NEXUS
[File created by TreeBASE:  7/26/07  21:06:00]
[Matrix accession#: M1992]

BEGIN TAXA;
	TITLE M1992;
	DIMENSIONS  NTAX=46;
	TAXLABELS
		6B_Guaymas	6A_Guaymas	4a_Guaymas	3H_Guaymas	1f_Guaymas	F03_Guaymas	C10_POB_9N	C05_Guaymas	B12_POB_9N	Methanococcus_jannaschii	Pyrococcus_furiosus	Archeoglobus_fuligidus	Alvinella_pompejana_symbiont	H02_Guaymas	H03_Guaymas	'848-2 Guaymas'	3E_Guaymas	2f_Guaymas	2d_Guaymas	H10_POB_9N	G10_POB_9N	G09_POB_9N	F12_POB_9N	F04_Guaymas	E12_POB_9N	G11_POB_9N	E05_Guaymas	D03_Guaymas	D02_Guaymas	C04_Guaymas	C01_Guaymas	B10_POB_9N	A11_POB_9N	A05_Guaymas	B02_Guaymas	Nautilia_sp._AmH	Persephonella_marina	E09_POB_9N	E06_Guaymas	B11_POB_9N	Candidatus_Arcobacter_sulfidicus	807_28_POB	807_22_Guaymas	807_21_Guaymas	H11_POB_9N	Helicobacter_pylori
	;
END;

BEGIN CHARACTERS;
	TITLE M1992;
	DIMENSIONS NCHAR=68;
	FORMAT DATATYPE = PROTEIN SYMBOLS = " 1 2 3 4 " MISSING = ? GAP = -  ;
	MATRIX
		6B_Guaymas                             PFPAEEVREALKD---CENVIVFDRGF-FGY-EG-ILTIDIRN?LYGE----APDVYSFIVGLGESD-
		6A_Guaymas                             PFPFDRIKEIAKK---AKLLAVLDRAVSQGF-AG-PVFGEVSGALANES--ERPIIMDFIIGLGESD-
		4a_Guaymas                             PFPIEEIRALAKK---AK?LAILEKDVSFGS-GG-AVFADVSRPLINEK--EKPVVLDFIIGLGESD-
		3H_Guaymas                             PFPIEEIKALAKK---AKVLAILEKDVSFGS-GG-AVFADVARSLINER--EKPIVLDFIIGLGGSD-
		1f_Guaymas                             PFPIEEIRALAKK---AKVLAILEKDVSFGS-GG-AVFADVSRSLINEK--EKPIVLDFIIGLGESD-
		F03_Guaymas                            PFPFKEILPLIKN---AKVVATLERNISMGY-GG-AVYADLSGALINEK--ERSTLIDFILGLGESD-
		C10_POB_9N                             PFPIEEIRALAKK---AKVLAILEKDISFGS-GG-AVSADVARSLINEK--EKPIVLDFIIGLGESD-
		C05_Guaymas                            PSPYDLVRDALDV-PSLKAVCCMDKSAPGGA-MG-ALFNEVSAAAYTTE--SRPMITNYIYGLGESD-
		B12_POB_9N                             RPFPYNEVAEKLKN---VKAVAALDRSMPMGT-TG-ALYNEVAGALAANG--QSAIMNKLYYGLGESD
		Methanococcus_jannaschii               RPFPKEDVKELLKD---ANNIAVLDKNISLGFNKG-ALGIEMASILKN------KKVCNYIVGLGGRD
		Pyrococcus_furiosus                    RPFPVEEIRELAKK---AKVLAFLEKNITIGL-YG-AVFTDASAALINES--EKPLMVDFIVGLGGRD
		Archeoglobus_fuligidus                 RPFPVEELREALKD---AEKVIVLDRSVSFGY-EG-PVSIELKSAIYGHS--S-AEIYSFAVGLGGRD
		Alvinella_pompejana_symbiont           PFPFDVVRDAIDISPNLKAIVCMDKSAPGGA-MG-ALFNEVSAAAYSTK--NRPIMTNYIYGLG----
		H02_Guaymas                            PFPYKELADVLSG---AKAIAVLDRVSPAGA-QGGPLFNEIRSALCDAN--NRPPVINYSYGFGESD-
		H03_Guaymas                            PFPTKELADILTN---LKAVAVLDRALSPGS-IGGPLFLDLRSALYEYE--KKPIMVDYIYGLGESD-
		'848-2 Guaymas'                        PFPYNEVAEKLAN---VKAIAALDRNSPMGA-MG-ALYNEVAGALSANG--QSAVMTNYIYGLGGSD-
		3E_Guaymas                             PFPYNEVAEKLAN---VKAIAALDRNSPMGA-MG-ALYNEVAGALAANG--QSAVMTNYIYGLGESD-
		2f_Guaymas                             PFPYKELADVLSG---AKAIAVLDRVSPAGA-QGGPLFNEIRSALYDAN--NRPPVINYSYGLGESD-
		2d_Guaymas                             PFPYNEVAEKLAN---VKAITALDRNSPMGA-MG-ALYNEVASALSANG--QSAVMTYYIYGLGESD-
		H10_POB_9N                             PFP?NEIAKKLAN---VKAVAALDRSAPMGT-TG-ALYNEVAGALAANG--ESAIMTNYIYGFGGSD-
		G10_POB_9N                             PFPYYDVMDALEASN-AKAVGVFDRAETFGA-VGGPLYSDIATAMYLRG--KTYPIVSFIYGLGGSD-
		G09_POB_9N                             PFPFDEIRDVLAN---VKAVAILDRSAPMGA-MG-ALFNEISAAMYTTP--H?PIINNYIYGLGESD-
		F12_POB_9N                             PFPYDEVREALAN---TKAIAVTDRSSPGGA-MG-AFFNEVSAAMYTSV--NRPIVTGFVYGLGESD-
		F04_Guaymas                            PFPFDQVRDILEN---AKSIAVLDRSSPGGA-MG-AFFNEVSAALYSTQ--NRPLVTNYIYGLGESD-
		E12_POB_9N                             PFPYNEIAEKLRN---VKAIAALDRSAPMGT-TG-ALYNEVAGALAAKG--YSAIMTNYIYGLGESD-
		G11_POB_9N                             PFPYERLGQDLKN---LKALAILDKSSPAGA-MG-AMFNEVTSTVYQTQGTKHPVVSNYIYGLGGSD-
		E05_Guaymas                            PFPYNEIREALAN---VKSVTVLDRSCPMGA-MG-ALYNEICGAMASTP--ANPLITNYIYGLGESD-
		D03_Guaymas                            PFPYKELADVLSG---AKAIAVLDRVSPAGA-QGGPLFNEIRSALYDVN--NRPLVINYSYGLGESD-
		D02_Guaymas                            PFPYRDIAEAISASN-AKVIGTLNKAETFGG-AGGPLFEEIATSLFLSG--IQIPLVDFIYGLGESD-
		C04_Guaymas                            PFPYNQVAEKLKN---IKAVAAPDRSAPMGA-MG-ALYNEVSGALAAKG--QSAIMTNYIYGLGGSD-
		C01_Guaymas                            PFPYNEIAEKLAN---VKAVAALDRNSPMGA-MG-ALYNEVAGALAANG--QS?VMTNYIYGLGGSD-
		B10_POB_9N                             PFPFDLVRDALEN---VKSVAVLDRSSPGGA-MG-AFYNEVAAALYTTP--NRPLVTNYIYGLGESD-
		A11_POB_9N                             PFPYNEVAEKLKN---VKAVAALDRSMPMGT-TG-ALYNEVAGALAANG--RSAIMTNYIYGLGGSD-
		A05_Guaymas                            PFPYDLVRDALDV-PSLKAVCCMDKSAPGGA-MG-ALFNEVSAAAYTTE--SRPMITNYIYGLGESD-
		B02_Guaymas                            PFPYNEIAEKLAN---VKAVAALDRNSPMGA-MG-ALYNEVAGALAANG--QSTVMTNIFTVSAEA--
		Nautilia_sp._AmH                       RPFPYNEIAKKLAN---VKAVAALDRSAPMGT-TG-ALYNEVAGALAANG--QSAIMTNYIYGLGESD
		Persephonella_marina                   RPFPVKEIAKALSN---AKGVAVLDRADSFDG-IGGPLFKDVASALLGTT--NRPFVHNFIYGLGESD
		E09_POB_9N                             SPFPFDLVRDALEN---VKSVAVLDRSSPGGA-MG-AFYNEVAAALYSTP--NSALVTNYIYGLGESD
		E06_Guaymas                            SPFPYNQVAEKLKD---VKAIATLDRSAPMGA-MG-ALYNEVSGALAANG--QSAIMTNYIYGLGESD
		B11_POB_9N                             RPFPYNEVAEKLRN---VKAVAALDRSMPMGT-TG-ALYNEVAGALAANG--QSAIMTNYIYGLGESD
		Candidatus_Arcobacter_sulfidicus       RPFPYEKLRDALEN---VKSIAVTDRSSPGGA-MG-AFYNEVAAAMATSK--SRPMVTNYIYGLGESD
		807_28_POB                             RPFPYNEVAEKLKS---VKAVAALDRSAPMGT-TG-ALYNEVAGALMANG--QSAVMTNYIYGLGANA
		807_22_Guaymas                         RPFPYKELADVLSG---AKAIAVLDGVSPAGA-QGGPLFNEIRSALYDAN--NRPPVINYSYGLGGSA
		807_21_Guaymas                         RPFPYNQVAEKLKD---VKAVAALDRSAPMGA-MG-ALYNEVSGALAAKG--QSAIMTNYIYGLGES-
		H11_POB_9N                             SPFPYNEVAEKLKN---VKAVAALDRSMPMGT-TG-ALYNEVAGALAANG--QSAIMNKLYYGFGGSD
		Helicobacter_pylori                    RPFPYERLGQDLKN---LKALAILDKSSPAGA-MG-AMFNEVTSAVYQTQGTKHPVVSNYIYGLGERD
	;
END;

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

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 EXSET * maskaa = 1 15 - 17 29 33 36 49 - 54 66 - 68 ; 
 END;