DOI: 10.5061/dryad.4tmpg4ffn
title: Proteome database of 36 million proteins from 4,351 species, including marine microbial sequences

description: A fasta-formatted database of 36,866,870 predicted proteins representing
 4,351 unique species from 117 phyla.
description: A database of 36,866,870 predicted proteins
 representing 4,351 unique species from 117 phyla (see table below) was
 constructed using the UniProt Reference Proteome (RP) at the 35%
 co-membership threshold including 4,295 Representative Proteome Groups
 (RPGs) (Chen et al. 2011) in addition to all taxonomically identifiable
 transcriptomes of the Marine Microbial Eukaryote Transcriptome Sequencing
 Project (MMETSP) (Keeling et al. 2014) that were processed through
 WinstonCleaner (https://github.com/kolecko007/WinstonCleaner). The database also included proteins inferred from the annotated and assembled genomes of <em>Aurantiochytrium limacinum</em> ATCC MYA-1381, <em>Schizochytrium aggregatum</em> ATCC 28209, and <em>Aplanochytrium kerguelensis</em> PBS07 from the U.S. Department of Energy’s Joint Genome Institute (JGI), all PFAM PF00494 <em>Aurantiochytrium sp.</em> KH105 proteome hits from the Okinawa Institute of Science and Technology Marine Genomics Unit genome browser, all of UniProt's annotated <em>Hondaea fermentalgiana</em> proteins, and the annotated proteins of the breviate <em>Lenisia limosa</em> and associated mutualistic epibionts (Hamann et al. 2016). Unique phyla are represented in the reference proteome database. Archaea Bacteria Eukaryota Candidatus Caudovirales Crenarchaeota Euryarchaeota Hyperthermophilic Nanoarchaeota Thaumarchaeota Abditibacteriota Acidobacteria Actinobacteria Aquificae Armatimonadetes bacterium Bacteroidetes Balneolaeota Calditrichaeota candidate Candidatus Chlamydiae Chlorobi Chloroflexi Chrysiogenetes Coprothermobacterota Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Elusimicrobia Fibrobacteres <br><br><br> Firmicutes Fusobacteria Gemmatimonadetes Haloplasmatales Ignavibacteriae Kiritimatiellaeota Lentisphaerae Natronospirillum Nitrospinae Nitrospirae Planctomycetes Proteobacteria Rhodothermaeota Spirochaetes Synergistetes Tenericutes Thermobaculum Thermodesulfobacteria Thermotogae Vampirococcus Verrucomicrobia Annelida Apicomplexa Apusomonadidae Arthropoda Ascomycota Bacillariophyta Basidiomycota Bigyra Blastocladiomycota Bolidophyceae Brachiopoda Breviatea Cercozoa Chlorophyta Choanoflagellata Chordata Chromeraceae Chromerida Chrysophyceae Chytridiomycota Ciliophora Cnidaria Cryptomycota Cryptophyta Dictyochophyceae Dinophyceae Discosea Echinodermata Endomyxa Euglenozoa Evosea Filasterea Foraminifera Fornicata Glaucocystophyceae Haptista Heterolobosea Ichthyosporea Microsporidia Mollusca Mucoromycota Nematoda Oomycetes Palpitomonas Parabasalia Pelagophyceae Perkinsozoa Phaeophyceae Pinguiophyceae Placozoa Platyhelminthes Porifera Raphidophyceae Rhodophyta Rotifera Rotosphaerida Stereomyxa Streptophyta Synchromophyceae Synurophyceae Tardigrada Tubulinea Vitrellaceae Xanthophyceae Zoopagomycota <strong>References</strong><br> Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R. 2011. Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation. <em>PLOS ONE</em>. 6(4):e18910. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. <em>PLoS Biol.</em> 12(6):e1001889. Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, Chen J, Milucka J, Viehweger B, Becker KW, et al. 2016. Environmental Breviatea harbour mutualistic <em>Arcobacter</em> epibionts. <em>Nature</em>. 534:254–258.