGRAGENCGILLRGTKRDDVERGQVLAKPGSINPHTTFESEV..YVLSKEEGGRHTPFFKGYRPQFYFRTTDVTGTI.ELPEGVE..............MVMPGDNIKMVVTLICPIAMDEGLRFAIREGGRTVGAGVVAKIIA..........   [394]
Bacillus        MAKEKFDRSKSHANIGTIGHVDHGKTTLTAAITTVL..HKKSGKGTAMAYDQIDGAPEERERGITISTAHVEYETETRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLSKNVGVPY..IVVFLNKCDMVDDE..ELLELVEMEVRDLLSEYDFPGDDVPVVKGSALKALE...........GDAEWEAKIFELMDAVDE.......YIPTPERDTEKPFMMPV.EDVFSITGRGTVATGRVERGQVKVGDEVEIIGLQEEN.KKTTVT.GVEMFRKLLDYAEAGDNIGALLRGVSREEIQRGQVLAKPGTITPHSKFKAEV..YVLSKEEGGRHTPFFSNYRPQFYFRTTDVTGII.HLPEGVE..............MVMPGDNTEMNVELISTIAIEEGTRFSIREGGRTVGSGVVSTITE..........   [396]
Mycopl_gen      MAREKFDRSKPHVNVGTIGHIDHGKTTLTAAICTVL...AKEGKSAATRYDEIDKAPEEKARGITINSAHVEYSSDKRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDSVMPQTREHILLARQVGVPK..MVVFLNKCDIASDE..EVQELVAEEVRDLLTSYGFDGKNTPIIYGSALKALE...........GDPKWEAKIHDLIKAVDE.......WIPTPTREVDKPFLLAI.EDTMTITGRGTVVTGRVERGELKVGQEVEIVGLKPI..RKAVVT.GIEMFKKELDSAMAGDNAGVLLRGVERKEVERGQVLAKPGSIKPHKKFKAEI..YALKKEEGGRHTGFLNGYRPQFYFRTTDVTGSI.ALAENTE..............MVLPGDNASITVELIAPIACEKGSKFSIREGGRTVGAGTVTEVLE..........   [394]
Streptococ      MAKEKYDRSKPHVNIGTIGHVDHGKTTLTAAITTVLARRLPSAVNQPKDYASIDAAPEERERGITINTAHVEYETEKRHYAHIDAPGHADYVKNMITGAAQMDGAILVVASTDGPMPQTREHILLSRQVGVKH..LIVFMNKIDLVDDE..ELLELVEMEIRDLLSEYDFPGDDLPVIQGSALKALE...........GDSKYEDIIMELMNTVDE.......YIPEPERDTEKPLLLPV.EDVFSITGRGTVASGRIDRGTVRVNDEIEIVGIKEET.QKAVVT.GVEMFRKQLDEGLAGDNVGVLLRGVQRDEIERGQVIAKPGSINPHTKFKGEV..YILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSI.ELPAGTE..............MVMPGDNVTIDVELIHPIAVEQGTTFSIREGGRTVGSGMVTEIEA..........   [398]
Micrococcu      MAKAKFERTKAHVNIGTIGHVDHGKTTLTAAISKVLYDKYP.DLNEARDFATIDSAPEERQRGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTREHVLLARQVGVPA..LLVALNKSDMVEDE..ELLERVEMEVRQLLSSRSFDVDEAPVIRTSALKALE...........GDPQWVKSVEDLMDAVDE.......YIPDPVRDKDKPFLMPI.EDVFTITGRGTVVTGRAERGTLKINSEVEIVGIRDV..QKTTVT.GIEMFHKQLDEAWAGENCGLLVRGLKRDDVERGQVLVEPGSITPHTNFEANV..YILSKDEGGRHTPFYSNYRAQFYFRTTDVTGVI.TLPEGTE..............MVMPGDTTEMSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK..........   [396]
Mycobactrm      MAKAKFQRTKPHVNIGTIGHVDHGKTTLTAAITKVLHDKFP.DLNETKAFDQIDNAPEERQRGITINIAHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHVLLARQVGVPY..ILVALNKADAVDDE..ELLELVEMEVRELLAAQEFDED.APVVRVSALKALE...........GDAKWVASVEELMNAVDE.......SIPDPVRETDKPFLMPV.EDVFTITGRGTVVTGRVERGVINVNEEVEIVGIRPST.TKTTVT.GVEMFRKLLDQGQAGDNVGLLLRGVKREDVERGQVVTKPGTTTPHTEFEGQV..YILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVV.TLPEGTE..............MVMPGDNTNISVKLIQPVAMDEGLRFAIREGGRTVGAGRVTKIIK..........   [396]
Gloeobacte      ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPN..IVVFLNKKDQLDDP..ELLELVELEVRE.LSKYDFPGDDVPIVAGSALMALE.KMASEPKLIRGKDDWVDCIYSLMDAVDA.......YIPTPERAIDKPFLMAV.EDLL.VSRRGTVAT.RIERGKVKVGETIELVGIR.T..RST.VT.GLEMFQ.SLDEGLAGDNIGVLLRGIKKEDVERGMVLAKPGSITPHTQFEGEV..YILSK.........................................................................................................   [229]
Prochlthx       ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLAKRVGVPN..IVVFLNKQDMVDDD..ELLELVELEVRELLTEYGFDGDSIPIVAGSALQAVD.AMIAKGTTKQSENEWVDKIHKLMAEVDA.......FIPTPERIIDKPFLMAI.EDVFSITGRGTVATGRIERGKVKVGE.IEIVGIRDN..RQSIVT.GVEMFRKLLDEGMAGDNVGVLLRGIQREDLERGMVLAKSRSITPHTKFESEV..YVLKK.........................................................................................................   [234]
Phormidium      ............................................................................................KNMITGAAQMDGAILVCSAADGPMPQTREHILLSKQVGVPH..IVVFLNKQDQVDDE..ELLELVELEVRELLSSYDFPGDDIPIVAGSALKAVE.ALQANSSIGKGEDEWVDKIHDLVAQVDE.......YIPAPERDIDKPFLMAV.EDVFSITGRGTVATGRIERGKVKVGEQIEIVGIRDT..TQSTVT.GVEMFQKTLDEGMAGDNVGVLLRGIQKEDILRGMVLAKPGSITPHTKFEAEV..YVLIG.........................................................................................................   [235]
Spirulina       MARAKFERNKPHVNIGTIGHVDHGKTTLTAAITMTL...AASGGAKARKYDDIDAAPEEKQRGITINTAHVEYETEQRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPS..IVVFLNKADMVDDE..ELLELVELEVRELLSSYDFPGDDIPIVSGSALKALD.FLTENPKTTRGENDWVDKIHALMDEVDA.......YIPTPERDIDKGLLDGLWEDVFSITGRGTVSTAGIERGKVKVGDTVELIGIKDT..RTTTVT.GAEMFQKTLEEGMAGDNVGLLLRGIQKNDVQRGMVIAKPKSITPHTKFEAEV..YILKKEEGGRHTPFFKGYRPQFYVRTTDVTGTI.DEFTADDGSTPE.........MVIPGDRINMTVQLICPIAIEQGMRFAIREGGRTVGAGVVAKIL...........   [409]
Anacystis       MARAKFERTKPHANIGTIGHVDHGKTTLTAAITTVL...AKAGMAKARAYADIDAAPEEKARGITINTAHVEYETGNRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPN..IVVFLNKEDMVDDA..ELLELVELEVRELLSSYDFPGDDIPIVAGSALQALE.AIQGGASGQKGDNPWVDKILKLMEEVDA.......YIPTPEREVDRPFLMAV.EDVFTITGRGTVATGRIERGSVKVGETIEIVGLRDT..RSTTVT.GVEMFQKTLDEGLAGDNVGLLLRGIQKTDIERGMVLAKPGSTTPHTKFESEV..YVLKKDEGGRHTPFFPGYRPQFYVRTTDVTGAI.SDFTADDGSAAE.........MVIPGDRIKMTVELINPIAIEQGMRFAIREGGRTIGAGVVSKILQ..........   [409]
Gloeothece      ............................................................................................KNMITGAAQMDGGILVVSAADGPMPQTREHILLAKQVGVPS..LVVFLNKEDQVDDA..ELLELVELEVRELLSIYDFPGDDIPIVIGSALKAVE.ALTATPTTKKGDNEWVDKILKLMDEVDE.......YIPTPEREIDKPFLMAV.EDVFSITGRGTVATGRIERGKIKVGETVELVGIRNT..RSTTVT.GVEMFQKVLEEGMAGDNVGLLLRGIQKEDIERGMVIAKPGSITPHTQFEGEV..YVLTK.........................................................................................................   [235]
Plectonema      ............................................................................................KNMITGATQMDGAILVVSAADGPMPQTREHILLAGQVGVPN..IVVFMNKQDQVDDE..ELLELVELEIRELLSSYDFPGDDIPVTAGSALKAVE.QLLSDPNTARGSDEWVDKIHALMDDGDK.......YIPTPSVKVDKPFLMAV.EDVFSITGRGTVATGRIERGLVKVGETVQLVGIADT..RETTVT.GVEMFQKTLDSGMAGDNVGVLLRGVQKEDIERGMVLAKSGSITPHTEFESEV..YVLNK.........................................................................................................   [235]
Plasmodium      MNNKLFLRNKQHINLGTIGHVDHGKTTLTTAISYLL...NLQGLSKKYNYSDIDSAPEEKIRGITINTTHIEYVSLTKHCAHIDCPGHSDYIKNMIIGATQMDIAILVISIIDGIMPQTYEHLLLIKQIGIKN..IIIFLNKEDLCDDV..ELIDFIKLEVNELLIKYNFDLNYIHILTGSALNVINIIQKNKDYELIKSNIWIQKLNNLIQIIDN........IIIPTRKINDYFLMSI.EDVFSITGRGTVVTGKIEQGCINLNDEIEILKFEKSSPNLTTVI.GLEMFKKQLTQAQSGDNVGILLRNIQKKDIKRGMILATPNKLKVYKSFIAET..YILTKEEGGRHKPFNIGYKPQFFIRTVDVTGEI.KNIY.LNENVQK.........VAIPGDKITLHIELKHYIVLTLNMKFSIREGGKTIGAGIITEIKN..........   [409]
Toxoplasma      MAKEIFKKQKPHINIGTIGHVDHGKTTLTAAITYVL...AKNNQAKLKTYKEIDCAPEEIARGITIKTSHIEYETAVRHYAHIDCPGHADYIKNMITGAAQMDGAILVVSAVDGPMPQTKEHLLLAKQIGISN..IIVFLNKIDLIDDN..EILELVELETRELLDKYNFSSD.TPIITGSALKALD........NNLTSNIWVDKIYELLTALDS.......YIPLPKRDLDKPFLLAI.EDIFSITGRGTVVTGKIERGSIKLGDTVTMLGFNIS..KNVVVI.GLEMFQKTLEIGEAGDNVGILLRGIQKTEVKRGMILSKPLTMTLHSIFQADV..YILTVAEGGREKPIFEGYCPQFYLYTINITGSI.KFSSETKETGTK.........MILPGDRVKLNVTLIYSIAIEKGMRFAIREGGRTIGAGIITDIIK*.........   [402]
Eimeria         MAKKFFEKTKTHLNIGTIGHVDHGKTTLTAAITSYL...SKINNTKAKSYSEIDSAPEEKARGITINTSHIEYETNLRHYAHIDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLAKQVGVPN..IIVFLNKIDMVEDN..ELLELVELEVRELLDIYEYNGDSTSIIKGSALKALE.....YIEKNDLNNKWVKNLKNLIEALDK.......SIPEPKRDINKPFLLSI.EDIFSITGRGTVVTGKIERGKVKLNDTVDILGFNLL..KTTTVT.GIEMFQKILNTAEAGDNVGILLRGIQKNEVRRGMVLAKPLSILTYSKFDAEV..YILSSSEGGRKKPFFEGYKPQFYFYTTDVTGTI.EFLRNPEKPE...........MILPGDKVKLRISLMYSIALEKGMRFAIREGGKTIGAGIIIDLIN*.........   [404]
Cyanophora      MARQKFDGNKPHVNIGTIGHVDHGKTTLTAAITTAL...ASQGKGKARKYDEIDAAPEEKARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPN..MVVFLNKEDQIDDA..DLLELVELEVRELLSKYDFPGDQIPFVSGSALLALE.SLSSNPKLMRGEDKWVDKILALMDAVDE.......YIPTPERPIDKSFLMAI.EDVFSITGRGTVATGRIERGAIKVGETVELVGLKDT..KSTTVT.GLEMFQKTLEEGMAGDMIGILLRGVQKTDIERGMVLAKPGSITPHTQFESEV..YVLTKDEGGRHTPFFSGYRPQFYVRTTDVTGSI.DAFTADDGSNAE.........MVMPGDRIKMTVSLVHPIAIEQGMRFRIREGGRTIGAGVVSKILK..........   [409]
Porphyridi      ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPQ..VVVFLNKEDQVDDK..EILELVELEVRELLSKYEFPGDDIPLAAGSALLALE.AMLANPKTVRGQNEWVDKIYTLMDHVDS.......YIPAPERDVDKPFLMAV.EDVFSITGRGTVATGRIESGIIKVGDTIEIVGLRET..RTTTIT.GLEMFQKTLEEGIAGDNIGILLRGIQKKDIERGMVLAKPGSIKPHNQFEAEV..YILSK.........................................................................................................   [235]
Porphyra        MARSKFERKKPHVNIGTIGHVDHGKTTLTAAISATL...STLGSTAAKKFDEIDAAPEEKARGITINTAHVEYETDNRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPT..LVVFLNKEDQVDDE..ELLELVELEGRELLSQYDFPGDDIPFVAGSALLALE.AVTKNTSIKKGEDKWVDKIFSLMEAVDT.......YIPTPERDVDKTFLMAV.EDVFSITGRGTVATGRIERGIIKVGDTIEIVGLRET..RTTTIT.GLEMFQKTLEEGLAGDNIGILLRGVQKKDIERGMVLAKPGTITPHTQFEAEV..YILTKEEGGRYTPFFPGYRPQFYVRTTDVTGTI.NQFTADDGTDAE.........MVMPGDRIKMTAELINAIAIEQGMLFAIREGGRTVGAGVVSKILK..........   [409]
Smithora        ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPT..LVVFLNKEDQVDDE..ELLELVELEGRELLSQYDFPGDDIPFVAGSALLALE.AVTKNPNIKQGEDKWVDKISSLMEAVDT.......YIPTPERDIDKTFLMAV.EDVFSITGRGTVATGRIERGIIKVGDTIEIVGLRET..RTTTIT.GLEMFQKTLEEGLAGDNIGILLRGVQKKDIERGMVLAKPGTITPHTQFEAEV..YILTK.........................................................................................................   [235]
Gracilaria      ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPN..IVVFLNKQDQVDDE..ELLELVELEVRELLGQYGFPGDNIPFVAGSALRALE.NITQNNTIQRGENEWVDKIHSLMDAVDE.......YIPTPVRDVEKTFLMAV.EDVFSITGRGTVTTGRIERGIIKVGDTIEIVGLRET..TTTTIT.GLEMFQKTLDEGMAGDNIGILLRGVQKKDIERGMVLAQPGTITPHTQFEAEV..YVLTK.........................................................................................................   [235]
Vaucheria       ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPN..IVVFLNKEDQVDDE..ELLELVELEVRELLSNYDFPGDTIAICPGSALQALN.AIALNPSLKQGEDKWVDKIFDLMTDVDT.......NIPTPVRDVDKAVLMAV.EDVFSITGRGTVATGRIERGVVKVGETIQIIGIQDT..RSTTVT.GVEMFQKTLDEGLAGDNVGILLRGVQKDDIQRGMVLAKPGTITPHKGFEGEV..YILTK.........................................................................................................   [235]
Costaria        ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLSKQVGVPH..IVVFLNKEDQVDDL..ELVELVELEVRELLSNYDFPGDDIPILTGSALQALD.AINNEPTLKKGDNKWVDKIYSLMESVDS.......YIPTPIRDVDKPFLMAI.EDVFSITGRGTVATGKIDRGIVKVGETVDLVGLGDT..KSTTVT.GVEMFQKTLDEGVAGDNVGILLRGLQKGDIERGMVLAKPGTITPHKGFEGEV..YILTK.........................................................................................................   [235]
Laminaria       ............................................................................................KNMITGAAQMDGAILVVSAADGPTPQTREHILLSKQVGVPH..IVVFLNKEDQVDDL..ELVELVELEVRELLSKYEFPGDDIPIRTGSALQALD.AINNEPPFKKGDNKWVDKIYTLMDSVDS.......YIPTPIRDVDKPFLMAI.EDVFSITGRGAVATGKIDRGIVKVGENVDLVGLGDT..KSTTVT.GVEMFQKTLDEGVAGDNVGILLRGLQKDEIERGMVLSKPGTITPHNTSESEL..YILTK.........................................................................................................   [235]
Odontella       ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTREHILLSKQVGVPD..IVVFLNKEDQVDDA..ELLELVELEVRELLSAYDFPGDDIDICPGSALQSVE.AISSNPAIKRGDNPWVDKIFALMDAVDE.......YIPTPERDIEKTFLMAI.EDVFSITGRGTVATGRIERGVVKVGDTVEIVGVGDT..RTTTIT.GTEMFQKTLDEGFAGDNVGILLRGVTREDIERGMVLSEPGTITPHTNFESEV..YVLTK.........................................................................................................   [235]
Coscinodis      ............................................................................................KNMITGAAHMDGAIIVVSAADGPMPQTREHILLSKQVGVPD.MIVVFLNKEDQVDDA..ELLELVELEVRELLSSYDFR.DDIPICPGSALQAIE.AISANPAIKKGDNPWVDKIFALMEAVDE.......YIPTPERDVEKTFLMAI.EDVFAITGRGTVATGRIERGIIKVGDTVEIVGISET..KTTTIT.GLKMFQKTLEEGFAGDNVGILLRGVTREEIERGMVLAQPGTTTPHTNFESEV..YVLTK.........................................................................................................   [235]
Cyclotella      MGPEKFARAKPHINIGTIGHVDHGKTTFTAAITATL...ANDGESFAKAYSDIDGAPEERARGITINTAHVEYQTRDRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLAKQVGVPH..IVVFLNKQDQVDDD..ELLELVELEVRELLSTYDFPGDDIPICPGSRLQAIE.AISSNPTLKRGDNPWVDKIYALMDAVDA.......YIPTPERDVEKTFLMAI.EDVFSITGRGTVATGRIERGVIKVGDNVEIVGIGDT..KTTTIT.GIEMFQKTLEEGFAGDNVGILLRGVTRENIERGMVLAKPGTITPHTNFESEV..YVLTKEEGGRHTPFFTGYSPIFYVITTDVTGSI.DQFTADDGSIVE.........MVMPGDRIKMTAELIYPVAIEEGMRFVIREGGRTIGAGVVSKIVK..........   [409]
Ochromonas      ............................................................................................KNMITGAAQMDGAILVVSAADGAMPQTREHILLARQVGVKK..LVVFLNKADQVDDP..EIISLVELELRDLLQSYDYPGDEIPFVAGSALLALE.AVTANPKIKKGENKWVDKIFELMDAVDN.......YIPTPEREVDKPFLMAI.EDVFSITGRGTVATGRIERGTILLGDTVELVGLGDT..KTTTVT.GLEMFQKTLDKGMAGDNIGILLRGIQKTDVLRGMVLSKPGSIKPHTKFEAEV..YILTK.........................................................................................................   [235]
Cryptomona      MARDKFERFKPHVNIGTIGHVDHGKTTLTAAISATL....SQYTGKSKKFDEIDSAPEERARGITINTAHVEYETDKWYYAHVDCPGHADYVKNMITGAAQMDGAILVCSAANGPMPQTREHILLAKQVGVPY..IVVFLNKADMVDDE..ELLELVQLEVQELLEKYDFPGSEIPFVAGSALLALE.AVANNPTIKRGEDKWVDTIYQLMDKVDE.......YIPTPERETDKAFLMAV.EDVFSITGRGTVATGRIERGKVKVGDTIEIVGLRET..RNTTIT.GLEMFQKSLDEALAGDNVGILVRGIQKTDIERGMVLAAPGSITPHTKFEGEV..YVLTKEEGGRHTPFFSGYRPQFYVRTTDVTGTI.AQFTSDDGSTAE.........MVMPGDRIKMTAQLIHPIAIEKGMRFAIREGGRTVGAGVVSKIIE..........   [408]
Euglena         MARQKFERTKPHINIGTIGHVDHGKTTLTAAITMAL...AATGNSKAKRYEDIDSAPEEKARGITINTAHVEYETKNRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPN..IVVFLNKEDQVDDS..ELLELVELEIRETLSNYEFPGDDIPVIPGSALLSVE.ALTKNPKITKGENKWVDKILNLMDQVDS.......YIPTPTRDTEKDFLMAI.EDVLSITGRGTVATGRVERGTIKVGETVELVGLKDT..RSTTIT.GLEMFQKSLDEALAGDNVGVLLRGIQKNDVERGMVLAKPRTINPHTKFDSQV..YILTKEEGGRHTPFFEGYRPQFYVRTTDVTGKI.ESFRSDNDNPAQ.........MVMPGDRIKMKVELIQPIAIEKGMRFAIREGGRTVGAGVVLSI............   [406]
Astasia         MSRQKFERIKPHINIGTIGHVDHGKTTLTAAITMAL...SVTGNTKSKKYEEIDSSPEEKARGITINTAHVEYETKNRHYAHVDCPGHADYIKNMITGAAQMDGAILVISATDGPMPQTKEHILLAKQVGVPN..LVVFLNKEDQIDDN..ELLELIELEIRETLNNYEFPGDEIPIITGSALLAIE.ALNKNPKIIKGENKWVDKILDLMDKIDS.......YIPTPIRDTDKDFLLAI.EDVLSITGRGTVATGRIERGKIKVGETVELIGLKNI..KSTTIT.GLEMFQKSLDEAIAGDNVGVLLRGIQKNEVERGMVIAKPGTIQPHIKFNSQV..YILTKEEGGRHTPFFEGYKPQFYVRTTDVTGKI.ESFKSDDGTTVQ.........MVMPGDKIKMIVELVQPIAIEKGMRFAIREGGKTVGAGVIINIID..........   [408]
Mantoniell      ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN..IVVFLNKEDQVDDD..ELLELVELEVRDTLSSYEFPGDDIPVVPGSALLALE.ALTEKPAMSAGENKWVDKIFALMDAVDS.......YIPTPERDTAKTFLMAI.EDVFSITGRGTVATGRVERGTVNCGDVVEIVGLGDT..REVTVT.GLEMFQKHLDESVAGDKVGVLLRGIQKDDIERGMVLAKKGTITPHTKFESQV..YVLSK.........................................................................................................   [235]
Pandorina       ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN..IVVFLNKEDQVDDQ..ELLELVELEVRELLDKYEFPGDEIPVVPGTALLALE.ALIANPKTQRGENKWVDKIYELMDKVDS.......YIPTPERETDKPFLLAV.EDVLSITGRGTVATGRVERGTLKISDNVEIVGLKPT..QTAVVT.GLEMF.KTLDETIAGDNVGVLLRGVQKKDIERGMVIAKPGTITPHTKFEAQV..YVLTK.........................................................................................................   [235]
Chlamydomo      MSRAKFERKKPHVNIGTIGHVDHGKTTLTAAITMTL...AAAGGSVGKKYDEIDSAPEEKARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN..VVVFLNKEDQVDDK..ELLELVELEVRETLDKYEFPGDEIPVVPGSALLALE.ALIENPKTQRGENKWVDKIYQLMDNVDS.......YIPTPQRETDKPFLLAV.EDVLSITGRGTVATGRVERGALRISDNVEIVGLRPT..QTAVVT.GLEMFKKTLDETLAGDNVGVLLRGVQKKDIERGMVIAKPGTTTPHTKFEAQV..YVLTKEEGGRHSAFMIGYQPQFYVRTTDVTGKV.VGFNHIQMRNPSSVAEEHSNKMAMPGDRISMTVELINPIAIEKGMRFAIREGGRTVGAGVVTNIVQ..........   [418]
Gonium          ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN..IVVFLNKEDQVDDK..ELLELVELEVRETLDKYEFPGDEIPVIPGSALLALE.ALIENPKTQRGENPWVDKIYQLMDKVDS.......YIPTPQRETDKPFLLAV.EDVLSITGRGTVATGRVERGTLKISDTVEFVGLKPT..QSAVVT.GLEMFKKTLDETLAGDNVGVLLRGVQKKDIERGMVIAKPGTITPHTKFEAQV..YVLTK.........................................................................................................   [235]
Draparnald      ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTTEHVLLAKQVGVPA..IVVFLNKADQVDDP..ELLELVELEVRDILDKYGFASDEVQILSGSALLALE.ALVENPNIKPGDSEWVDKIYNLMATVDE.......HIPTPKREMDKPFLLAV.EDVFSITGRGTVATGRVERN.IKINETVEIIGLRRNT.KTTTVT.AIEMFQKTLDETIAGDNVGILLRGVQKKDIERGMVIAKPGTIMPHTLFESQV..YVLTA.........................................................................................................   [235]
Chlorella       ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHLLLAKQVGVPN..IVVFLNKEDQVDDA..ELLELVELEIRETLDKYEFPGDEIPIIAGSRLLALE.ALSQNPQTQPGDNKWVDKIYNLMDQVDS.......YIPTPERETEKPFLMAI.EDVFSITGRGTVATGRVERGCVKIGDTVELVGLRDT..KTTTVT.GLEMFQKTLDESVAGDNVGILLRGVQKIDIERGMVLAKPGSIKPHTKFEAQV..YLFNK.........................................................................................................   [235]
Codium          MIREKFERIKPHLNIGTIGHVDHGKTTLTAAITMAL...AVKGYTKAKNYMDIDSAPEEKARGITINTAHVEYETDVRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPA..IVVFLNKADQVDDD..ELLELVELEIQETLTTYEYPGEEIPIITGSALLALE.SLTAKYVL.RIGNKWVQKIYDLMETVDE.......YIPLPKRDTEKPFLMAI.ENVVSITGRGTVATGRVERGMIEVGQTVELVGLKNT..KEAIIT.GLEMFHKTLEKSVAGDNVGILLRRIQKEEIQRGMVLAKPSSILPHQHFKAQV..YILKKEEGGRHTSFFAGYRPQFYVRTTDVTGHI.KTFQGKIDNTQIQ........MVMPGDRIQMEVELIRPIAIETRMRFAIREGGKTVGAGVVTTIVQ..........   [409]
Derbesia        ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPS..IVVFLNKADQVDDE..ELLELVELEVQETLSEYEYPGEEIPIISGSALLALE.ALTENPELDSANNEWVQKIYHLMDSVDD.......YIPLPERDTDKPFLMAI.EDVFSITGRGTVATGRVERGSVDVGENVELVGLKET..KETIIT.GLEMFQKTLDKSVAGDNVGILLRGIQKEEIQRGMVLAKPGSITPHRCFKAQV..YILKK.........................................................................................................   [235]
Bryopsis        ............................................................................................KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPS..IVVFLNKADQVDDE..ELLELVELEVRETLNEYEFPGDDIPIISGSALLALE.ALTENPDTNRTGDPWVKKIYDLMNEVDN.......YIPLPTRDTDKPFLMAI.ENVVSITGRGTVTTGRVERGADQVGDNIEIVGVKET..RQATIT.GLEMFQKTLEKSVAGDNVGVLLRGIQKEEVEPGMVLAKPGSTTPHKQFEAQV..YILKK.........................................................................................................   [235]
Raphidonem      ............................................................................................KNMITGAARMDGAILVVSGADGPMPQTKEHILLAKQVGVPN..VVVFLNKEDQVDDE..ELLELVELEVRETLDNYEFPGDEIPIVAGSALLALE.ALTENPELKRGENKWVDKIFDLMDQVDT.......YIPTPERDMDKAFLMAV.EDVFSITGRGTVATGRVERGSGKVGESIEIVGLRDT..RTTTVT.GLEMFQKTLEESVAGDNVGVLLRGIQKIDIERGMVLAKPGTITPHTKFESQV..YVLTK.........................................................................................................   [235]
Coleochaet      LLHMTFRNKKIHLNVGTIGHFSHGKTTLTAAITAVL...AGIGYTQPKQNDAIDSTSEEKARNMSIYVHHVEYETAAWHYSHLDCPGHVNYINNMITGVSQMDGAILVVSAVDGPMAQTKEHILLAKLLGISS..ILVFINKEDELDDQ..EVLPMLIQNMRQILIYYGFPGHTSPILCGSALLALE.AMNENPNFNRGKNKWVDKISSLIDHLDL.......YLPTPRRKLNKPFLMPI.ERVILIPSFGLVGTGTIEKGHINIGESVEIVGFKDT..QHSKVI.SLKMFNKTLEQAIAGDDIGIFLEGTNKNNFQKGMVIAKPNTIQSWNHFEAQI..YILRREEGGRRSPFFQGYCPQFYFRTIQITGRM.ESFEYEIGGKTW.........MVMPGEKIKAIIQLIFPIALKKKMRFVIREGGFTIGVGIILELIK..........   [409]
Chara           MAQEVFQRTKPHVNIGTIGHVDHGKTTLTAAITMTL...AVNSTCTPKKYDEIDAAPEERARGITINTAHVEYETALRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPS..IVVFLNKEDQVDDE..EILQLVDLEVRESLINYEFPGDKVPVVSGSALMALQ.ALTEKPNTSRGENKWVDKIYELMDAVDS.......YIPTPKRDIEKPFLMPI.EDVFSIQGRGTVATGRIERGILKLGDIVELIGLNEKI.RSTVVT.GLEMFRRLLEQGFAGENIGVLLRGIEKKDIERGMVIAQPGTIEPHTRFEAQV..YILRKEEGGRHSPFFAGYRPQFFVRTADVTGVI.EAFEYDNGDKTR.........MVMPGDRVKMIVNLICPIAIEKKMRFAIREGGRTIGAGVVYKY............   [408]
Nitella         ............................................................................................KNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPS..IVVFLNKEDQVDDD..EILQLVELEVRDYLNNYEFPGDEDPVICGSALMALQ.ALTEKPNLLRGQNAWVDKIYNLMDNVDS.......YIPTPKRDVEKPFLMPV.EDVFSIQGRGAVATGRIERGVIKLGDSIELVGLKEET.RSTVVT.GLEMFRRLLEQSFAGENIGVLLRGIEKKDIERGMVIAQPGTTKPHTRFEAQV..YILGK.........................................................................................................   [235]
Nico_tabac      AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMAL...ASMGNSAPKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSGADGPMPQTKEHILLAKQVGVPN..MVVFLNKQDQVDDE..ELLQLVELEVRELLSSYEFPGDDIPIISGSALLALE.ALMANPSIKRGENQWVDKIYELMDAVDS.......YIPIPVRQTELPFLMAI.EDVFSITGRGTVATGRVERGTVRIGDTVDIVGLKDT..RSTTVT.GVEMFQKILDEAMAGDNVGLLLRGIQKIDIQRGMVLAKPGTITPHTKFEAIV..YVLKKEEGGRHSPFFSGYRPQFYMRTTDVTGKV.TSITTDKGEESK.........MVMPGDRVNLVVELIMPVACEQGMRFAIREGGKTVGAGVIQKIIE..........   [409]
Nico_syl_A      AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMAL...ASMGNSAPKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSGADGPMPQTKEHILLAKQVGVPN..MVVFLNKQDQVDDE..ELLQLVELEVRELLSSYEFPGDDIPIISGSALLALE.ALMANPSIKRGENQWVDKIYELMDAVDS.......YIPIPVRQTELPFLMAI.EDVFSITGRGTVATGRVERGTVRIGDTVDIVGLKDT..RSTTVT.GVEMFQKILDEAMAGDNVGLLLRGIQKIDIQRGMVLAKPGTITPHTKFEAIV..YVLKKEEGGRHSPFFSGYRPQFYMRTTDVTGKV.TSITTDKGEESK.........MVMPGDRVNLVVELIMPVACEQGM...............................   [388]
Glycine         AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMAL...AALGNSAPKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIILAKQVGVPN..MVVFLNKQDQVDDE..ELLQLVEIEVRDLLSSYEFPGDDTPIVSGSALLALE.ALMANPAIKRGDNEWVDKIFQLMDEVDN.......YIPIPQRQTDLPFLLAV.EDVFSITGRGTVATGRVERGTIKVGETVDLVGLRET..RNTTVT.GVEMFQKILDEALAGDNVGLLLRGVQKTDIQRGMVLAKPGTITPHTKFSAIV..YVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKV.TSIMNDKDEEST.........MVLPGDRVKMVVELIVPVACEQGMRFAIREGGKTVGAGVIQSII...........   [408]
Arabidopsi      AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMAL...ASIGSSVAKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPD..MVVFLNKEDQVDDA..ELLELVELEVRELLSSYEFNGDDIPIISGSALLAVE.TLTENPKVKRGDNKWVDKIYELMDAVDD.......YIPIPQRQTELPFLLAV.EDVFSITGRGTVATGRVERGTVKVGETVDLVGLRET..RSYTVT.GVEMFQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGSITPHTKFEAII..YVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKV.TKIMNDKDEESK.........MVMPGDRVKIVVELIVPVACEQGMRFAIREGGKTVGAGVIGTILE..........   [409]
;
END;


BEGIN CODONS;
GENCODE UNIVNUC
;
END;

BEGIN ASSUMPTIONS;
[character sets and taxon sets  checked by CFD 8/29/95] 

	OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;

	CHARSET  small_indels = 37-39 134-135 188 217-221 239 276-277 284 337-338 380-393 439-. ;
	CHARSET  messybit = 188-208 ;
	
	EXSET  small_indels = 37-39 134-135 188 217-221 239 276-277 284 337-338 380-393 439-. ;
	EXSET  messybit = 188-208 ;
	
	TAXSET extra_plastids = 	
		ChlamydiaB Thermus_aq caeno_tufM	[extra bacteria]
		Porphyridi Smithora Gracilaria [reds]
		Vaucheria Costaria Laminaria Odontella Coscinodis [chromophytes] 
		Mantoniell Pandorina Gonium Chlorella Derbesia Bryopsis Raphidonem Nitella [greens]
		Glycine Nico_syl_A Arabidopsi [plants]
		;
	TAXSET extra_cyanos = 
		Phormidium Gloeothece Plectonema [cyanobacteria]
		;
	TAXSET extra_bacteria = 
		Thermotoga ChlamydiaA ChlamydiaB Thermus_aq Thermus_th Deinonema Flexistipe Borrelia_b
		Spirochaeta Chloroflexus Chlorobium Fibrobacter Thiobacillus yeast_tufM homo_tufM arab_tufM caeno_tufM 
		Bacteroide Pseudomona Ecoli Shewanella Bacillus Mycopl_gen Streptococ Micrococcu Mycobactrm	
		;
		
	TAXSET representatives = Thermotoga Deinonema Spirochaeta arab_tufM Ecoli Bacillus Gloeobacte Spirulina Plasmodium
		Toxoplasma Eimeria Cyanophora Porphyra Cyclotella Cryptomona Euglena Draparnald Coleochaet Chara Nico_tabac;

END;
;

BEGIN PAUP;			

[!Notes on analysis:
	
	Assuming the apicomplexan sequences are from plastids, where do they go?
	
	]
	set maxtrees=100;
	set increase=auto;
	set autoinc=100;
	set status=yes;
	set autoclose=yes;
	
	exclude small_indels;
	delete [extra_bacteria] extra_plastids extra_cyanos;
[	delete apicomplexa;]	
	outgroup thermotoga;
		
	set criterion = parsimony [distance];
[	hsearch [keep=1721] start=stepwise steepest=y swap=tbr 
				[addseq=simple]
				addseq=random nreps=100 rseed=675 rstatus	
				;
			savetrees brlens file=tufA995AAbestB+P.trees append;
]	
[	bootstrap bseed=99 nrep=100 keepall 
				[method=heuristic/addseq=simple]
				search=heuristic/addseq=random nreps=10 rseed=185 rstatus dstatus=600
				;
			savetrees file=tufA9_95AAbootPl.trees append;
	]			
	
	log stop;
	
	[quit;]

ENDBLOCK;

BEGIN MACCLADE;
v 3.0
-1404225164
1000&/0
0
0
END;