#NEXUS
[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.


Generated on November 10, 2026; 4:37 GMT

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Study reference:
Sant'anna F.H., Lebedinsky A.V., Sokolova T.G., Robb F.T., & Gonzalez J.M. 2015.
Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter
subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase
diversity. BMC Genomics, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S18113]

[ The following blocks are input data for analysis step 16748 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16748;
        DIMENSIONS NTAX=14;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_0112'
            'Caldanaerobacter subterraneus tengcongensis_3VTI'
            'Caldanaerobacter subterraneus tengcongensis_NP_621834.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM91357.1'
            'Thermoanaerobacter WP_004399980.1'
            'Thermoanaerobacter ethanolicus WP_003868948.1'
            'Thermoanaerobacter italicus YP_003477419.1'
            'Thermoanaerobacter mathranii YP_003677315.1'
            'Thermoanaerobacter siderophilus WP_006569909.1'
            'Thermoanaerobacter wiegelii YP_004818939.1'
            'Thermoanaerobacterium saccharolyticum YP_006391309.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1'
            'Thermoanaerobacterium xylanolyticum YP_004469852.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32981]

	TITLE HypE_alignment;
	LINK TAXA = TaxaForAnalysisStep16748;
	DIMENSIONS NCHAR=386;
	FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -;

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      ]
[                                                                       .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .      ]
'Caldanaerobacter subterraneus pacificus_CDSM653_0112'         -----------------------------MERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
'Caldanaerobacter subterraneus tengcongensis_3VTI'             --------------------------------------------GALIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
'Caldanaerobacter subterraneus tengcongensis_NP_621834.1'      ------MHGVFGRVLCSVLQVWRIRGDLM-ERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
'Caldanaerobacter subterraneus yonseiensis_ERM91357.1'         -----------------------------MERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NLTFTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDGIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIERLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGLDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
'Thermoanaerobacter WP_004399980.1'                            -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVENGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
'Thermoanaerobacter ethanolicus WP_003868948.1'                -----------------------------MDKVLLSHGGGGTMMENLIEEVFSKAFDNEYIKGMEDAALL---F---------------G--NITLTTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIENLKRIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
'Thermoanaerobacter italicus YP_003477419.1'                   -----------------------------MDKVLLSHGGGGTMMESLIEEVFSKAFDNEYIKGMEDAALL---F---------------G--NITFTTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPMEDLKKIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFINTSGIG-VVYENV-DVSIKNAKPGDVVLVSGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKDSVKHACEMMGFDFLHLANEGKLITVIDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
'Thermoanaerobacter mathranii YP_003677315.1'                  -----------------------------MDKVLLSHGGGGTMMESLIEEVFSKAFDNEYIKGMEDAALLFE--------------------NITFTTDSFIVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPMEDLKRIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFITTSGIG-VVYENV-DVSIKNAKPGDVVLVSGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKDSVKYACDMMGFDFLHLANEGKLIAVIDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTLNTIYGTSRIVDRPIGELLPRIC
'Thermoanaerobacter siderophilus WP_006569909.1'               -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVEKGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
'Thermoanaerobacter wiegelii YP_004818939.1'                   -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVENGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
'Thermoanaerobacterium saccharolyticum YP_006391309.1'         -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLSQMEDAALL---P---------------G--KTVFTTDSFVVKPIFFSGGDIGRLAICGTVNDISMRGAKPLFLSASFIIEEGFPIDDIKRIVDSMVDAANEAGVQIVTGDTKVVEKHSADGIFINTAGIG-ILHDEA-SVSIKNGKPGDAVIISGTIGDHGMAVMGDREGLDFEPPLLSDVSPLNKMVEKLMTLKDA-VKILRDPTRGGVAEVLYEIASMSNVGIKIYEDKLPVKESVKSACSMLGIDYLHLANEGKLVCVVDKDYAYKALEIMKDDKYGKDAAIIGEI--DDSG---LVTIETIYGTNRIVDRPIGELLPRIC
'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1'   -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLSQMEDAALL---P---------------G--KTVFTTDSFVVKPLFFPGGDIGRLSVCGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKRIVNSMEDTANEAGVQIVTGDTKVVEKNSADGIFINTAGIG-ILPDGA-SVSIKNGKPGDVVIVSGTIGDHGMAVMGAREGIDFDPPLLSDVSPLNKMVEKLMALRDA-VKILRDPTRGGVAEVLYEIAGMSNVGIKIYEDKLPVKENVKSACSMLGIDYLHLANEGKLVCVVDKDFAYKALEIMKDDKYGKDAAIIGEI--DDSG---LVTIETIYGTNRIVDRPIGELLPRIC
'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1'   -----------------------------MDKILMTHGGGGSMMQSFIDEIFISKFDNQYIKEMEDAALL---P---------------G--KIVFTTDSFVVKPLFFPGGDIGRLSVCGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKRIVNSMEDTANEAGVQIVTGDTKVVEKNSADGVFINTAGIG-ILPDGA-DISIKNGKPGDVVIISGTIGDHGMAVMSAREEINFEPPLFSDVSPLNKMVEKLATLKSA-VKILRDPTRGGVAEVLYEIANMSNVGIKIYEDKLPVKESVKSACSMLGLDYLHLANEGKLVCVVERDYADEALKLMKEDIYGKDASIIGEIND--TG---LVTIETVYGTTRIVDRPLGELLPRIC
'Thermoanaerobacterium xylanolyticum YP_004469852.1'           -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLNQMEDAALL---P---------------G--KTVFTTDSFVVKPVFFPGGDIGRLAICGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKKIVDSMVDAANEAGVQIVTGDTKVVEKNSADGIFINTAGIG-ILPDGA-YVSIKNGEPGDVVIVSGTIGDHGMAVMGAREGLDFDPPLFSDVSPLNKMVQKLMTLKDA-VKILRDPTRGGVAEVLYEIASMSNVGIKIHEDKLPVKESVKSACSMLGIDFLHLANEGKLICVVDKDFAYKALEIMKGDKYGKDAAIIGEI--DDSG---LVTIETVYGTNRIIDRPIGELLPRIC
;
END;

[ The following blocks are output data for analysis step 16748 ]
BEGIN TREES;
      TITLE HypE_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16748;
      TREE HypE_ML = [&R] (((('Thermoanaerobacterium saccharolyticum YP_006391309.1':0.031517,'Thermoanaerobacterium xylanolyticum YP_004469852.1':0.042239)0.9400:0.025978,'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1':0.011315)0.7340:0.054186,'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1':0.061975)0.9910:0.136071,((('Thermoanaerobacter mathranii YP_003677315.1':0.013433,'Thermoanaerobacter italicus YP_003477419.1':0.011126)0.5280:0.0189,((('Thermoanaerobacter wiegelii YP_004818939.1':1.0E-6,'Thermoanaerobacter WP_004399980.1':0.003409)0.8380:0.003407,'Thermoanaerobacter siderophilus WP_006569909.1':1.0E-6)0.9900:0.031345,'Thermoanaerobacter ethanolicus WP_003868948.1':0.004465)0.8510:0.023837)0.9800:0.074041,(('Caldanaerobacter subterraneus tengcongensis_3VTI':0.006911,('Caldanaerobacter subterraneus pacificus_CDSM653_0112':1.0E-6,'Caldanaerobacter subterraneus tengcongensis_NP_621834.1':1.0E-6)0.0000:1.0E-6)0.8900:0.010665,'Caldanaerobacter subterraneus yonseiensis_ERM91357.1':0.006626)0.9790:0.076519)0.6010:0.0965)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89916]


END;