SupplementaryMaterial 2
List of DFI organisms (Total 74). The sequences were retrieved from GenBank by BLAST search (Supplementary Material 1), initially using T. gondiiFCBP protein sequence as query, but later other DFI sequences were also used in order to identify all sequences with various degrees of similarity. This list is not meant to be exhaustive, as new organisms continue to be discovered and more genomes are sequenced. Over time, several organisms were reclassified and renamed, underscoring the novelty and exotic nature of the organisms. Only for a few, randomly selected organisms, we have also listed the single immunophilin sequences (CYN or FKBP) found in their genome, which shows that there is no relation between the presence of a DFI gene and the presence of CYN and FKBP genes.
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SpeciesDomain structureAccession #Phylogeny Number of single CYNs and FKBPs (and domain information)
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Phylum Apicomplexa
Babesia bigeminaFKBP-TPR-CYNXP_012768359.1Apicomplexa0 FKBP, 9 CYN (CeCYN16, SYF2, Ubox RING, WD40)
Babesia bovis T2BoFKBP-TPR-CYNXP_001608690.1Apicomplexa0 FKBP, 9 CYN (Ubox, WD40)
Babesia microti RIFKBP-TPR-CYNXP_012648744.1Apicomplexa
Eimeria brunettiFKBP-TPR-CYNCDJ53046.1Apicomplexa
Eimeria maximaFKBP-TPR-CYNXP_013335079.1Apicomplexa
Eimeria tenella FKBP-TPR-CYNAET50588.1Apicomplexa2 FKBP, 11 CYN (SYF2, WD40, ZnF-NOSIP)
Hammondia hammondiFKBP-TPR-CYNXP_008888049.1Apicomplexa2 FKBP, 12 CYN (CeCYN16, RING, WD40)
Neospora caninumFKBP-TPR-CYNXP_003883131.1Apicomplexa
Theileria equiFKBP-TPR-CYNXP_004832922.1Apicomplexa
Theileria parvaFKBP-TPR-CYNXP_765469.1Apicomplexa0 FKBP, 9 CYN (RING, WD40)
Toxoplasma gondii(3 strains)FKBP-TPR-CYNAAX51680.1Apicomplexa2 FKBP, 13 CYN (CeCYN16, RING, SYF2, WD40)
Phylum Spirochaetes
Borrelia hermsii DAH CYN-FKBPWP_012422177.1Spirochaetes
Treponema caldaria CYN-FKBPWP_013967678.1Spirochaetes
DSM 7334
Spirochaeta Africana CYN-FKBPWP_014456714.1Spirochaetes 2 CYN, 1 FKBP
Spirochaeta sp. BuddyCYN-FKBP WP_013608701.1Spirochaetes
Spirochaeta coccoides CYN-FKBP WP_013740452.1Spirochaetes
DSM 17374
Spirochaeta lutea CYN-FKBPWP_037548329.1 Spirochete 0 CYN, 1 FKBP
Treponema azotonutricium CYN-FKBPWP_015710234.1Spirochaetes
ZAS-9
Treponema brennaborenseCYN-FKBPWP_013757191.1Spirochaetes
DSM 12168
Treponema denticolaCYN-FKBPWP_002680321.1Spirochaetes0 CYN, 1 FKBP
Treponema primitiaCYN-FKBPWP_015709565.1Spirochaetes0 CYN, 2 FKBP
ZAS-2
Treponema putidumCYN-FKBPWP_044979872.1Spirochaetes
Treponema succinifaciens CYN-FKBPWP_013700291.1Spirochaetes
DSM 2489
Treponema vincentii CYN-FKBPWP_006188840.1Spirochaetes0 CYN, 1 FKBP
ATCC 35580
Phylum Bacteroidetes (mostly Flavobacteria)
Aquimarina agarivoransCYN-FKBPWP_010523173.1Flavobacteria
Aequorivita sp. D-24CYN-FKBPWP_062622682.1Flavobacteria
Capnocytophaga canimorsusCYN-FKBPWP_013997216.1Flavobacteria
Cc5
Capnocytophaga canimorsusCYN-FKBPWP_013997324.1Flavobacteria
Cc5
Capnocytophaga CYN-FKBPWP_002665439.1Flavobacteria
gingivalis ATCC 33624
Capnocytophaga CYN-FKBPWP_002667121.1Flavobacteria
gingivalis ATCC 33624
Capnocytophaga sputigena CYN-FKBP WP_002679844.1Flavobacteria1 CYN, 0 FKBP
Capno
Capnocytophaga ochracea CYN-FKBP WP_015782565.1Flavobacteria0 CYN, 0 FKBP
F0287
Capnocytophaga sp. oralCYN-FKBP WP_009411812.1Flavobacteria
taxon 324
Capnocytophaga sp. oralCYN-FKBP WP_009411339.1Flavobacteria
taxon 324
Cellulophaga algicolaCYN-FKBPWP_013551507.1Flavobacteria
DSM 14237
Cellulophaga algicolaCYN-FKBPWP_013549201.1Flavobacteria
DSM 14237
Cellulophaga lyticaCYN-FKBPWP_013619851.1Flavobacteria
DSM 7489
Chryseobacterium gleumCYN-FKBP WP_002980016.1Flavobacteria0 CYN, 2 FKBP
ATCC 35910
Croceibacter atlanticusCYN-FKBP WP_013187883.1Flavobacteria2 CYN, 1 FKBP
Dokdonia donghaensisCYN-FKBPWP_021778660.1Flavobacteria
multiple strains
Flavobacteria bacterium CYN-FKBPEAZ96145.1 Flavobacteria0 CYN, 0 FKBP
Flavobacteria bacteriumCYN-FKBPWP_006795114.1Flavobacteria
BBFL7
Flavobacteriales bacterium CYN-FKBPWP_013306554.1Flavobacteria
HTCC2170
Flavobacterium chungangenseCYN-FKBPWP_031454950.1 Flavobacteria 0 CYN, 1 FKBP
Flavobacterium daejeonenseCYN-FKBPWP_055090896.1 Flavobacteria 0 CYN, 0 FKBP
Flavobacterium frigoris CYN-FKBPWP_007137991.1Flavobacteria 0 CYN, 1 FKBP
Flavobacterium hibernum CYN-FKBPWP_041519349.1 Flavobacteria 0 CYN, 1 FKBP
Flavobacterium hydatis CYN-FKBPWP_035626885.1Flavobacteria 0 CYN, 3 FKBP
Flavobacterium johnsoniaeCYN-FKBPAAM92026Flavobacteria0 CYN, 2 FKBP
Flavobacterium johnsoniaeCYN-FKBPAAM92027Flavobacteria0 CYN, 2 FKBP
Flavobacterium psychrophilumCYN-FKBPYP_001296758.1 Flavobacteria0 CYN, 0 FKBP
JIP02/86
Flavobacterium psychrophilumCYN-FKBPYP_001296759.1 Flavobacteria0 CYN, 0 FKBP
JIP02/86
Flavobacterium reichenbachiiCYN-FKBPWP_035684065.1Flavobacteria 0 CYN, 0 FKBP
Flavobacterium seoulenseCYN-FKBPWP_035658288.1 Flavobacteria 0 CYN, 1 FKBP
Flavobacterium succinicans CYN-FKBPWP_024981134.1Flavobacteria 0 CYN, 1 FKBP
Fluviicola taffensis CYN-FKBPWP_013686748.1Flavobacteria
DSM 16823
Gaetbulibacter saemankumensis CYN-FKBPWP_027136884.1Flavobacteria 1 CYN, 2 FKBP
Gelidibacter mesophilusCYN-FKBPWP_027126492.1 Flavobacteria 1 CYN, 2 FKBP
Gramella forsetiiCYN-FKBPCAL65762 Flavobacteria1 CYN, 2 FKBP
Gramella forsetiiCYN-FKBPWP_011710397.1Flavobacteria1 CYN, 2 FKBP
Gramella echinicola CYN-FKBPWP_026933765.1Flavobacteria 1 CYN, 1 FKBP
Kordia algicida OT-1CYN-FKBPWP_007093789.1Flavobacteria1 CYN, 1 FKBP
Lacinutrix sp.CYN-FKBPWP_013870480.1Flavobacteria
5H-3-7-4
Leeuwenhoekiella blandensisCYN-FKBPWP_009781285.1Flavobacteria1 CYN, ~6 FKBP
Leeuwenhoekiella palythoaeCYN-FKBPWP_072983594.1Flavobacteria
Leeuwenhoekiella marinoflavaCYN-FKBPWP_073099465.1Flavobacteria
Mesoflavibacter zeaxanthinifaciensCYN-FKBPWP_010517508.1Flavobacteria 2 CYN, 3 FKBP
Nonlabens marinusCYN-FKBPWP_041496246.1Flavobacteria1 CYN, 1 FKBP
Nonlabens ulvanivoransCYN-FKBPGAL75631.1Flavobacteria
Polaribacter dokdonensisCYN-FKBPWP_053975013.1Flavobacteria 2 CYN, 1 FKBP
Polaribacter irgensii CYN-FKBPWP_004570747.1Flavobacteria 0 CYN, 4 FKBP
Psychroflexus torquis CYN-FKBPAFU67563.1Flavobacteria 1 CYN, 1 FKBP
Psychroserpens damuponensis CYN-FKBPWP_040278254.1Flavobacteria 1 CYN, 0 FKBP
Riemerella anatipestiferCYN-FKBPWP_013446672.1Flavobacteria
DSM 15868
Riemerella anatipestiferCYN-FKBPEFT35731.1Flavobacteria
RA-YM
Robiginitalea biformataCYN-FKBPWP_015754216.1Flavobacteria
Robiginitalea biformataCYN-FKBPWP_015755540.1Flavobacteria
HTCC2501
Salinimicrobium catenaCYN-FKBPSDL76680.1Flavobacteria
Sediminicola spCYN-FKBPWP_062055259.1 Flavobacteria 1 CYN, ~2 FKBP
Tamlana nanhaiensis CYN-FKBPWP_044625819.1 Flavobacteria 1 CYN, 2 FKBP
Tenacibaculum ovolyticum CYN-FKBPWP_028889491.1Flavobacteria 0 CYN, 3 FKBP
Tenacibaculum sp. CYN-FKBPWP_028891023.1Flavobacteria 0 CYN, 8 FKBP
Ulvibacter litoralisCYN-FKBPSDE92800.1Flavobacteria
Weeksella virosaCYN-FKBP WP_013598693.1Flavobacteria
DSM 16922
Winogradskyella spCYN-FKBPWP_045468090.1Flavobacteria 2 CYN, 0 FKBP
Zobellia galactanivoransCYN-FKBPWP_013994175.1Flavobacteria
Zobellia galactanivoransCYN-FKBPWP_013995030.1Flavobacteria
Zunongwangia mangroviCYN-FKBPSFC62278.1Flavobacteria
Zunongwangia profundaCYN-FKBPWP_013071163.1Flavobacteria1 CYN, 2 FKBP
SM-A87
Zunongwangia profunda CYN-FKBPWP_013070348.1Flavobacteria
SM-A87
Superphylum Heterokonta
Albugo candidaFKBP-TPR-CYNCCI40768.1Oomycetes
Albugo laibachiiFKBP-TPR-CYNCCA14206.1Oomycete
Phytophthora infestansFKBP-TPR-CYNXP_002906896.1Oomycetes5 FKBP (EF hand, TPR), 21 CYN (RRM, U-box, WD40)
Phytophthora parasitica FKBP-TPR-CYNETK71084.1Oomycetes
Phytophthora sojaeFKBP-TPR-CYNXP_009516060.1Oomycetes Similar to P. infestans
Plasmopara halstediiFKBP-TPR-CYNCEG39850.1Oomycetes
Saprolegnia diclinaFKBP-TPR-CYNXP_008614859.1Oomycetes
Aphanomyces invadans FKBP-TPR-CYNXP_008864835.1Oomycetes
Others
Candidatus Ruthia magnificaCYN-FKBPWP_011737713.1γ-proteobacteria1 CYN, 0 FKBP
Candidatus ThioglobusCYN-FKBPWP_053820422.1γ-proteobacteria1 CYN, 0 FKBP
Desulfotalea psychrophilaCYN-FKBPWP_011188886.1Proteobacteria0 CYN, 1 FKBP
Desulfobulbus propionicus CYN-FKBP WP_015723644.1Proteobacteria
DSM 2032
Ichthyophthirius multifiliisFKBP-TPR-CYNXP_004031957.1Ciliophora
Oxytricha trifallaxFKBP-TPR-CYNEJY68739.1Ciliophora
Paramecium tetraureliaFKBP-TPR-CYNXP_001444554.1Ciliophora
Paramecium tetraureliaFKBP-TPR-CYNXP_001445268.1Ciliophora
Perkinsus marinusFKBP-TPR-CYNXP_002768449.1Dinoflagellate
Phaeodactylum tricornutumFKBP-TPR-CYNXP_002184174.1Diatom
Pseudocohnilembus persalinusFKBP-TPR-CYNKRX10096.1Ciliophora
Stylonychia lemnaeFKBP-TPR-CYNCDW88109.1Ciliophora
Tetrahymena thermophilaFli-ATPase-FKBP-TPR-CYN XP_976669.2Ciliophora
Thalassiosira oceanicaFKBP-TPR-CYNXP_002286257.1Diatom
Thalassiosira pseudonanaFKBP-TPR-CYNXP_002286257.1Diatom
*Uncultured archaeonFKBP-CYNAAU82569 Archea?
GZfos18C8
*Uncultured archaeonFKBP-CYNCAI64202Archea?
GZfos18C8
Unidentified eubacteriumCYN-FKBPEDM43472.1Eubacteria?
SCB49
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*The genome of this single uncultured and tentatively characterized archaea, code-named GZfos18C8, contained two FCBP sequences, both lacking TPR. These two paralogs are highly similar to each other, with 85% amino acid identity, the major difference being the lack of 12-residue peptide sequence in one of them. According to PRED-SIGNAL, which predicts archaeal signal peptides with Hidden Markov Model, both proteins contain nearly identical signal peptides at the N-terminus (Reliability score >0.9, a perfect score being 1.0). These two FCBP paralogs possibly have a common but uncertain origin. We have ignored these two sequences in the rest of the paper, and until more definitive archaeal examples are found, we will maintain that the DFIs are absent in archaea.