#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 19, 2025; 3:47 GMT TreeBASE (cc) 1994-2008 Study reference: Bain P.A. 2016. De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water. BMC Genomics, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19998] BEGIN TAXA; TITLE Untitled_Block_of_Taxa; DIMENSIONS NTAX=32; TAXLABELS Bos_taurus_GPx7 Caenorhabditis_elegans_GPx3 Danio_rerio_GPx3 Homo_sapiens_GPx1 Homo_sapiens_GPx2 Homo_sapiens_GPx3 Homo_sapiens_GPx8 'Limulus polyphemus GPx-like' Macaca_fuscata_fuscata_GPx1 Macaca_fuscata_fuscata_GPx2 Macaca_fuscata_fuscata_GPx3 Macaca_fuscata_fuscata_GPx4 Metapenaeus_ensis_GPx Mus_musculus_GPx1 Mus_musculus_GPx4 Mus_musculus_GPx6 Mus_musculus_GPx8 Oreochromis_niloticus_GPx3 Oryzias_latipes_GPx3 'Parasteatoda tepidariorum GPx-like' 'Paratya australiensis TR11369|c0_g1_i1|m.1547' 'Paratya australiensis TR12356|c0_g1_i1|m.1706' 'Paratya australiensis TR41138|c2_g1_i1|m.32138' 'Paratya australiensis TR41138|c2_g1_i2|m.32139' Penaeus_monodon_GPx3 Pongo_pygmaeus_GPx1 Pongo_pygmaeus_GPx2 Procambarus_clarkii_GPx Rattus_norvegicus_GPx3 Rattus_norvegicus_GPx4 Rattus_norvegicus_GPx6 'Tetranychus urticae GPx-like' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M38542] TITLE Paratya_australiensis_GPx; LINK TAXA = Untitled_Block_of_Taxa; DIMENSIONS NCHAR=191; 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 ] [ . . . . . . . . . . . . . . . . . . . ] Bos_taurus_GPx7 DFYDFKAVNIRG-KLVSLEKYRGSVSLVVNVASECGFTDQHYRALQQLQRDLGPH-HFNVLAFPCNQFGQQEPDS--------NKEIESFARRTYSVSFPMFSKIAVTGTGAHPAFKYLTETSG-----------------------KEPTWNFWKYLVA-PDGKVIGAWDPTVS-VEEIRP-QITALVRK Caenorhabditis_elegans_GPx3 -IFDFQIETLQG-EYTDLSQYRGKVILLVNVATFCAYTQ-QYTDFNPMLEKYQAQ-GLTLVAFPCNQFYLQEPAE-NHELMNGLTYVRPGNGWTPHQELHIYGKIDVNGDNHHPLYEFVKESCPQTVD---KIG-KTDELMYNPVRPSDITWNFEKFLID-RNGQPRFRFHPTAWSHGDVVTPFIEQLLAE Danio_rerio_GPx3 SFHNYGAKTINGTQFIPFSHYAGKHVLVVNVATY-GLTF-QYVELNALHEELRHL-GFTILGFPCDQFGKQEPGE-NNEILSALKYVRPGNGFVP--NFQLFEKGDVNGDGEQALFTFLKNACPPVGE---SFGATSNRLFWEPLKVNDIKWNFEKFLLD-PDGRPVMRWFPRVN-VSEVRA-DILKYFHQ Homo_sapiens_GPx1 SVYAFSARPLAGGEPVSLGSLRGKVLLIENVASL-GTTVRDYTQMNELQRRLGPR-GLVVLGFPCNQFGHQENAK-NEEILNSLKYVRPGGGFEP--NFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVG-PDGVPLRRYSRRFQ-TIDIEP-DIEALLSQ Homo_sapiens_GPx2 SFYDLSAISLDG-EKVDFNTFRGRAVLIENVASL-GTTTRDFTQLNELQCRF-PR-RLVVLGFPCNQFGHQENCQ-NEEILNSLKYVRPGGGYQP--TFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIG-PEGEPFRRYSRTFP-TINIEP-DIKRLLKV Homo_sapiens_GPx3 TIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASY-GLTG-QYIELNALQEELAPF-GLVILGFPCNQFGKQEPGE-NSEILPTLKYVRPGGGFVP--NFQLFEKGDVNGEKEQKFYTFLKNSCPPTSE---LLG-TSDRLFWEPMKVHDIRWNFEKFLVG-PDGIPIMRWHHRTT-VSNVKM-DILSYMRR Homo_sapiens_GPx8 SFYAFEVKDAKG-RTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPS-HFSVLAFPCNQFGESEPRP--------SKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSK-----------------------KEPRWNFWKYLVN-PEGQVVKFWKPEEP-IEVIRP-DIAALVRQ 'Limulus polyphemus GPx-like' SIYDYAVPDILQEKNISFSDFRGKVVLVVNLATY-GLNW-HYPQLNALKEMFGNE-QFEILGFPCNQFGLQEPGANGTEIINGLKGVRPGNGFTP--NFVMFNKIEVNGENQHPLYAYLKTFCPSPLA---GFR-RQERLFYTPFHNRDIRWNFEKFLVN-KNGKPLMRYNPATR-PLNIAS-DIRSVLEH Macaca_fuscata_fuscata_GPx1 SVYAFSARPLAGGEPVSLGSLRGKVLLIENVASL-GTTVRDYTQMNELQRRLGPR-GLVVLGFPCNQFGHQENAK-NEEILNSLKYVRPGGGFEP--NFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLIAWSPVCRNDVAWNFEKFLVG-PDGVPVRRYSRRFQ-TIDIEP-DIEALLSQ Macaca_fuscata_fuscata_GPx2 SFYDLSAISLDG-EKVDFNTFRGRAVLIENVASL-GTTTRDFTQLNELQCRF-PR-RLVVLGFPCNQFGHQENCQ-NEEILNSLKYVRPGGGYQP--TFTLVQKCEVNGQNEHPVFAYLKDKLPYPHDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIG-PEVEPFRRYSRTFP-TINIEP-DIKRLLKV Macaca_fuscata_fuscata_GPx3 TIYEYGALTIDGEEYIPFKQYIGKYVLFVNVASY-GLTG-QYIELNALQEELAPF-GLVLLGFPCNQFGKQEPGE-NSEILPSLKYVRPGGGFVP--NFQLFEKGDVNGEKEQKFYTFLKNSCPPTSE---LLG-TSDRLFWEPMKVHDIRWNFEKFLVG-PDGIPVMRWHHRTT-ISNVKM-DILSYMRR Macaca_fuscata_fuscata_GPx4 SMHEFSAKDIDG-HMVNLDKYRGFVCIVTNVASQ-GKTEVNYTQLVDLHARYAEC-GVRILAFPCNQFGKQEPGS--------NEKIKEFAAG-YNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGI-----------------LGNAIKWNFTKFLID-KNGCVVKRYGPMEE-PLVIEK-DLPHYF-- Metapenaeus_ensis_GPx -------MALHEDKRIPLSEYSGKVVLIVNLATY-GLNF-QYHELNVLQETFP-E-DFVITGFPCNQFALQEPAANGTELIDGLMHVRPGNGFEP--NFRLFGKVEVNGENETPLYSYLKESCPSTMD---EFM-RSEMLHYAPLRNRDIRWNFEKFLIA-KDGKPFKRYNPMTR-PGEIEA-DVHQLLEI Mus_musculus_GPx1 TVYAFSARPLTGGEPVSLGSLRGKVLLIENVASL-GTTIRDYTEMNDLQKRLGPR-GLVVLGFPCNQFGHQENGK-NEEILNSLKYVRPGGGFEP--NFTLFEKCEVNGEKAHPLFTFLRNALPTPSDDPTALMTDPKYIIWSPVCRNDIAWNFEKFLVG-PDGVPVRRYSRRFR-TIDIEP-DIETLLSQ Mus_musculus_GPx4 SMHEFSAKDIDG-HMVCLDKYRGFVCIVTNVASQ-GKTDVNYTQLVDLHARYAEC-GLRILAFPCNQFGRQEPGS--------NQEIKEFAAG-YNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGM-----------------LGNAIKWNFTKFLID-KNGCEVKRYGPMEE-PQVIER-DLPCYL-- Mus_musculus_GPx6 TVYEYGANTIDGGEFVNFQQYAGKHILFVNVASFCGLTA-TYPELNTLQEELKPF-NVTVLGFPCNQFGKQEPGK-NSEILLGLKYVRPGGGYVP--NFQLFEKGDVNGDNEQKVFSFLKNSCPPTSE---LFG-SPEHLFWDPMKVHDIRWNFEKFLVG-PDGVPVMRWFHHTP-VRIVQS-DIMEYLNQ Mus_musculus_GPx8 SFYSFEVKDAKG-RTVSLEKFKGKASLVVNVASDCRFTDKSYQTLRELHKEFGPY-HFNVLAFPCNQFGESEPKS--------SKEVESFARQNYGVTFPIFHKIKILGPEAEPAFRFIVDSSK-----------------------KEPRWNFWKYLVN-PEGQVVKFWRPEEP-LEAIRP-HVSQMIGQ Oreochromis_niloticus_GPx3 TIYKYRAKTLNGSQTVNFSDYAGKAVLFVNVATY-GLTY-QYVELNALYEEMKLD-GLTILGFPCNQFGKQEPGQ-RHEILPGLKHVRPGNGFIP--NFLLFEKGDVNGKNEQEVYTFLKSSCPPVGI---DFGPMYGRLFWEPLKSTDIKWNFEKFLVG-RNGKPVMRWHPTIN-VSVVRA-DVRRYLLE Oryzias_latipes_GPx3 SIYKYHAKTLNGSQTVNFSDYIGKSVLFVNVATY?GYTY-QYVELNALHEELKPL-GFTIVGFPCNQFGKQEPGQ-NHEILPGLRHVRPGNGFVP--NFLLFNKGDVNGKYEQDVFTFLKGSCPPVGE---DFG-NTDRLFWEPLKIGDIKWNFEKFLVG-PEGKPVMRWHPSVN-VSTVRT-DIRNFLLK 'Parasteatoda tepidariorum GPx-like' NIYNYTLPDILQTRNISLSEFRGKHVLIVNVATY-GFTW-HYHQLNALKPRFNNHSNFDVLGFPCNQFAQQEPGGNGEEIMNGITYVRPGKGFKP--NFPIFQKIDVNGENEHPLFTFLKSLCPPTRD---DFS-DQKKLFYTPIKVRDIRWNFEKFLVN-EHGFPVKRYDPSTP-PDDIAT-DIEALLAS 'Paratya australiensis TR11369|c0_g1_i1|m.1547' -FYQFSANTLNGSTPISFEDYRGKVVLVYNVATY-GLTVPSYTQINALAEYYVDQ-EFVILGFPCHQFGLQEPGT-SVEIMNGIHYVRPGGNFVP--QMTLFEKTEVNGDNEDPIFTFLKSGCEYTDT---DFD-PG--VAYSPLRVGDIHWNFEKFVID-KNGKPYTRYHPAVVDTATLTP-DIDALLNA 'Paratya australiensis TR12356|c0_g1_i1|m.1706' -FYQFSAQLLNGSETINFSDYQGKVVLVYNVATY-GLTIPSYNQINALADEFAGQ-DLEILGFPCNQFGMQEPGVGAAEIMNGIRHVRPGGGFEP--KITLFDKTQVNGDSENEIFTFLKSACDYTET---TFS-SG--LNYSPMRVGDISWNFEKFLID-KTGKPFTRYHPSLVTTGSISA-DIAALLAA 'Paratya australiensis TR41138|c2_g1_i1|m.32138' TIYDFESPDLFEERNVSLSDYKGKVVLIVNVATY-GYTA-QYLDMNVLQESLT---NFVVLGFPCNLFGKQEPAANATELYNGIKYVRPGGGFEP--NFTIFKKLDVNGDKEHPLYTYLKSFCPATRD---AFS-DKDKLYYKPLKTNDIRWNWEKFLIT-KSGKPFMRYDPGTK-PNEIKN-DIMFLL-- 'Paratya australiensis TR41138|c2_g1_i2|m.32139' TIYDFESPDLFEERNVSLSDYKGKVVLIVNVATY-GYTA-QYLDMNVLQESLT---NFVVLGFPCNQFGKQEPAANSTELYNGIKYVRPGGGFEP--NFTIFKKLDVNGDKEHPLYSYLKAFCPATRD---SFS-DPDALYYKPLKKNDIRWNWEKFLIT-KSGKPFMRYDPGTK-PNEIKN-DIMFLLQQ Penaeus_monodon_GPx3 -FYQFSAKTLNGSNLIDFEEYRGKVLLVANVATY-GLTIPSYNQMNALAEYYEGQ-DFVILGFPCNQFGLQEPGATADELLNGVRYVRPGGGFEP--RMTIFQKTQVNGDSEDPIYTFLKSGCEYTDT---DFS-SG--LYYEPLRVGDLHWNFEKFLIN-REGKPVYRYHPSVVDPEDLKG-DINSLLNA Pongo_pygmaeus_GPx1 SVYSFSARPLAGGEPVSLGSLRGKVLLIENVASL-GTTVRDYTQMNELQRRLGPR-GLVVLGFPCNQFGHQENAK-NEEILNSLKYVRPGGGFEP--NFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVG-PDGVPLRRYSRRFQ-TIDIEP-DIEALLSQ Pongo_pygmaeus_GPx2 SFYDLSAISLDG-EKVDFNTFRGRAVLIENVASL-GTTTRDFTQLNELQCRF-PR-RLVVLGFPCNQFGHQENCQ-NEEILNSLKYVRPGSGYQP--TFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWNFEKFLIG-PEGEPFRRYSRTFP-TINIEP-DIKRLLKV Procambarus_clarkii_GPx -------MSLENGTDVSFEEFRGKVVLVINVATY-GLTVPSYTQMNALAEFYVDQ-DFVILGFPCNQFEMLEPAA-NAEIMNGIRYVRPGDGFEP--LMTLFEKTEVNGATEDPLFTFLKSACESTYT---EFY-SS--LFYEPIRIGDIQWNFEKFLIG-KDGKPYTRYHPDVVDPEALKD-DINTLLSA Rattus_norvegicus_GPx3 TIYEYGALTIDGEEYIPFKQYAGKYILFVNVASY-GLTD-QYLELNALQEELGPF-GLVILGFPCNQFGKQEPGE-NSEILPSLKYVRPGGGFVP--NFQLFEKGDVNGEKEQKFYTFLKNSCPPTAE---LLG-SPGRLFWEPMKIHDIRWNFEKFLVG-PDGIPIMRWYHRTT-VSNVKM-DILSYMRR Rattus_norvegicus_GPx4 SMHEFAAKDIDG-HMVCLDKYRGCVCIVTNVASQ-GKTDVNYTQLVDLHARYAEC-GLRILAFPCNQFGRQEPGS--------NQEIKEFAAG-YNVRFDMYSKICVNGDDAHPLWKWMKVQPKGRGM-----------------LGNAIKWNFTKFLID-KNGCVVKRYGPMEE-PQVIEK-DLPCYL-- Rattus_norvegicus_GPx6 TVYEYGANTLDGGEYVQFQQYAGKHILFVNVASFCGLTA-TYPELNTLQEELRPF-NVSVLGFPCNQFGKQEPGK-NSEILLGLKYVRPGGGFVP--NFQLFEKGDVNGDNEQKVFSFLKSSCPPTSE---LLG-SPEHLFWDPMKVHDIRWNFEKFLVG-PDGAPVMRWFHQTP-VRVVQS-DIMEYLNQ 'Tetranychus urticae GPx-like' -IYDYSIKDIYQENDISLGDHQSKAILLVNVATY-GYTH-HYIGMNALLERFG-HSSLAIIGFPCNQFGMQEPGSGAKEILNGIKHVRPGKGFVP--DFNLTIKIDVNGADEHPLWSFLKRSCPSTKI---NFA-RQSSLYYTPFHERDVKWNWEKFLIEPETGLVYKRYDASVD-PYYIAD-DIEYLLSR ; END;