#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 May 10, 2024; 3:53 GMT

TreeBASE (cc) 1994-2008

Study reference:
Susko E., Field C., Blouin C., & Roger A. 2003. Estimation of Rates-Across-Sites
Distributions in Phylogenetic Substitution Models. Systematic Biology, 52(5): 594-603.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1019]

BEGIN TAXA;
        TITLE  'Bacterial HMG-CoA';
        DIMENSIONS NTAX=14;
        TAXLABELS
            Archeoglobus_fulgidis
            Archeoglobus_profundus
            Archeoglobus_veneficus
            Enterococcus_faecalis
            Enterococcus_faecium
            Ferroglobus_placidus
            Pseudomonas_mevalonii
            Staphylococcus_aureus
            Staphylococcus_epidermidis
            Staphylococcus_haemolyticus
            Streptococcus_pneumoniae
            Streptococcus_pyogenes
            Thermoplasma_acidophilum
            Thermoplasma_volcanium
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M598]

	TITLE 'Bacterial HMG-CoA';
	LINK TAXA = 'Bacterial HMG-CoA';
	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" 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 ]
[                                        .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Archeoglobus_fulgidis           ENVIGTFELPLGIATNFLIDGKDYLIPMAIEEPSVVAAASNAARMAFTTDYTGSLMIGQIQVAKFEVDEIIERANECDPMCKDIEARVIVHLIVDVKDAMGANAVNTMCEKVAPFIGKVYLRIISNRLARAKAVFDKDVIEVVEGIMLAYAFDPFRCATKIMNGISALMIATGNDFRAIAGLTTYELVGTIEIPMAVGVIGGAKNPLAKISLKILGVAEEVAAALGLAQNFAALRALATEGIQRGHMELHA
Archeoglobus_profundus          ENVIGTFELPIGIATNFLIDGKDYLVPMVIEEPSVVAAASHGAKIAFSTLYTGSIMIGQIQVAKFEVDEIIEKANEIESSCKDLTVRVVVHLLIDVKDAMGANFINSVCERIAPFIGKVLLRILSNRLAIAKAVFDKKAVEVVEGIIKAYELDIYRCATKIMNGVCAVLIATGNDFRAVSALTHYELVGYIELPMSVGVVGGAKNPLARICLKILGVAEEVIASVGLAQNFAALRALVTEGIQRGHMELHA
Archeoglobus_veneficus          ENVIGTFELPLGIATNFLIDGKDYLIPMAIEEPSVVAAASNAAKMAFVTQATPPVMIGQIQVAKIEVDEIIQKANEQDSICKDIEARVIVHLLVDVRDAMGANAVNTMAEAVAPIIGKVRLRIISNRLARAKAVFDKDAIEVVDGIIEAYAFDPYRCATKIMNGVSAVVIATGNDFRAVAGLTTYELVGTIELPVAVGIVGGASNPMARVCLKILGVAEEVIAAVGLAQNFAALRALATEGIQRGHMELHA
Enterococcus_faecalis           ENQISETEVPMGVGLHLTVDETDYLVPMATEEPSVIAALSNGAKIAFKTVNQQRLMRGQIVFLIDELTEIFQQAELSYPSLRDLQYRASVDFLVDVKDAMGANIVNAMLEGVAELFQKILFSILSNSVVTMKTAIPVSRLEIAEKIVLASRYDPYRAVTKIMNGIEAVVLATGNDTRAVASLTSWTLIGEISVPLALATVGGAKLPKSQAAADLLAVAKEVVAAVGLAQNLAALRALVSEGIQKGHMALQA
Enterococcus_faecium            ENQVSEVEIPMGIAQNFQINGKKKWIPMATEEPSVIAAASNGAKICICAETPQRLMRGQIVLVINAVEELILCANESYPSVQDISTRESIDFLVDVKDAMGANMINSILESVANKLEEILFSILSNSLASACCEIPFERLQIAKKIQQAGEYDPYRAATKIMNGIEAVVAATGNDTRAVASLTDWQLVGKLTVPLAVATVGGANLPKAKASLAMLDIAKEVIAAVGLAQNLAALRALVTEGIQKGHMGLQA
Ferroglobus_placidus            ENVIGTFELPLGIATNFLIDGKEYLIPMAIEEPSVVAAASNAAKMAFFTDYSGNIMIGQIQVAKFEVEEIIEKANEQDPICKDVEARVIVHLLVDVKDAMGANAVNTMAEAVAPLIGKVYLRIISNRLARAKAIFDKNVIEVVEGIMQAYAFDPFRCATKIMNGISAVVIATGNDFRAVAGLTRYELVGTIELPMAVGVIGGAKNPLAKICLKILGVAEEVLAAVGLAQNFAALRALATEGIQRGHMELHA
Pseudomonas_mevalonii           ENVIGTFELPYAVASNFQINGRDVLVPLVVEEPSIVAAASYMAKLAFTTSSSAPLMHAQVQIARLSLDEIIELANRKDQLCRDIEVHTVAHLIVDVRDAMGANTVNTMAEAVAPLMGQVRLRILSNRLARAQVRITPQQLAVIEGILDAYAFDPYRAATKIMNGIDPLIVATGNDWRAVAGLTTWELVGTLEMPMPVGLVGGAKHPLAQLSLRILGVAQAIAVAVGLAQNLGAMRALATEGIQRGHMALHA
Staphylococcus_aureus           ENVIAQGALPVGLLPNIIVDDKAYVVPMMVEEPSVVAAASYGAKLVFKTVSSERIMIGQIVFLSADIKQIHKIADEAYPSYQRIAIDTSLKVFVDTKDAMGANMLNTILEAITAFLSDILMSILSNSVVKVQGEIDVKDLEVAKRMERASVLDIHRAATKVMNGIHAVVLATGNDTRGAASIATWRLIGTIEVPMTLAIVGGGKLPIAKASLELLNVAQEVVAAVGLAQNFAACRALVSEGIQQGHMSLQY
Staphylococcus_epidermidis      ENVIGQGALPVGLLPRIIVDDKEYVVPMMVEEPSVVAAASYGAKLVFKTISSERLMIGQIVFLANSISQIHQIADEAYPSYQRIEIDTSLKVFVDTKDAMGANMLITILEAITAHLQNVLMSILSNSVVQVQGEIDIEDLEVAQRMERASVLDIHRAATKVMNGIHAVVLATGNDTRGVASIATWELVGTIEVPMTLATVGGGKLPIAKASLNLLNVAQEVVAAVGLAQNFSACRALVSEGIQQGHMSLQY
Staphylococcus_haemolyticus     ENVIGQGTLPVGLLPKIIVDDKEYVVPMMVEEPSVVAAASYGAKLVFKTVKSERLMIGQIVFLAQAIPQIKQIAAEAYPSYRRIEIDTSLKVFVDTKDAMGANMLNTILEAITAHMRDVLMSILSNSVVRVQGEIDIKDLEVAQRMERASVLDIHRAATKVMNGIHAVVLATGNDTRGAASIATWKLVGTIEVPMTLAIVGGGKLPIAKASLELLNVAQEVVAAVGLAQNFSACRALVSEGIQKGHMSLQY
Streptococcus_pneumoniae        ENVVGTFSLPYSLVPEVLVNGQGYTVPYVTEEPSVVAAASYASKIIFTAQVHQRQMIGQVALAQEKIAELLELANQAYPSARDLHVEQVVYIHVDTQEAMGANMLNTMLEALKPVLGQSLMGILSNSLVTASCRIAFRYLEIAEKIALASQFDPYRAATKIFNGIDAILIATGNDWRAIAGLSCWTLVGEMTLPMPVATKGGSGNPRVALSHDLLGNAREIIVSIGLAQNFAALKALVSTGIQQGHMKLQA
Streptococcus_pyogenes          ENVLGRLALPFSIAPDFLVNGSTYQMPFVTEEPSVVAAASFAAKLIFKAQTLNRQMIGQIVLAKAAIKKLIALANKAYPSARTIHLEEIFYLTVDTQEAMGANMVNTMMEALVPDLGHCLMAILSNSLVTTSCEIPVRLLQLAQKIELASRLDPYRATTKIFNGIDAVVIATGNDWRAIAGLSQWHLLGQMTLPMPIASKGGSGNPTVSIAHDLLNQAKTLIASVGLAQNFAALKALTSSGIQAGHMKLHA
Thermoplasma_acidophilum        ENVITTIEMPMGIAVNFRINDRDYLIPMAIEEPSVVAAASNAAKVAFRAFATEPIMIGEIQVAKIALQKILDMANTRSKTARDLEVEIIVHLIVDVRDAMGANVINSMCEYVAPEIGRVNLRILSNRIAYASAVFPKEIIEAVDSIIEAYHMDIYRAATKIMNGVDAVLIATMNDWRSAANLARYELVGSIEIPMAVGTIGGTRIEKARIAMKILGVAKEVLAAVGLAQNFAALRALATEGIQRGHMELHS
Thermoplasma_volcanium          ENVITTIEMPLGIAVNFLINGKDYLIPMAIEEPSVVAAASNAAKVAFNAYATEPVMIGEIQVAKMNISRILELANTRSKTAKDIEVNVIVHLIVDVRDAMGANVVNSMCEYVAPEIGRVNLRILSNRVAYASAVFSKDIIEAVDNIVEAYRMDIYRASTKIMNGIDAVLVATMNDWRAAANLAKYELVGTIEIPIAVGTVGGTGIDKARIARKILGVATEVLAAVGLAQNFSAVRALATEGIQRGHMELHA
;
END;