#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 September 17, 2025; 22:56 GMT

TreeBASE (cc) 1994-2008

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 16689 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16689;
        DIMENSIONS NTAX=11;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_01585'
            'Caldanaerobacter subterraneus tengcongensis_NP_623301.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM92233.1'
            'Escherichia coli YP_006125371.1'
            'Escherichia coli YP_006125567.1'
            Geobacillus_sp._Y4.1MC1_YP_003989191.1
            'Geobacillus thermoglucosidasius YP_004587923.1'
            'Moorella thermoacetica YP_431022.1'
            'Thermacetogenium phaeum YP_006921296.1'
            'Thermoanaerobacter sp. YS13 THYS13_RS04685'
            'Thermococcus onnurineus TON_1022'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32848]

	TITLE HyfC_alignment;
	LINK TAXA = TaxaForAnalysisStep16689;
	DIMENSIONS NCHAR=318;
	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        ]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .        ]
'Caldanaerobacter subterraneus pacificus_CDSM653_01585'     ----MLDGKLFFVGLLQALLLMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
'Caldanaerobacter subterraneus tengcongensis_NP_623301.1'   ----MLDGKLFFVGLLQALLLMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
'Caldanaerobacter subterraneus yonseiensis_ERM92233.1'      ----MLDGKLFFVGLLQALLVMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLYALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFMAPEVTWAAFGFALLSFVFFLVNV
'Escherichia coli YP_006125371.1'                           MRQTLCDGYLVIFALAQAVILLMLTPLFTGISRQIRARMHSRRGPGIWQDYRDIHKLFKRQEVAPTSSG-LMFRLMPWVLISSMLVLAMALPLFITVSPFAGGGDLITLIYLLALFRFFFALSGLDTGSPFAGVGASRELTLGILVEPMLILSLLVLALIAGSTHIEMISNTLAMGWNSP--LTTVLALLACGFACFIEMGKIPFDVAEAEQELQEGPLTEYSGAGLALAKWGLGLKQVVMASLFVALFLSFGRAQELSLACLLTSLVVTLLKVLLIFVLASIAENTLARGRFLLIHHVTWLGFSLAALAWVFWLTGL
'Escherichia coli YP_006125567.1'                           --------MSVLYPLIQALVLFAVAPLLSGITRVARARLHNRRGPGVLQEYRDIFKLLGRQSVGPDASG-WVFRLTPYVMVGVMLTIATALPVVTVGSPLPQLGDLITLLYLFAIARFFFAISGLDTGSPFTAIGASREAMLGVLVEPMLLLGLWVAAQVAGSTNISNITDTVYHWPLSQS-IPLVLALCACAFATFIEMGKLPFDLAEAEQELQEGPLSEYSGSGFGVMKWGISLKQLVVLQMFVGVFIPWGQMETFTAGGLLLALVIAIVKLVVGVLVIALFENSMARLRLDITPRITWAGFGFAFLAFVSLLAA-
Geobacillus_sp._Y4.1MC1_YP_003989191.1                      ----MPEMKLLLIGLVQAVFLLLVAPFFTGLSRVLRAKAHSRKGPSILQDYRDIFKLIKRQEVVPAQSS-WVFRITPYVIMATMLLIAMIIPVLTLQAPLGMVGDLIVIVYLFTVFRFFFSIAGLDSGSSFAGIGASREMALGVLVEPTIILVLFVVALLSGSTDLGIISQKMATGEISYLSPAVLLGMVAFAVATFIESGKIPFDLAEAEAEIQEGPLTEYSGRSLAILKWSLGLKQMVVNALYLAIFFPFGNAAVVTPSAILVSMVLFLLKVVVIYVVAALLENSMARFVLFKTPAVTWVVFGIAMLSYVFYMVNI
'Geobacillus thermoglucosidasius YP_004587923.1'            ----MPEMKLLLIGLVQAVFLLLVAPFFTGLSRVLRAKVHSRKGPSILQDYRDIFKLIKRQEVVPAQSS-WVFRITPYVIMATMLLIAMIIPVLTLQAPLGMVGDLIVIVYLFTVFRFFFSIAGLDSGSSFAGIGASREMALGVLVEPTIILVLFVVALLSGSTDLGIISQKMATGEISYLSPAVLLGMVAFAVATFIESGKIPFDLAEAEAEIQEGPLTEYSGRSLAILKWSLGLKQMVVNALYLAIFFPFGNAAVVTPSAILVSMVLFLLKVVVIYVVAALLENSMARFVLFKTPAVTWVVFGIAMLSYVFYMVNI
'Moorella thermoacetica YP_431022.1'                        ----MPGIKLFLVGLMQALLVLLVAPLFAGLTRVLRARLHSRKGASIFQDYRDIFKLIKRQEVVPAQAS-WVFRFTPYVVMATTLLIAMVIPILTLQSPLGMAGDLIAVVYLFALLRFFFAVAGLDSGSGFAGIGASREMVLAILVEPTIILVLFVLALLTGSTDLGAISQKVAFGSISYYRPAVWLGMLAFAVATFIETGKLPFDLAEAEQELQEGPLTEYSGRSLAILKWSLSMKQVVVIALFLAVFFPFGSAAAVSTSSLLVSAAAFLLKVTGFYVIAALMENSSARLIIYKAPEVTWLAFGIALLSFVFYLVNV
'Thermacetogenium phaeum YP_006921296.1'                    ----MFDVNLFLLGILQAVFVVLAAPLLAGFARVLRAKMHSRTGPPILQYYYDLWKLLKRQDVSPAPAT-WVYRLTPYIVFSCAFLMAMIVPMVTLEAPLGYAGDLIVVIYLLAAIRFFTALSGIDSGSGFAGVGSIRELALSVLVEPALILVLLIMALFAGSTNLGSISLMIAQGEIPYTSPAVWLGMAALAVVSFVEMGKLPFDLAEAEQELQEGPLTEYSGRRLAVLEWGLFMKQVAVASLFLAVFFPFGSAASLSPPAVMAGLAFFLIKLAVCYFLAAVVENSMCRLTIYKAPGATWVALGIALLSFVFYLVEI
'Thermoanaerobacter sp. YS13 THYS13_RS04685'                ----MLDDKLFFVGLLQALLVMAVTPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDVGVITQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNVAVVNGFSILMSTAVFLLKVAIFYVIVALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
'Thermococcus onnurineus TON_1022'                          --------MNAVYAALNLIFIVLFAPLLDGIERKVKARLQSRQGPPLIQTWLDLLKLFRRPNVRPRESVRWLFEPAPAIALVSVLAASLFIPSL-LPGSLDTWGDIIAFIYLSTLSAVAIALGAFSTGSPYAQIGSHREVSIIMAEEFSLAFIVAALAASSG----GLSFSRLFPLQLK---VSTITGALAFAVMAYVAGARIPFDVAEAEPEIVEGPFIEFSGKGLGMLKLSIYVKRLLLTTILLNFFLPQDGT---------VRVLVYVIGLVIISVVYASIEAHYGRFRTKDAARFLKRFAIVGILSWILGVVGW
;
END;

[ The following blocks are output data for analysis step 16689 ]
BEGIN TREES;
      TITLE HyfC_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16689;
      TREE HyfC_ML = [&R] (((((('Thermoanaerobacter sp. YS13 THYS13_RS04685':0.014021,('Caldanaerobacter subterraneus tengcongensis_NP_623301.1':1.0E-6,'Caldanaerobacter subterraneus pacificus_CDSM653_01585':1.0E-6)0.730000:0.003476)0.732000:0.003867,'Caldanaerobacter subterraneus yonseiensis_ERM92233.1':0.01032)1.000000:0.139675,('Moorella thermoacetica YP_431022.1':0.082403,'Thermacetogenium phaeum YP_006921296.1':0.457843)0.740000:0.039928)0.964000:0.102146,(Geobacillus_sp._Y4.1MC1_YP_003989191.1:0.003457,'Geobacillus thermoglucosidasius YP_004587923.1':1.0E-6)0.966000:0.09735)0.521000:0.153155,'Thermococcus onnurineus TON_1022':1.646428)0.915000:0.205499,'Escherichia coli YP_006125371.1':0.397489,'Escherichia coli YP_006125567.1':0.497788)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89841]


END;