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YbiA-like family domain assignments


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Select to display   Genome       Domains   Proteins
No Yes ALL   11733 11733
No Yes Adineta vaga   5 5
No Yes Proterospongia sp. ATCC 50818   1 1
No Yes Mortierella verticillata NRRL 6337   1 1
No Yes Malassezia globosa CBS 7966   2 2
No Yes Piloderma croceum F 1598 v1.0   1 1
No Yes Serpula lacrymans var. lacrymans S7.9   5 4
No Yes Coniophora puteana   2 2
No Yes Hydnomerulius pinastri v2.0   3 3
No Yes Paxillus rubicundulus Ve08.2h10 v1.0   3 3
No Yes Pisolithus microcarpus 441 v1.0   3 3
No Yes Pisolithus tinctorius Marx 270 v1.0   2 2
No Yes Scleroderma citrinum Foug A v1.0   2 2
No Yes Pleurotus ostreatus Oyster mushroom 1 1
No Yes Amanita thiersii Skay4041 v1.0   2 2
No Yes Amanita muscaria Koide v1.0 Fly agaric 2 2
No Yes Galerina marginata v1.0   1 1
No Yes Hebeloma cylindrosporum h7 v2.0   1 1
No Yes Laccaria bicolor S238N-H82   2 2
No Yes Agaricus bisporus var. bisporus   1 1
No Yes Schizophyllum commune   3 3
No Yes Stereum hirsutum FP-91666 SS1 v1.0   3 3
No Yes Gloeophyllum trabeumv1.0   1 1
No Yes Punctularia strigosozonata v1.0   1 1
No Yes Sebacina vermifera MAFF 305830 v1.0   4 4
No Yes Tulasnella calospora AL13/4D v1.0   6 6
No Yes Postia placenta   2 2
No Yes Wolfiporia cocos MD-104 SS10 v1.0   2 2
No Yes Fomitopsis pinicolav1.0   5 5
No Yes Fomitopsis pinicola FP-58527 SS1 v3.0   4 4
No Yes Phanerochaete chrysosporium RP-78 2.1   4 3
No Yes Aspergillus carbonarius ITEM 5010   1 1
No Yes Dictyostelium discoideum   2 2
No Yes Dictyostelium purpureum   4 4
No Yes Selaginella moellendorffii   3 3
No Yes Eucalyptus grandis v201 Rose gum 2 2
No Yes Theobroma cacao B97-61/B2 v1 Cacao 1 1
No Yes Gossypium raimondii v221   3 3
No Yes Citrus clementina v165   6 6
No Yes Citrus sinensis v154 Sweet orange 1 1
No Yes Thellungiella halophila v173   1 1
No Yes Brassica rapa Chiifu-401 1.2 Field mustard 1 1
No Yes Capsella rubella v183   1 1
No Yes Arabidopsis lyrata Lyrate rockcress 1 1
No Yes Arabidopsis thaliana 10 Thale cress 1 1
No Yes Medicago truncatula Barrel medic 1 1
No Yes Phaseolus vulgaris v186 French bean 2 2
No Yes Glycine max v109 Soybean 1 1
No Yes Cucumis sativus v122 Cucumber 3 3
No Yes Fragaria vesca Wild strawberry 1 1
No Yes Malus domestica v196 Apple 3 3
No Yes Prunus persica v139 Peach 1 1
No Yes Linum usitatissimum v200 Flax 3 3
No Yes Manihot esculenta v147 Cassava 1 1
No Yes Populus trichocarpa v156 Black cottonwood 1 1
No Yes Vitis vinifera Wine grape 1 1
No Yes Mimulus guttatus v140 Spotted monkey flower 1 1
No Yes Solanum lycopersicum v.2.3 Tomato 1 1
No Yes Actinidia chinensis Hongyang   1 1
No Yes Aquilegia coerulea v195   1 1
No Yes Triticum urartu 22   1 1
No Yes Triticum aestivum 22 Bread wheat 3 3
No Yes Aegilops tauschii 22   1 1
No Yes Brachypodium distachyon Stiff brome 1 1
No Yes Oryza barthii 22 African wild rice 1 1
No Yes Oryza glumaepatula 22   1 1
No Yes Oryza glaberrima African rice 1 1
No Yes Oryza punctata 22   1 1
No Yes Oryza nivara 22   1 1
No Yes Oryza brachyantha 22 Malo sina 1 1
No Yes Oryza sativa ssp. japonica 5.0 Japanese rice 1 1
No Yes Phyllostachys heterocyclavar. pubescens Kikko-chiku 1 1
No Yes Panicum virgatum v202 Switchgrass 1 1
No Yes Setaria italica v164 Foxtail millet 1 1
No Yes Zea mays subsp. mays Maize 1 1
No Yes Zea mays v181 Maize 1 1
No Yes Musa balbisiana Balbis banana 1 1
No Yes Musa acuminata 22 Wild Malaysian banana 1 1
No Yes Amborella trichopoda 22   2 2
No Yes Physcomitrella patens   3 3
No Yes Coccomyxa subellipsoidea sp. C-169 v2   1 1
No Yes Asterochloris sp. Cgr/DA1pho v1.0   1 1
No Yes Chlorella variabilis sp. NC64A   1 1
No Yes Volvox carteri f. nagariensis   1 1
No Yes Chlamydomonas reinhardtii 4.0   1 1
No Yes Ostreococcus sp. RCC809   1 1
No Yes Ostreococcus lucimarinus CCE9901   1 1
No Yes Ostreococcus tauri   1 1
No Yes Bathycoccus prasinos   1 1
No Yes Micromonas sp. RCC299   1 1
No Yes Micromonas pusilla CCMP1545 v3.0   1 1
No Yes Cyanophora paradoxa   3 3
No Yes Trypanosoma cruzi strain CL Brener   1 1
No Yes Perkinsus marinus ATCC 50983   1 1
No Yes Tetrahymena thermophila SB210 1   3 3
No Yes Leptolyngbya sp. PCC 7376   1 1
No Yes Acaryochloris marina MBIC11017   2 2
No Yes Thermosynechococcus sp. NK55   1 1
No Yes Thermosynechococcus elongatus BP-1   1 1
No Yes Synechococcus sp. PCC 6312   1 1
No Yes Microcoleus sp. PCC 7113   2 2
No Yes Trichodesmium erythraeum IMS101   1 1
No Yes Geitlerinema sp. PCC 7407   1 1
No Yes Cyanothece sp. PCC 8802   1 1
No Yes Gloeocapsa sp. PCC 7428   1 1
No Yes Halothece sp. PCC 7418   1 1
No Yes Rivularia sp. PCC 7116   2 2
No Yes Calothrix sp. PCC 7507   2 2
No Yes Anabaena variabilis ATCC 29413   1 1
No Yes 'Nostoc azollae' 0708   1 1
No Yes Nostoc sp. PCC 7107   2 2
No Yes Nostoc punctiforme PCC 73102   2 2
No Yes Nostoc sp. PCC 7120   1 1
No Yes Nostoc sp. PCC 7524   2 2
No Yes Anabaena sp. 90   1 1
No Yes Nakamurella multipartita DSM 44233   1 1
No Yes Actinoplanes sp. SE50/110   1 1
No Yes Rothia dentocariosa ATCC 17931   1 1
No Yes Herpetosiphon aurantiacus DSM 785   1 1
No Yes Deinococcus maricopensis DSM 21211   1 1
No Yes Candidatus Desulforudis audaxviator MP104C   1 1
No Yes Coprococcus sp. ART55/1   1 1
No Yes Streptococcus parasanguinis ATCC 15912   1 1
No Yes Listeria welshimeri serovar 6b str. SLCC5334   1 1
No Yes Listeria monocytogenes serotype 4b str. CLIP 80459   1 1
No Yes Flavobacterium psychrophilum JIP02/86   1 1
No Yes Rhodopirellula baltica SH 1   1 1
No Yes candidate division WWE3 bacterium RAAC2_WWE3_1   1 1
No Yes Sorangium cellulosum 'So ce 56'   1 1
No Yes Burkholderia gladioli BSR3   1 1
No Yes Magnetococcus marinus MC-1   1 1
No Yes Erythrobacter litoralis HTCC2594   1 1
No Yes Jannaschia sp. CCS1   1 1
No Yes Ruegeria sp. TM1040   1 1
No Yes Vibrio sp. Ex25   1 1
No Yes Vibrio harveyi ATCC BAA-1116   1 1
No Yes Vibrio parahaemolyticus RIMD 2210633   1 1
No Yes Vibrio splendidus LGP32   1 1
No Yes Vibrio vulnificus MO6-24/O   1 1
No Yes Photobacterium profundum SS9   1 1
No Yes Shewanella baltica OS185   1 1
No Yes Marinobacter adhaerens HP15   1 1
No Yes Marinobacter sp. BSs20148   1 1
No Yes Hahella chejuensis KCTC 2396   2 2
No Yes Xenorhabdus nematophila ATCC 19061   1 1
No Yes Shigella sonnei Ss046   1 1
No Yes Shigella flexneri 5 str. 8401   1 1
No Yes Shigella boydii CDC 3083-94   1 1
No Yes Escherichia fergusonii ATCC 35469   1 1
No Yes Escherichia coli 'BL21-Gold(DE3)pLysS AG'   1 1
No Yes Methanobrevibacter ruminantium M1   1 1
No Yes Hordeum vulgare 22 Domesticated barley 5 5
No Yes Oryza sativa ssp. Indica (Subspecies) Long-grained rice 1 1
No Yes Chroococcidiopsis thermalis PCC 7203   1 1
No Yes Chamaesiphon minutus PCC 6605   3 3
No Yes Dactylococcopsis salina PCC 8305   1 1
No Yes Synechococcus sp. PCC 7002   1 1
No Yes Crinalium epipsammum PCC 9333   2 2
No Yes Oscillatoria nigro-viridis PCC 7112   2 2
No Yes Oscillatoria acuminata PCC 6304   2 2
No Yes Cyanothece sp. PCC 7822   1 1
No Yes Cyanothece sp. PCC 7425   1 1
No Yes Cyanothece sp. PCC 8801   1 1
No Yes Stanieria cyanosphaera PCC 7437   2 2
No Yes Calothrix parietina Calothrix sp. PCC 6303   1 1
No Yes Cylindrospermum stagnale PCC 7417   2 2
No Yes Anabaena cylindrica PCC 7122   2 2
No Yes Listeria monocytogenes EGD sequence   1 1
No Yes Listeria monocytogenes serotype 4b str. LL195   1 1
No Yes Listeria monocytogenes 07PF0776   1 1
No Yes Listeria monocytogenes M7   1 1
No Yes Listeria monocytogenes J1-220   1 1
No Yes Listeria monocytogenes SLCC2376   1 1
No Yes Listeria monocytogenes SLCC5850   1 1
No Yes Listeria monocytogenes ATCC 19117   1 1
No Yes Listeria monocytogenes L312   1 1
No Yes Listeria monocytogenes SLCC7179   1 1
No Yes Listeria monocytogenes SLCC2540   1 1
No Yes Listeria monocytogenes SLCC2378   1 1
No Yes Listeria monocytogenes serotype 1/2b str. SLCC2755   1 1
No Yes Listeria monocytogenes L99   1 1
No Yes Listeria monocytogenes HCC23   1 1
No Yes Listeria monocytogenes 10403S   1 1
No Yes Listeria monocytogenes Finland 1998   1 1
No Yes Listeria monocytogenes serotype 4b str. F2365   1 1
No Yes Sorangium cellulosum So0157-2   2 2
No Yes Myxococcus stipitatus DSM 14675   1 1
No Yes Simiduia agarivorans SA1 = DSM 21679   1 1
No Yes Vibrio parahaemolyticus BB22OP   1 1
No Yes Vibrio alginolyticus NBRC 15630 = ATCC 17749   1 1
No Yes Vibrio vulnificus CMCP6   1 1
No Yes Vibrio vulnificus YJ016   1 1
No Yes Shewanella baltica OS678   1 1
No Yes Shewanella baltica OS195   1 1
No Yes Shigella sonnei 53G   1 1
No Yes Shigella flexneri 2002017   1 1
No Yes Shigella flexneri 2a str. 2457T   1 1
No Yes Shigella flexneri 2a str. 301   1 1
No Yes Shigella boydii Sb227   1 1
No Yes Escherichia coli E24377A   1 1
No Yes Escherichia coli JJ1886   1 1
No Yes Escherichia coli LY180   1 1
No Yes Escherichia coli APEC O78   1 1
No Yes Escherichia coli O104:H4 str. 2009EL-2050   1 1
No Yes Escherichia coli O104:H4 str. 2009EL-2071   1 1
No Yes Escherichia coli O104:H4 str. 2011C-3493   1 1
No Yes Escherichia coli NA114   1 1
No Yes Escherichia coli P12b   1 1
No Yes Escherichia coli str. 'clone D i2'   1 1
No Yes Escherichia coli str. 'clone D i14'   1 1
No Yes Escherichia coli UM146   1 1
No Yes Escherichia coli 042   1 1
No Yes Escherichia coli IHE3034   1 1
No Yes Escherichia coli UMNK88   1 1
No Yes Escherichia coli ABU 83972   1 1
No Yes Escherichia coli KO11FL   1 1
No Yes Escherichia coli KO11FL   1 1
No Yes Escherichia coli ED1a   1 1
No Yes Escherichia coli UMN026   1 1
No Yes Escherichia coli 55989   1 1
No Yes Escherichia coli S88   1 1
No Yes Escherichia coli IAI1   1 1
No Yes Escherichia coli W   1 1
No Yes Escherichia coli W   1 1
No Yes Escherichia coli DH1   1 1
No Yes Escherichia coli DH1   1 1
No Yes Escherichia coli ATCC 8739   1 1
No Yes Escherichia coli BL21(DE3)   1 1
No Yes Escherichia coli BL21(DE3)   1 1
No Yes Escherichia coli SE15   1 1
No Yes Escherichia coli SE11   1 1
No Yes Escherichia coli APEC O1   1 1
No Yes Escherichia coli O103:H2 str. 12009   1 1
No Yes Escherichia coli UTI89   1 1
No Yes Escherichia coli 536   1 1
No Yes Escherichia coli HS   1 1
No Yes Escherichia coli ETEC H10407   1 1
No Yes Escherichia coli O26:H11 str. 11368   1 1
No Yes Escherichia coli CFT073   1 1
No Yes Escherichia coli O111:H- str. 11128   1 1
No Yes Escherichia coli str. K-12 substr. MDS42   1 1
No Yes Escherichia coli BW2952   1 1
No Yes Escherichia coli str. K-12 substr. MG1655   1 1
No Yes Escherichia coli str. K-12 substr. W3110   1 1
No Yes Escherichia coli str. K-12 substr. DH10B   1 1
No Yes Escherichia coli B str. REL606   1 1
No Yes Pseudomonas aeruginosa PA7   1 1
No Yes Malus x domestica (Duplicate) Apple 3 3
No Yes Ricinus communis (Early assembly) Castor bean 1 1
No Yes Nicotiana benthamiana 0.4.4 (Early draft)   2 2
No Yes Solanum pimpinellifolium A-1.0 (Early draft) Currant tomato 1 1
No Yes Solanum lycopersicum v2.3 (Early assembly) Tomato 1 1
No Yes Vibrio campbellii ATCC BAA-1116 (Duplicate of NC)   1 1
No Yes Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)   1 1
No Yes Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)   1 1
No Yes NCBI 2017_08 genome   9803 9802
No Yes Protozoadb 2010_08 (Protozoadb)   1 1
No Yes simHC - Simulated High Complexity Metagenome (meta-genome)   2 2
No Yes simLC - Simulated Low Complexity Metagenome (meta-genome)   1 1
No Yes simMC - Simulated Medium Complexity Metagenome (meta-genome)   2 2
No Yes Sludge/US, Jazz Assembly (meta-genome)   1 1
No Yes Sludge/US, Phrap Assembly (meta-genome)   1 1
No Yes Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2+ (meta-genome)   1 1
No Yes Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)   2 2
No Yes STRING v9.0.5 (STRING)   90 90
No Yes Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)   1 1
No Yes Uniprot 2018_03 genome   1231 1230
No Yes Global Ocean Sampling Expedition (GOS)   7 7
No Yes NCBI plasmid sequences (Plasmids)   3 3
No Yes NCBI viral sequences (Viral)   2 2
No Yes PDB chains (SCOP 1.75) (PDB)   1 1
No Yes Protein Data Bank (all PDB sequenc)   1 1
No Yes SCOP2 SCOPe CATH ECOD (all domain sequ)   2 2
No Yes TargetDB (Targets)   6 6
No Yes UniProt viral sequences (Viral)   1 1

Jump to [ Top of page · Assignment details · Add assignments from groups of genomes · Add assignments from individual genomes ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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