#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 19, 2025; 0:31 GMT TreeBASE (cc) 1994-2008 Study reference: Freitas T., Hou S., Dioum E., Salto J., Newhouse J., Gonzalez G., Gilles-gonzalez M., & Alam M. 2004. Ancestral hemoglobins in Archaea. Proceedings of the National Academy of Sciences of the United States of America, 101(17): 6675-6680. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1410] BEGIN TAXA; TITLE TaxonLabelSet12091; DIMENSIONS NTAX=38; TAXLABELS Aeropyrum_pernix_Pgb Ascaris_suum_Hb Bacillus_cereus_HemAT Bacillus_subtilis_HemAT Cerebratulus_lacteus_NHb Chloroflexus_aurantiacus_Pgb Cupriavidus_necator_FHb Equus_caballus_Mb Escherichia_coli_Hmp Glycera_dibranchiata_Hb Halobacterium_salinarum_HemAT Homo_sapiens_Cyg Homo_sapiens_HbA Homo_sapiens_HbB Homo_sapiens_HbD Homo_sapiens_HbE Homo_sapiens_HbG Homo_sapiens_HbT Homo_sapiens_Mb Homo_sapiens_Ngb Lucina_pectinata_Hb Lupinus_luteus_LHb Methanosarcina_acetivorans_Pgb Mus_musculus_Cyg Mus_musculus_HbA Mus_musculus_HbBm Mus_musculus_HbE Mus_musculus_Ngb Mycobacterium_tuberculosis_HbN Oryza_sativa_LHb Paramecium_caudatum_Hb Paramphistomum_epiclitum_Hb Physeter_catodon_Mb Riftia_pachyptila_Hb Synechocystis_sp._PCC6803_cyanoHb Thermobifida_fusca_Pgb Thermosynechococcus_elongatus_Gib Vitreoscilla_stercoraria_Hb ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1513] TITLE Globins; LINK TAXA = TaxonLabelSet12091; DIMENSIONS NCHAR=251; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y * 1 2" 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . ] Aeropyrum_pernix_Pgb -------------------------------MTPSDIPGYDYGRVEK--SPITDLEFDLLKKTVMLGEKDVMYLKKACDVLKDQVDEILDLWYGWVASN-EHLIIYYFSNPDT------GEPIKEYLERVRARFGAWILDTTCRDYN--REWLDYQYEVGLRHHRSK-----KGVTDGVRTVPHIPLRYLIAFIYPITA-TIKPFLAKKGGSPEDIEGMYNAWFKSVVLQVAIWSHPYTKENDW------- Ascaris_suum_Hb ------------------------------------------------------------ANKTRELCMKSLEHAKVDTS--NEARQDGIDLYKHMFENYPPLRKYFK--SREEYTAEDVQNDPFFAKQGQKILLACHVL-CAT-YDD-RETFNAYTRELLDRHARDHV--HMPPEVWTDFWKLFEEYLGKKTTL------DEPTKQAWHEIGREFAKEINKHGR-------------------------- Bacillus_cereus_HemAT ---------------------MLGVFKKHNNTTNVSILELSKNQQITFNVP-TNSELKIQMDMLHISKEDLQIVKVLQPFIYEEIDWITEKFYSNITKQ-PNLITIIERYS--------------SIPKLKQTLKTHIKELFSGDMH--ENFIEQRVRIAKRHVQIG-----LHRKWYTFLYQELFRSIMKILKTKITTQDDFSYSINVINKLLTLEQELVIASYESEYERMQKELEKEKEITA------- Bacillus_subtilis_HemAT ---------------------ML--FKKDRKQETAYFSDSNGQQKNRIQLTNKHADVKKQLKMVRLGDAELYVLEQLQPLIQENIVNIVDAFYKNLDEE-SSLMDIINDHS--------------SVDRLKQTLKRHIQEMFAGVIDD--EFIEKRNRIASIHLRIG-----LLPKWYMGAFQELLLSMIDIYEASITNIQELLKAIKATTKILNLEQQLVLEAFQSEYNQTRDEQEEKKNLLHQ------ Cerebratulus_lacteus_NHb -------------------------------------------------------------------------------MV--NWAAVVDDFYQELFKAHPEYQNKF--GFK-GVALGSLKGNAAYKTQAGKTVDYINAAIGGSAD----------AAGLASRHKGRN----VGSAEFHNAKACLAKACSAHGAP-----DLGHAIDDILSHL-------------------------------------- Chloroflexus_aurantiacus_Pgb MLEIRITYFTYYHSALRLSLQPEKGYSSRRWVMSEAIPGYTYGTAQVAQSPVSLEEWELLKQTVLWTAEDEQYLRMAGEVLGDQVDAILDLWYGFVASH-AHLVYYFTGSD--------GQPIADYLSRVRQRFGQWILDTCRRPYD---QDWLNYQMEIALRHYRTK----KNQTDGVQSVPMIPLRYMIAFIYPITA-TIREFLARKGHSAAEVDRMHQAWFKSIVLQVTLWSYPYTREGDF------- Cupriavidus_necator_FHb --------------------------------------------------------------MLTQKTKDIVKATAPVLAEH--GYDIIKCFYQRMFEAHPELKNVFN-MAHQE--------QGQQQQALARAVYAYAENIED------PNSLMAVLKNIANKHASL----GVKPEQYPIVGEHLLAAIKEVLGNA----ATDDIISAWAQAYGNLADVLMGMESELYERSAE------------------ Equus_caballus_Mb --------------------------------------------------------------GLSDGEWQQVLNVWGKVEAD--IAGHGQEVLIRLFTGHPETLEKFD-KFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGH------HEAELKPLAQSHATKH---KIPIKYLEFISDAIIHVLHSKHPGD----FGADAQGAMTKALELFRNDIAAKYKELGFQG-------------------- Escherichia_coli_Hmp --------------------------------------------------------------MLDAQTIATVKATIPLLVET--GPKLTAHFYDRMFTHNPELKEIFN-MSNQRN--------GDQREALFNAIAAYASNIEN------LPALLPAVEKIAQKHTSF----QIKPEQYNIVGEHLLATLDEMFS------PGQEVLDAWGKAYGVLANVFINREAEIYNENAS------------------ Glycera_dibranchiata_Hb --------------------------------------------------------------GLSAAQRQVVASTWKDIAGSDNGAGVGKECFTKFLSAHHDMAAVFG-FSGASD---PGVADLGAKVLAQIGVAVSHLGDEGK--------MVAEMKAVGVRHKGYGNK-HIKAEYFEPLGASLLSANEHRIGGK----MMAAAKDAWAAAYADISGALISGLQS------------------------- Halobacterium_salinarum_HemAT ---------------------MS---NDNDTLVTADVRNGIDGHALADRIGLDEAEIAWRLSFTGIDDDTMAALAAEQPLFEATADALVTDFYDHLESY-ERTQDLFANST-------------KTVEQLKETQAEYLLGLGRGEYD---TEYAAQRARIGKIHDVLG----LGPDVYLGAYTRYYTGLLDALADDVVADRGEEAAAAVDELVARFLPMLKLLTFDQQIAIDTYIDSYAQRLHDE------ Homo_sapiens_Cyg ---------------------------------------------MEKVPGEMEIERRERSEELSEAERKAVQAMWARLYAN--CEDVGVAILVRFFVNFPSAKQYFS-QFKHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPD---KVSSVLALVGKAHALKH---KVEPVYFKILSGVILEVVAEEFASD----FPPETQRAWAKLRGLIYSHVTAAYKEVGWVQQVPNATTPPATLPSSGP--- Homo_sapiens_HbA -------------------------------------------------------------MVLSPADKTNVKAAWGKVGAH--AGEYGAEALERMFLSFPTTKTYFP-HF-DLSH-----GSAQVKGHGKKVADALTNAVAHVDD------MPNALSALSDLHAHKL---RVDPVNFKLLSHCLLVTLAAHLPAE----FTPAVHASLDKFLASVSTVLTSKYR-------------------------- Homo_sapiens_HbB ------------------------------------------------------------MVHLTPEEKSAVTALWGKVN----VDEVGGEALGRLLVVYPWTQRFFE-SFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDN------LKGTFATLSELHCDKL---HVDPENFRLLGNVLVCVLAHHFGKE----FTPPVQAAYQKVVAGVANALAHKYH-------------------------- Homo_sapiens_HbD -------------------------------------------------------------VHLTPEEKTAVNALWGKVN----VDAVGGEALGRLLVVYPWTQRFFE-SFGDLSSPDAVMGNPKVKAHGKKVLGAFSDGLAHLDN------LKGTFSQLSELHCDKL---HVDPENFRLLGNVLVCVLARNFGKE----FTPQMQAAYQKVVAGVANALAHKYH-------------------------- Homo_sapiens_HbE ------------------------------------------------------------MVHFTAEEKAAVTSLWSKMN----VEEAGGEALGRLLVVYPWTQRFFD-SFGNLSSPSAILGNPKVKAHGKKVLTSFGDAIKNNDN------LKPAFAKLSELHCDKL---HVDPENFKLLGNVMVIILATHFGKE----FTPEVQAAWQKLVSAVAIALAHKYH-------------------------- Homo_sapiens_HbG ------------------------------------------------------------MGHFTEEDKATITSLWGKVN----VEDAGGETLGRLLVVYPWTQRFFD-SFGNLSSASAIMGNPKVKAHGKKVLTSLGDAIKHLDD------LKGTFAQLSELHCDKL---HVDPENFKLLGNVLVTVLAIHFGKE----FTPEVQASWQKMVTAVASALSSRYH-------------------------- Homo_sapiens_HbT -------------------------------------------------------------MALSAEDRALVRALWKKLGSN--VGVYTTEALERTFLAFPATKTYFS-HL-DLSP-----GSSQVRAHGQKVADALSLAVERLDD------LPHALSALSHLHACQL---RVDPASFQLLGHCLLVTLARHYPGD----FSPALQASLDKFLSHVISALVSEYR-------------------------- Homo_sapiens_Mb -------------------------------------------------------------MGLSDGEWQLVLNVWGKVEAD--IPGHGQEVLIRLFKGHPETLEKFD-KFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGH------HEAEIKPLAQSHATKH---KIPVKYLEFISECIIQVLQSKHPGD----FGADAQGAHNKALELFRKDMASNYKELGFQG-------------------- Homo_sapiens_Ngb ---------------------------------------------------------------MERPEPELIRQSWRAVSRS--PLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLS---SLEEYLASLGRKHRAVG----VKLSSFSTVGESLLYMLEKCLGPA----FTPATRAAWSQLYGAVVQAMSRGWDGE------------------------ Lucina_pectinata_Hb -------------------------------------------------------------MSLSAAQKDNVKSSWAKASAA--WGTAGPEFFMALFDAHDDVFAKFSGLFKGAAKGT-VKNTPEMAAQAQSFKGLVSNWVDNLDN---AGALEGQCKTFAANHKAR----GISAGQLEAAFKVLIAGFMKSYGG-------D--EGAWTAVAGALMGEIEPNN--------------------------- Lupinus_luteus_LHb -------------------------------------------------------------GALTESQAALVKSSWEEFNAN--IPKHTHRFFILVLEIAPAAKDLFS-FLKGTSE--VPQNNPELQAHAGKVFKLVYEAAIQLEVTG-VVVTDATLKNLGSVHVSK----GVADAHFPVVKEAILKTIKEVVGAK----WSEELNSAWTIAYDELAIVIKKEMDDAA----------------------- Methanosarcina_acetivorans_Pgb -------------------------------VSVEKIPGYTYGETEN-RAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSH-PHILLYYFTSPD-------GTPNEKYLAAVRKRFSRWILDTCNRSYD---QAWLDYQYEIGLRHHRTK----KNQTDNVESVPNIGYRYLVAFIYPITA-TMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF------- Mus_musculus_Cyg ---------------------------------------------MEKVPGDMEIERRERSEELSEAERKAVQATWARLYAN--CEDVGVAILVRFFVNFPSAKQYFS-QFRHMEDPLEMERSPQLRKHACRVMGALNTVVENLHDPD---KVSSVLALVGKAHALKH---KVEPMYFKILSGVILEVIAEEFAND----FPVETQKAWAKLRGLIYSHVTAAYKEVGWVQQVPNTTTPPATLPSSGP--- Mus_musculus_HbA -------------------------------------------------------------MVLSGEDKSNIKAAWGKIGGH--GAEYGAEALERMFASFPTTKTYFP-HF-DVSH-----GSAQVKGHGKKVADALASAAGHLDD------LPGALSALSDLHAHKL---RVDPVNFKLLSHCLLVTLASHHPAD----FTPAVHASLDKFLASVSTVLTSKYR-------------------------- Mus_musculus_HbBm ------------------------------------------------------------MVHLTDAEKAAVSCLWGKVNSD----EVGGEALGRLLVVYPWTQRYFD-SFGDLSSASAIMGNAKVKAHGKKVITAFNDGLN{DN}LDS------LKGTFASLSELHCDKL---HVDPENFRLLGNMIVIVLGHHLGKD----FTPAAQAAFQKVVAGVATALAHKYH-------------------------- Mus_musculus_HbE ------------------------------------------------------------MVNFTAEEKTLINGLWSKVN----VEEVGGEALGRLLVVYPWTQRFFD-SFGNLSSASAIMGNPRVKAHGKKVLTAFGESIKNLDN------LKSALAKLSELHCDKL---HVDPENFKLLGNVLVIVLASHFGNE----FTAEMQAAWQKLVAGVATALSHKYH-------------------------- Mus_musculus_Ngb ---------------------------------------------------------------MERPESELIRQSWRVVSRS--PLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLS---SLEEYLTSLGRKHRAVG----VRLSSFSTVGESLLYMLEKCLGPD----FTPATRTAWSRLYGAVVQAMSRGWDGE------------------------ Mycobacterium_tuberculosis_HbN ---------------------------------------------------------MGLLSRLRKREPISIYDKIG---GHEAIEVVVEDFYVRVLAD--DQLSAFF-SGTN--------MSRLKGKQ-VEFFAAALGGPEPYT-----------GAPMKQVHQGR----GITMHHFSLVAGHLADALTAAG-------VPSETITEILGVIAPLAVDVTSGESTTAPV--------------------- Oryza_sativa_LHb --------------------------------------------------MALVEDNNAVAVSFSEEQEALVLKSWAILKKD--SANIALRFFLKIFEVAPSASQMFS-FLRNSDV--PLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKY----GVGDAHFEVVKFALLDTIKEEVPADM---WSPANKSAWSEAYDHLVAAIKQEMKPAE----------------------- Paramecium_caudatum_Hb -------------------------------------------------------------------------SLFEQLGGQAAVQAVTAQFYANIQADAT-VATFFNGID--------------MPNQTNKTAAFLCAALGGPNA------WTG--RNLKEVHANMG----VSNAQFTTVIGHLRSALTGAG--------VAAALVEQTVAVAETVRGDVVTV--------------------------- Paramphistomum_epiclitum_Hb -------------------------------------------------------------TLTKHEQDILLKELGPHVDTPAHIVETGLGAYHALFTAHPQYISHFSRLEGHTIENVMQSEGIKHYARTL-TEAIVHMLKEISN----DAEVKKIAAQYGKDHTSRK----VTKDEFMSGEPIFTKYFQNLVKD-----AEGKAAVEKFLKHVFPMMAAEI----------------------------- Physeter_catodon_Mb -------------------------------------------------------------MVLSEGEWQLVLHVWAKVEAD--VAGHGQDILIRLFKSHPETLEKFD-RFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKG------HHEAELKPLAQSHATKH---KIPIKYLEFISEAIIHVLHSRHPGD----FGADAQGAMNKALELFRKDIAAKYKELGYQG-------------------- Riftia_pachyptila_Hb ---------------------------------------------------------DYVCGPLQRLKVKRQWAEAYGSG--NSREEFGHFIWSHVFQHSPAARDMFKRVR------GDNIHTA2PAFRAHATRVLGGLDMCIALLDD-EPVLNTQLAHLAKQHETRG----VEAAHYDTVNHAVMMGVENVIGSE------VFDQDAWKPCLNVITNGIQG----------------------------- Synechocystis_sp._PCC6803_cyanoHb --------------------------------------------------------------------MSTLYEKLG---GTTAVDLAVDKFYERVLQD--DRIKHFF-ADVD--------KAKQRAHQ-KAFLTYAFGGTDKYDG-----------RYMREAHKELVENHGLNGEHFDAVAEDLLATLKEMGV------PEDLIAEVAAVAGAPAHKRDVLNQ--------------------------- Thermobifida_fusca_Pgb -----------------MQLAQSSTARRVGMATKTLIPGYTYGTEQVAKSPIGLEDLNKLKTTVMFTSADEEALRMAGDVLEDQVEDVLDVWYGFVADH-PHLLAYFSTPD--------GHPIQEYLDRVRERFGQWILDTCRRPYN--QEWLDYQQEIALRHTPEK-----KNVTDNANSVDNIPLRYVIAFIYPVTA-TLRPFLAKKGHSADQVEANYQAWFKSVTMQIALWSQPYTRDGYW------- Thermosynechococcus_elongatus_Gib ----------------------------------MVIQSFEVKKMTIEPINFMATMVRRVQLTDEDKSLLAEFLPWGKEI----APQMADTFYDYLGRD--EEMNAILNAT----------EGRIHRLHQTFVDWFYEMFTGMDSWG--KAYAERRWKIGLVHVRIG-----IGPQHVVPAMAVVVNAVRQKLREANKSEALSDALGKICMIDLAFIEQAYFEVSSQAVLKETGWTQALFQRLIATGAAAM Vitreoscilla_stercoraria_Hb ----------------------------------------------------------------MLDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFD-MGRQ-----------ESLEQPKALANTVLAAAQNIEN---LPAILPAVKKIAVKHCQAG----VAAAHYPIVGQELLGAIKEVLGDA----ATDDILDAWGKAYGVIADVFIQVEADLYAQAVE------------------ ; END;