#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; 22:55 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 16676 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16676;
        DIMENSIONS NTAX=14;
        TAXLABELS
            'Acetonema longum WP_004093938.1'
            'Caldanaerobacter subterraneus tengcongensis_NP_623305.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM92237.1'
            'Desulfitobacterium hafniense WP_005811732.1'
            'Desulfitobacterium hafniense YP_517887.1'
            'Desulfotomaculum kuznetsovii YP_004516877'
            'Geobacillus sp. YP_003989187.1'
            Geobacillus_thermoglucosidasius_EID44394.1
            'Geobacillus thermoglucosidasius YP_004587919.1'
            'Moorella thermoacetica YP_430061.1'
            'Thermacetogenium phaeum YP_006920225.1'
            'Thermoanaerobacter sp. YS13 THYS13_RS04705'
            'Thermococcus onnurineus TON_1019'
            'Thermodesulfobacterium thermophilum WP_022856203.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32839]

	TITLE CooC_alignment;
	LINK TAXA = TaxaForAnalysisStep16676;
	DIMENSIONS NCHAR=275;
	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     ]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .     ]
'Acetonema longum WP_004093938.1'                           ---MKIAVSGKGGVGKTMVAANLARMFAQNGYKVYAVDADPDASLGSAIGLADDVLARVKPMIEMQQVIAERS------GGGAFYTLNPQVDDILDSYSIQ-LGNIRFLRMGGVKQGGSACYCRENSFLRAIVDALLLGQQDVVVLDMGAGIEHLTRGTSRGVDVMLVVTEPTKNSVQTAKVVKNLADDLEVKKIRFIGNKIRQSKEAAFLQDQFPSGGLI--GLLPFDESVPEAAMAGP-VDVPDSSRPIGAEMQRIYHYILSDC---------
'Caldanaerobacter subterraneus tengcongensis_NP_623305.1'   ---MKIAISGKGGVGKTTIAAGLIKYFAQKGYQVYAVDADPDTSLGMILGLPEERIGSLKPIVAMRELIAERTG-----GNGAFFSLNPDVDSILEDYTIR-NGNILFLKMGAVKPGGSECYCRENTVLNALVNSIILKRKEIVVMDMSAGIEHLTRGTARGVDIMLIVTEPTLVSIQTARTIQKLATELGISKIKFVANKIRQSKDEEFILSHLPPGDVI--GLIPFQTEILDQA-AGF-NSEQS-FTAAG--ITELATRLLN-----------
'Caldanaerobacter subterraneus yonseiensis_ERM92237.1'      ---MKIAISGKGGVGKTTIAAGLIKYFAQKGYQVYAVDADPDTSLGMVLGLPEERIGSLKPIVAMRELIAERTG-----GNGAFFSLNPDVDSILEDYTIR-NGNILFLKMGAVKPGGSECYCRENTVLNALVNSIILKRKEIVVMDMSAGIEHLTRGTARGVDFMLIVTEPTLVSIQTARTIQKLATELGISKIKFVGNKLRQPKDEEFIMKHLSPDDVI--GLIPFQTEILDQA-AGF-IDEEQ-FVAAG--ITELANKLLS-----------
'Desulfitobacterium hafniense WP_005811732.1'               MKSMKIAISGKGGVGKTTFAANLAHYLSEQGMRVLAVDADPDASLGTVLGIAEDALNRLRPIVDMKELIEQRMG-----GSGAFYPLNPQVDDILDDYSVQ-VGPIRFFRMGNVKGGGTACYCKENSFLHALVNSLILSEQDTVILDMGAGIEQLTRGTAQGVDVLVIVTEASTVSAHTVRVIQKLAQELGIPKVSVIGNKIRSSKDEDFLKAQFTEDELL--GLIPFSEELLDMS-IHTDNSSFP-KGAPGSQLESVYRKLMEGRDI-------
'Desulfitobacterium hafniense YP_517887.1'                  ---MKIAISGKGGVGKTTFAANLAHYLSEQGMRVLAVDADPDASLGTVLGIAEDALNRLRPIVDMKELIEQRMG-----GSGAFYPLNPQVDDILDDYSVQ-VGPIRFFRMGNVKGGGTACYCKENSFLHALVNSLILSEQDTVILDMGAGIEQLTRGTAQGVDVLVIVTEASTVSAHTVRVIQKLAQELGIPKVSVIGNKIRSSKDEDFLKAQFTEDELL--GLIPFSEELLDMS-IHTDNSSFP-KGAPGSQLESVYRKLMEGRDI-------
'Desulfotomaculum kuznetsovii YP_004516877'                 ---MKLAISGKGGVGKTTIAAALAKSFAETHQTVYAIDADPDACLAAAIGIPEEVASELKPIVEMRDLIRAKT------GEGAFYTLNPQVNDVLDDYSYQ-YKNIKFIRMGGIKKGGSECYCRENTFLNAVVSSLLLDSNEVVIMDMGAGIEHLSRGTARGVDLMLVVVEPSRNSINTAHLVKRLAADLGIRKVRIIGNKIRTAREKEYIENHFSPEEIL--GFIEFNNEIWEKA-MEP-NSDAAGELLAG--MREVREKILREAGDR------
'Geobacillus sp. YP_003989187.1'                            ---MKLAISGKGGVGKTTIAANLIKNFASQGYQVYAVDADPDTSLGMALGLPEEQIGSLKPIVDMREVIAERTG-----GSGAYFSLNPEVDSLLEDYTIK-SGNIRFLKMGAIKPGGSACYCRENTVLNAIINSLILKHQEMVILDMSAGIEHLTRGTARGVNLMLIVTEPTLVSVQTALVVRKLASDIGVEKIKFVGNKLRHPKDEEFILSHLPPDDVI--GLIPFQTKILDQA-AGF-VEDQS-FTAEG--IADLAVRLLDEALLNH-----
Geobacillus_thermoglucosidasius_EID44394.1                  ---MKLAISGKGGVGKTTIAANLIKNFASQGYQVYAVDADPDTSLGMALGLPEEQIGSLKPIVDMREVIAERTG-----GSGAYFSLNPEVDSLLEDYTIK-SGNIRFLKMGAIKPGGSACYCRENTVLNAIINSLILKHQEMVILDMSAGIEHLTRGTARGVNLMLIVTEPTLVSVQTALVVRKLASDIGVEKIKFVGNKLRHPKDEEFILSHLPPDDVI--GLIPFQTKILDQA-AGF-VEDQS-FTAEG--IADLAVRLLDEALLNH-----
'Geobacillus thermoglucosidasius YP_004587919.1'            ---MKLAISGKGGVGKTTIAANLIKNFASQGYQVYAVDADPDTSLGMALGLPEEQIGSLKPIVDMREVIEERTG-----GSGAYFSLNPEVDSILEDYTIK-SGNIRFLKMGAIKPGGSACYCRENTVLNAIINSLILKHQEMVILDMSAGIEHLTRGTVRGVNLMLIVTEPTLVSVQTALVVRKLASDIGVEKIKFVGNKLRHPKDEEFILSHLPPDDVI--GLIPFQTKILDQA-AGF-VEDQS-FTAEG--IADLAVRLLNEALSAH-----
'Moorella thermoacetica YP_430061.1'                        ---MKLAISGKGGVGKTTIAAGLIKYFAGQGYQVYAVDADPDTSLGMVLGLPEERLGTLKPIVDMRQIIAERTG-----GEGAFFALNPEVDSLLEDFTIK-NDNILFLKMGAIKPGGSTCYCRENTVLNAMINSLLLKRREMVVLDMGAGIEHLTRGTARGVDTMLIVTEPTLVSIQTARVIQKLASELGIEQIKFIGNKLRHHRDEEFILNHLPSGEVI--GLIPFQPAILDQA-AGI-TSTQS-FIATG--ITELASRLIEN----------
'Thermacetogenium phaeum YP_006920225.1'                    ---MKIAVTGKGGVGKTTLAAGLAKHFARCGYQVYAVDADPDISLGTTLGVPEEQLAAQPPLIEMKELIKERTG-----AGGAFYILNPQVDDVLDKYSID-LSNIKLLRMGGYKQAGTACYCPENSFLNAVVNSLLLGNHDVVILDFGAGIEHLTRGTARGVDLMLIVTEPTRVSVETARVIQKLAREIGVPKIRIVGNKVRNSREKEFLMSSFDKDELL--GVMQYNDELWEKSMLDEPREMEE-ILINS--VSNIFNLIRGGDVEAGTAAKS
'Thermoanaerobacter sp. YS13 THYS13_RS04705'                ---MKIAISGKGGVGKTTIAAGLIKYFAQKGYQVYAVDADPDTSLGMVLGLPEERIGSLKPIVAMRELIAERTG-----GNGAFFSLNPDVDSILEDYTIR-NGNILFLKMGAVKPGGSECYCRENMVLNALVNSIILKRKEIVVMDMSAGIEHLTRGTARGVDIMLIVAEPTLVSIQTARTIQKLATELGISKIKFVANKIRQSKDEEFIMKHLSPDNVI--GFIPFQTEILDQA-AGF-IDEYS-FSVTA--ITELAAKLLN-----------
'Thermococcus onnurineus TON_1019'                          ---MKILVAGKGGVGKTTTTALLAHIIADKGYNVLTLDTDSVPNLAQSLGVPYDEALDIVPLSRNEELAQERTGAKPGSGWGVLFSLTPKVDDLVDMYGIRIKPNLSLVVVGSTEQPKEGCLCPSIALAKAFLNHVLLREKDIVIVDSEAGAEVFGRGLAEKFDVMLCVAEPTLKSLTIAKKLLKMGEELNISNLMLIINKVHDSMEAAKLYSRVFSDYLVPYHLVHFDTSVIKADNEGLGVNSIPRDSRIYRDVESLANKLLSMKKRSKVV---
'Thermodesulfobacterium thermophilum WP_022856203.1'        ---MKIAISGKGGVGKTTIAAGLIKYFAQKGYQVYAVDADPDTSLGMVLGLPEERIGSLKPIVAMRELIAERTG-----GNGAFFSLNPDVDSILEDYTIR-NGNILFLKMGAVKPGGSECYCRENTVLNALVNSIILKRKEIVVMDMSAGIEHLTRGTARGVDLMLIVTEPTLVSIQTARVVQKLAAELGISKIKFVGNKLRQPKDEEFILSHLPPGDVI--GLIPFQTEILDQA-AGF-NSEQS-FTAAG--ITELATRLLS-----------
;
END;

[ The following blocks are output data for analysis step 16676 ]
BEGIN TREES;
      TITLE CooC_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16676;
      TREE CooC_tree = [&R] (('Acetonema longum WP_004093938.1':0.230213,(('Thermacetogenium phaeum YP_006920225.1':0.389874,'Desulfotomaculum kuznetsovii YP_004516877':0.439216):0.079254,(((((('Caldanaerobacter subterraneus yonseiensis_ERM92237.1':0.029043,'Thermoanaerobacter sp. YS13 THYS13_RS04705':0.046112):0.033941,'Caldanaerobacter subterraneus tengcongensis_NP_623305.1':0.009121):0.024362,'Thermodesulfobacterium thermophilum WP_022856203.1':0.00376):0.075746,'Moorella thermoacetica YP_430061.1':0.155746):0.046521,('Geobacillus thermoglucosidasius YP_004587919.1':0.010588,(Geobacillus_thermoglucosidasius_EID44394.1:1.0E-6,'Geobacillus sp. YP_003989187.1':1.0E-6):0.005662):0.095275):0.336733,('Desulfitobacterium hafniense YP_517887.1':1.0E-6,'Desulfitobacterium hafniense WP_005811732.1':1.0E-6):0.437313):0.057904):0.156774):0.44248,'Thermococcus onnurineus TON_1019':1.220573);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89828]


END;