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Supplemental Information a homology-based pipeline for global prediction of post-translational modification sites Xiang Chen1, Shao-Ping Shi1,2, Hao-Dong Xu1, Sheng-Bao Suo1, Jian-Ding Qiu1,3


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Supplemental Table 4. Organism index of 340 cellular conditions in PTMProber V1.0.

Taxonomy ID

Organism Name

taxid=2880

Ectocarpus siliculosus (Brown alga)

taxid=3055

Chlamydomonas reinhardtii

taxid=3067

Volvox carteri (Green alga)

taxid=3694

Populus trichocarpa (Western balsam poplar)

taxid=3702

Arabidopsis thaliana (Mouse-ear cress)

taxid=3847

Glycine max (Soybean)

taxid=3988

Ricinus communis (Castor bean)

taxid=4533

Oryza brachyantha

taxid=4538

Oryza glaberrima (African rice)

taxid=4558

Sorghum bicolor (Sorghum)

taxid=5660

Leishmania braziliensis

taxid=5664

Leishmania major

taxid=5671

Leishmania infantum

taxid=5693

Trypanosoma cruzi

taxid=5722

Trichomonas vaginalis

taxid=5759

Entamoeba histolytica

taxid=5762

Naegleria gruberi (Amoeba)

taxid=5786

Dictyostelium purpureum (Slime mold)

taxid=5811

Toxoplasma gondii

taxid=5823

Plasmodium berghei (strain Anka)

taxid=5825

Plasmodium chabaudi

taxid=5851

Plasmodium knowlesi (strain H)

taxid=5865

Babesia bovis

taxid=5874

Theileria annulata

taxid=5875

Theileria parva (East coast fever infection agent)

taxid=5888

Paramecium tetraurelia

taxid=6183

Schistosoma mansoni (Blood fluke)

taxid=6238

Caenorhabditis briggsae

taxid=6239

Caenorhabditis elegans

taxid=6279

Brugia malayi (Filarial nematode worm)

taxid=6293

Wuchereria bancrofti

taxid=6334

Trichinella spiralis (Trichina worm)

taxid=6669

Daphnia pulex (Water flea)

taxid=6945

Ixodes scapularis (Black-legged tick)

taxid=7029

Acyrthosiphon pisum (Pea aphid)

taxid=7070

Tribolium castaneum (Red flour beetle)

taxid=7091

Bombyx mori (Silk moth)

taxid=7159

Aedes aegypti (Yellowfever mosquito)

taxid=7165

Anopheles gambiae (African malaria mosquito)

taxid=7176

Culex quinquefasciatus (Southern house mosquito)

taxid=7209

Loa loa (Eye worm)

taxid=7217

Drosophila ananassae (Fruit fly)

taxid=7220

Drosophila erecta (Fruit fly)

taxid=7222

Drosophila grimshawi (Fruit fly)

taxid=7227

Drosophila melanogaster (Fruit fly)

taxid=7230

Drosophila mojavensis (Fruit fly)

taxid=7234

Drosophila persimilis (Fruit fly)

taxid=7238

Drosophila sechellia (Fruit fly)

taxid=7240

Drosophila simulans (Fruit fly)

taxid=7244

Drosophila virilis (Fruit fly)

taxid=7245

Drosophila yakuba (Fruit fly)

taxid=7260

Drosophila willistoni (Fruit fly)

taxid=7425

Nasonia vitripennis (Parasitic wasp)

taxid=7460

Apis mellifera (Honeybee)

taxid=7668

Strongylocentrotus purpuratus (Purple sea urchin)

taxid=7719

Ciona intestinalis (Transparent sea squirt)

taxid=7739

Branchiostoma floridae (Florida lancelet)

taxid=7897

Latimeria chalumnae (West Indian ocean coelacanth)

taxid=7955

Danio rerio (Zebrafish)

taxid=7998

Ictalurus punctatus (Channel catfish) (Silurus punctatus)

taxid=8022

Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)

taxid=8083

Xiphophorus maculatus (Southern platyfish) (Platypoecilus maculatus)

taxid=8084

Xiphophorus helleri (Green swordtail)

taxid=8090

Oryzias latipes (Medaka fish)

taxid=8128

Oreochromis niloticus (Nile tilapia)

taxid=8260

Platichthys flesus (European flounder) (Pleuronectes flesus)

taxid=8364

Xenopus tropicalis (Western clawed frog)

taxid=9031

Gallus gallus (Chicken)

taxid=9103

Meleagris gallopavo (Common turkey)

taxid=9258

Ornithorhynchus anatinus (Duckbill platypus)

taxid=9305

Sarcophilus harrisii (Tasmanian devil)

taxid=9483

Callithrix jacchus (White-tufted-ear marmoset)

taxid=9541

Macaca fascicularis (Crab-eating macaque)

taxid=9543

Macaca fuscata fuscata (Japanese macaque)

taxid=9544

Macaca mulatta (Rhesus macaque)

taxid=9595

Gorilla gorilla gorilla (Lowland gorilla)

taxid=9598

Pan troglodytes (Chimpanzee)

taxid=9601

Pongo abelii (Sumatran orangutan)

taxid=9606

Homo sapiens (Human)

taxid=9615

Canis familiaris (Dog)

taxid=9646

Ailuropoda melanoleuca (Giant panda)

taxid=9749

Delphinapterus leucas (Beluga whale)

taxid=9785

Loxodonta africana (African elephant)

taxid=9796

Equus caballus (Horse)

taxid=9823

Sus scrofa (Pig)

taxid=9913

Bos taurus (Bovine)

taxid=9986

Oryctolagus cuniculus (Rabbit)

taxid=10029

Cricetulus griseus (Chinese hamster)

taxid=10090

Mus musculus (Mouse)

taxid=10116

Rattus norvegicus (Rat)

taxid=10141

Cavia porcellus (Guinea pig)

taxid=10181

Heterocephalus glaber (Naked mole rat)

taxid=10228

Trichoplax adhaerens

taxid=12957

Atta cephalotes (Leafcutter ant)

taxid=12968

Blastocystis hominis

taxid=13037

Danaus plexippus (Monarch butterfly)

taxid=13616

Monodelphis domestica (Gray short-tailed opossum)

taxid=13642

Polysphondylium pallidum (Cellular slime mold)

taxid=13686

Solenopsis invicta (Red imported fire ant)

taxid=15368

Brachypodium distachyon (Purple false brome)

taxid=28377

Anolis carolinensis (Green anole)

taxid=29159

Crassostrea gigas (Pacific oyster)

taxid=29760

Vitis vinifera (Grape)

taxid=30611

Otolemur garnettii (Small-eared galago)

taxid=31033

Takifugu rubripes (Japanese pufferfish)

taxid=31234

Caenorhabditis remanei

taxid=34765

Oikopleura dioica (Tunicate)

taxid=35128

Thalassiosira pseudonana (Marine diatom)

taxid=36329

Plasmodium falciparum (isolate 3D7)

taxid=39947

Oryza sativa subsp. japonica (Rice)

taxid=40830

Barbus barbus (Barbel) (Cyprinus barbus)

taxid=43151

Anopheles darlingi (Mosquito)

taxid=43179

Spermophilus tridecemlineatus (Thirteen-lined ground squirrel)

taxid=44056

Aureococcus anophagefferens (Harmful bloom alga)

taxid=44689

Dictyostelium discoideum (Slime mold)

taxid=45351

Nematostella vectensis (Starlet sea anemone)

taxid=46245

Drosophila pseudoobscura pseudoobscura (Fruit fly)

taxid=51511

Ciona savignyi (Pacific transparent sea squirt)

taxid=54126

Pristionchus pacificus

taxid=59463

Myotis lucifugus (Little brown bat)

taxid=59729

Taeniopygia guttata (Zebra finch)

taxid=61853

Nomascus leucogenys (Northern white-cheeked gibbon)

taxid=69293

Gasterosteus aculeatus (Three-spined stickleback)

taxid=70448

Ostreococcus tauri

taxid=73239

Plasmodium yoelii yoelii

taxid=79923

Clonorchis sinensis (Chinese liver fluke)

taxid=81824

Monosiga brevicollis (Choanoflagellate)

taxid=81972

Arabidopsis lyrata subsp. lyrata (Lyre-leaved rock-cress)

taxid=88036

Selaginella moellendorffii (Spikemoss)

taxid=94908

Tetraodon miurus (Congo puffer)

taxid=99883

Tetraodon nigroviridis (Spotted green pufferfish)

taxid=103372

Acromyrmex echinatior (Panamanian leafcutter ant)

taxid=104421

Camponotus floridanus (Florida carpenter ant)

taxid=121224

Pediculus humanus subsp. corporis (Body louse)

taxid=126793

Plasmodium vivax (strain Salvador I)

taxid=135651

Caenorhabditis brenneri (Nematode worm)

taxid=145481

Physcomitrella patens subsp. patens (Moss)

taxid=159749

Thalassiosira oceanica (Marine diatom)

taxid=164328

Phytophthora ramorum (Sudden oak death agent)

taxid=184922

Giardia intestinalis (strain ATCC 50803 / WB clone C6)

taxid=214684

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)

taxid=222929

Coccidioides posadasii (strain C735) (Valley fever fungus)

taxid=226230

Saccharomyces kudriavzevii (strain ATCC MYA-4449 / AS 2.2408 / CBS 8840 / NBRC 1802 / NCYC 2889)

taxid=227321

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)

taxid=229533

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (Wheat head blight fungus)

taxid=235443

Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)

taxid=237561

Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

taxid=237631

Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus)

taxid=237895

Cryptosporidium hominis

taxid=240176

Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (Inky cap fungus)

taxid=242507

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (Rice blast fungus)

taxid=246409

Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) (Mucormycosis agent)

taxid=246410

Coccidioides immitis (strain RS) (Valley fever fungus)

taxid=246437

Tupaia chinensis (Chinese tree shrew)

taxid=281687

Caenorhabditis japonica

taxid=283643

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)
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