#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

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 16730 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16730;
        DIMENSIONS NTAX=11;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_0106'
            'Caldanaerobacter subterraneus tengcongensis_NP_621828.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM91339.1'
            'Thermoanaerobacter WP_004399986.1'
            'Thermoanaerobacter ethanolicus WP_003868942.1'
            'Thermoanaerobacter italicus YP_003477425.1'
            'Thermoanaerobacter wiegelii YP_004818933.1'
            'Thermoanaerobacterium saccharolyticum YP_006391303.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_003850795.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1'
            'Thermoanaerobacterium xylanolyticum YP_004469846.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32956]

	TITLE EchF_alignment;
	LINK TAXA = TaxaForAnalysisStep16730;
	DIMENSIONS NCHAR=721;
	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       590       600       610       620       630       640       650       660       670       680       690       700       710       720 ]
[                                                                       .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
'Caldanaerobacter subterraneus pacificus_CDSM653_0106'         ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKET-----------------------------------------------------------------------------------------------------------------------------------------------KASAEKE-------EKEGI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Caldanaerobacter subterraneus tengcongensis_NP_621828.1'      ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKET-----------------------------------------------------------------------------------------------------------------------------------------------KASAEKE-------EKEGI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Caldanaerobacter subterraneus yonseiensis_ERM91339.1'         ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKEV-----------------------------------------------------------------------------------------------------------------------------------------------KAPTEKE-------EKEGI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacter WP_004399986.1'                            ----------------MLDMLKNVVSNLTHKPVTRKYPF-EKRE---PFEKARGHIE-NDIDKCILCGICQRVCPSNCIQVNRKE----GTWAFQPFECIICGVCVESCPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------AKEYRP-ISNEKYEIVQKKEV-------------------------------------------------------------------------------------------------------------------------Q---------------------NPPNKDK-------KEGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacter ethanolicus WP_003868942.1'                ----------------MLDMLKNVVSNLTHKPATRKYPF-EKRE---PFERARGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWGFEPFACIICGVCVDACPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------LREYRP-ISNDKYVVLQKKEV-----------------------------------------------------------------------------------------------------------------------------------------------KNPPEKD-------KKEGI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacter italicus YP_003477425.1'                   ----------------MLDMLKNVLSNLIHKPVTRKYPF-EKRE---PFERARGHIK-NDIDKCILCGICQRVCPSNCIQVNRKE----GKWVFQPFECVICGACVENCPTKSLKM----------------------------------------------------------------------------------------------------------------------------------------EAEYRA-VSNEKYEIVHKKEV-------------------------------------------------------------------------------------------------------------------------K---------------------NPPTKDK-------KEVA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacter wiegelii YP_004818933.1'                   ----------------MLDMLKNVVSNLTHKPVTRKYPF-EKRE---PFEKARGHIK-NDIDKCILCGICQRVCPSNCIQVNRKE----GTWAFQPFECIICGVCVESCPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------AKEYRP-ISNEKYEIVQKKEV-------------------------------------------------------------------------------------------------------------------------Q---------------------NPPNKDK-------KEGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacterium saccharolyticum YP_006391303.1'         ----------------MLDMLKSVFSNLSKKPVTRMYPF-EERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCIKVDRKT----GVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacterium thermosaccharolyticum YP_003850795.1'   ----------------MLDMLKSVFSNLSRKPVTRMYPF-VERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCIKVDRKT----SVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1'   ----------------MLDMLKSVFSNLSKKPATRMYPF-VERK---PFDINRGHLE-NDIEKCIFCSMCQRVCPSNCIKVDRKN----GVWEYDPFECVICGVCVEKCPKKCLRL----------------------------------------------------------------------------------------------------------------------------------------DTHYRS-CTDKKYDVHLERHE-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
'Thermoanaerobacterium xylanolyticum YP_004469846.1'           ----------------MLDMLKNVFSNLSKKPVTRMYPF-EERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCISVDRKT----SVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
;
END;

[ The following blocks are output data for analysis step 16730 ]
BEGIN TREES;
      TITLE EchF_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16730;
      TREE EchF_ML = [&R] (((('Thermoanaerobacterium thermosaccharolyticum YP_003850795.1':0.009577,'Thermoanaerobacterium xylanolyticum YP_004469846.1':0.019778)0.7850:0.009896,'Thermoanaerobacterium saccharolyticum YP_006391303.1':1.0E-6)0.9580:0.084827,'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1':0.01935)1.0000:0.305725,((('Caldanaerobacter subterraneus yonseiensis_ERM91339.1':1.0E-6,('Caldanaerobacter subterraneus tengcongensis_NP_621828.1':1.0E-6,'Caldanaerobacter subterraneus pacificus_CDSM653_0106':1.0E-6)0.0000:1.0E-6)0.9920:0.109235,'Thermoanaerobacter ethanolicus WP_003868942.1':0.027611)0.4820:0.034472,('Thermoanaerobacter WP_004399986.1':1.0E-6,('Thermoanaerobacter wiegelii YP_004818933.1':1.0E-6,'Thermoanaerobacter italicus YP_003477425.1':0.115544)0.8300:0.009615)0.8690:0.05456)0.9540:0.140674)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89893]


END;