NEXUS [File created by TreeBASE: 7/26/07 21:03:14] [Matrix accession#: M1601] BEGIN TAXA; TITLE M1601; DIMENSIONS NTAX=36; TAXLABELS Antirrhinum_majus_cyc Antirrhinum_majus_dich Besleria_labiosa_Gcyc1 Calceolaria_arachnoidea_Ccyc1 Calceolaria_arachnoidea_Ccyc2 Chrysothemis_pulchella_Gcyc1 Cyrtandra_apiculata_Gcyc1 Cyrtandra_apiculata_Gcyc2 Didymocarpus_citrinus_Gcyc1C Didymocarpus_citrinus_Gcyc1D Epithema_benthamii_Gcyc1 Epithema_benthamii_Gcyc2 Fieldia_australis_Gcyc1E Fieldia_australis_Gcyc1F Gesneria_humilis_Gcyc1 Jovellana_punctata_Ccyc2 Kohleria_eriantha_Gcyc1 Loxostigma_sp._Gcyc1C Loxostigma_sp._Gcyc1D Mitraria_coccinea_Gcyc1E Napeanthus_reitzii_Gcyc1 Nicotiana_tabacum_cyc1 Nicotiana_tabacum_cyc2 Paulownia_tomentosa_Pcyc1 Paulownia_tomentosa_Pcyc2 Ramonda_myconi_Gcyc1 Ramonda_myconi_Gcyc2 Schizanthus_x_wisetonensis_cyc1 Schizanthus_x_wisetonensis_cyc2 Scrophularia_canina_Scyc1 Scrophularia_canina_Scyc2 Sinningia_schiffneri_Gcyc1 Streptocarpus_holstii_Gcyc1A Streptocarpus_holstii_Gcyc1B Tetranema__mexicanum_Tcyc2 Titanotrichum_oldhamii_Gcyc1 ; END; BEGIN CHARACTERS; TITLE M1601; DIMENSIONS NCHAR=340; FORMAT DATATYPE = PROTEIN SYMBOLS = " 1 2 3 4 " MISSING = ? GAP = - ; MATRIX Antirrhinum_majus_cyc MLGFDKPSKTLDWLLTKSKTAIKEL---VQSK--------ST---KSN---SSSPCD-DCE-EVVSV-----D--SENVT----D-HSKGK-SL--KA-------NNKCKE-AMDSHQAA---AKESRAKARARARERTKEKMCIKQLNEAI--------------VL-----RNH-QFEV----SGTR--------------------------E------A-----------FV----------HP--VFGFHQQN-----------YG-NASH-------------------ENWD-QSNLS-----------------SQSNQLCAIL--NQHKFI Antirrhinum_majus_dich MLGFDKPSKTLDWLLTKSKEAIKEL---VQSK--------SS---KSN--ISNSPS--ECDQEVLSA-----DLP-----YI---GSSKGKAAVGLNS--------NKCKG-GRD----AVDLAKESRAKARARARERTKEKMCIKQLNQE-RN-KS-YE-W-NPSVL-FQSK-SSQQFEV----SGPS-----------------------TN-----------YEELNQ-ESIMIKRKLK--QNHP-SMFGF-QPE----------------------------------NATENWDYYSNFT-----------------SQSNQLCAIL--DQHKFI Besleria_labiosa_Gcyc1 MLGFDKPSKTLEWVLKKSKAGIKEL---VQTKENSGNANASASAAKS----ISSPS--EC--EVVSAG-NYGEAPYENGSYVACAADSRKK-----------------------DPQKNVLNLAKMSRAKARARARERTREKMCIKKFNES-RNNMCGPDHLINPSSSSIHS-RN-DMFEVC--PM-SN--------------------------VASSAAAAPN-EDLIQ-ESIVIKRMLK----HPSSFFGF-QQNL-IISRDL--NCT-LPSP----------------NVSDNWD-ISSFN-----------------SQSN-LCDIL--DQHKFI Calceolaria_arachnoidea_Ccyc1 MLGFDKPSKTLEWLLTKSKSAIKE------TK-E-----------KC---TSSSPS--EC----VSAG-N-GE-------FL----DSKGK-S----------------KGSGKE----ALNLAKESRDKERARARERTREKMNLKKLDES-----------------------N-QVFD---------------------------HFPS-SS---------TA-EDLIR-ESILVKRMMR----HP-SIFGF-QQND-TVSRH--SNFNNFQSH----------------NVNENWD-LSNLN-----------------SQSN-LSDIL--DQHKFI Calceolaria_arachnoidea_Ccyc2 MLGFDKPSKTLDWLLTKSKAAIKEL---VQNK-Q-------GTD-KN-------IY--ECD-EV-----------IENGN------ISKRK-S--------------KCKGVVKDP---ALNSVKESRDKARARARERTREKVNAKKIDEC-RNNMCSSD-L------------N-NMF-------SSN-------------------FSL-PN-E-----AVVT-EDFTQ-ESILIKRMMK----NP-SIFGF-QQNI-GG--------S-FPCPN---------------NVGENWD-MSSLN-----------------SQTN-LCDIL--DQHKFI Chrysothemis_pulchella_Gcyc1 MLGFDKPSKTLDWLLTKSKAAIKEL---VQAK-KS----GSGSA-KS----ISSPS--EC--EVVSAG-N-GET-FENGSYL--DADSKKK-SLPVNP-------NYKCKEYSKDPQQSALNLAKVSRAKARARARERTREKMCIKKLNES-RS-MD-PD-L-NPSNQ-IQ---------------------------------PTLHCPL-TNNV----PAATT-EDLIQ-ESIVIKRMLK---QYP-PFFGF-QQNL-IISRDL--NCH-LPSP----------------NINDNWD-INSLT-----------------SQSN-LCDIL--DQHKFI Cyrtandra_apiculata_Gcyc1 MLGFDKPSKTLEWLLTKSKVAIKDL---VHTK-KS------SSA-RS----TSSPS--EC--GVVL---N-GEA-FENGSCLL-GADLKRK-SVSMNA--------NKCKG-AKDPTQSASTLAKESRAKARARARERTKEKMCIKKQNES-RN-MC-SN-L-NPSVP-IQ--RN-NLFEVCR-PFASN---------------SILHCPI-TN-EATASTVAATHEDLIQ-ESNVIKRMLR---HHS-SFFGF--------------HCS-LPSP----------------NVNENWD-VSSLT-----------------SQSN-FCDIL--DQHKFI Cyrtandra_apiculata_Gcyc2 MLGFDKPSKTLEWLLTKSKTAIKEL---VQIK-KS---DAPTCTNKR----ISSPS--GC--EV-----I-E---LENGNYL--DADYNGN-LVPANT--------YRCRR-AKDAQQDVWNLAKDSRAKARTRARERTREKMCMKKLTES-SN-MA-SD-L-NLSIP-SQA-RK-SFSEVCKVPP-SN-------------TEPRLHFPL-TN------TAAAT-EDLIQ-ESLVIRRMLK----HN-SMLGF-QQN-----------------------------------VNQNWD-ISSLT-----------------ARSN-LCDIL--DQHKFI Didymocarpus_citrinus_Gcyc1C MLGFDKPSKTLDWLLTKSKVAIKDL---LHTK-KS------SSA-RS----TSSPS--EC---VGL---N-GKD-FEYGSRLL-PADSKRK-SELMNA--------NKCKG-AKDPTQSASTLSKESRAKARARARERTKEKMCIKKLNES-RN-L------------------N-SLFEVHR-PSSSN-------------SQPILHCPI-SN-EATAATVAAT-EHLIQ-ESNVVKRMLRHHYYHP-SFFGF--------------HCS-FPSP------------------NENWD-VSSLT-----------------SQTN-FCDIL--DQHKFI Didymocarpus_citrinus_Gcyc1D MLGFDKPSKTLEWLLTKSKVAIKDL---VHAK-KS------SSA-RG----TSSPS--EC--EVVL---N-GEA-FENGTCLV-GADSKRK-WVSINA--------NKCKG-AKDPSQSASTLAKESRAKARARARERTKEKMCIKQLNES-RN-MG-SI-L-NPSVP-IQ--RN-NLFEVCR-PSASN---------------SILLCPI-TS-EATTATVAATHEDLIQ-DSNVIKRMLR---HHS-SFFGF--------------HCS-LPAP----------------NVNEDWN-VSSLT-----------------SQSN-FCDIL--DQHKFI Epithema_benthamii_Gcyc1 MLGFDKPSKTLEWLLTKSKAAIKDL---VLSK-KC----ASSSA-KS----TSSPS--E----VV----N-GED-FETGNSLV--ADSKRK-LVVT-----------RCRG-GKDPQLAVPNHEKESRAKARARAMERTKEKMCMKKLNET-RN-LG-PD-V-NPAMP-MQ---------------------------------PIFQCPL-TN-E----AASN--EDLIQ-ESFTVRRMSK---HQP--FFGF-QQ-------------------------------------NENWD-ITSLP-----------------SQSN-LCDIL--DQHKFI Epithema_benthamii_Gcyc2 MLGFDKPSKTLEWLLTKSKAAINEL---VQMK-KS---TTSTST--S-------AR--EC--QAPSTG-NDTQA-LENG---------------------------NKCKR-GKDLP---LNVAKESRVKARARARERTQEKMCIKKLNES-RN-L-SSG-L-HSSDP-IQS-RN----------------------------------HL-NN-I----SAASS-DDLIQ-ESVLIKRMLK----DP-SFFGF-QENL-IISRDL--SYS-IPYD----------------SANENWD-ISTLS-----------------EQSN----IL--DQHKFI Fieldia_australis_Gcyc1E MLGFDKPSKTLEWLLTKSKAAIKEL---MQTK-KR----ASASA-KS----ISSPS--EC--EVVSAG-N-GEA-FENGNYL--DADSKRK-SVLLNA--------YKCKE-AKDPQQAALNLAKVSRAKARARARERTREKMCIKKLNES-RN-LD-PD-L-NPSNP-IQF-RN-NLFEICKL-SASN-------------SEPILHCPL-TN-V----AAAAT-EDLIQ-ESIVIKRMLK----HP-SFFGF-QQNL-IISRDL--NCS-LPSP----------------NINDNWD-ISSLT-----------------SQSN-LCDIL--DQHKFI Fieldia_australis_Gcyc1F MLGFDKPSKTLEWLLTKSKSAIKEL---VQTK-KS----GSASA-KS----ISSPS--ES--EVVSAG-N-GEA-FENGNYV--GAD-----DRPLNYQKNFKLNAYNCKE-AKDPQQAAINLAKVSRSKARARARERTREKMCIKNLNES-RN-MD-LD-L-NPS-T-IQS-RN-NLFEVCKL-SASN-------------IQPLLHCPL-TN-E----TAAAT-EDLIQ-ESIVIKRMLK----HP-SFFGF-QQNL-TISRDL--NCS-LPSP----------------NINDNWD-INSLT-----------------SQSN-ICDIL--DQHKFI Gesneria_humilis_Gcyc1 MLGFDKPSKTLDWLLSKSKAAIKEL---VQAK-KS----GSGSA-KC----ISSPS--EC--EVVSAG-T-GET-FENVSYL--DADSKKK-SLSLNP-------IYKCKEYSKDPQQSALNLAKVSRAKARARARERTREKMCIKKLNES-RN-MD-PD-L-NPSNQ-IQ---------------------------------PTLHCPL-TNSV----PAATT-EDLIQ-ESIVIKRMLK---QYP-SFFGF-QQNL-IMSRDL--NCN-LPSP----------------NINDNWD-INSLT-----------------SQSN-LCDIL--DQHKFI Jovellana_punctata_Ccyc2 MLGFDKPSKTLEWLLTTSKADIKEL---VQTK-Q-------STA-KN-------IS--EC--EAVS---N-GEV-LENGNCVW--ADLKRK-S--------------KCIG-VNDP---ALNLAKESRDKARARARERTREKVNAKKLDEC-RRNMGSSD-L------------N-NLF---------NT-----------------HFPL-PN-E-----AAAT-EDFTQ-ESVLIKRMMK----LP-SIFGF-QQNL-SS--------S-FPCS----------------NVGENWD-ISNLN-----------------SQSN-RCDIL--DQHKFI Kohleria_eriantha_Gcyc1 MLGFDKPSKTLDWLLTKSKAAIKEL---VQAK-KS----GSGSA-KS----ISSPS--EC--EVVSAG-T-GET-FENGSYL--DADSKKK-SLPLNS-------NYNCKEYSKDPQQSALNLAKVSRAKARARARERTREKMSIKKLNES-RN-MN-PD-L-NPSNQ-IQ---------------------------------PTLHCPL-TNSV----PAATN-EDLIQ-ESIVIKRMLK---QYP-SFFGF-QQNL-IISRDL--NCN-LPSP----------------NINYNWD-VNSLT-----------------SQSN-LCDIL--DQHKFI Loxostigma_sp._Gcyc1C MLGFDKPSKTLEWLLTKSKAAIKDL---VHTK-KS------SSS-RS----TSSPS--EC--EVVL---N-REA-FEFGSCLL-PADSKRK-SVLMNA--------NKCKG-AKDPTQSASTLAKESRAKARARARERTKEKMGIKKLNES-RN-M------------------N-NLFEVCR-PSASN-------------IQPILHCPI-TN-EATADTVVAT-KHLIQ-ESNVVKRMLR---HHP-SFFGF--------------HCS-LPST----------------NVNDNWD-VSSLT-----------------SQSN-FCDIL--DQHKFI Loxostigma_sp._Gcyc1D MLGFDKPSKTLEWLLTKSKVAIKDL---VHTK-KS------SSA-RS----TSSPS--EC--EVVL---N-DEA-FENGSYLL-GADSKRK-WVSMNA--------NKCKG-AKDPTQSASTLAKESRAKARARARERTKEKMCIKKLNES-RN-MG-SN-L-NPSVP-IQ--RN-NLFEVCR-PSASN---------------SFLHCSI-TN-EATAATVAATHEDLIQ-ESNVIKRMLR---HHS-SFFGL--------------YCS-LPSP----------------NVNENWD-ASSLT-----------------SQSN-FCDIL--DQHKFI Mitraria_coccinea_Gcyc1E MLGFDKPSKTLEWLLTKSKAAIKEL---VQTK-KS----ASASA-KS----ISSPS--EC--EVVSAG-N-GEA-FENGNYL--GADSNRK-SVLLNA--------YKCKE-AKDPQQPALNLAKVSRAKARARAREGTREKMCIKKLNES-RY-MD-PD-S-NPSNP-IQS-RN-NLIEICKS-SASN-------------SEPILHCPL-TN-V----AAAST-EDLIQ-ESIVIKRMLK----HP-SFFGY-QQNL-IISRDL--NCS-LPSP----------------NINDNWD-ISSLT-----------------SQSN-LCDIL--DQHKFI Napeanthus_reitzii_Gcyc1 MLGFDKPSKTLEWLLTKSKAAIKEL---VHTK-KS----ASASA-KS----NSSPS--EC--EVVSAG-N-GEA-FDYGNYL--GADSKKK-SALMNA--------YKCKG-PKDPQQAALNLAKESRAKARARARERTREKMSIKKLNES-IN-LV-PD-L-NPSNP-IQS-TN-NPFD--------------------------LHCPL-TN-V----AAPET-EDLIQ-ESIVIKRMLK----HP-SFFGF-QQNL-IISRDL--NCS-LPSA----------------NINENWD-ISSIT-----------------SQSN-LCDIL--DQHKFI Nicotiana_tabacum_cyc1 MLGFDKPSKTLDWLFTKSKLAIEELTT-AQIK-ITS-PNESSAAKKST-SSIN----SECE-DVVLA--------------------------------------RAKQEE------AILNLVARESRAKARARARERTIKKIWAQI--EA-KLN--------SSSVV-----KEQTKID--------------------EI-----------------------KEM-IH-GSVLVERKNI---------------------KSSSSTWVFITRISVVLKRLQLIRTTIAPLLPEIGI------MM------------------------L-IEQ---- Nicotiana_tabacum_cyc2 ILGFDKPSKTLDWLFTNSKLAIEELANWSTH--QDHHPK-IAGATKSSCNETAKDCASQCE-DLAIT---------TN-------EGSERK--------------PKRAKE-KKEVKDDLVLVARESRAKARARARERTIKKMWSRI--ETSQRS--TSQ-L-IRSSF------HPNF--------------------SAPI------------------------------ES------------------------STTYYGSSSFN-------------------------TENLD--KGTT-SE-LQ----GRW-------KQL-DSCHSNQ---- Paulownia_tomentosa_Pcyc1 MLGFDKPSKTLDWLLTKSKTAIKHL---VQTK-QH----TTAGA-KS----VSSPS--EC--EVESEG-N-GEA-FENGKSL--GADSKGK-SVMMKA--------NKHKG-GKDPQQAALNLAKESRVKARARARERTREKLCIKQLNES-RN-TG-YD-L-NPSIP-IQY-MN-NQLEVCKI-SGSTS------KVDAGI----LHCPP-TY-E------AATHEDLIQ-ESIVIKRKVK----HP-SIFGF-QPNH-IISRDSSSNYS-IPSPY---------------NSTENWD-ISNFT-----------------SQSN-ICAIL--DQHKFI Paulownia_tomentosa_Pcyc2 MLGFDKPSKTLDWLLTKSKAAIKEL---VQTK-QN----ASASA-KSS----SSSS--EC--ELLSSVGN-GDV-FEYGNSL--GAGSKRK-F-G-----------NKHKG-AKDPQQAASNLAKESRAKARARARERTREKMCIKQLNGA-RN-TG-SD-L-NPSIP-MQY-RN-NQLEVFQLSAGSSSNNLSCLKANAGIREPIFHCPL-TN-E------AAT-EDLIQ-ESIVIKRKSK----NP-SFFGF-QQNL-IVSRDLSSNYG-IPSA----------------NTTENWD-ICSFT-----------------SQSN-LCAIL--DQHKFI Ramonda_myconi_Gcyc1 MLGFDKPSKTLDWLLTKSKVAIKDL---VHTK-KSSS--PSASA-RG----ISSPS--EC--EVVL---N-GE-------------DSKKK-----------------SKE-AKDPTQIASTLAKESRAKARARARERTKEKMCIKKLNES-GK-MV-SH-L-SPTI-------------------------------------PI-HCPIMTD-E------ATN--DMIQ-ESNLIKRMMR---PHP-SIFGF--------------HR----------------------DVNENWD-ISSLT----------------SSQSN-FCDIL--DQHKFI Ramonda_myconi_Gcyc2 MLGFDKPSKTLEWLLTKSKAAIKEL---VQMK-KN---DSTTCTNMS---VVSSPS--DC--D---------------GNYI--DPDSNA----PANYFA------YGCGR-TKDPQQDVMNLAKESRAKARARARERTREKMCKKKLNDS-RN-MASPSSL-NFPLA-----NN-------------------------------------TA-A----AAAAT-EELIH-ESLVIRRMLK--QNH--SNFGF-HQN-----------------------------------LNQNWD-MSNLT-----------------AQSE-LCDIL--DQHKFI Schizanthus_x_wisetonensis_cyc1 MLGFDKPSKTLDWLFTNSKLAIDDL---------------ITRA-KS---AIS-----QC-HEETI----------NEAN-----PPAKTK--TSSHD---------HQKQEAKT----LHVLARESRDKARARARERTINKLWPR-LVGG-KK---------SNSSL-----KEHTQMD-------------------KPIC------------------------------------------VKPSLILGFHGQNLTTAPKGSISNYS-NCFSN-----------------TQNWD-VSNTLMSSSLSAAMTTSANNYSSQ---VFQSC--DQ---- Schizanthus_x_wisetonensis_cyc2 MLGFEKPSKTLDWLFTNSKLAIEVL---------------SAR--KNPASSIS-----QCEQKPPV-----DQIA-KS-----------------STG--------KKQKQ-VKTHDQATVL-ARESRARARARARERTINKMWTRIVTG--KRS------------LSC----PH--MD------------------IQPLCDY--------------------KRA---CDS-AIKEMMI----KPWVILGF-------SPKSQSSNHGFFCCCY---------------TTT-----------------------------------TL-------- Scrophularia_canina_Scyc1 MLGFDKPSRTLDWLLTESKPAIKELA-------------ASGRGNKSR---ISSPSD-QC--EVVSV---------ENASS--DSKSTKGK-----------------------EPRHQLADLAKESRAKARARASERTREKMCIKQINGA-TN-TTLHE--------------HQIPFRV-----SSN---------------------------------SST-GNH--HE-----GMVN-------SIFEF-QQNL-FVSRDFTSNHNMNPTH-------------------ENWD----------------------------VCAIL--DQHKFI Scrophularia_canina_Scyc2 MLGFDKPSKTLDWLLTESKASIKDL---ILKK-KS---------QNGV--VSSSPF--EC--EVISSR-N-----LE---------HSNRK-SICL--------------------------SAKEMRVKARARARERTREKMCIKQLNEAIRRN-G-YD-L-SPSIP-IHYNMNNNN-----------CNNG-------GISESIFDYPI-NY-E-----ASSNHEDLI-HESILIRRKFK---QYPPSIFGF-QHNL-IFSRDSSSN----ATP----------------FTTQS-D----------------------------VWAIL--DQHKFI Sinningia_schiffneri_Gcyc1 MLGFDKPSKTLDWLLIKSKAAIKEL---VQAK-KS----GS--A-KS----ISSPS--EC--EVVFAG-N-GET-FENGSYL--DAESKKK-SMPLNP-------NYKCKEYSKDPQQSALNLAKVSRAKARARARERTKEKMCIKKLNES-RN-MD-PD-L-NPSNQ-IQ---------------------------------PTLHCHL-TNNV----SAATT-EDLIQ-ESIVFKRMLK---QYP-SFFGF-QQNL-IISRDL--NCN-LPSP----------------NINDNWD-INSLT-----------------SQSN-LCDIL--DQHKFI Streptocarpus_holstii_Gcyc1A MLGFDKPSKTLDWLLTKSKVAIKDL---VLNK-TS------SSS-RS----TSSPS--EC--EVVL---N-GEA-FEDGNCLP-HPDS-RK-SSSMNA--------KKC----KDPAQRASKLAKESRAKARARARERTKEKMCIKKLNES-RN-M-----------------NN-NFF-------ASD-------------SHPVFHCPI-TN-EAT-----ATHEDLIQ-ESSVIKRMLR---HHQSSFFGF--------------QFG-LPSP----------------YVNENWD-VGSLT-----------------SQSN-LCDIL--DQHKFI Streptocarpus_holstii_Gcyc1B MLGFDKPSKTLDWLLTKSKVAIKDL---VLTN-KS------SSS-RS----PSSPS--EC--EVAL---N-DEA-FQDGSCLL-PPDSKRN-SAST----------------ARDPAQSASTLAKESRAKARARARERTKEKLCIKKLNES-RN-M-----------------NN-NLF-------TSN-------------SQPVLHCPI-TN-EAT-----ATQQDLIQ-ESSVIKRMLR---HHQ-SFFGF--------------HCAALPSP----------------DVNENWD-AGSLT-----------------SQSN-LCDIL--DQHKFI Tetranema__mexicanum_Tcyc2 MLGFDKPSKTLDWLLTKSKAAIKEL---VQSK----------SA-KS---ASSSPS--ECE-EVVSAGGN-GEA-SENGNYL--GADSKGK-SVLLSS--------NKCKG-AKDSQQAALNLAKESRAKARARARERTKEKMCIKQLNEA-RN-KGSSD-W-NPSIL-IQSKHHH-QFEV----SGSR--------------EPILHYPL-AY-E------AAT-EDLIHHESIMIKRKLK----HP-SISALHQQNL-SGSRNLNSNCS-IPSA----------------SATENWD-YSNFI-----------------AQSNQLCAIL--DQHKFI Titanotrichum_oldhamii_Gcyc1 MLGFDKPSKTLEWLLTKSKAAIKEL---VQTK-KST----SASA-KS----ISSPS--EC--EVVSAG-H-GET-FENRNYL--GADSKKK-SVLLNS--------YKCKE-AKDPQQAALNLAKVSRAKARARARERTREKMCIKKLNES-RN-MG-PD-L-NP----IQS-RN-NLFEACKL-SASN-------------SDPILHCPL-TN-V----AAAAT-EDLIQ-ESIVIKRMLK----HP-SFFGF-QQNL-IISRDL--NCS-IPSP----------------NVNDNFD-ISSLT-----------------SQSN-LCDIL--DQHKFI ; END; BEGIN CODONS; CODESET * UNTITLED = Universal: all ; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; EXSET amb = 39 45 51 154 - 155 176 221 - 226 ; END;