#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; 19:41 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 16746 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16746;
        DIMENSIONS NTAX=13;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_0111'
            'Caldanaerobacter subterraneus tengcongensis_NP_621833.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM91343.1'
            'Thermoanaerobacter ethanolicus WP_003868947.1'
            'Thermoanaerobacter italicus YP_003477420.1'
            'Thermoanaerobacter mathranii YP_003677316.1'
            'Thermoanaerobacter siderophilus WP_006569908.1'
            'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1'
            'Thermoanaerobacter wiegelii YP_004818938.1'
            'Thermoanaerobacterium saccharolyticum YP_006391308.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_003850800.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1'
            'Thermoanaerobacterium xylanolyticum YP_004469851.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32980]

	TITLE HypD_alignment;
	LINK TAXA = TaxaForAnalysisStep16746;
	DIMENSIONS NCHAR=427;
	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       ]
[                                                                       .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
'Caldanaerobacter subterraneus pacificus_CDSM653_0111'         --------------------------------------------MQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEARERNIKNYSVYSLHKTMPEALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPVGDEIEIKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
'Caldanaerobacter subterraneus tengcongensis_NP_621833.1'      -------------------------------------------MMQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEAKERKIKNYSVYSLHKTMPEALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPVGDEIEIKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
'Caldanaerobacter subterraneus yonseiensis_ERM91343.1'         -------------------------------------------MMQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEARERNIKNYSVYSLHKTMPKALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPIGDEIEVKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter ethanolicus WP_003868947.1'                -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GLFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVVELA--NRNVVIATFGDLIRVPGS-KS-SLQLERAAGKEVKVFYSPLDALNYAEGNPSKEVVFIGIGFETTVPTVAVTIKEAKEKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIDEIFEPCDSTWRGLGKIKGSGLRIKDKYKDFDAAVKFDIKPIGEEIKIKG---CRCGDVLKGSIYPNECPLFGRACTPENPVGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter italicus YP_003477420.1'                   --------------------------------------------MQ-QTEMIK----KAKEIIDVF----NPG--VQFNIMEVCGSHTMAISKFGLRQILPKNIRLISGPGCPVCVTAQNEIDSIIELS--NKNVVIATFGDLIRVPGS-KS-SLQQQRAAGKEIKVFYSPLDALKYAEENPTKEVVFLGIGFETTIPTVAVTIKEAKKKNIKNYSVYCLHKTMPEALRVLLEEGS-KVQGFLLPGHVSAITGSKIYEFIPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NSSIEIQYKRVVREEGNVKAQKIIEEIFEPCDSTWRGLGKIKGSGLKMKDKYKDFDAAVKFDIKPIGEEFEIKG---CRCGDVLKGSIYPNECPLFGNVCTPENPVGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter mathranii YP_003677316.1'                  --------------------------------------------MQ-QTEMIK----KAKEIIDVF----NPG--VQFNIMEVCGSHTMAISKFGLRQILPKNIRLISGPGCPVCVTAQNEIDSIIELS--NKNVVIATFGDLIRVPGS-KS-SLQQQRAAGKEIKVFYSPLDALKYAEENTTKEVVFIGIGFETTIPTVAVTIKEAKEKNIKNYSVYCLHKTMPETLRALLEGGS-NVQGFLLPGHVSAITGSKIYEFIPKEFGVSGVISGFEAMDILMSIIMLLKNYK---NSSIEIQYKRVVRKEGNIKAQKIIEEIFEPCDSTWRGLGKIKGSGLRIKDKYKDFDAAVKFDIKPIGGEIEIKG---CRCGDVLKGSIYPNECPLFGKACTPENPVGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter siderophilus WP_006569908.1'               -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVVELA--NRNVVIATFGDLIRVPGS-KS-SLQLERAAGKEVKVFYSPLDALKYAEGNPSKEVVFIGIGFETTVPTVAVTIKEAKEKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFIPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1'      -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVIELA--NKNVVIATFGDLIRVPGN-KS-SLQAERAAGKEVKVFYSPLDALKYAEENPSKEVVFIGIGFETTVPTVAVTIKEAREKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacter wiegelii YP_004818938.1'                   -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVIELA--NKNVVIATFGDLIRVPGN-RS-SLQAERAAGKEVKVFYSPLDALKYAEENPSKEVVFIGIGFETTVPTVAVTIKEAREKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
'Thermoanaerobacterium saccharolyticum YP_006391308.1'         -----------------------------------------------MQGIIN----RAKELIDRY----NTG--EFIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDASISLA--SQGVTIATFGDLVRVPGN-DS-SLQEERAKGKDVRVFYSPLDALDYAMANPSKEVVFIGIGFETTIPSVAMTIKEAYTRKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVSAITGSSIYGFLVDKYKIGGVVSGFEATDILMSVVMILKNLK---DPKIEIQYKRVVKEGGNTEAQRLMDEIFEESDAEWRGLGMIEGSGLKIREKYSEYDAEKKFNIKKPNSRTEIKG---CRCGDVLKGLITPKQCPLFGKACTPLNPVGPCMVSSEGSCAAYYKYGE---------
'Thermoanaerobacterium thermosaccharolyticum YP_003850800.1'   -----------------------------------------------MQDIIK----SARKLIDKY----NSG--EPIKIMEVCGSHTMAISRYGLRQILPENIKLISGPGCPVCVTAQNEIDAVISLA--GQGITIATFGDLIRVPGN-NS-SLQEERAKGKDVKVFYSPLDALEYAEANPSKEVVFIGIGFETTIPSVALTIKEAYTKKIKNYSVYCLHKTMPKALEALVINGS-DIQGFLLPGHVSAITGSTIYNFLVDKYKIGGVVSGFEAQDILISIIMILKNME---NPKIEIQYKRVVREEGNTDAKKLIEEVFEDSDATWRGLGMIEGSGLKIRDLYSEYDAEKKFHIQKPSEQIEING---CRCGDVLMGIISPHQCPLFGKACTPVNPIGPCMVSSEGSCAAYYKYGE---------
'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1'   -----------------------------------------------MQDIIN----TAKKLIDKY----NIG--EPIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDAVISLA--GKGMTIATFGDLIRVPGN-NS-SLQEERAKGKDVKVFYSPIDALEYAKANTSKEVVFIGIGFETTIPSVALTIKEAHAKKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVSAITGSNIYNFLVDKYKIGGVVSGFEAQDILMSVVMILKNMK---NPKIEIQYKRVVREEGNADAKKLIEEVFEDSDATWRGLGMIEGSGLKIRDLYSEYDAEKKFHIQKPSEQIEING---CRCGDVLMGIISPHQCPLFGKACTPVNPIGPCMVSSEGSCAAYYKYGA---------
'Thermoanaerobacterium xylanolyticum YP_004469851.1'           -----------------------------------------------MQGIIN----TAKELIDRY----NIG--ESIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDASISLA--SQGVTIATFGDLVRVPGN-NS-SLQEERAKGRNVRVFYSPLDALDYAIANPSKEVVFIGIGFETTIPSVALTIKEAYTKKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVAAITGSTIYNFLVDKYKIGGVVSGFEASDILMSVVMILKNLR---DPKIEIQYKRVVKEEGNTDAQSLIEEVFEESDAEWRGLGMIEGSGLKIREKYSEYDAEKKFNIKKPNSSTEIKG---CRCGDVLKGIITPKQCPLFGKACTPLNPVGPCMVSSEGSCAAYYKYGE---------
;
END;

[ The following blocks are output data for analysis step 16746 ]
BEGIN TREES;
      TITLE HypD_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16746;
      TREE HypD_ML = [&R] ((('Thermoanaerobacterium xylanolyticum YP_004469851.1':0.016796,'Thermoanaerobacterium saccharolyticum YP_006391308.1':0.034917)0.9840:0.053301,('Thermoanaerobacterium thermosaccharolyticum YP_003850800.1':0.018305,'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1':0.023577)0.9450:0.033068)1.0000:0.159863,((('Thermoanaerobacter italicus YP_003477420.1':0.025521,'Thermoanaerobacter mathranii YP_003677316.1':0.016937)0.9990:0.060029,(('Thermoanaerobacter wiegelii YP_004818938.1':0.002614,'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1':1.0E-6)0.0000:1.0E-6,('Thermoanaerobacter siderophilus WP_006569908.1':0.002524,'Thermoanaerobacter ethanolicus WP_003868947.1':0.029756)0.7690:0.016163)0.6210:0.020392)0.8530:0.027171,(('Caldanaerobacter subterraneus yonseiensis_ERM91343.1':0.005247,'Caldanaerobacter subterraneus pacificus_CDSM653_0111':1.0E-6)0.0000:1.0E-6,'Caldanaerobacter subterraneus tengcongensis_NP_621833.1':0.00525)0.9190:0.037643)0.9190:0.072549)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89915]


END;