NEXUS
[File created by TreeBASE:  7/26/07  21:06:00]
[Matrix accession#: M1991]

BEGIN TAXA;
	TITLE M1991;
	DIMENSIONS  NTAX=32;
	TAXLABELS
		'Uncultured bacteria SBII-2'	Methanococcus_jannaschii	FII_F1_POB_9N	FII_E4_POB_9N	FII_E1_POB_9N	FII_C3_POB_9N	FII_C1_POB_9N	FII_B1_POB_9N	FII_G02_POB_9N	FII_f6_POB_9N	Riftia_pachyptila_endosymbiont	Thiobacillus_denitrificans_b	Rhodobacter_capsula	Rhodspirillum_rubrum	3838_RT	Alcaligenes_eutrophus	Thiobacillus_ferrooxidans	Rhodobacter_veldkampii	Pogonophora_sp._JT1_endosymbiont	h04_POB_9N	e05_POB_9N	d05_POB_9N	g05_POB_9N	c07_POB_9N	c04_POB_9N	Synechococcus_sp._WH7803	Hydrogenovibrio_marinus	Hydrogenophilus_thermoluteolus	Thiobacillus_sp.	Thiobacillus_denitrificans	f06_POB_9N	a05_POB_9N
	;
END;

BEGIN CHARACTERS;
	TITLE M1991;
	DIMENSIONS NCHAR=129;
	FORMAT DATATYPE = PROTEIN SYMBOLS = " 1 2 3 4 " MISSING = ? GAP = -  ;
	MATRIX
		'Uncultured bacteria SBII-2'           EPFAEAAYQFWLGGDFIKNDEPQGN-------QVFCPMKKVIPLVYDAMKRAMDETGRAKLFSANITADDHYEMIARGEYVLETFGPDADKVAFLVDGYVG---------GPGMITTARRNFPSQYLHY
		Methanococcus_jannaschii               KDDENLTSQEFNKFEDRIYKTLEMRDKAEEETGERKA-YMPNITAPYREMIRRAEIA-EDAGSEYVMIDVVVCGFSAVQSFRE--EDFKFIIHAHRA--------------------------------
		FII_F1_POB_9N                          N-------QVLCPMKKVIPLVADAMKRAQDETGEAKLFSANITADDHSEMIARGEYILETFGPDADKVAFLVDGYVG---------GPGMVTTARRY--------------------------------
		FII_E4_POB_9N                          N-------QVFAPMKKVIPLVVDAMKRAQDETGQAKLFSANITADSHAEMIARGEYILEAFGEFADHVAFLVDGYVG---------GPGMVTTARRR--------------------------------
		FII_E1_POB_9N                          N-------QVFCPMKKVIPLVVNTMKRAQDKTGQAKLFSANITANSHAEMIARGEYILEQFGPDADKVAFLVDGYIG---------GPGMVTTARR---------------------------------
		FII_C3_POB_9N                          N-------QVFCPMKKVIPLVVDAMKRAQDETGQAKLFSANITADDHAEMIARGEYILEAFGPDADKVAFLVDGYVG---------GPGMVTTARRY--------------------------------
		FII_C1_POB_9N                          N-------QVFCPMKKVIPPVVDAMKRAQDETGQAKLFSANITADSHAEMIARGEYILEQFGPDADKVAFLVDGYVG---------GPGMVTTARRW--------------------------------
		FII_B1_POB_9N                          N-------QTFAPMREIIPLIADAMRRAQDETGEAKIFSGNITAGDPFEMIARGEYILETFGPDADKVAFLVDGYVG---------GPGMVTTARR---------------------------------
		FII_G02_POB_9N                         N-------QVFCPMKKVIPLVADAMKRAQDETGEAKLFSANITADDHSEMIARGEYILETFGPDADKVAFLVDGYVG---------GPGMVTTARR---------------------------------
		FII_f6_POB_9N                          N-------QVFCPNKKVIPLVVDAMKRAQDETGQAKLFSANITADSHAEMIARGEYVLEQFGPDADKVAFLVDGYVG---------GPGMVTTARRW--------------------------------
		Riftia_pachyptila_endosymbiont         N-------QPFSPMKKTIPLVADAMRRAQDETGEAKLFSANITADDPAEMIARGEFVLETFGFEASQVAFLVDGYVA---------GPTAVATARRK--------------------------------
		Thiobacillus_denitrificans_b           N-------QVFCPLKKVLPLVYDAMKRAQDDTGQAKLFSMNITADDHYEMCARADYALEVFGPDADKLAFLVDGYVG---------GPGMVTTARRQ--------------------------------
		Rhodobacter_capsula                    N-------QTFAPLKETIRLVADAMKRAQDETGEAKLFSANITADDHYEMVARGEYILETFGENADHVAFLVDGYVT---------GPAAITTARRS--------------------------------
		Rhodspirillum_rubrum                   N-------QPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGENASHVALLVDGYVA---------GAAAITTARRR--------------------------------
		3838_RT                                KDDEDVNSQPFMRWRHRFDYVAEAVHQAEAETGERKGHYLNVTAPDVEQMYQRAEYA-KSLGMRVIMHDFLTAGFTAHTSLSNWCCHNGMLLHIHRA--------------------------------
		Alcaligenes_eutrophus                  KDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFA-KSLGSVIIMID-LIVGWTCIQSMSNWCRQNDMILHLHRA--------------------------------
		Thiobacillus_ferrooxidans              KDDENVNSQPFMRWRQRFDFVMEAIQKAEAETGERKGHYLNVTAPTPEEMYKRAEYA-KEIGAPIIMHDYITGGFCANTGLANWCRDNGMLLHIHRA--------------------------------
		Rhodobacter_veldkampii                 KDDENVNSQPFMRWRDRFLFCQEAIEKAEAETGERKGHYMNVTAATMEEMYERAEFA-KEIGTPIIMSDYLTVGWAAHTSLSKWCRKNGMLLHVHRA--------------------------------
		Pogonophora_sp._JT1_endosymbiont       KDDENVNSQPFMRWRDRFEFVQEATEKAQAETGEIKGHYLNVTAPDIEEMYKRAEFA-KEIGAPIIMSDYLTMGWAAQQSLSKWCRNNGMLLHVHRA--------------------------------
		h04_POB_9N                             --------QPFMRWRDRSLFVQEACEKAEAETGERKGHYLNVTAPTVEEMFKRAEFA-KEIGARIIMSDYLTLGWAAHTSLSKWCRDNGILLHVHRA--------------------------------
		e05_POB_9N                             KDDENVNSQPFMRWRDRFLFVQEACEKAEAETGERKGHDLNVTAPTVEEMFKRAEFA-KEIGARIIMSDYLTLGWAAHTSLSKWCRDNGILLHVHRA--------------------------------
		d05_POB_9N                             KDDENVNSQPFMRWRDRFLFVQEAIEKAEAETGERKGHYLNVTAPDVEEMYKRAEFA-KEIGSRIIMSDYLTLGWAAHQSLSKWCRDNGMLLHVHRA--------------------------------
		g05_POB_9N                             KDDENVNSQSFMRWRDRFEFVAEAVMKAQDETGERKGHYLNVTAATPEEMYKRAEFA-KELGMPIIMHDFLTGGFTANTGLANWCRDSGMLLHIHRA--------------------------------
		c07_POB_9N                             KDDENINSQPFQRWQDRFEFVANAVDKATIETGERKGHYLNVTSGDVEQMMKRAEFA-KELGQPIIMHDFLTAGFTANTTLAKWCRDNGMLLHIHRA--------------------------------
		c04_POB_9N                             KDDENINSQPFQRWQDRFEFVANAVDKATLDTGERKGHYLNVTSGDVEQMMKRAEFA-KELGQPIIMHDFLTAGFTANTTLAKWCRDNGMLLHIHRA--------------------------------
		Synechococcus_sp._WH7803               KDDENINSQPFQRWQNRFEFVAEAIKLSEQETGERKGHYLNVTANTPEEMYERAEFA-KELGMPIIMHDFITGGFTANTGLSKWCRKNGMLLHIHRA--------------------------------
		Hydrogenovibrio_marinus                KDDENINSQPFQRWRDRFEFVAEAVDKATAETGERKGHYLNVTAGTVEEMMKRAEFA-KELGQPIIMHDFLTAGFTANTTLANWCRENGMLLHIHRA--------------------------------
		Hydrogenophilus_thermoluteolus         KDDENVNSQPFMRWRDRFLFCQEAIEKAQAETGERKGHYMNVTGPTMEEIYKRAEFA-KEIGTPIIMIDYLTVGWAATQSLSKWCRDNGMLLHVHRA--------------------------------
		Thiobacillus_sp.                       KDDENVNSQPFMRWRHGFDFVMEAIEKAERETGERKGHYLNVTAPTPDEMFKRAEYA-KEIGAPIIMHDYITGGFTANTGLAQWCRDNGVLLHIHRA--------------------------------
		Thiobacillus_denitrificans             KDDENVNSQPFMRWRQRFDFVMEAIQKSERETGERKGHYLNVTAPTPEEMYKRAEYA-KEIGAPIIMHDYITGGFCANTGLANWCRDNGMLLHIHRA--------------------------------
		f06_POB_9N                             KDDENVNSQPFMRWRDRFLFVEEGRRKAEAETGERKGHYLNVTAPTVEEMFKRAEFA-KEVGAPIIMSDYLTLGWAAHNSLSKWCRDNGMLLHVHRA--------------------------------
		a05_POB_9N                             KDDENVNSQFFMRWRDRFLFVQEACEKAEAETGERKGHYLNVTAPTVEEMYKRAEFA-KEIGARIIMSDFLTLGWAAHTSLSKWCRDNGLLLHVHRA--------------------------------
	;
END;

BEGIN CODONS;
CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 EXSET * mask = 1 - 32 62 82 102 - 110 121 - 129 ; 
 END;