#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; 22:44 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 16693 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16693;
        DIMENSIONS NTAX=11;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_01581'
            'Caldanaerobacter subterraneus tengcongensis_NP_623297.1'
            'Caldanaerobacter subterraneus yonseiensis_WP_022587809.1'
            'Escherichia coli YP_006125375.1'
            'Escherichia coli YP_006125566.1'
            'Geobacillus sp. Y4.1MC1 YP_003989195.1'
            'Geobacillus thermoglucosidasius YP_004587926.1'
            'Moorella thermoacetica YP_431018.1'
            'Thermacetogenium phaeum YP_006921300.1'
            'Thermoanaerobacter sp. YS13 THYS13_RS04635'
            'Thermococcus onnurineus TON_1023'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32861]

	TITLE HyfG_alignment;
	LINK TAXA = TaxaForAnalysisStep16693;
	DIMENSIONS NCHAR=583;
	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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580   ]
[                                                                     .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .   ]
'Caldanaerobacter subterraneus pacificus_CDSM653_01581'      --VENEIKAQQDRKKYVRALYSKFGASILEEKWQTPDQVTLT-VKLNILPEIVEEAYYGQGGWLSNVIGNDERSINGHFAVYYVLSIEAEKDPDKNLWLTVKALVPADKPEFPSVAPRVPAAVWYEREVRDMLGLEPVGLPDARRLVLPDDWPDNLYPLRKD-MDY--RLRPEPAAEEENYEFIEVKGEGIVEV-PLGPLHITSDEPGHFRLYVDGEYIVDADYRLFYVHRGLEKLAESRMDYNQVTFLAERICGICGYAHSVAYAMAVEAANRIEVPLRAQYIRTILLEVERIHSHLLNIGLAAHLVGFDSGFMHFFRIREKAMQMAEILTGGRKTYGMNLIGGVRRDILKEEKVQALRLISEIRSELKELIDMLLNTPNFISRTQGVGRLDPKVARNFGSVGPNLRGSGYGRDTRADHPYCAYKHVSWNVISKEGCDVLSRVLVRAEELFESLDIIERCLSDLPPGPILHEGFTYTPYTFALGYTEAPRGENVHWVMTANQHQVYRWRVRASTYNNWPVLRYMFYGNTVADAPLIVASIDPCYSCAERVTLVDVRKKRAKTVQYQELEQYCRERKYSPLKN
'Caldanaerobacter subterraneus tengcongensis_NP_623297.1'    --MENEIKAQQDRKKYVRALYSKFGASILEEKWQTPDQVTLT-VKLNILPEIVEEAYYGQGGWLSNVIGNDERSINGHFAVYYVLSIEAEKDPDKNLWLTVKALVPADKPEFPSVAPRVPAAVWYEREVRDMLGLEPVGLPDARRLVLPDDWPDNLYPLRKD-MDY--RLRPEPAAEEENYEFIEVKGEGIVEV-PLGPLHITSDEPGHFRLYVDGEYIVDADYRLFYVHRGLEKLAESRMDYNQVTFLAERICGICGYAHSVAYAMAVEAANRIEVPLRAQYIRTILLEVERIHSHLLNIGLAAHLVGFDSGFMHFFRIREKAMQMAEILTGGRKTYGMNLIGGVRRDILKEEKVQALRLISEIRSELKELIDMLLNTPNFISRTQGVGRLDPKVARNFGSVGPNLRGSGYGRDTRADHPYCAYKHVSWNVISKEGCDVLSRVLVRAEELFESLDIIERCLSDLPPGPILHEGFTYTPYTFALGYTEAPRGENVHWVMTANQHQVYRWRVRASTYNNWPVLRYMFYGNTVADAPLIVASIDPCYSCAERVTLVDVRKKRAKTVQYQELEQYCRERKYSPLKN
'Caldanaerobacter subterraneus yonseiensis_WP_022587809.1'   --MENEIKAQQDRKKYVRALYSKFGASIFEEKWQTPDQVTLT-VNLNILPEIVEEAYYGQGGWLSNVIGNDERSINGHFAVYYVLSIEAEKDPDKNLWLTVKALVPADKPEFPSVAPRVPAAVWYEREVRDMLGLEPVGLPDARRLVLPDDWPDNLYPLRKD-MDY--RLRPEPAAEEENYEFIEVKGEGIVEV-PLGPLHITSDEPGHFRLYVDGEYIVDADYRLFYVHRGLEKLAESRMDYNQVTFLAERICGICGYAHSVAYAMAVEAANRIEVPLRAQYIRTILLEVERIHSHLLNIGLAAHLVGFDSGFMHFFRIREKAMQMAEILTGGRKTYGMNLIGGVRRDILKEEKVQALRLISEIRSELKELIDMLLNTPNFISRTQGVGRLDPKVARNFGSVGPNLRGSGYGRDTRADHPYCAYKHVSWNVISKEGGDVLSRVLVRAEELFESLDIIERCLSDLPPGPILHEGFTYTPYTFALGYTEAPRGENVHWVMTANQHQVYRWRVRASTYNNWPVLRYMFYGNTVADAPLIVASIDPCYSCAERVTLVDVRKKRAKTVPYQELEQYCRERKYSPLKN
'Escherichia coli YP_006125375.1'                            --VNVNSSSNRGEA-ILAALKTQFPGAVLDEERQTPEQVTIT-VKINLLPDVVHYLYYQHDGWLPVLFGNDERTLNGHYAVYYALSMEGAE----KCWIVVKALVDADSREFPSVTPRVPAAVWGEREIRDMYGLIPVGLPDQRRLVLPDDWPEDMHPLRKDAMDY--RLRPEPTTDSETYAFINE-GNSDARVIPVGPLHITSDEPGHFRLFVDGEQIVDADYRLFYVHRGMEKLAETRMGYNEVTFLSDRVCGICGFAHSVAYTNSVENALGIEVPQRAHTIRSILLEVERLHSHLLNLGLSCHFVGFDTGFMQFFRVREKSMTMAELLTGSRKTYGLNLIGGVRRDILKEQRLQTLKLVREMRADVSELVEMLLAMPNMEQRTQGIGILDRQIARDYSPVGPLIRGSGFARDLRFDHPYADYGNIPKTLFTFTGGDVFSRVMVRVKETFDSLAMLEFALDNMPDTPLLTEGFSYKPHAFALGFVEAPRGEDVHWSMLGDNQKLFRWRCRAATYANWPVLRYMLRGNTVSDAPLIIGSLDPCYSCTDRVTLVDVRKRQSKTVPYKEIERYGIDRNRSPLK-
'Escherichia coli YP_006125566.1'                            --MSEEKLGQH----YLAALNEAFPGVVLDHAWQTKDQLTVT-VKVNYLPEVVEFLYYKQGGWLSVLFGNDERKLNGHYAVYYVLSMEKGT----KCWVTVRVEVDANKPEYPSVTPRVPAAVWGEREVRDMYGLIPVGLPDERRLVLPDDWPDELYPLRKDSMDY--RQRPAPTTDAETYEFINELGDKKNNVVPIGPLHVTSDEPGHFRLFVDGENIIDADYRLFYVHRGMEKLAETRMGYNEVTFLSDRVCGICGFAHSTAYTTSVENAMGIQVPERAQMIRAILLEVERLHSHLLNLGLACHFTGFDSGFMQFFRVRETSMKMAEILTGARKTYGLNLIGGIRRDLLKDDMIQTRQLAQQMRREVQELVDGLLSTPNMEQRTVGIGRLDPEIARDFSNVGPMVRASGHARDTRADHPFVGYGLLPMEVHSEQGCDVISRLKVRINEVYTALNMIDYGLDNLPGGPLMVEGFTYIPHRFALGFAEAPRGDDIHWSMTGDNQKLYRWRCRAATYANWPTLRYMLRGNTVSDAPLIIGSLDPCYSCTDRMTVVDVRKKKSKVVPYKELERYSIERKNSPLK-
'Geobacillus sp. Y4.1MC1 YP_003989195.1'                     --MENKMKSDQGKK-YVEALRSKFGTAILDESWQTPDQVTLT-VKLNSLPEVVEEVYYRQGGWLANVIGNDERSLNGHFALYYVLSMEQAQDSRQNFWLTVKALIPSHKPEFPSVTPRVPAAVWYEREVRDMFGLEPVGLPDTRRLVLPDDWPDHHYPLRKD-ANV---FRPDPAVEEESYKFIEVEGEGIVEV-PIGPLHIANDEPGHFRLYVDGEYIIDADYRLFYVHRGIEKLAETRMDYHQVNFLVERICGICGYTHSVAYATALETANGIEVPLRAQYIRTILLEVERLHSHLLNLGVAAHLVGFDSGFMHFFRVREKSMKMAEILTGGRKTYGMNLIGGVRRDILKEERDQVLRLVSEMRTDLDELLDIMVNTTNFISRTKGVGRLDPKVARDYSPVGPNLRGSGFARDTRMTHPYAAYDRITWNVISKDGCDVLSRQLVRAAELFQSLDIIEKCLSEMPPGPVLVEGFSYKPYTFAVGYTEAPRGENVHWVMTGSGQNVYRLRARASTYNNWPSLRYMFQGNTVSDAPLIIASIDPCYSCCDRVTVIDVRKRKAKTIEYRELERYCQERKDSPLKL
'Geobacillus thermoglucosidasius YP_004587926.1'             --MENKVKSDQGKK-YVKALRSKFGTAILDESWQTPDQVTLT-VKLNSLPEVVEEVYYRQGGWLANVIGNDERSLNGHFALYYVLSMEQAQDFRQNFWLTVKALIPSHKPEFPSVTPRVPAAVWYEREVRDMFGLEPVGLPDTRRLVLPDDWPDHHYPLRKD-ANV---FRPDPAVEEESYKFIEVEGEGIVEV-PIGPLHIANDEPGHFRLYVDGEYIIDADYRLFYVHRGIEKLAETRMDYHQVNFLVERICGICGYTHSVAYATALETANGIEVPLRAQYIRTILLEVERLHSHLLNLGVAAHLVGFDSGFMHFFRVREKSMKMAEILTGGRKTYGMNLIGGVRRDILKEERDQVLRLVSEMRTDLDELLDIMVNTTNFISRTKGVGRLDPKIARDYSPVGPNLRGSGFARDTRMTHPYAAYDRITWNVISKDGCDVLSRQLVRAAELFQSLDIIEKCLSEMPPGPVLVEGFSYKPYTFAVGYTEAPRGENVHWVMTGSGQNVYRLRARASTYNNWPSLRYMFQGNTVSDAPLIIASIDPCYSCCDRVTVIDVRKRKAKTIEYRELERYCQERKDSPLKL
'Moorella thermoacetica YP_431018.1'                         --MGQGSESKRAQK-YIKDLRSKFPGAILEESSQAPDQITVT-VKLNDLPGIVEELYYRHNGWLSTMLGNDERELNGCFALYYVLSMEGNSNKRENTWITVKALVPEKEPQFPSVTPRVPAAVWYEREVRDMFGLEPVGIPDARRLVLPDDWPDNLHPLRKDAMDY--RYRPEPV--EENYNFIEVEGEGIVEV-PLGPLHITSDEPGHFRLFVDGEYIVDADYRLFYVHRGMEKLAENRMDYDQITFLAERICGICGYAHSVAYAAAVETANGIEVPPRAQYIRTILLEVERLHSHLLNLGLAAHLVGFDSGFMHFFRVREKAMQMAEILTGGRKTYGINLIGGVRRDIFKEERDQVLRLIAEIRTELDELLDILINTPNFISRTQGVGRLERQVARDFSPVGPNMRGSGYARDTRADHPYGAYDRVSWEVISKDGCDVLSRELVRAAELYESFNIIERCLTEMPPGPVLTEGFAYKPHTFALGYTEAPRGENVHWLMTGNNQKLYRWRVRAATYNNWPALRYMFRGNTVSDAPLIVASIDPCYSCTERVTMVDVRKKKARTIEYKELERYCRERKYSPLKF
'Thermacetogenium phaeum YP_006921300.1'                     MNPQTEPVKSNGKKEEVESLRSGFGQAILDETWQTPDQVTLT-VDLDYLPQVVAAAYYRLGGWLSSVIGNDERRLNGAFALYYVLSMEHER-PEENFWLTIKALVPPEKLEFPSVTPLVPAAAWYERDVRDLLGIHPVNHPDPRRLVLPDDWPDGLHPLRKDAMDY--RFRPEAATDEETYEFVNVEGEGIMEV-PLGPLHVTSDEPGHFRLFVDGETIVDADYRLFYCHRGLEKLAENRMDYDQVHFLAERICGICGYAHSIAYTTAVERAIGLEVPERARYLRTILLEVERLHSHLLNLGLACHFTGFDSGFMQFFRVREKAMRIAEILSGARKTYGVNLIGGVRRDILKEERDQVVDLLAECRRETDDLIAILLNTPNLRKRTVGVGVLDRKVARDFSPVGPNVRGSGFQRDTRSDHPYLAYDSIPWEVVTAEGCDVFSRVLVRAKEVYETFNIIQHCLQELPGGPVLVEGFTYKPHRYALGYVEAPRGEDIHWVMTCDNQKLYRWRPRASSYNNWPAIRFMLRGNAISDAPLIIASIDPCYSCTERVTVVDIKKKKAKDISYKELERYCIEKKDSPLKG
'Thermoanaerobacter sp. YS13 THYS13_RS04635'                 --VENEIKA-QDRKKYVRALYSKFGASILEEKWQTPDQVTLT-VKLNILPEIVEEAYYGQGGWLSNVIGNDERSINGHFAVYYVLSIEAEKDPNKNLWLTVKALVPADKPEFPSVAPRVPAAVWYEREVRDMLGLEPVGLPDARRLVLPDDWPDNLYPLRKD-MDY--RLRPEPAAEEENYEFIEVKGEGIVEV-PLGPLHITSDEPGHFRLYVDGEYIVDADYRLFYVHRGLEKLAESRMDYNQVTFLAERICGICGYAHSVAYAMAVEAANRIEVPLRAQYIRTILLEVERIHSHLLNIGLAAHLVGFDSGFMHFFRIREKAMQMAEILTGGRKTYGMNLIGGVRRDILKEEKVQALRLISEIRSELKELIDMLLNTPNFISRTQGVGRLDPKVARNFGSVGPNLRGSGYGRDTRADHPYCAYKHVSWNVISKEGCDVLSRVLVRAEELFESLAIIERCLSDLPPGPILHEGFTYTPYTFALGYTEAPRGENVHWVMTANQHQVYRWRVRASTYNNWPVLRYMFYGNTVADAPLIVASIDPCYSCAERVTLVDVRKKRAKTVQYQELEQYCRERKYSPLKN
'Thermococcus onnurineus TON_1023'                           --M------------VFDILK---GCKILEHN----DKMTVAEVGASNIREIARALF-ERGYYYSSGMGVDERPINGRFAMYHIFNCDTE-----GRYVVLKITSPEGSPEVPSITPVIKGAEWSEREAMDMLGIVFSGHPKPERLILPDDWPEGVYPLRKD-FPYNKKLPPSKPIEKER-----EHKKDVMEI-PLGPYHPSLHEPEYFELYVKGDKVVDAEYRGFHIHRGMEKLAESRMTINQIPFLAERICGICGCTHSAAYCQAVEDAAGIYVPERAQYIRTIMLEVERIHSHLLWFGVVCHLLGFDSGFMHIWRAREYIMDIAELITGNRKTYGINIVGGVRRDITEDKKEKTLKLLDMVEKESREVLDNIAEMKELRERMEGVGVLPKKEAREIGVVGPMARSSGIDTDVRRDHPYAAYKDLDFKVPVYKEGDVFARFLVRYEEIFESFNMIRQALENMPPGELINDEYEIPPFKLGIGVTEAPRGENIHAVITWGENMIYRWHPRAATYNNLPAVPIMLRGNDVADAPLIIASIDPCFSCTDHVSIIDSESGK---ILWRGPLKEGVRRV------
;
END;

[ The following blocks are output data for analysis step 16693 ]
BEGIN TREES;
      TITLE HyfG_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16693;
      TREE HyfG_ML = [&R] ((((((('Caldanaerobacter subterraneus pacificus_CDSM653_01581':1.0E-6,'Thermoanaerobacter sp. YS13 THYS13_RS04635':0.001892)0.853000:0.001891,'Caldanaerobacter subterraneus tengcongensis_NP_623297.1':1.0E-6)0.000000:1.0E-6,'Caldanaerobacter subterraneus yonseiensis_WP_022587809.1':0.007603)1.000000:0.13135,('Geobacillus sp. Y4.1MC1 YP_003989195.1':0.001946,'Geobacillus thermoglucosidasius YP_004587926.1':0.001817)1.000000:0.131969)0.935000:0.036167,'Moorella thermoacetica YP_431018.1':0.08955)0.986000:0.08993,('Thermacetogenium phaeum YP_006921300.1':0.153267,'Thermococcus onnurineus TON_1023':1.018311)0.253000:0.050987)1.000000:0.224463,'Escherichia coli YP_006125566.1':0.168471,'Escherichia coli YP_006125375.1':0.199901)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89845]


END;