Reference tree for APSES domains

How this tree was computed

The input sequence alignment was derived from the Probcons MSA of 74 fungal APSES domains (from Assignment 3). The PHYLIP input file appears below. Columns that represented regions of uncertain alignment were deleted, as well as large gapped sections. Using the PHYLIP suite and the program promlk (an ML tree building program that constructs a tree under the assumption of a "molecular clock") with default paramaters, the following tree was constructed. Likelihood of branches is reported beneath the Tree.

PHYLIP Input File

  74  72
MBP1_SACCEIMKRKKDDW-VNATHILKAANF-AKA--KRTREKVQGGFGKYQGTWVPLNIAKQLAEKF--SVYDQLK-PLF
MBP1_YARLIVMRRKSDGW-VNATHILKVAGF-DKP--QRTREKVQGGYGKYQGTWVPLERAREIATLY--DVDSHLA-PIF
5821_NEUCRVMRRRHDDW-VNATHILKAAGF-DKP--ARTREKIQGGYGRYQGTWIPLEQAEALARRN--NIYERLK-PIF
9090_CRYNEVMRRRSDAY-LNATQILKVAGF-DKP--QRTREKVQGGYGKYQGTWIPIERGLALAKQY--GVEDILR-PII
MBP1_ASPNIVMRRRSDDW-INATHILKVAGF-DKP--ARTREKVQGGYGKYQGTWIPLQEGRQLAERN--NILDKLL-PIF
MBP1_KLULAIMKRKADNW-VNATHILKAAKF-PKA--KRTREKVQGGFGKYQGTWIPLELASKLAEKF--EVLDELK-PLF
MBP1_GIBZEVMRRRNDSW-LNATQILKVAGV-DKG--KRTKEKVQGGYGKYQGTWIKFERGLQVCRQY--GVEELLR-PLL
MBP1_ASPTEVMRRRADDW-INATHILKVAGF-DKP--ARTREKVQGGYGKYQGTWIPLPEGRLLAERN--NIIDKLR-PIF
MBP1_CANALIMRRKKDSW-INATHILKIAKF-PKA--KRTREKVQGGYGKYQGTYVPLDLGAAIARNF--GVYDVLK-PIF
MBP1_CANGLIMKRKNDGW-VNATHILKAANF-AKA--KRTREKVQGGFGKYQGTWVPLNIAINLAEKF--DVYQDLK-PLF
1770_YARLIVMRRRTDSS-LNATQILKVAGV-EKS--KRTKEKVQGGYGKYQGTWIPYERGVDLCRQY--SVYDVLQ-PLL
2974_MAGGRVMRRRVDDW-INATHILKAAGF-DKP--ARTREKVQGGYGKYQGTWIPLEAGEALAHRN--NIFDRLR-PIF
1485_USTMAVMRRRGDGW-LNATQILKIAGI-EKT--RRTKEKIQGGYGKFQGTWIPLQRAQQVAAEY--NVSHLLQ-PIL
MBP1_USTMAVMRRRSDDW-LNATQILKVVGL-DKP--QRTREKVQGGYGKYQGTWIPLDVAIELAERY--NIQGLLQ-PIT
0560_GIBZEVMRRRSDDW-INATHILKAAGF-DKP--ARTREKIQGGYGKYQGTWIPLESGQALAERH--SVIDRLR-PIF
4232_ASPFU-MRRRGDDW-INATHILKVAGF-DKP--ARTREKVQGGYGKYQGTWIPLHEGRLLAERN--NIIDKLR-PIF
MBP1_CRYNEVMRRASDSW-VNATQILKVAGV-HKS--ARTKEKIQGGYGKYQGTWVPLDRGRDLAEQY--GVGSYLS-SVF
MBP1_NEUCRVMRRQKDGW-VNATQILKVANI-DKG--RRTKEKVQGGYGKYQGTWIPFERGLEVCRQY--GVEELLS-KLL
MBP1_DEBHAIMRRKLDSW-INATHILKIAKF-PKA--KRTREKVQGGYGKYQGTYVPLDLGADIAKNF--GVFDSLR-PIF
2876_CANALIMRRCKDDW-VNATQILKCCNF-PKA--KRTKEKVQGGFGRFQGTWIPLEDARRLAKTY--GVTEELA-PVL
MBP1_MAGGRVMKRIGDSK-LNATQILKVAGV-EKG--KRTKEKVQGGYGKYQGTWIKYERALEVCRQY--GVEELLR-PLL
4319_ASPNIVMKRRSDGW-LNATQILKVAGV-VKA--RRTKEKVQGGYGKYQGTWVNYQRGVELCREY--HVEELLR-PLL
MBP1_ASPFUVMKRRSDSW-LNATQILKVAGV-VKA--RRTKEKVQGGYGKYQGTWVNYQRGVELCREY--HVEELLR-PLL
MBP1_SCHPOVMRRRRDSW-LNATQILKVADF-DKP--QRTREKVQGGYGKYQGTWVPFQRGVDLATKY--KVDGIMS-PIL
5548_ASPTEVMKRRSDSW-LNATQILKVAGV-VKA--RRTKEKVQGGYGKYQGTWVNYQRGVDLCREY--HVEELLR-PLL
5496_SCHPOLMKRCHDNW-LNATQILKIAEL-DKP--RRTREKIQGGCGKYQGTWVPSERAVELAHEY--NVFDLIQ-PLI
7246_DEBHAIMRRCKDDW-VNATQILKCCNF-PKA--KRTKEKIQGGYGRFQGTWIPLADAQRLAASY--GVTPDLA-PVL
MBP1_EREGOIMKRKADDW-VNATHILKAAKF-AKA--KRTREKVQGGFGKYQGTWVPLDIARRLAQKF--EVLEELR-PLF
6370_EREGOVMRRLHDDW-VNITQVFKVATF-SKT--QRTKEKIQGGYGRFQGTWIPLDSAKGLVAKY--EITDIVVLTVI
SWI4_SACCEVMRRTKDDW-INITQVFKIAQF-SKT--KRTKEKVQGGYGRFQGTWIPLDSAKFLVNKY--EIIDPVVNSIL
4890_KLULAIMRRCNDNW-LNITQVFKAGSF-TKA--QRTKEKIQGGYGRFQGTWIPWESTKYLVEKY--NINNKVVKRIV
4966_CANGLVMRRTMDDW-VNVTQVFKIAQF-SKT--QRTKEKVQGGYGRFQGTWVPLEAAKFMTTKY--NIDNPVVNTI-
9785_DEBHAVVRRADNNM-INGTKLLNVAQM-TRG--RRDGHVVKIGSMHLKGVWIPFERALAMAQRE--GIVDLLY-PLF
3009_ASPNIVMWDYNIGL-VRTTHLFKCNDY-SKT--TPAKHSITGGALAAQGYWMPYEAAKAIAATFCWKIRFALT-PLF
SOK2_SACCEVVRRADNDM-VNGTKLLNVTKM-TRG--RRDGHVVKIGSMHLKGVWIPFERALAIAQRE--KIADYLY-PLF
9680_CANGLVVRRADNDM-VNGTKLLNVTGM-TRG--RRDGDVVKGGPMTLKGVWIPIDRARAIARQE--GIEQWLY-PLF
3001_EREGOVVRRADNDM-INGTKLLNVAKM-TRG--RRDGHVVKIGSMHLKGVWIPFERALALAQRE--KIVDMLF-PLF
4197_CANALVVRRADNNM-INGTKLLNVAQM-TRG--RRDGHVVKIGSMHLKGVWIPFERALAMAQRE--QIVDMLY-PLF
4237_CANALVVRRADNNM-INGTKLLNVAQM-TRG--RRDGHVVKIGSMHLKGVWIPFERALAMAQRE--QIVDMLY-PLF
8256_ASPTEVARREDNSM-INGTKLLNVAGM-TRG--RRDGHVVKIGPMHLKGVWIPFERALEFANKE--KITDLLY-PLF
3440_ASPNIVARREDNGM-INGTKLLNVAGM-TRG--RRDGNVVKIGPMHLKGVWIPFDRALEFANKE--KITDLLY-PLF
2292_YARLIVARREDNDM-INGTKLLNVAGM-TRG--RRDGHVVKAGAMHLKGVWIPYDRALEFANKE--KIIDLLF-PLF
1102_YARLIVARREDNNM-INGTKLLNVVGM-TRG--RRDGHVVKIGAMHLKGVWIPYERALAFAQRE--RIVDVLY-PLF
5125_ASPFUVARREDNHM-INGTKLLNVAGM-TRG--RRDGHVVKIGPMHLKGVWIPFERALEFANKE--KITDLLY-PLF
PHD1_SACCEVVRRADNNM-INGTKLLNVTKM-TRG--RRDGEVVKIGSMHLKGVWIPFERAYILAQRE--QILDHLY-PLF
8847_CANGLVVRRADNDM-INGTKLLNVTKM-TRG--KRDGKVVKIGSMHLKGVWIPFERALFIAKRE--KIVDLLY-PLF
5499_YARLIIIWDYHTGY-VHLTGLWKAIGN-SKA--DIVKRRVRGGYLKIQGTWVPYDIARALASRTCYFIRFALI-PLF
5299_KLULAVVRRADNDM-INGTKLLNVTRM-TRG--RRDGHVVKIGSMHLKGVWIPFERALVMAQRE--KIVDLLY-ALF
0305_GIBZEVARREDNHM-INGTKLLNVAGM-TRG--RRDGHVVKIGPMHLKGVWIPYDRALDFANKE--KITELLY-PLF
0837_NEUCRVARREDNAM-INGTKLLNVAGM-TRG--RRDGHVVKIGPMHLKGVWIPFERALDFANKE--KITELLY-PLF
8552_MAGGRVARREDNHM-INGTKLLNVAGM-TRG--RRDGHVVKIGPMHLKGVWIPFERALDFANKE--KITELLY-PLF
0447_DEBHAVSRREDTNY-VNGTKLLNVAGM-TRG--KRDGSVVKVGAMNLKGVWIPFERASEIARNE--GIDGLLY-PLF
9978_GIBZEVMWDYNIGL-VRMTPFFKCRGY-GKT--IPAKHSITGGSIAAQGYWMPYRCAKAICATFCHPIAGALI-PIF
1513_CANALVSRREDTNY-INGTKLLNVIGM-TRG--KRDGNVVKVGSMNLKGVWIPFDRAYEIARNE--GVDSLLY-PLF
6132_SCHPO-LRRCPDSY-FNISQILRLAGT-SSS--ENAKENVDSKHPQIDGVWVPYDRAISIAKRY--GVYEILQ-PLI
1244_ASPFUVMWDYNIGL-VRTTHLFKCNDY-SKM--LNA-HSITGGALAAQGYWMPYEAAKAVAATFCWKIRHALT-PLF
0925_USTMAMMIDVDTSF-VRFTSITQALGK-NKV--NFGRTKLKGGYLSIQGTWLPFDLAKELSRRIAWEIRDHLV-PLF
2599_ASPTEIMWDYNIGL-VRTTPLFRSQNY-SKT--TPAKHSITGGAIVKPGYWIPFEAAKAVAATFCWRIRYALT-PIF
9773_DEBHAIIWDYETGF-VHLTGIWKASIN-DEVKADIVKKRIRGGFLKIQGTWLPFDLCKMLAKRFCYHIRFQLI-PIF
0918_CANALVIWDYETGW-VHLTGIWKASLT-IDGKADIVKKRIRGGFLKIQGTWLPYKLCKILARRFCYYLRYSLI-PIF
9901_DEBHAILRRVQDSY-INISQLFSILLKISEA--QLTNSSGGHEVRDLRGLWIPYDRAVSLALKF--DIYELAK-SLF
7766_ASPNILMRRSKDGY-VSATGMFKIAFP-WAK--LEEETRPESEDEIAGNVWISPVLALELAAEY--KMYDWVR-ALL
5459_GIBZELMRRSYDGF-VSATGMFKASFP-YAE--ASDESLPTSHEETAGNVWIPPEQALILAEEY--KISPWIR-ALL
2267_NEUCRLMRRSQDGY-ISATGMFKATFP-YAS--QEEESIPTSSEETAGNVWIPPEQALILAEEY--QITPWIR-ALL
3510_ASPFULMRRSKDGY-VSATGMFKIAFP-WAK--LEEETREGSEDEIAGNIWVSPLLALELAKEY--QMYDWVR-ALL
3762_MAGGRLMRRSSDGY-VSATGMFKATFP-YAD--AEDESLPASKEETAGNVWISPDQALALAEEY--SIATWIR-ALL
3412_CANALVLRRVQDSF-VNVTQLFQILIKLPTS--QVDNGSSSHQNIYLQGIWIPYDKAVNLALKF--DIYEITK-KLF
6166_SCHPOLMRMAKDSS-ISATSMFRSAFP-KAT--QEEEDNLNIEDKRVAGLWVPPADALALAKDY--SMTPFIN-ALL
XBP1_SACCE---------------RDLICQS-YKD--F--LKRIRGGYIKIQGTWLPMEISRLLCLRFCFPIRYFLV-PIF
6355_ASPTETY-FLMDGY-VSATGMFKIAFP-WAK--LDEESREESEDEIAGNVWISPKLALELAGEY--QMYNWVR-ALL
9301_MAGGRVMWDYGCGL-VRMTHFFKCRGY-TKT--VPGKYSITGGSISAQESPIDREEAESMYGRSMQAQAQQQG-PLR
5262_KLULAYI---DLHWHLNP------TLS-TLL--G--QKRIRGGYIKIQGTWLPYPVSKELCSRFCYPLRYLLV-PLF
3869_EREGOYT---DVHWNVDPTWKQRLCRL-YQQ--E--KKRIRGGYIKIQGTWLPMEICKRLCIRFCFPIRYFLV-PIF
6482_CANGLSVNYLDFHW-FDISEKVRSQIF-EQF--K--QQRIRGGYIKIQGTWVPWYIAKLICIRFCFPIRYLLV-PIF