#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; 6:35 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 4476 ] BEGIN TAXA; TITLE TaxaForAnalysisStep4476; DIMENSIONS NTAX=45; TAXLABELS Arabidopsis_korshinskyi_45 Arabidopsis_thaliana_44 Arabis_gemmifera_43 Aspergillus_nidulans_14 Bacillus_anthracis_6 Bacillus_circulans_5 Beta_vulgaris_28 Betula_pendula_36 Betula_pendula_37 Candida_albicans_20 Capsicum_annum_42 Cicer_arietinum_32 Coccidioides_immitis_13 Enterococcus_faecalis_8 Glycine_max_26 Glycine_max_31 Hypocrea_virens_16 Listeria_innocua_9 Nicotiana_tabacum_34 Nicotiana_tabacum_35 Oryza_sativa Oryza_sativa_24 Oryza_sativa_27 Oryza_sativa_29 Oryza_sativa_38 Oryza_sativa_39 Oryza_sativa_40 Pseudomonas_aeruginosa_11 Pseudomonas_fluorescens_12 Rhizopus_microsporus_18 Rhizopus_virens_17 Saccharomyces_crevisiae_19 Serratia_marcescens_10 Shewanella_oneidensis_7 Streptomyces_coelicolor_1 Streptomyces_lividans_2 Trichoderma_harzianum_15 Triticum_aestivum_21 Triticum_turgidum_22 Vibrio_cholerae_3 Vigna_unguiculata_25 Vigna_unguiculata_41 Vigna_unguuiculata_33 Xanthomonas_sp_4 Zea_mays_30 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3808] TITLE 'Class III like chitinases, Fig. 3'; LINK TAXA = TaxaForAnalysisStep4476; DIMENSIONS NCHAR=408; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_korshinskyi_45 SRGGIAIYWGQN-GN---------EGNLSATCA-TGRYAYVNVAFLVKFG----NGQTPELNLAGHCN------PAANT-------CT-HFGSQVKYCQSRGIKVMLSLGGG----IGNYSIGSKEDAKVVADYLWNNFLGG----KS--SSRPLG-DAVLDGIDFNIELGS------PQHWDD--------LARSLSKLSH--RG------RK---VYLTGAPQC-PFPD----------RLMGNALNTR---RFDYVWIQFYN-NPP--CSYTS--G--------NTQNL----FDSWNKWTT--S-------ITAQ-KIFLGLPAAPEASGS---G----YIPPDVLTSQILPTLKKS-----------RKYGGVMLWSKFWDD----KD-----GYSSSILATV Arabidopsis_thaliana_44 SRGGIAIYWGQN-GN---------EGNLSATCA-TGRYAYVNVAFLVKFG----NGQTPELNLAGHCN------PAANT-------CT-HFGSQVKDCQSRGIKVMLSLGGG----IGNYSIGSREDAKVIADYLWNNFLGG----KS--SSRPLG-DAVLDGIDFNIELGS------PQHWDD--------LARSLSKFSH--RG------RK---VYLTGAPQC-PFPD----------RLMGSALNTK---RFDYVWIQFYN-NPP--CSYTS--G--------NTQNL----FDSWNKWTT--S-------IAAQ-KIFLGLPAAPEAAGS---G----YIPPDVLTSQILPTLKKS-----------RKYGGVMLWSKFWDD----KN-----GYSSSILASV Arabis_gemmifera_43 SRGGIAIYWGQN-GN---------EGNLSATCA-TGRYAYVNVAFLVKFG----NGQTPELNLAGHCN------PAANT-------CT-RFGSQVKDCQSRGIKVMLSLGGG----IGNYSIGSREDAKVVADYLWNNFLGG----KS--SSRPLG-DAVLDGIDFNIELGS------PQHWDD--------LARSLSKLSY--KG------RK---VYLTGAPQC-PFPD----------RLMGSALNTR---LFDYVWIQFYN-NPP--CSYTS--S--------NTQNL----FDSWNKWTT--S-------ITAQ-KIFLGLPAAPEAAGS---G----YIPPDVLTSQILPVLKKS-----------RKYGGVMLWSKFWDD----KN-----GYSSSILPGV Aspergillus_nidulans_14 AKSNIAVYYGQG-VN---------QPRLAEFCA-ETSYDIINIGFINSFPEQNPLTGLPGSDFGNQCWADT--FVVDGIASQLYSHCP-NIAEDIPKCQAAGKKVFLSLGG---AT-PTYWFDTIDASTKLADFLWGAFGPVTDAWTVADKPRPFG-NAVVDGFDFDIEFFGS-----K-GYAN--------MIKRFRRRFG--EV------PD-QTFYISAAPQC-SIPD----------EQLSVAIKNA---VIDFVWVQFYN-TPG--CSARDFVL--------GTKNG--FNYDSWVEVIKA-G-------ANPNAKLYVGLPASGAAANL---GY---YLT-PEEVKPLVKKYMDKYP---------ETFGGVMLWEATQAR----NNQIDGVGYNEKIREIL Bacillus_anthracis_6 SK-LLVGYWHNFDNGTG---------IIKLRDV-SPKWDVINVSFGETGGD---RS-TVEFSPVYG--------------------TDAEFKSDISYLKSKGKKVVLSIGG-------QNGVVLLPDNAAK-QRFINSIQSL---------IDKYG----FDGIDIDLE-SGIYLNGNDTNFKNPTTPQIVNLISAIRTISDH-YG------PD---FLLSMAPETAYVQGGYSAYRSIWGAYLPIIYGVKD--KLTYIHVQHYNAGSG--IG-MDGNN-----YNQGTADYEVAMADMLLHGFPIGGNANNMFPALRSDQVMIGLPATPAAAPS---GGYISPTEMKKALDYIIKGIPFGGKYKLSNESGYPAFRGLMSWSINWD-----AKN--NFEFSSNYRTYF Bacillus_circulans_5 SK-WLIGYWHNFDNGST---------NIKLRNV-STAYDVINVSFAEPISP---GSGTLAFTPYNA--------------------TVEEFKSDIAYLQSQGKKVLISMGG-------ANGRIELTDATKKRQQFEDSLKSI---------ISTYG----FNGLDIDLEGSSLSLNAGDTDFRSPTTPKIVNLINGVKALKSH-FG------AN---FVLTAAPETAYVQGGYLNYGGPWGAYLPVIHALRN--DLTLLHVQHYNTGSM--VG-LDGRS-----YAQGTADFHVAMAQMLLQGFNVGGSSGPFFSPLRPDQIAIGVPASQQAAG----GGYTAPAELQKALNYLIKGVSYGGSYTLRQPAGYVGLKGIMTWSINWD-----AYT--NNQFSNAHRPFL Beta_vulgaris_28 HGSQIVIYWGQN-GD---------EGSLADTCN-SGNYGTVILAFVATFG----NGQTPALNLAGHCD------PATN--------CN-SLSSDIKTCQQAGIKVLLSIGGG----AGGYSLSSTDDANTFADYLWNTYLGG----QS--STRPLG-DAVLDGIDFDIESGD------GRFWDD--------LARALAGHNN--GQ------KT---VYLSAAPQC-PLPD----------ASLSTAIATG---LFDYVWVQFYN-NPP--CQYDT-----------SADNL----LSSWNQWT---T-------VQAN-QIFLGLPASTDAAGS---G----FIPADALTSQVLPTIKGS-----------AKYGGVMLWSKAYD------S-----GYSSAIKSSV Betula_pendula_36 EAGVITVYWGQN-GN---------EGSLADACA-TGNYGIVNIAFLSTFG----NGQTPSINLAGHCSTN----PATNE-------CTAGFSNDIKACQNQGIKVMLSIGGA----EGSYSLSSADDARSVANYLWNNFLGG----QS--DSRPFG-DAVLDGIDFDIEGGGT-----AEHWDE--------LAKALAEFSQ--Q-------KK---VYLTAAPQC-PFPD????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Betula_pendula_37 ??????????????N---------EGSLADACA-TGNYGIVNIAFLSTFG----NGQTPSINLAGHCSTV----PATNE-------CTAGFSNDIKACQNQGIKVMLSIGGAVVPGGGSYSLSSADDARSVANYLWNNFLGG----QS--DSRPFG-DAVLDGIDFDIEGGGT-----AEHWDE--------LAKALAEFSQ--Q-------KK---VYLTAAPQC-PFPD----------ALLGGALNTG---LFDYV????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Candida_albicans_20 ???NIAAYWGQN-AGG-------DQQTLGDYCS-SSPASIIILSFLDGFP---NLS----LNFANQC-------SGTFS--SGLAHCS-QIGSDIKSCQQQGKTILLSLGG---AT-GNYGFSSDSEAVQFAGTLWNKFGGGK---DS---ERPFD-DAIVDGFDFDIENKDQ-----T-GYAA--------LATQLRKYF---ST------GT-KSYYLSAAPQC-PYPD----------ESVGDLMSQV---DLDFAFIQFYN-NY---CS---------------LNQQ--FNWNSWSNYAR-----------GKSIKLYLGLPGSSSSAGS---G----FVG-LSTVQRVVASIKGD-----------SSFGGISIWDISSAE----NG??????????????? Capsicum_annum_42 S--GIAIYWGQN-GN---------EATLNDTCA-SGNYAYVNLSFLNKFG----NGQTPEINLAGHCN------PAVNG-------CT-ILGPQIKFCQKLGVKVMLSMGGG----VGNYSLASKKDAKDVARYLYNNFLGG----RS--SFRPLG-NARLDGIDFDIELGS------SLYYED--------LAQYLKRYSK--LG------RK---MYLTAAPQC-PFPD----------RLLGTALNTG---LFDNVWIQFYN-NPS--CQYTT--N--------NVDDL----KNSWTRWTT--S-------VNAR-RIFLGLPAAPQAAGS---G----FIPAEVLTGGILPVIKKS-----------RKYGGVMLWSKFWDE----QT-----GYSASIVKSV Cicer_arietinum_32 NAAGIAVYWGQN-GN---------EGSLQDACN-TNNYQFVNIAFLSTFG----NGQNPQINLAGHCD------PSTNG-------CT-KFSPEIQACQAKGIKVLLSLGGG----AGSYSLNSAEEATTLANYLWNNFLGG----TS--TSRPLG-DAVLDGIDFDIESGG------Q-HYDE--------LAKALNGFS----Q------QK---VYLSAAPQC-PYPD----------AHLDSAIQTG---LFDYVWVQFYN-NPQ--CQYSN--G--------NINNL----VNAWNQWT---S-------SQAK-QVFLGVPASDAAAPS---G---GLIPADVLTSQVLPAIKTS-----------PKYGGVMIWDRFNDA----QS-----GYSNAIKGSV Coccidioides_immitis_13 AKSNLAVYWGQG-AG---------QNRLSYFCE-KTSFDIIVVGFINVFPDQGP-AGWPGSNFGNQC-ADSYYYTKNGTKTKLLDGCY-QIKEDLPKCKALGKTILLSLGGG--AVHDFYEVKSEESALNFADFLWGAFGPLTPDWTG---PRPFG-EASVDGFDFDIEKGSN-----F-GYSI--------MVRRLRELFL--QD------PL-NRYYISAAPQC-IMPD----------KYLSHAISNS---AFDFIFIQFYN-NPS--CSAKRWVT--------NPKSVT-YTVDDWVKYIRK-S-------GNPLAKLFIGLPASKSAAAK---ED---YLT-PGEATKIVSTYMAKYP---------STFGGMMVWEATASE----NNKLGGLPYADIMKEVL Enterococcus_faecalis_8 GKKVLVGYWHNWASKGRDGYKQGTSASLNLSEV-NQAYNVVPVSFMKSDGT---T-RIPTFKP-------------YNQ-------TDTAFRQEVAQLNSQGRAVLLALGG-------ADAHIQLVKGDEQ--AFANEIIRQ---------VETYG----FDGLDIDLEQLAITAGDNQTVIPA--------TLKIVKDHYRA-QG------KN---FIITMAPEFPYLK------PG--AAYETYITSLNG--YYDYIAPQLYNQGGD--GVWVDEIM----TWVAQSNDALKYEFLYYMSDSLIHGTRG--YLQIPNDKLVLGLPANRDAAGS---GYVVEATPVAKTFDQL-AKDGNP-------------IRGLMTWSANWDVGQDVNGKSYNNEFATRYSNLV Glycine_max_26 TTGGITIYWGQN-ID---------DGTLTSTCD-TGNFEIVNLAFLNAFG----CGITPSWNFAGHCG-D----WN--P-------CS-ILEPQIQYCQQKGVKVFLSLGGA----KGTYSLCSPEDAKEVANYLYQNFLSG--------KPGPLG-SVTLEGIDFDIELG-S-----NLYWGD--------LAKELDALRH--QN------DHY--FYLSAAPQC-FMPD----------YHLDNAIKTG---LFDHVNVQFYN-NPP--CQYSP--G--------NTQLL----FNSWDDWTSN-V-------LPNN-SVFFGLPASPDAAPS---G---GYIPPQVLISEVLPYVKQA-----------SNYGGVMLWDRYHDV----LN-----YHSDQIKDYV Glycine_max_31 HAAGIAIYWGQN-GG---------EGTLAEACN-TRNYQYVNIAFLSTFG----NGQTPQLNLAGHCD------PNNNG-------CT-GLSSDIKTCQDLGIKVLLSLGGG----AGSYSLSSADDATQLANYLWQNFLGG----QT--GSGPLG-NVILDGIDFDIESGG------SDHYDD--------LARALNSFSS---Q------RK---VYLSAAPQC-IIPD----------AHLDRAIQTG---LFDYVWVQFYN-NPS--CQYSS--G--------NTNNL----INSWNQWI---T-------VPAS-QIFMGLPASEAAAPS---G---GFVPADVLTSQVLPVIKQS-----------SKYGGVMLWNRFNDV----QN-----GYSNAIIGSV Hypocrea_virens_16 SKQNIAVYWGQNSANSQS-----TQQRLSFYCN-DANINVIDIAFLNGIT---P----PMTNFANAG--DR---CTPFSDNPWLLSCP-EIEADIKTCQANGKTIILSLGGD--SYTQGGWSSAS-AAQSAANQVWAMFGPVQSGSTV---HRPFG-SAVVDGFDFDFEATTN-------NLAA--------FGTQLKSRTN--AA------GG-KKYYFSAAPQC-FFPD----------AAVGALINAV---PMDWIQIQFYN-NP---CGVSGFTP--------GTSTQNNYNYQTWENWAKT-S-------PNPNVKLLVGIPAGPTAGRG--------YVS-GSQLT-SVFQYSKQF----------STFAGAMMWDMSQLF----QN----TGFEAQVVNAL Listeria_innocua_9 NKQVLVGYWHSWKSSGKDGYQQGTSADIALKDT-PKAYNVVDVSFMKGDGV---N-RIPTFKP-------------VGI-------NDSDFRAQVGALNKEGRAVLLALGG-------ADGHVELKAGDEQ--AFANEIIRQ---------VETYG----FDGLDIDLEQSAITAGDNKTVIPA--------ALKIVKDHYKA-QG------KN---FLITMAPEFPYLK------PG--SAYESYLTSLAN--YYDYIAPQLYNQGGD--GVWVDETN----QWIAQNNDTLKESFLYYMADSFINGTRG--YLKIPANKFVFGLPANVDAAAT---GYVKDPQIVQNVFNRLQAK-GTP-------------VKGVMTWSVNWDAGKNSAGVAYNNGFSNAYGPIV Nicotiana_tabacum_34 KAGDIVVYWGQD-VG---------EGKLIDTCN-SGLYNIVNIAFLSSFG----NFQTPKLNLAGHCE------PSSGG-------CQ-QLTKSIRHCQSIGIKIMLSIGGG----TPTYTLSSVDDARQVADYLWNNFLGG----QS--SFRPLG-DAVLDGIDFDIELG-------QPHYIA--------LARRLSEHGQ--QG------KK---LYLTAAPQC-PFPD----------KLLNGALQTG---LFDYVWVQFYN-NPE--CEFMS--N--------S-ENF----KRRWNQWT---S-------IPAK-KLYIGLPAAKTAAGN---G----YIPKQVLMSQVLPFLKGS-----------SKYGGVMLWNRKFDV----QC-----GYSSAIRGAV Nicotiana_tabacum_35 EAGDIVIYWGQN-GN---------EGSLADTCA-TNNYAIVNIAFLVVFG----NGQNPVLNLAGHCD------PNAGA-------CT-GLSNDIRACQNQGIKVMLSLGGG----AGSYFLSSADDARNVANYLWNNYLGG----QS--NTRPLG-DAVLDGIDFDIEGG-T-----TQHWDE--------LAKTLSQFSQ--Q-------RK---VYLTAAPQC-PFPD----------TWLNGALSTG---LFDYVWVQFYN-NPP--CQYSG--G--------SADNL----KNYWNQWN---A-------IQAG-KIFLGLPAAQGAAGS---G----FIPSDVLVSQVLPLINGS-----------PKYGGVMLWSKFYDN-----------GYSSAIKANV Oryza_sativa KTGQMTVFWGRN-KN---------EGTLKETCD-TGLYTTVVISFYSVFG----HGRYWG-DLSGHDL-------R-------------VIGADIKHCQSKNIFVFLSIGGA----GKDYSLPTSKSAADVADNIWNAHMDGRR--PG--VFRPFG-DAAVDGIDFFIDQGAP------DHYDD--------LARNLYAYNKMYRA------RTP--VRLTATVRC-AFPD----------PRMKKALDTK---LFERIHVRFYD-DAT--CSYNH--A--------GLAGV----MAQWNKWT-A-R-------YPGS-HVYLGLAAAN--VP----GKND-NVFIKQLYYDLLPNVQKA-----------KNYGGIMLWDRFYDK----QT-----GYGKTVKYWA Oryza_sativa_24 RRRNVVVFWGGN-KN---------EGSLRSVCD-SGLYNIVIISFYSLFG----HGRYWD-DLSGHDL-------R-------------HIGADITHCHFKAVYVLLSIGGGD---GKDYSLPSSKSAADVADNLYNSFLGGSR--PG--VYHPFGDDVTVVGIDFFIDRGQP------DHYYE--------IAERINYDTRHWRD------PIG--FKLTATVSC-AYDDS--------DPRMKKALETY---LFRRIHVRFYD-DPR--CSYNH--A--------GLAGV----MAQWNRWS-A-S-------YPYNGKIYLGLAAAN--LT----GKND-MVAVGELYRKLLPAVQKT-----------DTYGGVMLWNSYYDS----IT-----HYGRYVSAWA Oryza_sativa_27 GGVNIAVYWGQN-GS---------EGTLGETCG-TGLYAYVNLAFLSTFG----AGRAPVLNLADHCD------APSGT-------CA-SLAADIASCQAAGVKVLLSIGGG----ALGYNLSSPSDARDLAAYLWDNFLGGGA--TG--ASRPLG-DAVLDGVDFDIESPS-------RFYDD--------LARNLASLYT--RAPRPPRGGKT--YLLTAAPQC-PYPD----------ASLAAALATG---LFDHVWVQFYN-NPP--CQYAAP-G--------DASAL----RSAWAQWTA--G-------LPAA-TVFLGLPASLDAADS---G----FVDADTLASQVLPVVEGA-----------ANYGGIMLWSRSYDK----DS-----SFSVKLQAAL Oryza_sativa_29 RAGDIAVYWGQN-GD---------EGSLADACN-SGLYAYVMVAFLSTFG----NGQTPVLNLAGHCE------PSSGG-------CT-GQSSDIQTCQSLGVKVILSIGGG----AGSYGLSSTQDAQDVADYLWNNFLGG----SS--GSRPLG-DAVLDGVDFDIETGN------PAHYDE--------LATFLSRYSA--QGGG----KK---VILTAAPQC-PYPD----------ASLGPALQTG---LFDSVWVQFYN-NPP--CQYAN--G--------DASNL----VSAWNTWTG--G-------VSAG-SFYVGVPAAEAAAGS---G----YVAPGDLTSAVLPAVQGN-----------AKYGGIMVWNRFYDV----QN-----NFSNQVKSSV Oryza_sativa_38 RAGDIAIYWGQN-GN---------EGTLAQTCA-TGNYRFVIVAFLPVFG----KGQTPVLNLAGHCD------PASNG-------CT-GVGADIKSCQSLGIKVMFSIGGG----VGNYGLSSRDDAKQVAAYLWNNYLGG----TS--PSRPLG-DAVMDGIDFDIESGG------GMYWDD--------LARYLKAYSR--QGSS----KKP--VYLTAAPQC-PFPD----------ASLGVALSTG---LFDYVWVQFYN-NPP--CQYSSS-N--------GVGNL----ASAWKQWT---S-------IPAG-RVFLGLPAAAEAAGS---G----FVETSDLVSKVLPVVKKS-----------PKYGGIMLWSRYYDG----LT-----GYSDKVKSSV Oryza_sativa_39 QAGSIAIYWGQN-NG---------EGTLADTCA-TGNYKFVNIAFLAAFG----NGQPPVFNLAGHCD------PTNGG-------CA-SQSSDIKSCQSRGVKIMLSIGGG----AGSYYLSSSEDAKNVATYLWNNFLGG----QS--SSRPLG-DAVLDGIDFDIEGGT------NQHWDD--------LARYLKGYSN--SG------RR---VYLTAAPQC-PFPD----------ACIGDALNTG---LFDYVWVQFYN-NPP--CQYSS--G--------STSNL----ADAWKQWL---S-------VPAK-QIFLGLPASPQAAGS---G----FIPADDLKSQVLPVIKSS-----------GKYGGIMLWSKYYDD----QD-----DYSSSVKSDV Oryza_sativa_40 HAGGIAVYWGQN-DG---------EASLAETCA-SGNYEFVIIAFLPKFG----KGQTPRVDLASHCD------PASGG-------CT-GQSKDIRACQRRGVKVLLSIGGG----DGSYGLSSPGDARQVAMYLWNNFLGG----SS--SSRPLG-DAVLDGIDFDIELGG------AKFWDD--------LARDLKSLGR--SGG-----RR---VVLSAAPQC-PFPD----------EWDGGAISTG---LFDAVWVQFYN-NPE--CQFSA-----------GRGAF----MDAWRKWE---S-------VPAG-RLFLGLPASKDAAGT---G----FVPAGELNSRVLPLIRGS-----------PKYGGVMLWSKYYDD----QT-----GYSSAIKSHV Pseudomonas_aeruginosa_11 GKKILMGFWHNWPAGAADGYQQGSFANIALEDV-PSEYNVVAVAFMKGRG-------IPTFQP-------------YNL-------SDAEFRRQVGVLNAQGRAVLISLGG-------ADAHIELHAGQEQ--ALAAEIVRL---------VETYG----FDGLDIDLEQSAIDLADNQRVLPA--------ALKLVREHYAG-QG------KH---FIVSMAPEFPYLH------KN--GKYVPYLQALEG--VYDFIAPQYYNQGGD--GLWVQEANGGKGAWIAQNNDAMKEDFLYYLTESLATGSRD--FVRIPAQRLAIGLPSNVDAAAT---GYVIDPAAVSNAFRRLEAA-GHA-------------IKGLMTWSVNWDDGLNKRGERYNWEFRKRYASLI Pseudomonas_fluorescens_12 GKKILMGFWHNWPAGPSDGYQRGQFANIALENV-PKEYNVVAVAFMKGSG-------IPTFKP-------------FNV-------SDAEFRRQVGVLNSQGRAVLISLGG-------ADAHIELRAGQEQ--PLANEIIRL---------VETYG----FDGLDIDLEQSAIDFAANKTVLPA--------ALKLVKDHYAG-QG------KH---FIISMAPEFPYLT------TS--GKYVGYLQALEG--YYDFIAPQFYNQGGD--GVWVPEANNGNGAWIAQNNDTMKEDFLYYLTESLVTGTRG--FTKIPADKFVIGLPANVDAAAT---GYVIDKTVVGNAMKRLAVK-GHP-------------IKGLMTWSVNWDNGTSKDRVPYDWEFSRRYGPLI Rhizopus_microsporus_18 HGPNVMYYWGQNSAGGSN-----TQASLGTYCE-SGQVDAVLLSFLHVF----NVGGIPEINLSSAC-------AGTYFPNTQLLSCP-AVGADIKKCQDKGVKVILSLGG---AA-GVYGFTSDAQGQQFAQTIWNLFGGGN---SD---TRPFG-DAVIDGVDLDIEGGSS-----T-GYVA--------FVNALRQKF------------S-SNFLIGAAPQC-PFPD----------AILGSVLNSA---SFDYVNVQFYN-NY---CS-A-------------TGSS--FNFDTWDNWAKTTS-------PNKNVKIMFTVPGSSTAAGS---G----YVP-MSTLQTIVPSLASKY----------SSYGGVSVWDASQAW----NN----GGFNSQLYSLV Rhizopus_virens_17 NGVNVMYYWGQNSAGGSN-----TQGSLVSYCQ-SGQVDVIILSFLNKF----NMGGLPEINLASAC-------EQTFFPNTNLLHCP-TVGSDIKTCQSNGVKVLLSLGG---AA-GSYGFSSDSEGQTFAETIWNLFGGGT---SD---TRPFD-DAVIDGIDLDIEGGSS-----T-GYAA--------FVTALRSK---------------GHFLIGAAPQC-PFPD----------AILGSVIDAV---GLDFVNVQFYN-NV---CSVA-------------SGSS--FNFDVWNDWAKNKS-------PNKNIKVMLTVPGSSTAAGS---G----YAS-IAELGPIVSSVISQY----------SSFGGVSVWDASQAW----NN----NGFHSELYSIV Saccharomyces_crevisiae_19 ANTNIAVYWGQN-SAG-------TQESLATYCE-SSDADIFLLSFLNQFP---TLG----LNFANAC-------SDTFS--DGLLHCT-QIAEDIETCQSLGKKVLLSLGG---AS-GSYLFSDDSQAETFAQTLWDTFGEGTG--AS---ERPFD-SAVVDGFDFDIENNNE-----V-GYSA--------LATKLRTLF---AE------GT-KQYYLSAAPQC-PYPD----------ASVGDLLENA---DIDFAFIQFYN-NY---CS---------------VSGQ--FNWDTWLTYAQTVS-------PNKNIKLFLGLPGSASAAGS---G----YISDTSLLESTIADIASS-----------SSFGGIALWDASQAF----SN----E-LNGEPYVEI Serratia_marcescens_10 ?KKILMGFWHNWAAGASDGYQQGQFANMNLTDI-PAEYNVVAVAFMKGQG-------IPTFKP-------------YNL-------SDAEFRRQVGVLNSQGRAVLISLGG-------ADAHIELKTGDED--KLKDEIIRL---------VEVYG----FDGLDIDLEQAAIGAANNKTVLPA--------ALKKVKDHYAA-QG------KN---FIISMAPEFPYLR------TN--GTYLDYINALEG--YYDFIAPQYYNQGGD--GIWVDELN----AWITQNNDAMKEDFLYYLTESLVTGTRG--YAKIPAAKFVIGLPSNNDAAAT---GYVIDKQAVYNAFSRLDAK-NLS-------------IKGLMTWSINWDNGKSKAGVAYNWEFKTRYAPLI Shewanella_oneidensis_7 QAGVVVGYWHNWCGGA--GYKGGVAPCVSLAQV-NPQYNVVDISFMKVYGA---TGSIPTFKLDPA----------VGL-------SEAQFIDQIGELNRQGRAVLIALGG-------ADAHIELRKGQEH--DLANEIIRL---------VEKYG----FDGLDIDLEQAAVTAADNQIVIPA--------ALRIVKDHYRK-QQ------KN---FLITMAPEFPYLT------TG--GKYVPYINALEG--YYDWINPQFYNQGGD--GIYIEGIG-----WIAQNNDSLKQEFIYHISDALVNGTNG--FTKIPHDKLVFGIPTNIDAAAT---GYVSDPNALFAAFEQLKNQ-GQP-------------LRGLMTWSVNWDMGKNAAGQAYNESFIKAYGPFI Streptomyces_coelicolor_1 PKHAVTGYWQNFNNGAT---------VQKISDV-PSAYDIIAVAFADATTT----PGAVTFNLDSAGLG--------GY-------TVDQFKADVRAKQAAGKKVIISVGG-------EKGTVSVNSSASA-TNFANSVYSV---------MREYG----FDGVDIDLE-NG--LNPT---YMT----------QALRALSAK-AG------PD---MILTMAPQTIDMQ----STQG--G-YFQTALNVKD--ILTVVNMQYYNSGTM--LG-CDGKV-----YAQGTVDFLTALACIQLEG----G--------LAPSQVGLGLPASTRAAG----GGYVSPSVVNAALDCLTKATNCG---SFKPSKTYPDLRGAMTWSTNWD-----ATA--GNAWSNSVGAHV Streptomyces_lividans_2 PKHAVTGYWQNFNNGAT---------VQKISDV-PSAYDIIAVAFADATTT----PGAVTFNLDSAGLG--------GY-------TVDQFKADVRAKQAAGKKVIISVGG-------EKGTVSVNSSASA-TNFANSVYSV---------MREYG----FDGVDIDLE-NG--LNPT---YMT----------QALRALSAK-AG------PD---MILTMAPQTIDMQ----STQG--G-YFQTALNVKD--ILTVVNMQYYNSGTM--LG-CDGKV-----YAQGTVDFLTALACIQLEG----G--------LAPSQVGLGLPASTRAAG----GGYVSPSVVNAALDCLTKATNCG---SFKPSKTYPDLRGAMTWSTNWD-----ATA--GNAWSNSVGAHV Trichoderma_harzianum_15 SKQNIAVYWGQNSANSQS-----TQQRLSFYCN-DANINVIDIAFLNGIT---P----PMTNFANAG--DR---CTPFSDNPWLLQCP-EIEADIKTCQANGKTILLSLGGD--SYTQGGWSSTG-AAQSAADQVWAMFGPVQSGSSV---HRPFG-SAVVDGFDFDFEATTN-------NLAA--------FGAQLKSRTN--AA------GG-KKYYFSAAPQC-FFPD----------AAVGALINAV---PMDWIQIQFYN-NP---CGVSGFTP--------GTSTQNNYNYQTWENWAKT-S-------PNPNVKLLVGIPAGPGAGRG--------YVS-GSQLT-SVFQYSKGF----------STFAGAMMWDMSQLY----QN----TGFETQVVNAL Triticum_aestivum_21 KTGQVTVFWGRN-KA---------EGSLREACD-SGMYTMVTMSLLDVFGA---NGKYHL-DLSGHDL-------S-------------SVGADIKHCQSKGVPVSLSIGGY----GTGYSLPSNRSALDLFDHLWNSYFGGSK--PS--VPRPFG-DAWLDGVDLFLEHGTP-----ADRYDV--------LALELAKHN--IRG------GPGKPLHLTATVRC-GYPP---------AAHVGRALATG---IFERAHVRTYESDKW--CNQN---L--------GWEG-------SWDKWT-A-A-------YPAT-RFYVGLTADD--KS------HQ-WVHPKNVYYGVAPVAQKK-----------DNYGGIMLWDRYFDK----QT-----NYSSLIKYYA Triticum_turgidum_22 QTGQLTVFWGRN-AG---------EGTLREACD-TGLYSTVVISFYSVFG----HGRYWG-DLSGHPL-------A-------------GVGADIKHCQSRNILVLLSIGGP----RNGYSLPSSASATAVADNLWNAHLGGRR--NG--VYRPFG-DAAVDGIDFYIDQGAP------DHYDE--------LASRLDGHNRFYRG------RKG--VRLTATPRC-GLPD----------PRLGAALRTG---LFERIHVRFYG-NDS--CSLGK--G--------DTYGV----VEQWEKWT-A-A-------FPRT-QVYLGLAPAESGVPEWAQG-TV-AVYLKYLYYDLLPKVQKA-----------NNYGGVMVWDRFTDK----KT-----RWSSVVSGWA Vibrio_cholerae_3 KKHRLIGYWHNFVNGAGC--------PIRLADM-SQAWDVIDIAFAENDRN---STGTVHFNLYAGDIYS----SCPAL-------DPAQFKQDMKALQAKGKVFVLSLGG-------AEGTITLNTDQDE-ANFVSSLTAL---------IKEWG----FDGLDVDLE-SGSNLVHG-SQIQA-------RLGRALKQIEKN-IG------GD---MFLTMAPEHPYVQGGMVAYSGIWGAYIPVINEVRD--TLDILHVQLYNNGGL--PNPYTPSA-----APEGSVDMMVAQSKMLIEGFTLAN--GTRFEPLRDDQVAIGLPSGPSSAN----SGQAPTQNILDALDCLTKGTRCG---TIKPAFAYPNYAGVMTWSINWD-----KHD--GFNFSKPVGDKL Vigna_unguiculata_25 ?NGGIAVYWGQD-AR---------EGNLIATCD-SGKYAIVLLAFLHQFG----AGRTPTLNFAGHCG-D----SSGRS-------CG-LLQPQINYCQAKGIKVLLSIGGP----TGGYWLSSAEDAKDVANYLFINFLSG--------EFGPLG-SVMLDGVDFHVET--S-----EDYWDD--------LARELDLLRQ--TT------GRY--FYLSAAPQCPTDPI----------PYLGKAIATN---LFDYIFVQFYD-NPS--CSYTD--G---------TSAL----LESWDKWVDS-V-------ASNN-SLFVGVPAAPSAG-----D---GYIPPEVLNDEVLPHAKEA-----------SNYGGVMLWDRYRDV----QN-----GYSDSIMSNV Vigna_unguiculata_41 ???GIAIYWGQN-GN---------EGTLSEACD-TGRYTHVNIAFLNKFG----NGQTPEMNLAGHCN------PATNS-------CT-KFSAQIKYCQSKNIKVLLSIGGG----IGTYTLASVEDAGTVSTFLWNTFLGG----HS--STRPLG-DAELDGIDFDIEQGS------TQNYDH--------LARFLKAYSK--KG------KKR--VYLGAAPQC-PIPD----------RFLGTALDTG---LFDFVWVQFYN-NPP--CQYAD--G--------NVTNL----LNSWKRWTS--T-------VPAG-KIFLGLPAPPAAAGS---G----FVPADVLTSKILPVIKKS-----------RKYGGVMLWSRFFDV----QN-----GYSTSIIGSV Vigna_unguuiculata_33 ????ISVYWGQN-GN---------EGSLADACN-TGNYKYVNIAFLSAFG----GGQTPQLNLAGHCN------PSINN-------CN-VFSDQIKGCQSRGIKVLPSLGGA----SGSYSLSSADDATQVANYIWNNFLGG----QS--SSRPLG-DAVLDGVDFDIEAGS------GNHWDD--------LARSLKGNN-----------SQ---LLLAAAPQC-PIPD----------AHLDSAIKTG---LFDYVWVQFYN-NPP--CQYSS--G--------NTNSL----ISSWNQWT---S-------SQAK-QLFLGVPASTAAAGS---G----FIPANDLISQVLPAIKGS-----------SKYGGVMLWD?????????????????????????? Xanthomonas_sp_4 PRHALVGYWHNFTNPSGP--------TIPISQV-SNDFDVI-VRFGDDAGN-----GAVSFTVDPG-----------AG-------TEAQFKADVAAARARGKKVVLSLGG-------QNGTVTLNNATQV-ANFVNSMEDL---------IRYYG----FDGVDIDLE-SGAGVYHG-AAVQT-------NLVAAIKQLSAR-IG------PS---FYLSMAPEHPYVQGGFVAYSGIWGAYLPIIDGLRQ--ELDLIHVQYYNNGAL--YTPYSQNG-----LPEGSVDMLVGASLMLIEGFRTNNNTGVVFNGLRPDQVALGLPSGPSSAN----SGQASSATIANALNCLTRLQNCG---TIRPQQAYPTFRGVMTWSINWD-----RRD--GFIFSRPVRATL Zea_mays_30 SAGNIAVYWGQN-GN---------EGSLADACN-SGLYAYVNIAFLTTFG----NGQTPVLNLAGHCD------PGSGS-------CT-GQSSDIQTCQSLGIKVLLSIGGA----SGSYGLSSTDDANSVADYLWDNFLGG----SG--SSRPLG-AAVLDGIDFDIENGQ------SAHYDD--------LANALK-------GKG----S----VLLTAAPQC-PYPD----------ASLGPALQTG---QFDNVWIQFYN-NPG--CAYAN--G--------DDTNL----VNAWNTWTS--S-------ITAG-SFYLGVPASPQAAGS---G----TSTP-ALTGTVIPAIRGI-----------GNYGGIMVWDRFNDV----QN-----NYSSQVKGSV ; END; [ The following blocks are output data for analysis step 4476 ] BEGIN TREES; TITLE Tb9248; LINK TAXA = TaxaForAnalysisStep4476; TREE Fig._3 = [&R] (((((((((Glycine_max_31,(Cicer_arietinum_32,Vigna_unguuiculata_33)),((((Betula_pendula_36,Betula_pendula_37),Nicotiana_tabacum_35),Nicotiana_tabacum_34),(((Oryza_sativa_39,Oryza_sativa_40),Oryza_sativa_38),((((Arabidopsis_thaliana_44,Arabidopsis_korshinskyi_45),Arabis_gemmifera_43),Capsicum_annum_42),Vigna_unguiculata_41)))),(Oryza_sativa_29,Zea_mays_30)),Beta_vulgaris_28),Oryza_sativa_27),(Vigna_unguiculata_25,Glycine_max_26)),((Triticum_turgidum_22,(Oryza_sativa,Oryza_sativa_24)),Triticum_aestivum_21)),((Coccidioides_immitis_13,Aspergillus_nidulans_14),((Trichoderma_harzianum_15,Hypocrea_virens_16),((Rhizopus_virens_17,Rhizopus_microsporus_18),(Saccharomyces_crevisiae_19,Candida_albicans_20))))),(((Vibrio_cholerae_3,Xanthomonas_sp_4),((Bacillus_circulans_5,Bacillus_anthracis_6),(((Serratia_marcescens_10,(Pseudomonas_aeruginosa_11,Pseudomonas_fluorescens_12)),(Enterococcus_faecalis_8,Listeria_innocua_9)),Shewanella_oneidensis_7))),(Streptomyces_coelicolor_1,Streptomyces_lividans_2))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3092] END;