#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; 22:56 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 16688 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16688;
        DIMENSIONS NTAX=10;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_CDSM653_01586'
            'Caldanaerobacter subterraneus tengcongensis_NP_623302.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM92234.1'
            'Escherichia coli YP_006125370.1'
            'Escherichia coli YP_006125568'
            'Geobacillus sp. Y4.1MC1 YP_003989190.1'
            'Geobacillus thermoglucosidasius YP_004587922.1'
            'Moorella thermoacetica YP_431023.1'
            'Thermoanaerobacter sp. YS13 THYS13_RS04690'
            'Thermococcus onnurineus TON_1021'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32847]

	TITLE HyfB_alignment;
	LINK TAXA = TaxaForAnalysisStep16688;
	DIMENSIONS NCHAR=695;
	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     ]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .     ]
'Caldanaerobacter subterraneus pacificus_CDSM653_01586'     -MTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGIYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTIDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLLPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGASA--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGQVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAASTKGSALIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGVPIGAGYIANVASALLHVSSPQLSDGLSIFPASSEQAMLS--TLLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYLLFSPAYLLRTAFTKAGCFIILLFKKAMAYISQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR---
'Caldanaerobacter subterraneus tengcongensis_NP_623302.1'   MMTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGVYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTSDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLSPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGAAT--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGYVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAVSTKGSVLIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGAPVGAGYIANVASALLHVSSPKVSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYPLFSPVYLLRTAFTEAGRFIILLFKKAMAYISQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR---
'Caldanaerobacter subterraneus yonseiensis_ERM92234.1'      -MIVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAVPVLIEGKGFILEGMEFIP--FGRFTINVDPLSAFMTLVISLLSIATGVYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTSDNAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLSPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGAAT--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENVGIILMGVGAGMMGIATGYVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFTYHTLFAVSTKGSVLIRMAFPLAAVALALTGALTSLCFVKAYGVTFTGPFRGGNELKIKEVPVTMLIGMGLLAIGCFVLGLGAPVGAGYIANVASALLHVSSPKVSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYPLFSPVYLLRTAFTEAGRFIILLFKKAMAYISQIELM--WERYIYYPLFHFMVYIGKRAQTFQTGNVRIYCLYIILTLGVLLIATVR---
'Escherichia coli YP_006125370.1'                           -MDALQLLTWSLILYLFASLASLFLLGLD---RLAIKLSGITSLVGGVIGIISGITQLHAGVTLVARFATPFD--FADFTLRMDSLSAFMVLVISLLVVVCSLYSLTYMREYEGKGAAAMGFFMNLFIASMVALLVMDNAFWFIVLFEMMSLSSWFLVIARQ-DKTSINAGMLYFFIAHAGSVLIMIAFLLMGRES-GSLDFA--SFRTLSLSPGLASAVFLLA---FFGFGAKAGMMPLHSWLPRAHPAAPSHASALMSGVMVKIGIFGILKVAMDLLAQTGLPLWWGILVMAIGAISALLGVLYALAEQDIKRLLAWSTVENVGIILLAVGVAMVGLSLHDPLLTVVGLLGALFHLLNHALFKGLLFLGAGAIISRLHTHDMEKMGALAKRMPWTAAACLIGCLAISAIPPLNGFISEWYTWQSLFSLSRVEAVALQLAGPIAMVMLAVTGGLAVMCFVKMYGITFCGAPRSTHAEEAQEVPNTMIVAMLLLAALCVLIALSASWLAPKIMHIAHAFTNTPPVTVASGIALVPGT-FHTQVT--PSLLLLLLLAMPLLPGLYWLW-CRSRRAAFRRTGDAWACGYGWENAMAPSGNGVMQPLRVVFSALFRLRQQL-DPTLRLNKGFAHVTARAQSTEPF--WDERVIRPIVSATQRLAKEIQHLQSGDFRLYCLYVVAALVVLLIAIAV---
'Escherichia coli YP_006125568'                             -MSAISLINSGVAWFVAAAVLAFLFSFQK---ALSGWIAGIGGAVGSLYTAAAGFTVLTGAVGV----SGALS--LVSYDVQISPLNAIWLITLGLCGLFVSLYNIDWHRHAQVKCNG---LQINMLMAAAVCAVIASNLGMFVVMAEVMALCAVFLTSNSK-------EGKLWFALGRLGTLLLAIACWLLWQRY-GTLDLRLLDMRMQQLP--LGSDIWLLG---VIGFGLLAGIIPLHGWVPQAHANASAPAAALFSTVVMKIGLLGMLT--LSLLGGNA-PLWWGIALLVLGMITAFVGGLYALMEHNIQRLLAYHTLENIGIILLGLGAGVTGIALEQPALIALGLVGGLYHLLNHSLFKSVLFLGAGSVWFRTGHRDIEKLGGIGKKMPVISIAMLVGLMAMAALPPLNGFAGEWVIYQSFFKLSNSGAFVARLLGPLLAVGLAITGALAVMCMAKVYGVTFLGAPRTKEAENATCAPLLMSVSVVALAICCVIGGVAAPWLL---------------PMLSAAVPL-PLEPANTTVS--QPMITLLLIACPLLP-FIIMAICKGDRLPSRSRGAAWVCGYDHEKSMVITAHGFAMPVKQAFAPVLKLRK------------------WLNPVSLVPGWQC---------------------EGSALLFRRMALVELAVLVVIIVSRGA
'Geobacillus sp. Y4.1MC1 YP_003989190.1'                    -MNVQQLFLLSVFLYVAGALGSLAMNRVG---KAANYVSSGSAFLAACAGIALSIPAIAGGADFMMESAGVVP--FAKFVIKIDPLSAFMILVISLLTAASAVYSLAYQNEYVGRGNGVLGFLNNIFIASMILVVASDNAFYFLVFWELMTLASYFLVCFDQKNKEAIHAGFTYHVVAHAGTALIMISFILFFLQT-GTFDFA--AFRSANLSPVMKDLAFLLA---FFGFGAKAGIMPFHTWLPQAHPAAPSNVSSLMSGVMVKIAIYGIIRVGVDFLGASV--WWWGLTVLAFGAISALLGILYAASENDLKRLLAYSSIENVGIILMGIGVGMIGVASGQPVLGVLGILAGLYHLLNHAVFKGLLFLGTGSIIYRIGTKNMEEMGGLAKQMPWTGFAFLTGALAISAIPPLNGFVSEWFLYQSLFMAGKSDILTFKVLSPLFAVMLALTGALAAMCFVKAYGVTFVGPFRSDRVREAREVPVPMIAGMVILVAGCIVLGLGAPMIAPYIGIVASALLGTNPVWVSDDMMVFPGSNSQAMLS--TPLMFLLLIGLVMFS-LFIVWIQGGMKAGRRIDSVPWACGYAYSSRMAATANAFVQPLRILFHPIYLLRNALIGLGNKIASYSKQAVDYIDRLELI--WENNIYGLLARGMFHLGKRVQVIQVGNVQVYCMYIIITLVVLLITTVR---
'Geobacillus thermoglucosidasius YP_004587922.1'            -MNVQQLFLLSVFLYVAGALGSLAMNRVG---KAANYVSAISTFTAAIAGLISTIIVLVRETPIVTELSGFVP--FARFTIEMDHLSAFMILVISLLAAATAIFTLTYDDQYVGKNAGIFGFLNNSYILSMVLAVASSNAFYFLVFWEIMTLASYFLVVVKQ-DEEAIHSGFVYFAVAHAAATAIIISFVVLFLYT-GSFSFT--DFRSVEISQATKNLVFLLS---FIGFGTKAGIVPFHIWLPRTYSSAPSTVSALMS---TKVAIYGLIRVGVDFLGASV--WWWGLTVLTIGAISAFLGILYASGENDLNRQLAYSSTENVGIILMGIGVGMIGVASGQPVLGVLGILAGLYHLLNHAVFKGLLFLGTGSIIYRIGTKNMEEMGGLAKQMPWTGFAFLTGALAISAIPPLNGFVSEWFLYQSLFMAGKSDILTFKVLSPLFAVMLALTGALAAMCFVKAYGVTFVGPFRSDRVREAREVPVPMIAGMVILVAGCIVLGLGAPMIAPYIGIVASALLGTNPVWVSDDMMVFPGSNSQAMLS--TPLMFLLLIGLVMFS-LFIVWIQGGMKAGRRIDSVPWACGYAYSSRMAATANAFVQPLRILFHPIYLLRNALIGLGNKIASYSKQAVDYIDRLELI--WENNIYGLLARGMFHLGKRVQVIQVGNVQVYCMYIIITLVVLLITTVR---
'Moorella thermoacetica YP_431023.1'                        -MLTQQLLLLSVLLYVAGALASLALNRAG---KIANYASGISALAAAGTGMASAVQVLAGGAAFTWEAAGFIP--FAKFIIKVDPLSAFMLLVISLLTGATALYSLSYLDEYTGKGAGVMGFFNNLFIASMVLVVISGNAFYFLIFWELMTLASYFLVSFDQEDSEAVKAGFIYLFMAHAGTALIMLAFILFFVYT-GTFDFA--SFRGANLPVFTKSLIFLLA---FLGFGAKAGIIPLHIWLPKAHPAAPSNASALMSGVMIKTAIYGILRVSVDFLGASV--WWWGFIVLASGAISAVLGVLYALGEHDIKRLLAYHSVENVGIILMGAGAGMIGIAAGQPVLGVLGILAGLYHLLNHAVFKGLLFLGAGSVIYRTHTKHMEELGGLARRMPWTALAFLVGAVAISAIPPLNGFVSEWFTYQSLFIASTSSILAVRVFAPLFVVMLALTGALAAMCFVKAYGVTFGGPCRSGHAREAREVPIPMLAGMAILAISCIILGVGAPVVAPYIGKVASALLAITAVQVSDGLLVFPANSMQAMLS--TPLIAILLVGLATLP-LLIIGIQGGFQAGRRIDAEPWACGYKYSPRMAYTATAFAQPLRVLFRPVYSLRTTLDGPGYTVASYFKGAVVYIASVESL--WERYIYAPLARGTVYLGKKLQAFQIGNVRLYCLYIIITLVVLLLATVR---
'Thermoanaerobacter sp. YS13 THYS13_RS04690'                -MTVQQLFLLSIFLYVVGALISLGLNRDG---KIANYVSGTTAFLAGCTGVASAIPVLIEGKGFILEGMEFIT--FGRFTINVDPLSAFMILVISLLSIATGIYSISYQEEYIGKGTGVMGFLNNIFIVSMILVVTIENAFYFLVFWELMTLVSYFLVCFEQENREAIKAGFVYFVMAHVGTVLIMISFILFYVYT-GTFDFA--AFRNANLLPVIKNLAFLLA---FLGFGVKAGIVPFHFWLPQAHPAAPSNVSALMSGVMIKTAIYGIIRVGVDFLGASA--WWWGLTVLAFGAISAVFGVLYAVSENDLKRLLAYSSIENLGIILMGVGAGMMGIATGQVSVGILGILAGLYHLINHAVFKGLLFLGAGSVVYRLHTRNMEEMGGLARYMPWTGLTFFIGALSISALPPLNGFVSKWFIYHTLFVASTKGSVPIRMAFPLAAVALALTGALTSLCFVKAYGVPFTGPFRGGNELKIKEVPVTMLIGMGLLAICCFVLGLGVPIGPGHIVNMASALLHVSSPQLSDGLSIFPASSEQAMLS--TPLVLVFVVGLAILP-LLIIG-TGGKRAGRRVDFEPWACGYKYSSRMAWTSTAFAHSLYLLFSPAYLLRTAFTKVGCFIILLFKKAMAYIAQIELM--WERYIYYPLLHFMVYIGKRAQTFQTGNVRMYCLYIILTLGVLLIATVR---
'Thermococcus onnurineus TON_1021'                          -MEV--IFLFIVIILSVASFIGV-FSRSAILTKLVNALSALGSLTIAYAGIVGLKESVELNITLLHLKSDSIINAFSTLTLKVDPLSGFFMIILGILGFCTSVYGIAYLDMYKGD-KRLYAFNYPLFLLFMFLVLVSWNLLWFVVFWELMTLFSQFLVAFER-NEKTLIATLKYFCMTKAAADFMLIAIVLVLITISGGGDYDILSSQLVNYFRSHPLEMYLVSAGFMIGLGVKAALVPFHVWLPDAYVEAPSNVSSLLSGAMEKMPVYMMFRFFLSFTPLTP---NIGLLIALFGTLTLFFGTMYALKQTDSKRLLAYHSVGQIGYVVFALGAGIYLLSKGYTTFGALALMASLFHALNHAFFKGLLFLTAGSILYRTGSRDLDHLGGLARFMPITAFAALIGSLSIAGMPPFNGFVSKWMIYVSTLPTPT----LVSLFGALALFI----SAVTTASFVKYFTSIFVRPP--AKEITVKEVPVSMWASQLILAVLCVIFGV-YPALPLEAISKAVDSVGVTTPSIT----VFPGLIVSDGIGNIAPLALLVFSGALTAV-LLAIF-------PYKISLPVWTTGTRRSLAMRLPASSYYASFEEEFEDVYSW-------GEWCVCTTKRL------------WDA--TKAVLSNFEEVSFDLDKMMTGAWLMLLILLTILGGVLL--------
;
END;

[ The following blocks are output data for analysis step 16688 ]
BEGIN TREES;
      TITLE HyfB_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16688;
      TREE HyfB_ML = [&R] (((((('Caldanaerobacter subterraneus yonseiensis_ERM92234.1':0.003787,'Caldanaerobacter subterraneus tengcongensis_NP_623302.1':1.0E-6)0.903000:0.011585,('Caldanaerobacter subterraneus pacificus_CDSM653_01586':0.00191,'Thermoanaerobacter sp. YS13 THYS13_RS04690':0.021044)0.921000:0.013368)1.000000:0.238237,('Geobacillus thermoglucosidasius YP_004587922.1':0.155964,'Geobacillus sp. Y4.1MC1 YP_003989190.1':0.04098)1.000000:0.152214)0.953000:0.085963,'Moorella thermoacetica YP_431023.1':0.090643)0.944000:0.143417,'Thermococcus onnurineus TON_1021':1.287552)0.935000:0.197195,'Escherichia coli YP_006125370.1':0.409023,'Escherichia coli YP_006125568':1.002222)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89840]


END;