#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 21, 2025; 13:33 GMT TreeBASE (cc) 1994-2008 Study reference: Lohtander K., Pasonen H., Aalto M., Palva T., Pappinen A., & Rikkinen J. 2008. Phylogeny of chitinases and implications for estimating horizontal gene transfer from chitinase transgenic silver birch (Betula pendula). Environmental Biosafety Research, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2145] [ The following blocks are input data for analysis step 4474 ] BEGIN TAXA; TITLE TaxaForAnalysisStep4474; DIMENSIONS NTAX=55; TAXLABELS Arabidopsis_thaliana_14 Arabidopsis_thaliana_23 Arabidopsis_thaliana_25 Arabidopsis_thaliana_27 Arabidopsis_thaliana_30 Arabidopsis_thaliana_34 Arabidopsis_thaliana_44 Arachis_hypogaea_35 Beta_vulgaris_10 Beta_vulgaris_11 Betula_pendula_15 Betula_pendula_16 Betula_pendula_28 Betula_pendula_29 Betula_pendula_45 Betula_pendula_46 Betula_pendula_52 Betula_pendula_53 Betula_pendula_54 Betula_pendula_55 Brassica_napus_22 Burkholderia_gladioli_2 Cynodon_dactylon_31 Glycine_max_51 Nicotiana_tabacum_43 Nicotiana_tabacum_49 Nocardiopsis_prasina_7 Oryza_japonica_26 Oryza_sativa_20 Oryza_sativa_21 Oryza_sativa_33 Oryza_sativa_37 Oryza_sativa_38 Oryza_sativa1BAA9_32 Persea_americana_42 Phaseolus_vulgaris_12 Phaseolus_vulgaris_47 Phytophthora_infestans_1 Picea_glauca_9 Pinus_strobus_36 Pisum_sativum_50 Poa_pratensis_39 Saccharum_officinale_19 Secale_cereale_40 Streptomyces_coelicolor_4 Streptomyces_griseus_8 Streptomyces_lavendulae_3 Streptomyces_olivaceoviridis_5 Streptomyces_thermoviolaceus_6 Triticum_aestivum_24 Triticum_aestivum_41 Vigna_sesquipedalis_48 Vigna_unguiculata_13 Zea_mays_17 Zea_mays_18 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3810] TITLE 'Group IV Chitinases, Fig. 1'; LINK TAXA = TaxaForAnalysisStep4474; DIMENSIONS NCHAR=271; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_14 IVTQEFFNGIISQAASS-CAGNRFYSRGAFLEALDSY--SRFGRVGSTDDSRREIAAFFAHVTHETGR????????????NFCYIEEIDG----ASKDYCDEN-A---TQYPCNPNKGYYGRGPIQLS-----------WNFNYGPAGTAIGFDGLNAPETVATDPVISFKTALWYWTNR????????????????????VQPVIS--QGFGATIRAINGALECD--GANTATVQA-RVRYYTDYCRQLG?????VDPGNNLTCTTATA?T Arabidopsis_thaliana_23 IVTQIFFNNIINQAGNG-CAGKSFYTRDSFINATNTF--PSFANT????VTRREIATMFAHFTYETG?????????????HFCYIEEING----ASRVMCDQN-N---RQYPCAPAKSYHGRGPLLLS-----------WNFNYGACGQSLGLDLLRQPELVSSNPVVAFRTALWFWMKS????????????????????VRPVLN--QGFGATIRAISG-FDCD--GRNLGGVNA-RIGYYRDYCGQLG?????LDPGANITCTAATA?T Arabidopsis_thaliana_25 ?VTPDFFNSILNQ--RGDCPGKGFYTHDTFMAAANSY--PSFGAS????ISKREIAAFFAHVAQETG?????????????FMCYIEEIDGPAKAASGEYCDTE-K---PEFPCAQGKGYYGRGAIQLS-----------WNYNYGLCGKALDENLLASPEKVAQDQVLAFKTAFWFWTTN????????????????????VRTSFK--SGFGATIRAVNS-RECS--GGDSTAKAANRIKYFQDYCGKLG?????VAPGDNLTCTAATA?T Arabidopsis_thaliana_27 ????QFENLFSKRNS-PVAHAVGFWDYRSFITAAAEYQPLGFGTAGEKLQGMKEVAAFLGHVGSKTSCGYGVATGGPLAWGLCYNKEMSP-----DQLYCDDYYKLT---YPCTPGVSYHGRGALPVY-----------WNYNYGQTGEALKVDLLSHPEYLENNATLAFQAAIWRWMTPPKKHLPSAHDVFVGKWKPTKNDTAAKRTPGFGATINVLYGDQICN--SGFDNDEMNNIVSHYLYYLDLIGVGREEAGPHEKLSCTTTTTTA Arabidopsis_thaliana_30 ????QFEQLFSKRNT-PIAHAVGFWDYQSFITAAALFEPLGFGTTGGKLMGQKEMAAFLGHVASKTSCGYGVATGGPLAWGLCYNREMSP-----MQSYCDESWKFK---YPCSPGAEYYGRGALPIY-----------WNFNYGAAGEALKADLLNHPEYIEQNATLAFQAAIWRWMTPIKRAQPSAHDIFVGNWKPTKNDTLSKRGPTFGSTMNVLYGEYTCG--QG-SIDPMNNIISHYLYFLDLMGIGREDAGPNDELSCTTTTTTA Arabidopsis_thaliana_34 LVPRTLYDQIFIHKDNNACPAKGFYPYEAFVEATRSF--PKFGSVGNFWTRRREVAAFLAQISHETTGGWATAPDGPYAWGLCFKEEV-----SPQSNYCDASNK----DWPCVSGKSYKGRGPIQLS-----------WNYNYGQAGRALGFDGLQNPELVANNSVLAFKTALWFWMTEQTPK-PSCHNVMVNRYRPTKADRAANRTVGYGLVTNIINGGLECG--IPGDGRVTD-RVGYFQRYAQLFK?????VTTGPNLDCTTTTTTT Arabidopsis_thaliana_44 IISSSQFDDMLKHRNDAACPARGFYTYNAFITAAKSF--PGFGTTGDTATRKKEVAAFFGQTSHETTGGWATAPDGPYSWGYCFKQEQ-----NPASDYCEPSAT-----WPCASGKRYYGRGPMQLS-----------WNYNYGLCGRAIGVDLLNNPDLVANDAVIAFKAAIWFWMTAQPPK-PSCHAVIAGQWQPSDADRAAGRLPGYGVITNIINGGLECG--RGQDGRVAD-RIGFYQRYCNIFG?????VNPGGNLDCTTTTTTT Arachis_hypogaea_35 LISKTLFDSIFLHKDDNACPARNFYTYESFVEATSSF--PAFGSTGCSATRKREVAAFLAQISHETTGGWATAPDGPYAWGLCFKEEV-----SPQSDYCDSSNK----EWPCYPGKSYKGRGPIQLS-----------WNYNYGPAGKALGFDGLKNPDIVSNNSVIAFKTALWFWMTEQKPK-PSCHNVMVGNYVPTASDRAANRTLGFGLVTNIINGGLECG--VPDDARVND-RIGYFQRYAKLFN?????VDTGPNLDCTTTTTTT Beta_vulgaris_10 IVSQAFFDGIIGQAAAS-CPGKNFYTRAAFLSAVD----PKFGNEGSSDDNKREIAAFFAHISHETT?????????????NLCHIEERDG---DVGDAYCDQDKA---AQYPCAAGKKYYGRGPLQLS-----------WNYNYALAGQAIGFDGLGNPEKVATDVNTSFKAAMWFWMTN????????????????????VHSVMN--QGFGATTKAINGALECN--GQNQDQAND-RIQFYKKYCADFG?????VAPGDNLTCTTATA?T Beta_vulgaris_11 LVTDAFFNRIINQASAS-CAGKRFYTRAAFLSALRFY--PQFG-SGSSDVVRREVAAFFAHVTHETG?????????????HFCYIEEIAK----ST--YCQSS-----AAFPCNPSKQYYGRGPLQIT-----------WNYNYIPAGRSIGFDGLNAPETVANNAVTAFRTAFWFWMNN????????????????????VHSVIVNGQGFGASIRAING-IECN--GGNSAAVTA-RVGYYTQYCQQLG?????VSPGNNLRCTTATA?T Betula_pendula_15 ?VTAEFFNGILDEADAS-CAGKNFFTRAAFLEALNSF--NEFGRIGSVDDSKREIAAFFAHVTHETG?????????????HFCYIEEIDG----ASKDYCDET-N---TEYPCNPDKGYYGRGPIQLS-----------WNFNYGPAGKSIGFDGLNSPETVANDPT?????????????????????????????????????????????????????????????????????????????????????????????????TTATA?? Betula_pendula_16 IVTPDFFNGILNQASGD-CPGKSFYTREAFLDALKSY--TQFGTTDSADDSKREIAAFFAHVTHETG?????????????FLCHIEEIDG----ASKDYCKHT-D---TEYPCNPNKNYYGRGPLQLS-----------WNYNYGAAGKSIEFDGLNSPET???????????????????????????????????????????????????????????????????????????????????????????????????????TTATA?? Betula_pendula_28 ?????????????????????????????????????QPDGFGTTGGKLSGMKEVAAFLGHVGSKTSCGYGVATGGPLAWGLCYNKELSP-----DSSYCDEYYKLT---YPCAPGAAYYGRGALPIY-----------WNYNYGKAGEALKVDLLNHPEYIEQNATLAFHAAIWRWMTPVKKHQPSAHDAFVGNWKPTKNDTLSKRLPGFGTTMNVLYGDGVCG--QG-DSDSMNNIVSHYQYYLDLMGVGREEAGPHEVLSC?TTTTTA Betula_pendula_29 ????????????????????????????????????????????????????????????????ETSCGYGVATGGPLAWGLCYNKEMSP-----SQTYCDDSYKYT---YPCTPGAEYYGRGALPIY-----------WNFNYGATGEALKVNLLDHPEYIEQNATLAFQAAIWRWITPIKKSQPSAHDAFVGNWKPTKNDTLSKRVPGFGATMNILYGDLVCG--QG-DIDPMNTIISHYLYYYELMGGNREDAGTNEVLSC?TTTTTA Betula_pendula_45 ???????????????????PAKGFYTYDVFIAAAKSF--PGFATTGDTATRKREIAAFLAQTSHETTGGWASAPDGPYSWGYCYLREQ-----NPGS-YCASDPN-----YPCASGRQYYGRGPIQLS-----------WNYNYGRCGKAIGVDLLNNPDLVATDAVISFKTAIWFWMTPQSPK-PSC????????????????????????????????????????????????????????????????????????????TTTTTT? Betula_pendula_46 ??????????LKHRNDAGCQAKGFYTFDAFIAAAKSF--SGFATTGDTDTRKREIAAFLAQTSHETTGGWESAPDGPYAWGYCYLKEQ-----NPGS-YCSSDKT-----YPCASGKQYYGRGPIQIS-----------WNYNYGRCGKAIGVDLLNNPDRVSTDAVISFKTAIWFWMTPQSPK-PSCHDVITGKWKPSDADKSANRNAGYG????????????????????????????????????????????????????TTTTTT? Betula_pendula_52 IISASLFDQFLKYRNDGRCKSNGFYTYNAFIAAARSF--GAFGTNGDVNTRKREVAAFLAQTSHETTGGWPSAPDGPYAWGYCFITET-----N-KADYCTPSKE-----WPCAAGKQYYGRGPIQLT-----------HNYNYGQAGKAIGSGLLNNPDLVATDATISFKTALWFWMTPQGNK-PSSHDVIIGKWTPSATDMSAGRVAGYGVITNIIN?????????????????????????????????????????????TTTTTT? Betula_pendula_53 ?????????????????????????????????????????????GDDTTRKREIAAFLAQTSHETTGGWASAPDGPYAWGYCFITET-----N-PADYCTPSTE-----WPCASGKQYYGRGPIQLT-----------HNYNYGPAGKAIGADILNNPDLVATDAITSFKTAIWFWMTPQGNK-PSSHDVIIGQWTPSAADTSAGRVPGYGVITNIINGGLECG--HGADDRVAD-RIGFYKRYCDLLG?????VSYGDNLDC?TTTTTT Betula_pendula_54 ????????????????????????????????????F--GAFGTNGDVTTRKREVAAFLAQTSHETTGGWANAPDGPYAWGYCFVSEN-----N-KADYCSPSKQ-----YPCAAGKKYYGRGPIQLT-----------YNYNYGQAGKAIGSNLLANPDLVAIDATISFKTALWFWMTPQGNK-PSSHDVITGKWKPTAADASAGRLPGYGLITNIINGGLECG--RGPNNRVAD-RIGFFKRYCDIMG?????VSYGNN????TTTTTT Betula_pendula_55 ???????????????????????FYTYNAFIAAARSF--GAFGTNGDVTTRKREVAAFLAQTSHETTGGWANAPDGPYAWGYCFVSEN-----N-KADYCSPSRQ-----YPCAPGKKYYGRGPIQLT-----------YNYNYGQAGKAIGAGLLANPDLVATDAIISFKTALWFWMTPQGNK-PSSHDVITGKWKPTVADSSAGRLPGYGLITNIINGGLECG--RGADNRVAD-RIGFFKRYCDILG?????VSYGN?????TTTTTT Brassica_napus_22 IVTQAFFNGIINQAGGG-CAGKNFYTRDSFINAANTF--PNFANS????VTRREIATMFAHFTHETG?????????????HFCYIEEING----ASRDYCDEN-N---RQYPCAPGKGYFGRGPIQLS-----------WNYNYGACGQSLNLNLLGQPELVSSNPTVAFRTGLWFWMNS????????????????????VRPVLN--QGFGATIRAING-MECN--GGNSGAVNA-RIRYYRDYCGQLG?????VDPGPNLSCTAATA?T Burkholderia_gladioli_2 ?LSRATFEQMFPT???????RNSFYTYDGLVGALKSY--PDFAGEASQDVRKQEIAAFLANVSHETG?????????????GLVYIRESNQ-ANWN--SYCSSGN--------CG-GKQYYGRGPMQLS-----------WDYNYKAAGDALGLNLLGNPDWVATDATISWATAIWFWMTQSGAG-T????????????MTPHQAMASGRGFGETIRSINGSLECN--GRNPAQVQS-RVDAYKRFA??????????????????ATAT?A? Cynodon_dactylon_31 LVSERLYNSLFLHKDDPACPAKGFYTYSSFIQAARAF--PKFAGTGDLATRKRELAAFFAQISHETTGGWATAPDGPYSWGLCYKEEI-----RPASNYCDATDK----KWPCYPAKSYHGRGPIQLS-----------WNFNYGPAGQALGFDGLRNPEIVANCSDTAFRTALWFWMTPRRPK-PSCHEVMVGEYRPIAVDVAGNRMPGFGLVTNIVNGGLECN--RTDDARVNN-RIGFYRRYCQIFN?????VDTGPNLDTTTTTTTT Glycine_max_51 LISSSLFDQMLKYRNDGRCSGHGFYRYDAFIAAAGSF--NGFGTTGDDNTRKKEIAAFLAQTSHETTGGWASAPDGPYAWGYCFINEQ-----N-QATYCDG-GN-----WPCAAGKKYYGRGPIQLT-----------HNYNYGQAGKALGLDLINNPDLVATDATVSFKTALWFWMTAQGNK-PSSHDVITGRWTPSSADSSAGRAPGYGVITNIINGGLECG--HGQDNRVQD-RIGFYRRYCQMMG?????ISPGDNLDCTTTTTTT Nicotiana_tabacum_43 IISSSMFDQMLKHRNDNACQGKGFYSYNAFINAARSF--PGFGTSGDTTARKREIAAFFAQTSHETTGGWATAPDGPYAWGYCWLREQ-----GSPGDYCTPSGQ-----WPCAPGRKYFGRGPIQIS-----------HNYNYGPCGRAIGVDLLNNPDLVATDPVISFKSALWFWMTPQSPK-PSCHDVIIGRWQPSSADRAANRLPGFGVITNIINGGLECG--RGTDSRVQD-RIGFYRRYCSILG?????VSPGDNLDCTTTTTTT Nicotiana_tabacum_49 IVTNDLFNEMLKNRNDGRCPANGFYTYDAFIAAANSF--PGFGTSGDDTARRKEIAAFFGQTSHETTGGSLSA--EPFTGGYCFVRQN?????????????????????????DQSDRYYGRGPIQLT-----------NQNNYEKAGNAIRQDLVNNPDLVATDATISFKTAIWFWMTPQDNK-PSSHDVIIGSWTPSAADQSANRAPGYGVITNIINGGIECG--VGPNAAVED-RIGYYRRYCGMLN?????VAPGDNLDCTTTATTT Nocardiopsis_prasina_7 VVSEAQFNQMFPN???????RNPFYTYSGLTTALSSY--PGFTNTGSVEVQRREAAAFLANVSHETG?????????????GLVYIKEINE-DNYP--HYCDLSQP---FGCPAG-QSAYYGKGPIQLA-----------WNYNYKAAGDALGIDLLNNPYLVEQDASIAWRTGLWFWNTQSGAG-T????????????MSGHTAIVDGHGFGESIRSINGSIECN--GGNPGQVQS-RINTFTQFTQILG?????TTTGSNLSCATAT?AT Oryza_japonica_26 ?????FEELFAHRNDRSLAHAAGFWDYHAFITAAALFEPRGFGTTGGKEVGMKEVAAFLGHVGAKTSCGYSVATGGPLAWGLCYNHELSP-----SQSYCDNSNEL----YPCVEGVEYYGRGALPVY-----------WNYNYGIIGQGIKQDLLNHPELLEQNATLAFEAAIWRWMTPMKRKQPSAHDVFVGNWKPTKNDTLSKRYPGFGATMNILYGDLICG--QG-SIDKMNVIVSHYQHYLDLMGVGSDKAGDN--LDCTTTTTTA Oryza_sativa_20 VVTEAFFNGIKNQAPNG-CAGKNFYTRQSFLNAAHSY--SGFARDRTNDDSKREIAAFFAHVTHETG?????????????HMCYINEING----ASMDYCDKN-N---KQWPCQPGKKYYGRGPLQIS-----------WNYNYGPAGQNIGFDGLRDPDRVAQDPTISFKTALWFWMNN????????????????????VHQVML--QGFGATIRAINGALECN--GKNPGAVNA-RVNYYKDYCRQFG?????VDPGGNLYCTTATA?T Oryza_sativa_21 VVTEAFFNGIKNQAPNG-CAGKSFYTRQSFLNAARSY--SGFANDRTNDDSKREIAAFFAHVTHETG?????????????HMCYINEING----ANMDYCDKS-N---KQWPCQPGKKYYGRGPLQIS-----------WNFNYGPAGKNIGFDGLRDPDKVAQDPTISFKTALWFWMNN????????????????????VHQVMS--QGFGATIRAINGALECN--GKNPGAVNA-RVNYYKDYCRQFG?????VSPGGNLYCTTATA?T Oryza_sativa_33 ???EQLYASLFLHKDDAACPARGFYTYASFVRAATKF--PRFAATGCADARKREVAAFLAQISHETTGGWATAPERPYAWGLCYKEEI-----NTAAQLLRTADKQSYKQWLCYPGKSYHGQGPIQIS-----------WNFNYGPAGQALGFDRLRNPEIVANCSDIAFQTALWFWMTPRDTK-PSCHHVMVGEYRPGPADVAANRTAGFGLVTNIVNSGLECN--RAGDARVNN-RIGFYRRYCQVLG?????VDT??????TTTTTTT Oryza_sativa_37 IVSRSLFDQMLLHRNDAACPAKNFYTYDAFVAAANAF--PSFATTGDAATRKREVAAFLAQTSHETTGGWATAPDGPYSWGYCFKEENNG---NVGSDYCVQSSQ-----WPCAAGKKYYGRGPIQIS-----------YNYNYGPAGQAIGSNLLSNPDLVASDATVSFKTAFWFWMTPQSPK-PSCHAVMTGQWTPNGNDQAAGRVPGYGVVTNIINGGVECG--HGADSRVAD-RIGFYKRYCDMLG?????VSYGANLDCTTTTTTT Oryza_sativa_38 ?????LFDQMLLHRNDQACAAKGFYTYDAFVAAANAY--PDFATTGDADTCKREVAAFLAQTSHETTGGWPTAPDGPYSWGYCFKEENNG---NA-PTYCEPKPE-----WPCAAGKKYYGRGPIQIT-----------YNYNYGPAGQAIGSDLLNNPDLVASDATVSFKTAFWFWMTPQSPK-PSCHAVITGQWTPSADDQAAGRVPGYGEITNIINGGVECG--HGADDKVAD-RIGFYKRYCDMLG?????VSYGDNLDCTTTTTTT Oryza_sativa1BAA9_32 IVSEQLYASLFLHKDDAACPARGFYTYASFVRAATRF--PRFAATGCADARKREVAAFLAQISHETTGGWATAPDGPYAWGLCYKEEI-----NPQSSYCDATDK----QWPCYPGKSYHGRGPIQISCHQRNVCMMMSRNFNYGPAGQALGFDGLRNPEIVANCSDIAFQTALWFWMTPRDTK-PSCHQVMVGEYRPGPADVAANRTAGFGLVTNIVNGGLECN--RAGDARVNN-RIGFYRRYCQVLG?????VDVGPNLDCTTTTTTT Persea_americana_42 LISQSVFNQMLKHRNDAACQAKGFYTYNAFIAAANSF--NGFASVGDTATRKREIAAFLAQTSHETTGGWATAPDGPYAWGYCFLKEQ-----GNPPDYCVPTAQ-----WPCAPGKKYYGRGPIQIS-----------YNYNYGPAGRAIGYDLINNPDAVATDPVISFKTALWFWMTPQSPK-PSCHNVITGRWTPSAADRAAGRLPGYGVITNIINGGIECG--KGFNDKVAD-RIGFYKRYCDLLG?????VSYGSNLDCTTTTTTT Phaseolus_vulgaris_12 IVTADFFNGIIDQADSG-CAGKNFYTRDAFLSALNSY--TDFGRVGSEDDSKREIAAAFAHFTHETG?????????????HFCYIEEIDG----ASKDYCDEESI---AQYPCSSSKGYHGRGPIQLS-----------WNFNYGPAGSANNFDGLGAPETVSNDVVVSFKTALWYWMQH????????????????????VRPVIN--QGFGATIRAINGALECD--GANPTTVQA-RVNYYTEYCRQLG?????VATGDNLTCTTATA?T Phaseolus_vulgaris_47 LISRSTFDQMLKHRNDGACPAKG-YTYDAFIAAAKAY--PSFGNTGDTATRKREIAAFLGQTSHETTGGWATAPDGPYAWGYCFVRER-----NPST-YCSATPQ-----FPCAPGQQYYGRGPIQIS-----------WNYNYGQCGRAIGVDLLNKPDLVATDSVISFKSALWFWMTAQSPK-PSSHDVITSRWTPSSADVAARRLPGYGTVTNIINGGLECG--RGQDSRVQD-RIGFFKRYCDLLG?????VGYGNNLDCTTTTTTT Phytophthora_infestans_1 ????????????????????????YNFNGLVDAASKY--SEFANTGNDDNDKRELAAFLAQTAHECD?????????????SFKAAEEYAR-DTYSVWQYCDNAT----YTCAPG-RR-YHGRGPIQLS-----------WNYNYYNAGEALGIDLLNNPDIVATDTTVTWMTALWYWMTPHGG---????????????RVIHDIVAGENGFAQSTDIINGGLECGPDAPNTSNEQQ-RITYFTKMCEALG?????VEPLGATSC?TAT?AT Picea_glauca_9 IISQSFFNGLAGGAGSS-CEGKGFYTYNAFIAAANAF--SGFGTTGSNDVKKRELAAFFANVMHETG?????????????GLCYINEKNP-----PMKYCQSS-----STWPCTSGKSYHGRGPLQLS-----------WNYNYGAVGKSIGFDGLNNPEKVGKDPTTSSKTAVWFWMKNR??????????????????NCHSAITSGKGLGGTIKAINS-MECN--GGNSGEVNS-RVNYYKKICSQLG?????VDPGANVSCTTATA?T Pinus_strobus_36 IISEDVFHQFLKHRNDDACSAKGFYTYSAFIAAANSF--PDFGNIGDQDSRKRELAAFFGHTSQETTGGWPTAPDGPYAWGYCFKDQV?????????????????????????NSTDRYRGRGPIQLT-----------GDYNYKAAGNALGYDLINNPDLVATDATVSFKTAVWFWMTAQSPK-PSCHDVILGRLTPSVTDTAAGRVAGYGMLTDIINGGPECG--TGTISDVQQGRIGFYQRYCKMLG?????VDVGSNLDYTTTATTT Pisum_sativum_50 LVPSSLFDQMLKYRNDGRCAGHGFYTYDAFIAAARSF--NGFGTTGDDNTKKKELAAFLAQTSHETTGGWPTAPDGPYAWGYCFVSEQ-----NTQEVYCSP-KD-----WPCAPGKKYYGRGPIQLT-----------HNYNYGLAGQAIKEDLINNPDLLSTNPTVSFKTAIWFWMTPQANK-PSSHDVITGRWTPSAADSSAGRVPGYGVITNIINGGIECG--HGQDNRVDD-RVGFYKRYCQIFG?????VDPGGNLDCTTTTTTT Poa_pratensis_39 ???QSLFEQMLLHRNDAACLAKGFYTYNAFIAAANSF--AGFGTTGSTDVRKREVAAFLAQTSHETTGGWPTAPDGPYSWGYCFKQEQ-----GATSDYCSPSSQ-----WPCAPGKKYFGRGPIQIS-----------YNYNYGPAGQAIQTDLLNNPDLVATDPTVSFKTALWFWMTAQSPK-PSSHAVITGQWSPSSADQAAGRVPGYGVITNIINGGLECG--KGQDNRVAD-RIGFYKRYCDLLG?????VSYGNNLDCTTTTTTT Saccharum_officinale_19 VVTDAFFNGIKNQAGNG-CEGKNFYTRSAFLSAADSY--KGFGGG--SVEGKREIAAFFAHVTHETG?????????????HFCYISEIN-----KNNAYCDSS-N---RQWPCAAGQKYYGRGPLQIS-----------WNYNYGPAGRDIGFNGLGDPNRVAQDAVIAFKTALWFWTNN????????????????????VHRVMS--QGFGATIRAINGALECN--GNNPAQMNA-RVGYYKQYCQQLG?????VDPGPNLTCTTATA?T Secale_cereale_40 IISQSLFDQMLLHRNDAACLAKGFYNYGAFIAAANSF--SAFATTGGTDVRKREVAAFLAQTSHETTGGWPTAPDGPYSWGYCFNQER-----GAPSDYCSPSSQ-----WPCAPGKKYFGRGPIQIS-----------YNYNYGPAGRAIGTDLLNNPDLVATDATVSFKTALWFWMTPQSPK-PSSHDVITGRWSPSGADQAAGRVPGYGVITNIINGGLECG--RGQDARVAD-RIGFYKRYCDLLG?????VSYGHNLDCTTTTTTT Streptomyces_coelicolor_4 VVSEAQFDQMFPS???????RNSFYTYSGLTAALSAY--PGFSNTGSDTVKKQEAAAFLANVGHETG?????????????GLVYVVEQNT-ANYP--HYCDASQP---YGCPAG-NDKYYGRGPVQLS-----------WNFNYKAAGDALGIDLLNNPDLVQNDSAVAWKTGLWYWNTQTGPG-T????????????MTPHDAMVNGAGFGETIRSINGSLECD--GGNPGQVQS-RIDNYERFTQLLG?????VEPGGNLSCATAT?AT Streptomyces_griseus_8 VVSEAQFNQMFPN???????RNAFYTYKGLTDALSAY--PAFAKTGSDEVKKREAAAFLANVSHETG?????????????GLFYIKEVNE-ANYP--HYCDTTQS---YGCPAG-QAAYYGRGPIQLS-----------WNFNYKAAGDALGINLLANPYLVEQDPAVAWKTGLWYWNSQNGPG-T????????????MTPHNAIVNNAGFGETIRSINGALECN--GGNPAQVQS-RINKFTQFTQILG?????TTTGPNLSCATAT?AT Streptomyces_lavendulae_3 LVSEAQFKQMFPK???????RNAFYTYKGLVAALKAY--PGFAGTGSAEVRKQEAAAFLANVAHETG?????????????GLVYVVEQNT-ANYP--HYCDRSRP---YGCPAG-QAAYYGRGPLQIS-----------WNFNYKAAGDALGIDLLHNPSLVQKDAAVSWKTGLWYWNTQRGPG-T????????????MTPHEAMVNHRGFGQTIRSINGALECD--GHNPAQVQS-RVANYQRFTKILG?????VAPGGNLSCATAT?AT Streptomyces_olivaceoviridis_5 VVTEAQFNQMFPN???????RNSFYSYSGLTAALSAY--PGFANTGSDTTKKQEAAAFLANVSHETG?????????????GLVHVVEQNQ-ANYP--HYCDWSRP---YGCPAG-QAAYYGRGPIQLS-----------WNFNYKAAGDALGIDLLNSPWLVERDSAVAWKTALWYWNTQTGPG-T????????????MTPHNAMVNGAGFGQTIRSINGSLECD--GKNPAQVQS-RVNNYQRFTQILG?????VSPGGNLYCATAT?AT Streptomyces_thermoviolaceus_6 VVSEAQFNQMFPN???????RNPFYTYQGLVDALSAF--PGFANTGDDTTKKQEAAAFLANVNHETG?????????????GLQYVVEQNT-ANYP--AYCDWSQP---YGCPAG-QDAYYGRGPIQLS-----------WNFNYKAAGDAIGVDLLNNPWLVENDPAIAWKTGLWYWNTQSGPG-T????????????MTPHDAMVNHAGFGQTIRSINGSLECD--GRNPAQVQS-RVDAYQRFTSILG?????VAPGDNLYCATAT?AT Triticum_aestivum_24 VVTDAFFDGIKSQAADGGCPGKSFYTRQFFLDGAQAN--PDFGKGGTSDDGKREIAAFFAHFTHETG?????????????YMCYIEEKDG----ASQNYCDTN-Y---PLWPCTSGKAYYGRGPLQLT-----------WNYNYGAAGQKLGFNGLDNPEKVAQDPALTFQAAFWFWMTN????????????????????VHQVVP--QGFGETSRKINS-GECN--GGNAPAMNA-RANYYVEYCKQFG?????VDPGNNLTCTTATA?T Triticum_aestivum_41 IISQSLFDQMLLHRNDAACLAKGFYNYGAFVAAANSF--SGFATTGSTDVKKREVAAFLAQTSHETTGGWPTAPDGPYSWGYCFNQER-----GATSDYCTPSSQ-----WPCAPGKKYFGRGPIQIS-----------HNYNYGPAGQAIGTDLLNNPDLVASDATVSFKTALWFWMTPQSPK-PSSHDVITGRWSPSGADQAAGRVPGYGVITNIINGGLECG--RGQDGRVAD-RIGFYKRYCDLLG?????VSYGDNLDCTTTTTTT Vigna_sesquipedalis_48 LIPRATFDQMLKHRNDGACPARGFYTYDAFIAAARAF--PSFGNTGDTATRKREIAAFLGQTSHETTGGWPSAPDGPYAWGYCFVREQ-----NPSA-YCSPTPQ-----FPCASGQQYYGRGPIQIS-----------WNYNYGQCGNAIGVDLINNPDLVATDPVVSFKSAIWFWMTPQSPK-PSSHDVITSQWTPSAADVAAGRLPGYGTVTNIINGGLECG--RGQDSRVED-RIGFFKRYCDLFG?????VGYGNNLDCTTTTTTT Vigna_unguiculata_13 IVTDAFFNGIIDQADSG-CVGKSFYARDAFLSALDSY--TDFGRVGSEDDSKREIAAAFAHFTHETG?????????????HFCYIEEIDG----ASKDYCDEDSI---AQYPCSSSRGYT-VVPIQLS-----------WNFNYGPAGEANNFDGLGPPETVSNDVVVSFKTALWYWMQH????????????????????VRPVIN--QGFAATIRAINGQLECD--GANPSTVQA-RVNYYTEYCRQLG?????VDTGDNLTCTTATA?T Zea_mays_17 VVTSSFFNGIKNQAGSG-CEGKNFYTRSAFLSAVKGY--PGFAHGGSQVQGKREIAAFFAHATHETG?????????????HFCYISEIN-----KSNAYCDPT-K---RQWPCAAGQKYYGRGPLQIS-----------WNYNYGPAGRAIGFDGLGDPGRVARDAVVAFKAALWFWMNS????????????????????VHGVVP--QGFGATTRAMQRALECG--GNNPAQMNA-RVGYYRQYCRQLG?????VDPGPNLTCTTATA?T Zea_mays_18 VVTDAFFNGIKNQAGSG-CEGKNFYTRSAFLSAVNAY--PGFAHGGTEVEGKREIAAFFAHVTHETG?????????????HFCYISEIN-----KSNAYCDAS-N---RQWPCAAGQKYYGRGPLQIS-----------WNYNYGPAGRDIGFNGLADPNRVAQDAVIAFKTALWFWMNN????????????????????VHGVMP--QGFGATIRAINGALECN--GNNPAQMNA-RVGYYKQYCQQLR?????VDPGPNLICTTATA?T ; END; [ The following blocks are output data for analysis step 4474 ] BEGIN TREES; TITLE Tb9246; LINK TAXA = TaxaForAnalysisStep4474; TREE Fig._1.4 = [&R] ((((((Streptomyces_olivaceoviridis_5,(Streptomyces_thermoviolaceus_6,(Nocardiopsis_prasina_7,Streptomyces_griseus_8))),Streptomyces_coelicolor_4),Streptomyces_lavendulae_3),Burkholderia_gladioli_2),(Phytophthora_infestans_1,Glycine_max_51)),(((((((Phaseolus_vulgaris_12,Vigna_unguiculata_13),(Arabidopsis_thaliana_14,(Betula_pendula_15,Betula_pendula_16))),Beta_vulgaris_11),((((Brassica_napus_22,Arabidopsis_thaliana_23),(Arabidopsis_thaliana_25,Triticum_aestivum_24)),(Oryza_sativa_20,Oryza_sativa_21)),((Zea_mays_18,Saccharum_officinale_19),Zea_mays_17))),Beta_vulgaris_10),Picea_glauca_9),(((((Oryza_sativa1BAA9_32,Oryza_sativa_33),Cynodon_dactylon_31),(Arabidopsis_thaliana_34,Arachis_hypogaea_35)),((((Arabidopsis_thaliana_30,Betula_pendula_29),Betula_pendula_28),Arabidopsis_thaliana_27),Oryza_japonica_26)),(((((Persea_americana_42,(Phaseolus_vulgaris_47,Vigna_sesquipedalis_48)),Nicotiana_tabacum_43),((Betula_pendula_45,Betula_pendula_46),Arabidopsis_thaliana_44)),((Pisum_sativum_50,(Pinus_strobus_36,Nicotiana_tabacum_49)),((Betula_pendula_52,Betula_pendula_53),(Betula_pendula_54,Betula_pendula_55)))),(((Secale_cereale_40,Triticum_aestivum_41),Poa_pratensis_39),(Oryza_sativa_37,Oryza_sativa_38)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5294] END; BEGIN TREES; TITLE Tb9246; LINK TAXA = TaxaForAnalysisStep4474; TREE Fig._1.2 = [&R] ((((((Streptomyces_olivaceoviridis_5,(Streptomyces_thermoviolaceus_6,(Nocardiopsis_prasina_7,Streptomyces_griseus_8))),Streptomyces_coelicolor_4),Streptomyces_lavendulae_3),Burkholderia_gladioli_2),(Phytophthora_infestans_1,Glycine_max_51)),(((((((Phaseolus_vulgaris_12,Vigna_unguiculata_13),(Arabidopsis_thaliana_14,(Betula_pendula_15,Betula_pendula_16))),Beta_vulgaris_11),((((Brassica_napus_22,Arabidopsis_thaliana_23),(Arabidopsis_thaliana_25,Triticum_aestivum_24)),(Oryza_sativa_20,Oryza_sativa_21)),((Zea_mays_18,Saccharum_officinale_19),Zea_mays_17))),Beta_vulgaris_10),Picea_glauca_9),(((((Oryza_sativa1BAA9_32,Oryza_sativa_33),Cynodon_dactylon_31),(Arabidopsis_thaliana_34,Arachis_hypogaea_35)),((((((Persea_americana_42,(Phaseolus_vulgaris_47,Vigna_sesquipedalis_48)),Nicotiana_tabacum_43),((Betula_pendula_45,Betula_pendula_46),Arabidopsis_thaliana_44)),((Pisum_sativum_50,Nicotiana_tabacum_49),((Betula_pendula_52,Betula_pendula_53),(Betula_pendula_54,Betula_pendula_55)))),(((Secale_cereale_40,Triticum_aestivum_41),Poa_pratensis_39),(Oryza_sativa_37,Oryza_sativa_38))),Pinus_strobus_36)),((((Arabidopsis_thaliana_30,Betula_pendula_29),Betula_pendula_28),Arabidopsis_thaliana_27),Oryza_japonica_26)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5292] END; BEGIN TREES; TITLE Tb9246; LINK TAXA = TaxaForAnalysisStep4474; TREE Fig._1.1 = [&R] ((((((Streptomyces_olivaceoviridis_5,(Streptomyces_thermoviolaceus_6,(Nocardiopsis_prasina_7,Streptomyces_griseus_8))),Streptomyces_coelicolor_4),Streptomyces_lavendulae_3),Burkholderia_gladioli_2),(Phytophthora_infestans_1,Glycine_max_51)),(((((((Phaseolus_vulgaris_12,Vigna_unguiculata_13),(Arabidopsis_thaliana_14,(Betula_pendula_15,Betula_pendula_16))),Beta_vulgaris_11),((((Brassica_napus_22,Arabidopsis_thaliana_23),(Arabidopsis_thaliana_25,Triticum_aestivum_24)),(Oryza_sativa_20,Oryza_sativa_21)),((Zea_mays_18,Saccharum_officinale_19),Zea_mays_17))),Beta_vulgaris_10),Picea_glauca_9),((((((Oryza_sativa1BAA9_32,Oryza_sativa_33),Cynodon_dactylon_31),(Arabidopsis_thaliana_34,Arachis_hypogaea_35)),(((((Persea_americana_42,(Phaseolus_vulgaris_47,Vigna_sesquipedalis_48)),Nicotiana_tabacum_43),((Betula_pendula_45,Betula_pendula_46),Arabidopsis_thaliana_44)),(((Secale_cereale_40,Triticum_aestivum_41),Poa_pratensis_39),(Oryza_sativa_37,Oryza_sativa_38))),((Pisum_sativum_50,Nicotiana_tabacum_49),((Betula_pendula_52,Betula_pendula_53),(Betula_pendula_54,Betula_pendula_55))))),Pinus_strobus_36),((((Arabidopsis_thaliana_30,Betula_pendula_29),Betula_pendula_28),Arabidopsis_thaliana_27),Oryza_japonica_26)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5291] END; BEGIN TREES; TITLE Tb9246; LINK TAXA = TaxaForAnalysisStep4474; TREE Fig._1.3 = [&R] ((((((Streptomyces_olivaceoviridis_5,(Streptomyces_thermoviolaceus_6,(Nocardiopsis_prasina_7,Streptomyces_griseus_8))),Streptomyces_coelicolor_4),Streptomyces_lavendulae_3),Burkholderia_gladioli_2),(Phytophthora_infestans_1,Glycine_max_51)),(((((((Phaseolus_vulgaris_12,Vigna_unguiculata_13),(Arabidopsis_thaliana_14,(Betula_pendula_15,Betula_pendula_16))),Beta_vulgaris_11),((((Brassica_napus_22,Arabidopsis_thaliana_23),(Arabidopsis_thaliana_25,Triticum_aestivum_24)),(Oryza_sativa_20,Oryza_sativa_21)),((Zea_mays_18,Saccharum_officinale_19),Zea_mays_17))),Beta_vulgaris_10),Picea_glauca_9),(((((Oryza_sativa1BAA9_32,Oryza_sativa_33),Cynodon_dactylon_31),(Arabidopsis_thaliana_34,Arachis_hypogaea_35)),(((((Persea_americana_42,(Phaseolus_vulgaris_47,Vigna_sesquipedalis_48)),Nicotiana_tabacum_43),((Betula_pendula_45,Betula_pendula_46),Arabidopsis_thaliana_44)),((Pisum_sativum_50,(Pinus_strobus_36,Nicotiana_tabacum_49)),((Betula_pendula_52,Betula_pendula_53),(Betula_pendula_54,Betula_pendula_55)))),(((Secale_cereale_40,Triticum_aestivum_41),Poa_pratensis_39),(Oryza_sativa_37,Oryza_sativa_38)))),((((Arabidopsis_thaliana_30,Betula_pendula_29),Betula_pendula_28),Arabidopsis_thaliana_27),Oryza_japonica_26)))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5293] END; BEGIN TREES; TITLE Tb9246; LINK TAXA = TaxaForAnalysisStep4474; TREE Fig._1.5 = [&R] ((((((Streptomyces_olivaceoviridis_5,(Streptomyces_thermoviolaceus_6,(Nocardiopsis_prasina_7,Streptomyces_griseus_8))),Streptomyces_coelicolor_4),Streptomyces_lavendulae_3),Burkholderia_gladioli_2),(Phytophthora_infestans_1,Glycine_max_51)),(((((((Phaseolus_vulgaris_12,Vigna_unguiculata_13),(Arabidopsis_thaliana_14,(Betula_pendula_15,Betula_pendula_16))),Beta_vulgaris_11),((((Brassica_napus_22,Arabidopsis_thaliana_23),(Arabidopsis_thaliana_25,Triticum_aestivum_24)),(Oryza_sativa_20,Oryza_sativa_21)),((Zea_mays_18,Saccharum_officinale_19),Zea_mays_17))),Beta_vulgaris_10),Picea_glauca_9),(((((Oryza_sativa1BAA9_32,Oryza_sativa_33),Cynodon_dactylon_31),(Arabidopsis_thaliana_34,Arachis_hypogaea_35)),((Arabidopsis_thaliana_30,(Betula_pendula_29,(Betula_pendula_28,Arabidopsis_thaliana_27))),Oryza_japonica_26)),(((((Persea_americana_42,(Phaseolus_vulgaris_47,Vigna_sesquipedalis_48)),Nicotiana_tabacum_43),((Betula_pendula_45,Betula_pendula_46),Arabidopsis_thaliana_44)),((Pisum_sativum_50,(Pinus_strobus_36,Nicotiana_tabacum_49)),((Betula_pendula_52,Betula_pendula_53),(Betula_pendula_54,Betula_pendula_55)))),(((Secale_cereale_40,Triticum_aestivum_41),Poa_pratensis_39),(Oryza_sativa_37,Oryza_sativa_38)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5295] END;