#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

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 16744 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16744;
        DIMENSIONS NTAX=13;
        TAXLABELS
            'Caldanaerobacter subterraneus tengcongensis_NP_621830.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM91341.1'
            'Caldanaerobacter_subterraneus_subsp.pacificus_CDSM653_108'
            'Thermoanaerobacter WP_004399984.1'
            'Thermoanaerobacter ethanolicus WP_003868944.1'
            'Thermoanaerobacter italicus YP_003477423.1'
            'Thermoanaerobacter mathranii YP_003677319.1'
            'Thermoanaerobacter siderophilus WP_006569906.1'
            'Thermoanaerobacter wiegelii YP_004818935.1'
            'Thermoanaerobacterium saccharolyticum YP_006391305.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_003850797.1'
            'Thermoanaerobacterium thermosaccharolyticum YP_007297555.1'
            'Thermoanaerobacterium xylanolyticum YP_004469848.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32962]

	TITLE HypB_alignment;
	LINK TAXA = TaxaForAnalysisStep16744;
	DIMENSIONS NCHAR=307;
	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       ]
[                                                                       .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
'Caldanaerobacter subterraneus tengcongensis_NP_621830.1'      --------------------------------------------------------------------------MEEIVIIRDVLETNKNIASENKAIKDERNILMVNLIGSPGAGKTSFIIKAIEHMK---VPCAVIEGDVTS-DIDARKMAERN-IPVVQINTGGACHLNAASVNKALQALNFDN-GIVFIENVGNLICPSAFELGEDFKLAMANVPEGDDKPYKYPALFSKAKAVVLNKIDMLPYFEFDRKFFYDGVRAL-NQEAPIFEVSARTGEGFGEFARWLEEEYHKFRQGK--------
'Caldanaerobacter subterraneus yonseiensis_ERM91341.1'         --------------------------------------------------------------------------MEEIVIIRDVLETNKNIASENKAIKDERNILMVNLIGSPGAGKTSFIIKAIEHIK---VPCAVIEGDVTS-DIDARKMAERN-IPVVQINTGGACHLNAASVNKALQALNFDN-GIVFIENVGNLICPSAFELGEDFKLAMANVPEGDDKPYKYPALFSKAKAVVLNKIDMLPYFEFDKKFFYDGVRAL-NQEAPIFEVSARTGEGFGEFARWLEEEYHKFRQGK--------
'Caldanaerobacter_subterraneus_subsp.pacificus_CDSM653_108'    --------------------------------------------------------------------------MEEIVIIRDVLETNKNIASENKAIKDERNILMVNLIGSPGAGKTSFIIKAIEHMK---VPCAVIEGDVTS-DIDARKMAERN-IPVVQINTGGACHLNAASVNKALQALNFDN-GIVFIENVGNLICPSAFELGEDFKLAMANVPEGDDKPYKYPALFSKAKAVVLNKIDMLPYFEFDRKFFYDGVRAL-NQEAPIFEVSARTGEGFGEFARWLEEEYHKFRQGK--------
'Thermoanaerobacter WP_004399984.1'                            --------------------------------------------------------------------------MEEIVIIRDVLEANNNVASENKAIKDERNILMVNIIGSPGAGKTSFILRAIEHLK---VPCGVIEGDVTS-DIDAKKMAEKK-IPVVQINTGGSCHLNAGSVNRALQSLSFDN-GIVFIENVGNLICPSEFELGEDFKLAMANVPEGDDKPYKYPALFTKAKAVVLNKIDMLPYFEFDKKFFYDGIRAL-NPDAPIFEISARTGEGFGEFAKWLEEEYQKFRQNK--------
'Thermoanaerobacter ethanolicus WP_003868944.1'                --------------------------------------------------------------------------MEEIVIIRDVLEVNNNVAHENKVIKDEKNILMVNLIGSPGAGKTTFILRAIENLK---VPCAVIEGDVTS-DIDARKMAERN-IPVVQINTGGSCHLNAGSVNKALKALSFDD-GIVFIENVGNLICPSAFELGEDFKLAMANVPEGDDKPYKYPALFTKAKAVVLNKIDMLPFFEFNKKFFYDGIRAL-NPDAPIFEVSARTGEGFGEFAKWLEEEYHKFRQDK--------
'Thermoanaerobacter italicus YP_003477423.1'                   --------------------------------------------------------------------------MEEIIIIRDVLEANNNVASENKAIKDERNILMVNIIGSPGTGKTSFILKAIEHLK---VPCGVIEGDVTS-DIDAKKMAEKK-IPVVQINTGGSCHLNAGSVNRALQSLAFDN-GIVFIENVGNLICPSGFELGEDFKLAMANVTEGDDKPYKYPLLFTKAKAVVLNKIDMLPYFEFNKKFFYDGVRAL-NPNAPIFEVSARTGEGFGELAKWLEEEYQKFRQNK--------
'Thermoanaerobacter mathranii YP_003677319.1'                  --------------------------------------------------------------------------MEEIIIIRDVLEANNNVASKNKAIKDERNILMVNIIGSPGTGKTSFILKAIEHLK---VPCGVIEGDVTS-DIDAKKMAEKK-IPVVQINTGGSCHLNAGSVNRALQSLAFDN-GIVFIENVGNLICPSGFELGEDFKLAMANVTEGDDKPYKYPLLFTKAKAVVLNKIDMLPYFEFNKKFFYDGVRAL-NLNAPIFEVSARTGEGFGELAKWLEEEYQKFRQNK--------
'Thermoanaerobacter siderophilus WP_006569906.1'               -------------------------------------------------------------------------MEEIIVIIRDVLEANNNVASENKAIKDERNILMVNIIGSPGAGKTSFILRAIEHLK---VPCGVIEGDVTS-DIDAKKMAEKK-IPVVQINTGGSCHLNAGSVNRALQSLSFDN-GIVFIENVGNLICPSEFELGEDFKLAMANVPEGDDKPYKYPALFTKAKAVVLNKIDMLPYFEFDKKFFYDGIRAL-NPDAPIFEVSARTGEGFGEFAKWLEEEYQKFRQNK--------
'Thermoanaerobacter wiegelii YP_004818935.1'                   --------------------------------------------------------------------------MEEIVIIRDVLEANNNVASENKAIKDERNILMVNIIGSPGAGKTSFILRAIEHLK---VPCGVIEGDVTS-DIDAKKMAEKK-IPVVQINTGGSCHLNAGSVNRALQSLSFDN-GIVFIENVGNLICPSEFELGEDFKLAMANVPEGDDKPYKYPALFTKAKAVVLNKIDMLPYFEFDKKFFYDGIRAL-NPDAPIFEVSARTGEGFGEFAKWLEEEYQKFRQNK--------
'Thermoanaerobacterium saccharolyticum YP_006391305.1'         ---------------------------------------------------------------------------MEIKIIKDVLEANNNIAEENKNIKDERKIMMVNIIGSPGTGKTSFILKLIENMD---IPCGVIEGDVAS-DIDARKMAERN-IPVVQINTGGACHLNANSINKALSTLDFEG-GILFIENIGNLICPSDFELGEDFKLAMANVAEGDDKPYKYPLLFSKAKAVVINKIDLLPYFDFNKQYFYDGVKTL-NDEAEIFEVSARTGEGFEVLAKWLKKKYSEYVQGK--------
'Thermoanaerobacterium thermosaccharolyticum YP_003850797.1'   ---------------------------------------------------------------------------MEIKIIKNVLEANNNIAEENKNIKDERKILMVNIIGSPGTGKTSFILKLIENMD---IPCGVIEGDVAS-DIDARKMAERN-IPVVQINTGGECHLNANSVNKALSSIDFHD-GILFIENIGNLICPSEFELGEDFKLAMANVAEGDDKPYKYPLLFSKAKAVVLNKIDLLPYFDFNKQYFYDGVKTL-NDKAEIFEVSSRTGEGFEVLAKWLKEIYNQYMQSK--------
'Thermoanaerobacterium thermosaccharolyticum YP_007297555.1'   ---------------------------------------------------------------------------MEIKIIKNVLEANNNIAEENKNIKDERKILMVNIIGSPGTGKTSFILKLIENMD---IPCGVIEGDVAS-DIDARKMAEMN-IPVVQINTGGECHLNANSVNKALSSIDFHD-GILFIENIGNLICPSEFELGEDFKLAMANVAEGDDKPYKYPLLFSKAKVVVLNKIDLLPYFDFNKQYFYDGVKTL-NDKAEIFEVSSRTGEGFEVLAKWLKEIYNQYMQSK--------
'Thermoanaerobacterium xylanolyticum YP_004469848.1'           ---------------------------------------------------------------------------MEIKIIKDVLEANNNIAEENKSIKDGRKIMMVNIIGSPGTGKTSFILKLIENMD---IPCGVIEGDVAS-DIDARKMAERN-IPVVQINTGGACHLNANSINKALSTLDFEG-GILFIENIGNLICPSDFELGEDFKLAMANVAEGDDKPYKYPLLFSKAKAVVINKIDLLPYFDFNKQYFYDGVKTL-NDEAEIFEVSARTGEGFEVLAKWLKEKYDEYVQGK--------
;
END;

[ The following blocks are output data for analysis step 16744 ]
BEGIN TREES;
      TITLE HypB_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16744;
      TREE HypB_ML = [&R] ((('Thermoanaerobacterium thermosaccharolyticum YP_007297555.1':0.008967,'Thermoanaerobacterium thermosaccharolyticum YP_003850797.1':1.0E-6)0.9460:0.036462,('Thermoanaerobacterium xylanolyticum YP_004469848.1':0.012322,'Thermoanaerobacterium saccharolyticum YP_006391305.1':0.007514)0.9130:0.02985)0.9490:0.081589,(((('Thermoanaerobacter mathranii YP_003677319.1':0.009274,'Thermoanaerobacter italicus YP_003477423.1':1.0E-6)0.9850:0.047586,(('Thermoanaerobacter siderophilus WP_006569906.1':1.0E-6,'Thermoanaerobacter wiegelii YP_004818935.1':1.0E-6)0.0000:1.0E-6,'Thermoanaerobacter WP_004399984.1':0.004612)0.0000:1.0E-6)0.9480:0.040615,'Thermoanaerobacter ethanolicus WP_003868944.1':0.047797)0.3090:0.037259,('Caldanaerobacter subterraneus yonseiensis_ERM91341.1':0.004487,('Caldanaerobacter subterraneus tengcongensis_NP_621830.1':1.0E-6,'Caldanaerobacter_subterraneus_subsp.pacificus_CDSM653_108':1.0E-6)0.7640:0.004709)0.9290:0.035525)0.9650:0.111914)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89899]


END;