Supplementary Table 1: List of the 93 genomes queried to build the manually curated 3D structure-guided multiple sequence alignments. Names of genomes are classified according to the belonging to alpha-proteobacteria, cyanobacteria, bacteria, archaea and eukarya. Taxonomy ID (NCBI) / home-defined MiSynPat sequence name nomenclature / species name (binomiale nomenclature)


alpha-proteobacteria
181661 / Agro.tume / Agrobacterium tumefaciens
770 / Anap.marg / Anaplasma marginale
38323 / Bart.hens / Bartonella henselae
803 / Bart.quin / Bartonella quintana
375 / Brad.japo / Bradyrhizobium japonicum
235 / Bruc.abor / Brucella abortus
29459 / Bruc.meli / Brucella melitensis
29461 / Bruc.suis / Brucella suis
335992 / Cand.Pela / Candidatus Pelagibacter ubique
155892 / Caul.cres / Caulobacter crescentus
944 / Ehrl.cani / Ehrlichia canis
302409 / Ehrl.rumi / Ehrlichia ruminantium Gardel
254945 / Ehrl.rumi / Ehrlichia ruminantium Welgevonden
442 / Gluc.oxyd / Gluconobacter oxydans
381/ Meso.loti / Mesorhizobium loti
1076 / Rhod.palu / Rhodopseudomonas palustris
781 / Rick.cono / Rickettsia conorii
42862 / Rick.feli / Rickettsia felis
782 / Rick.prow / Rickettsia prowazekii
785 / Rick.typh / Rickettsia typhi
89184 / Sili.pome / Silicibacter pomeroyi
382 / Sino.meli / Sinorhizobium meliloti
292805 / Wolb.endo / Wolbachia endosymbiont of B. malayi
163164 / Wolb.endo / Wolbachia endosymbiont of D. melano
542 / Zymo.mobi / Zymomonas mobilis

cyanobacteria
1172 / Anab.vari / Anabaena variabilis
1177 / Anab.sp / Nostoc
1142 / Syne.sp / Synechocystis

bacteria
63363 / Aqui.aeol / Aquifex aeolicus
29544 / Azoa.sp. / Azoarcus sp.
1392 / Baci.anth / Bacillus anthracis
818 / Bact.thet / Bacteroides thetaiotaomicron
216816 / Bifi.long / Bifidobacterium longum
139 / Borr.burg / Borreliella burgdorferi
197 / Camp.jeju / Campylobacter jejuni
129958 / Carb.hydr / Carboxydothermus hydrogenoformans
83560 / Chla.muri / Chlamydia muridarum
83558 / Chla.pneu / Chlamydia pneumoniae
1097 / Chlo.tepi / Chlorobaculum tepidum
61435 / Deha.ethe / Dehalococcoides ethenogenes
1299 / Dein.radi / Deinococcus radiodurans
562 / Esch.coli / Escherichia coli
851 / Fuso.nucl / Fusobacterium nucleatum
35554 / Geob.sulf / Geobacter sulfurreducens
33959 / Lact.john / Lactobacillus johnsonii
1575 / Leif.xyli / Leifsonia xyli
173 / Lept.inte / Leptospira interrogans
28227 / Myco.pene / Mycoplasma penetrans
487 / Neis.meni / Neisseria meningitidis
1747 / Prop.acne / Propionibacterium acnes
265606 / Rhod.balt / Rhodopirellula baltica
1280 / Stap.aure / Staphylococcus aureus
1313 / Stre.pneu / Streptococcus pneumoniae
1143 / Syne.sp. / Synechocystis sp.
2336 / Ther.mari / Thermotoga maritima
2039 / Trop.whip / Tropheryma whipplei
670 / Vibr.para / Vibrio parahaemolyticus

archae
56636 / Aero.pern / Aeropyrum pernix
2234 / Arch.fulg / Archaeoglobus fulgidus
2243 / Halo.sp. / Halobacterium sp.
145262 / Meth.ther / Methanothermobacter thermautotrophicus
2190 / Meth.jann / Methanocaldococcus jannaschii
2320 / Meth.kand / Methanopyrus kandleri
2209 / Meth.maze / Methanosarcina mazei
160232 / Nano.equi / Nanoarchaeum equitans
13773 / Pyro.aero / Pyrobaculum aerophilum
2261 / Pyro.furi / Pyrococcus furiosus
2287 / Sulf.solf / Sulfolobus solfataricus
2303 / Ther.acid / Thermoplasma acidophilum

eukaryota
3702 / Arab.thal / Arabidopsis thaliana
7955 / Dani.reri / Danio rerio
6239 / Caen.eleg / Caenorhabditis elegans
7719 / Cion.inte / Ciona intestinalis
5207 / Cryp.neof / Cryptococcus neoformans
45157 / Cyan.mero / Cyanidioschyzon merolae
44689 / Dict.disc / Dictyostelium discoideum
7227 / Dros.mela / Drosophila melanogaster
6035 / Ence.cuni / Encephalitozoon cuniculi
5759 / Enta.hist / Entamoeba histolytica
9031 / Gall.gall / Gallus gallus
5741 / Giar.inte / Giardia intestinalis
9606 / Homo.sapi / Homo sapiens
5664 / Leis.majo / Leishmania major
4530 / Oryz.sati / Oryza sativa
5833 / Plas.falc / Plasmodium falciparum
4932 / Sacc.cere / Saccharomyces cerevisiae
4896 / Schi.pomb / Schizosaccharomyces pombe
7668 / Stro.purp / Strongylocentrotus purpuratus
5911 / Tetr.ther / Tetrahymena thermophila
35128 / Thal.pseu / Thalassiosira pseudonana
5875 / Thei.parv / Theileria parva
5722 / Tric.vagi / Trichomonas vaginalis
5693 / Tryp.cruz / Trypanosoma cruzi