#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 November 15, 2026; 18:05 GMT

TreeBASE (cc) 1994-2008

Study reference:
Xu L., Huang H., Wei W., Zhong Y., Tang B., Yuan H., Zhu L., Huang W., Ge M., Yang
S., Zheng H., Jiang W., Chen D., Zhao G., & Zhao W. 2014. Complete genome sequence
and comparative genomic analyses of the vancomycin-producing Amycolatopsis
orientalis. BMC Genomics, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S15601]

[ The following blocks are input data for analysis step 13423 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep13423;
        DIMENSIONS NTAX=20;
        TAXLABELS
            Amycolatopsis_mediterranei
            Amycolatopsis_orientalis_orf0553
            Amycolatopsis_orientalis_orf5636
            Bacillus_cereus
            Bacillus_pumilus
            Bacillus_subtilis
            Corynebacterium_diphtheriae
            Corynebacterium_glutamicum_ATCC13032
            Corynebacterium_pseudotuberculosis
            Frankia_sp_CcI3
            Listeria_monocytogenes_EGD
            Mycobacterium_bovis_AF2122
            Mycobacterium_tuberculosis_H37Rv
            Nocardia_farcinica
            Rhodococcus_erythropolis
            Saccharopolyspora_erythraea
            Staphylococcus_epidermidis_ATCC12228
            Staphylococcus_haemolyticus
            Streptococcus_pneumoniae_TIGR4
            Streptomyces_coelicolor
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M21510]

	TITLE 'Isp-MP';
	LINK TAXA = TaxaForAnalysisStep13423;
	DIMENSIONS NCHAR=370;
	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]
[                                                 .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .]
Amycolatopsis_mediterranei               VPSPAPGAGSLPAAPGGALDDLRASVGLQIA-DETLLRSIAGGLTEVEKLLREVVRS--DVQAVNDAALHLVEAGGKRFRPLFTLLAAQFGP-KQDDHVIV-AAAAVELVHLATLYHDDV--MDEATMRRGAESVNARWDNTIAILTGDFLFAHASRLVADLG-TDAARIIAETFGELVTGQMRETVGPGPGD------DAVAHYLTVIAQKTGSLIATSGRFGGMMSGAAEEHIEALRRFGDIIGTAFQISDDIIDIASPSDELGKAQGTDLREGVRTLPMLYALADPET-DPRLIELLS-----GPIADDALVQEALELLRVSSGLDRARVTLSDYAQRARAELTALPASPARDACESVADYLVARTR
Amycolatopsis_orientalis_orf0553         -------------------------VGLQIA-DEQLLRTLATGLADVETLLREVVRS--DVKAVEDAASHLVEAGGKRFRPLFTLLASQFGP-KQGDQVVT-AAAAVELVHLATLYHDDV--MDEATMRRGAESVNARWDNTIAILTGDFLFAHASRLVADLG-TDAARIIAETFGELVTGQMRETVGPADGD------DAVEHYLTVIAQKTGSLIATSGRFGGMMSGAPDEYIDALRRFGDIIGTAFQISDDVIDIASASDELGKAQGTDLREGVRTLPMLYALADPAT-DPRLVELLS-----GPISDDKLVAEALGLLRASSGLERARETLSDYARRARAELAALPASPARDACESVADYLVARTH
Amycolatopsis_orientalis_orf5636         --------------VNTTTIVTELGLDPALERHRRFAAELRTGLARVEERLQEVLHSP-GQPELTEAATHLVRAGGKRLRPLMALAGAAFGD--GRDEAIS-AAVLVELVHVATLYHDDV--MDEAPMRHGVASANSLWGNKKAVLIGDYVLACAARVGAGLG-DYALRSQAETFGRLVRGQFLETTGPFEDCG---RHAPYEHHIQVMADKSASLIAMAGRLGAQVSGADERTIETLGQYGELIGVAFQISDDVLDISASSTDLGKSAGTDLREGIVTLPMLHSLDDEGPGAARLREIIG----HGPVSDPAVRQEALGLLRDSAGVVRALAEAHGYAAKAKDLALSLPDRPARALLVGLSAFVVDRGE
Bacillus_cereus                          ---------------------------MNNMKLQLMYSFLRSDINVIEKELKKTVA-S-EQPLVEEAALQLIEAGGKRIRPVFVLLAG-KFGDYKLDAIKH-VAVALELIHMASLVHDDV--IDAAFLRRGSATVNAKWGDRIAMYTGDYLFAKSLECITNIEIPEAHQALSHTILEVCKGEIEQIKDKYNYD------QNLRTYLRRIKRKTALLIAASCQLGAIAAGANRDTVNRLFWYGYFVGMSYQIIDDILDFVSTEEKLGKPAGGDLLQGNITLPALYAME-DPVLRQKITSVHE-------NSTASEMQEIIDAVKNSTAIDQAFAFSERYLHKALEIIKPLPRGKAKYALQNVAKYIGKRKF
Bacillus_pumilus                         ------------------------------MKLKAMISFLNHDIDIIEKELEQTVR-S-DYALLSEAGLHLLQAGGKRIRPVFVLLSG-MFGDYDINKIKY-VAVALELIHMASLVHDDV--IDDAELRRGKPTIKAKWDNRIAMYTGDYMFARSLEYMTKINHPMAHEILSKMVVELCLGEIEQVKDKYNMD------QNLRTYLRRIKRKTALLIAGSCQLGAIAAGTDEKTHKALYWFGYYVGMSYQIIDDVLDFTSTEEELGKPVGGDLLQGNVTLPVLYALK-NPTLEGQLKLINS-------ETTEMQLKPVIEHLKQTDAIDRSIRVSEMYLKKAFEQLDKLPRGRARTSLASIAKYIGKRKF
Bacillus_subtilis                        --MLNIIRLLAESLPRISDGNENTDVWVNDMKFKMAYSFLNDDIDVIERELEQTVR-S-DYPLLSEAGLHLLQAGGKRIRPVFVLLSG-MFGDYDINKIKY-VAVTLEMIHMASLVHDDV--IDDAELRRGKPTIKAKWDNRIAMYTGDYMLAGSLEMMTRINEPKAHRILSQTIVEVCLGEIEQIKDKYNME------QNLRTYLRRIKRKTALLIAVSCQLGAIASGADEKIHKALYWFGYYVGMSYQIIDDILDFTSTEEELGKPVGGDLLQGNVTLPVLYALK-NPALKNQLKLINS-------ETTQEQLEPIIEEIKKTDAIEASMAVSEMYLQKAFQKLNTLPRGRARSSLAAIAKYIGKRKF
Corynebacterium_diphtheriae              -MGN--------------------GTRVDLG-EQNLNEEIAAGMIRVEDLLREELSK--GEDFLVEKVMHLAEAGGKRFRPMFALLASQYGSQPMSENVIK-AAVVVEMTHLATLYHDDV--MDEADKRRGVDSANFRWNNSVAILAGDILLAHVARLMADLG-VETVAHFSETFAELVTGQMRETIGARDG-------DPIEHYLNVINEKTGVLIASAGFLGSMHAGASAEHVEALRAYGRAIGMVFQIVDDIIDIFSDTTDSGKTPGTDLREGVFTLPVLYALSEDTAVGEELRSILT-----GPLTDDATVAHALDLLARSTGRERALADVHRYLEEAERQLALLPQNSTTDALRSLAHYTVKRVG
Corynebacterium_glutamicum_ATCC13032     -MSSGRTVPTRSHGLGKEGVSTTGASQVEFG-DPELTARINDAMVQVEELLHTELSS--GEDFLVDIVMHLTRAGGKRFRPMFALLASEFGEKPLSENVIK-AAVVVEITHLATLYHDDV--MDEASMRRGVPSANARWDNSVAILAGDILLAHASGLMSQLG-TDTVAHFAETFGELVTGQMRETVGPRDT-------DPIEHYTNVIREKTGVLIASAGYLGAMHAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVFTLPVLYALREDTPVGAELRDILT-----GPLEDDETVNHVLELLSQSGGRQAALDEVYRYMDIANAELDRLPDSTVKEALRNLATFTVKRVG
Corynebacterium_pseudotuberculosis       -MSNG-----------AEGLSTSTGTRVDLG-NPALNEDISAGMTRVEELLQKELCV--GEDFIVEKVKHLANAGGKRFRPMFALLASQYGDHPVSEDVIK-AAVVVEMTHLATLYHDDV--MDEAAKRRGVESANARWNNSVAILAGDILLAHVSRLMADLG-TDTVRHFSETFGDLVTGQMRETIGVGEG-------DPIEHYMAVIREKTGVLIASAGYLGALHSGATADHIEALRAYGAAIGMVFQIVDDIIDIFSDSEDSGKTPGTDLREGVFTLPVLYALREQTPIGEELRATLT-----GPVTDDTTVARVLDLLTQSTGRDRALADVHHYLNEAEAQLELLPQNATTEALRNLARFTVQRVG
Frankia_sp_CcI3                          -------------------MSAIGLDVVGIRTDPDLEKAVRVGLARVEDLLRESVRS--ESAFVTETSRHLVDAGGKRFRPIVVLLAAQFAD-PEAVGVVP-AAVAIELTHLSTLYHDDV--MDEAPRRRGAASANTRWTNTVAILTGDYLFARASDITADLG-PEATRILARTIATLCEGQIRETVGPAPGQ------DPVEHYLRVITDKTASLIATSGRLGAMLAGADPITVDTLATFGELFGVAFQLSDDIIDVASDPVDSGKTPGTDLREGIPTLPVLYALQADDRAAGRLRELITTGFAPGDGNTEDRVGEALDLLRGHVGMARARAELISWSSRARECLASLPDNPAKTALESLADFVVDRTG
Listeria_monocytogenes_EGD               ------------------------------MKLNFLYANMQKDIDSVEKELKKALSGA-AADTTSAAALHLLEAGGKRIRPMFVCLSARLAANADFNAVKN-ASVAIELIHMASIVHDDV--VDDADLRRGRETIKSKWGNHIAMYTGDFLFAKSLEYMTEIKDVAAHKMLSHVTVELSTGEIEQLKDKYNFD------QSVRNYLRRIKRKTALLIAASCGLGGVVSGQSEADYQKLYRFGYYVGMAFQITDDVLDFVGTEKELGKPAGEDLRQGNVTLPVFFAME-DPFLKKRISQITE-------ETPAEEIAVLVEEVKKTGAK-QAEDVATTYLKKAVEILDSLPQVPELKPLKQIVRVLDKRNY
Mycobacterium_bovis_AF2122               -----------------MRTPATVVAGVDLG-DAVFAAAVRAGVARVEQLMDTELRQ--ADEVMSDSLLHLFNAGGKRFRPLFTVLSAQIGPQPDAAAVTV-AGAVIEMIHLATLYHDDV--MDEAQVRRGAPSANAQWGNNVAILAGDYLLATASRLVARLG-PEAVRIIADTFAQLVTGQMRETRGTSENV------DSIEQYLKVVQEKTGSLIGAAGRLGGMFSGATDEQVERLSRLGGVVGTAFQIADDIIDIDSESDESGKLPGTDVREGVHTLPMLYALRESGPDCARLRALLN-----GPVDDDAEVREALTLLRASPGMARAKDVLAQYAAQARHELALLPDVPGRRALAALVDYTVSRHG
Mycobacterium_tuberculosis_H37Rv         -----------------MRTPATVVAGVDLG-DAVFAAAVRAGVARVEQLMDTELRQ--ADEVMSDSLLHLFNAGGKRFRPLFTVLSAQIGPQPDAAAVTV-AGAVIEMIHLATLYHDDV--MDEAQVRRGAPSANAQWGNNVAILAGDYLLATASRLVARLG-PEAVRIIADTFAQLVTGQMRETRGTSENV------DSIEQYLKVVQEKTGSLIGAAGRLGGMFSGATDEQVERLSRLGGVVGTAFQIADDIIDIDSESDESGKLPGTDVREGVHTLPMLYALRESGPDCARLRALLN-----GPVDDDAEVREALTLLRASPGMARAKDVLAQYAAQARHELALLPDVPGRRALAALVDYTVSRHG
Nocardia_farcinica                       -MSTS--AVS----GSAVSGSSTVVAGVELG-DAELAATVRNGLEEVEKLLIAELSD--GEDFLQDAALHLAKAGGKRFRPLFTILTGQLGPRPTDPALIT-AGTVVELVHLATLYHDDV--MDEATMRRGAPSVNSRWGNNIAILAGDYLFAHASRLTSTLG-PDAVRIIAETFAELVTGQMRETMGARESQ------DPVEHYLRVVWEKTGSLIAAAGRFGGTFSGADTAHIERLARLGDAVGTAFQISDDIIDISSASEQSGKTPGTDLREGVHTLPVLYALREEGAEADRLRTLLD-----HPLHSDDEVAEALELLGRSQGMVLAKEKLQSYADQAYAELAALPSGPANDALEQLVRYTIERVG
Rhodococcus_erythropolis                 -MGTD--IVSTEKTAADATASSTVVAGIDLG-DEQLAAVVRGGLSDVEELLVSELSD--GEDFLTEAALHLARAGGKRFRPLFTILTAQLGPVPNDPSIIT-AATVTELVHLATLYHDDV--MDEASMRRGAPSANARWGNSVAILAGDYLFAHASRLVSTLG-PEAVRIIAETFAELVTGQMRETIGVKKEQ------DPVEHYLKVVWEKTGSLIAASGRFGGTFSGADAAHIERLERLGDAVGTAFQISDDIIDISSVSAQSGKTPGTDLREGVHTLPVLYAFREEGADADRLRELLA-----GPVTEDALVEEALELLERSPGMVKAKAKLGEYAVSAKAQLAELPQGPANEALVRLVDYTIERVG
Saccharopolyspora_erythraea              MSRPAGDPNSYLRG------GVPGPTGFEIT-DSALAESVRQGIADVEALLHESVRS--DLEFATRTSLHLVDAGGKRFRPLFALLAAQFGD-PRTENVIK-SAAVVEMVHLATLYHDDV--MDEATMRRGATSANARWDNSVAILTGDFLFAQASRLVADLG-TDAAREMARTFEALVTGQMRETVGVGRDE------DPVDFYLKVIYEKTGSLIAIAGRFGALFSGASPEQVTAMERLGRILGTAFQISDDVIDIASPAVESGKTPGTDLREGVRTLPMLFALADEGT-DVRLRELLA-----GPLEHDADVEEALKLLRECDGLTRARRTLDEYAAEARTELAALPDVPARDALATLVEYVVARTR
Staphylococcus_epidermidis_ATCC12228     --------------MALLQCTLAIKKTVLAKVINVAKLNINNEIKKVEKRLEEAII-S-SDQTLQEASFHLLSSGGKRVRPAFVILSGQFGSNNKPSEDTYRVAVALELIHMATLVHDDV--IDKSDKRRGRLTISKKWDQSTAILTGNFLLAMGLKHLSEISDTRVHSTISKSIVDVCRGELFQFQDQFNSN------QTITNYLRRINRKTALLIQLSTQVGAITSNASNDVIRKLKMIGHYIGMSFQIIDDVLDFTSSEKKLGKPVGSDLMNGHITLPVLLEMRKNKTFKDKISQLNP-------DSPQHAFETCITIIRQSESIEQSKQISEKYLNKAINLIDELEDGPNKELFRKLIKKMGSRNK
Staphylococcus_haemolyticus              ----------------------------------MAKLNMNSEIKNVEKRLQKAIE-S-NDPILREASSHLLSSGGKRVRPAFVILSSQFGPQKK-TEDTYRVAVALELIHMATLVHDDV--IDKSDKRRGRLTIVKKWDVTTAILTGNFLLALGLEHLSEIRDNRIHHIISNSIVNVGLGELFQFQDQFNSE------QSITNYLRRINRKTALLIQLATEVGAITSEANDETIRKLKMIGHYIGMSFQIVDDILDFTSTEKKLGKPVGSDLMNGHITLPVLLEMKKDTSFKKKIAALNH-------QSESQEFKPLIEQIRNSYSIKESKAISDKYLAKALKLIDELDEPNAQSLFIKLIKKMGSRSV
Streptococcus_pneumoniae_TIGR4           -------------------------------------MKKQEKLALVESALEDFYGDQQFASSLRESVLYSIHAGGKRIRPFLLLEVLEALQVTIKPAHAQ-VATALEMIHTGSLIHDDLPAMDDDDYRRGRLTNHKKFGEAMAILAGDALFLDSYALIAQADLPSQIKVDLIANLSLASGSLGMVAGQVLDMEGEHQHLSLEELQTIHANKTGKLLAYPFQAAAIIAELSPEMQVKLKTVGELIGLAFQVRDDVLDVTASFEEIGKTPQKDLQAEKSTYPALLGLEESIAFCNQTLDQAN--------------------------------------EKLEEIAQQLP--FETESIVSVVESLRING-
Streptomyces_coelicolor                  -------------------MTVVGPFGLSVR-DQALEADVQAGLVAVEEGLLEATKS--EVPFITEAAQHLVRAGGKRFRPLLVMLSAQFGD-PYAPGIVP-SAVVVELTHLATLYHDDV--MDEAAVRRGVPSANTRWDNSVAVLTGDFLFARASQILADLG-PEAVRVQALAFERLVTGQILETAGPQDGR------DPVDHYLDVLGGKTGSLVAVSCRFGAMMSGADETVVDVLTQYGERLGVAFQLADDVLDIASDSDESGKTPGTDLREGIPTLPVLR-LRERAARLGLAEDLALCELLDSDLSDDARHAEALRLLRAHPALEQARRDTVRYAEEARAALAPLRECDAKAALVELCDAVVHRAG
;
END;

[ The following blocks are output data for analysis step 13423 ]
BEGIN TREES;
      TITLE 'Isp-MP';
      LINK TAXA = TaxaForAnalysisStep13423;
      TREE 'Isp-MP' = [&R] ((((((Rhodococcus_erythropolis:1.0,Nocardia_farcinica:1.0):1.0,(Mycobacterium_tuberculosis_H37Rv:1.0,Mycobacterium_bovis_AF2122:1.0):1.0):1.0,(Saccharopolyspora_erythraea:1.0,(Amycolatopsis_mediterranei:1.0,Amycolatopsis_orientalis_orf0553:1.0):1.0):1.0):1.0,(Amycolatopsis_orientalis_orf5636:1.0,(Frankia_sp_CcI3:1.0,Streptomyces_coelicolor:1.0):1.0):1.0):1.0,(Corynebacterium_glutamicum_ATCC13032:1.0,(Corynebacterium_diphtheriae:1.0,Corynebacterium_pseudotuberculosis:1.0):1.0):1.0):1.0,((Staphylococcus_epidermidis_ATCC12228:1.0,Staphylococcus_haemolyticus:1.0):1.0,(Listeria_monocytogenes_EGD:1.0,(Bacillus_cereus:1.0,(Bacillus_subtilis:1.0,Bacillus_pumilus:1.0):1.0):1.0):1.0):1.0,Streptococcus_pneumoniae_TIGR4:1.0);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr72353]


END;