#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; 22:57 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 16694 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16694;
        DIMENSIONS NTAX=11;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_01580'
            'Caldanaerobacter subterraneus tengcongensis_NP_623296.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM92229.1'
            'Escherichia coli YP_006125376.1'
            'Escherichia coli YP_006125565.1'
            'Geobacillus sp. Y4.1MC1 YP_003989196.1'
            'Geobacillus thermoglucosidasius YP_004587927.1'
            'Moorella thermoacetica YP_431017.1'
            'Thermacetogenium phaeum YP_006921301.1'
            'Thermoanaerobacter sp. YS13 THYS13_RS04630'
            Thermococcus_onnurineus_NA
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32862]

	TITLE HyfH_alignment;
	LINK TAXA = TaxaForAnalysisStep16694;
	DIMENSIONS NCHAR=199;
	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         ]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
'Caldanaerobacter subterraneus pacificus_CDSM653_01580'     MLRLLKKALQVGEATVEYPFKPVEVAQGFRGKPAYDFSRCIGCGACATACPSNAITMDCDLDRGIKSWNINYGRCIFCGRCEEVCPTGAIVLSTEFELAVIKKEDMYCRAEFQLCRCIFCGEYFETFREIEYVREILEQTGLTKKSLESW-VQLLKVCPKCRRHKVARIAALDNWHVDLNGRREEKWNQKLSYKNLKQS
'Caldanaerobacter subterraneus tengcongensis_NP_623296.1'   MLRLLKKALQVGEATVEYPFKPVEVAQGFRGKPAYDFSRCIGCGACATACPSNAITMDCDLDRGIKSWNINYGRCIFCGRCEEVCPTGAIVLSTEFELAVIKKEDMYCRAEFQLCRCIFCGEYFETFREIEYVREILEQTGLTKKSLESW-VQLLKVCPKCRRHKVARIAALDNWHVDLNGRREEKWNQKLSYKNLKQS
'Caldanaerobacter subterraneus yonseiensis_ERM92229.1'      MLRLLKKALEVGEATVEYPFKPVEVAQGFRGKPAYDFSRCIGCGACATACPSNAITMDCDLDKGIKSWNINYGCCIFCGRCEEVCPTGAIVLSKEFELAVIKKEDMYCRAELKLCRCIFCGEYFETFREIEYVREVLEQTGLTKKSLESW-DQLLKVCPKCRRHKVARIAALDNWHVDLNGRREE---------NGTRS
'Escherichia coli YP_006125376.1'                           MLKLLKTIMRAGTATVKYPFAPLEVSPGFRGKPDLMPSQCIACGAC--ACPANALTIQTDDQQNSRTWQLYLRRCIYCGRCEEVCPTRAIQLTNNFELTVTNKADLYTRATFHLQRCSRCERPFAPQKTVALAAELLAQQQNAPQNREML-RAQASVCPECKQR-----ATLINDDTDVPLVAKEQL------------
'Escherichia coli YP_006125565.1'                           MFTFIKKVIKTGTATSSYPLEPIAVDKNFRGKPEQNPQQCIGCAACVNACPSNALTVETDLATGELAWEFNLGRCIFCGRCEEVCPTAAIKLSQEYELAVWKKEDFLQQSRFALCNCRVCNRPFAVQKEIDYAIALLKHNG--DSRAENH-RESFETCPECKRQKCL----VPSDRIELTRHMKEAI------------
'Geobacillus sp. Y4.1MC1 YP_003989196.1'                    MLKLLKKALQVGEATVKYPFKPLEVAPGFRGKPVYDFSQCIACGACATACPSNAITMEHDFKRGIVSWNINYGRCIFCGRCDEVCPTGAIALSEEFELAASRKEDLYCRAEIQLCKCSSCGKHFAPYRELEYVLANLEQVGLTDHDKEKW-KQLVNVCPECRRRQVA-----APWVHN---------------------
'Geobacillus thermoglucosidasius YP_004587927.1'            MLKLLKKALQVGEATVKYPFKPLEVAPGFRGKPVYDFSQCIACGACATACPSNAITMEHDFKRGIVSWNINYGRCIFCGRCDEVCPTGAIALSEEFELAASRKEDLYCRAEIQLCKCSSCGKHFAPYRELEYVLANLEQVGLTDHDKEKW-KQLVNVCPECRRRQVA-----APWVHN---------------------
'Moorella thermoacetica YP_431017.1'                        MLKLLKKALQVGEATVEYPFKPVEVAPGFRGKPEYNFDRCIACGACATACPPNAITMEYDLKQGTKTWNIFYGRCIFCGRCEEVCPTGAIALTTEFELAVASKEDLYYRAEVQLRKCSCCGEYFAPSRELEYVMSTLEQSGLPEGDRQGW-RQLLEKCPQCRRRQAAVSVAEATGSRDRVQGGGQ--------------
'Thermacetogenium phaeum YP_006921301.1'                    MIKLLRKVLQVGEATEKYPFTPATVSPGMRGKPEYHFQSCISCGACAGACPANAITLESDPDLGTRRWAIFYGRCIFCGRCEEVCPTGAITLSQDFELAAVNRDDLITTAEFRLTKCRACGRFFAPARELTYLLTSLMENGLPLEEAEEK-RRLLRTCPECRRK--ISICNLRKATTGLTGKGVTR-------------
'Thermoanaerobacter sp. YS13 THYS13_RS04630'                MLRLLKKALQVGEATVEYPFKPVEVAQGFRGKPAYDFSRCIGCGACATACPSNAITMDCDLDRGIKSWNINYGRCIFCGRCEEVCPTGAIVLSTEFELAVIKKEDMYCRAEFQLCRCIFCGEYFETFREIEYVREILEQTGLTKKSLESW-VQLLKVCPKCRRHKVARIAALDNWHVDLNGRREEKWNQKLSYKNLKQS
Thermococcus_onnurineus_NA                                  RL------------------------------------------------PPQAIRVFTDEARGIRVVHLFIGRCIFCGRCQDVCPVGAIKLTTQFELATSDHDELHQIVELQMARCSECGKSFDTYR---HLIASLEK-------IHPWERKNLLLCPECRAKKTS------EWRV---------WG-----------
;
END;

[ The following blocks are output data for analysis step 16694 ]
BEGIN TREES;
      TITLE HyfH_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16694;
      TREE HyfH_ML = [&R] ((((('Caldanaerobacter subterraneus pacificus_CDSM653_01580':1.0E-6,'Thermoanaerobacter sp. YS13 THYS13_RS04630':1.0E-6)0.000000:1.0E-6,'Caldanaerobacter subterraneus tengcongensis_NP_623296.1':1.0E-6)0.000000:1.0E-6,'Caldanaerobacter subterraneus yonseiensis_ERM92229.1':0.069992)1.000000:0.310025,(Thermococcus_onnurineus_NA:1.083969,(('Thermacetogenium phaeum YP_006921301.1':0.54779,('Escherichia coli YP_006125376.1':0.55778,'Escherichia coli YP_006125565.1':0.631149)0.872000:0.321304)0.663000:0.099432,'Moorella thermoacetica YP_431017.1':0.214397)0.692000:0.080076)0.127000:0.042502)0.981000:0.216265,'Geobacillus thermoglucosidasius YP_004587927.1':1.0E-6,'Geobacillus sp. Y4.1MC1 YP_003989196.1':1.0E-6)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89846]


END;