Zerkle, House, and Brantley (2005) American Journal of Science [PDF]

Combined Data Matrix Files - nexus format:         (abbreviations found below)
zero.nex (13 groups based on gene presence in > 0% taxa, including single taxa; 'z' = 0%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphaz,betaz,crenz,cyanoz,epsilonz,bsaz,ccsz,gammaz,hgcz,ltz,methz,pyroz,thermoz     

ten.nex (13 groups based on gene presence in > 10% taxa, including single taxa; 'ten' = 10%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphaten,betaten,crenten,cyanoten,epsilonten,bsaten,ccsten,gammaten,hgcten,ltten,methten,pyroten,thermoten     

fifteen.nex (13 groups based on gene presence in > 15% taxa, including single taxa; 'fifteen' = 15%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphafifteen,betafifteen,crenfifteen,cyanofifteen,epsilonfifteen,bsafifteen,ccsfifteen,gammafifteen,hgcfifteen,ltfifteen,methfifteen,pyrofifteen,thermofifteen     

twenty.nex (13 groups based on gene presence in > 20% taxa, including single taxa; 'twenty' = 20%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphatwenty,betatwenty,crentwenty,cyanotwenty,epsilontwenty,bsatwenty,ccstwenty,gammatwenty,hgctwenty,lttwenty,methtwenty,pyrotwenty,thermotwenty     

twentyfive.nex (13 groups based on gene presence in > 25% taxa, including single taxa; 'tf' = 25%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphatf,betatf,crentf,cyanotf,epsilontf,bsatf,ccstf,gammatf,hgctf,lttf,methtf,pyrotf,thermotf     

fifty.nex (13 groups based on gene presence in > 50% taxa, including single taxa; 'f' = 50%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphaf,betaf,crenf,cyanof,epsilonf,bsaf,ccsf,gammaf,hgcf,ltf,methf,pyrof,thermof     

ninetynine.nex (13 groups based on gene presence in > 99% taxa, including single taxa; 'nn' = 99%)
fn,aa,dr,cte,tm,af,hsp,mj,mk,mt,alphann,betann,crennn,cyanonn,epsilonnn,bsann,ccsnn,gammann,hgcnn,ltnn,methnn,pyronn,thermonn    

finalgroups.nex (13 groups based on gene presence in > 20% taxa, excluding single taxa)
alpha,beta,cren,cyano,epsilon,lgc,gamma,hgc,meth1, meth2,pyro,thermo     


Supplemental Data Tables:
Dowload MS excel file - Fe, Zn, Cu, Mn, Mo, Ni, Co, V, and W -containing metallo-enzymes (when number of moles per enzyme unknown, assumed 1)
Compiled from Burgess and Lowe, 1996; Dismukes, 1996; Hille, 1996; Holm and others, 1996; Johnson and others, 1996; Lipscomb and Str
ter, 1996; Ragsdale and Kumar, 1996; Berman and others, 2000; Frausto da Silva and Williams, 2001; Lvov and others, 2002; and references therein.


Prokaryote Abbreviations:
ap    Aeropyrum pernix
at    Agrobacterium tumefaciens
aa    Aquifex aeolicus
af    Archaeoglobus fulgidus
bh    Bacillus halodurans
bs    Bacillus subtilis
bm    Brucella melitensis
cj    Campylobacter jejuni
cc    Caulobacter crescentus (vibroides)
cte    Chlorobium tepidum
ca    Clostridium acetobutylicum
cpe    Clostridium perfringens
cg    Corynebacterium glutamicum
dr    Deinococcus radiodurans
ec    Escherichia coli
fn    Fusobacterium nucleatum
hi    Haemophilus influenzae Rd
hsp    Halobacterium sp.
hp    Helicobacter pylori
ll    Lactococcus lactis
ml    Mesorhizobium loti
mt    Methanobacterium thermoautotrophicum
mj    Methanococcus jannaschii
mk    Methanopyrus kandleri
ma    Methanosarcina acetivorans
mma    Methanosarcina mazei
mle    Mycobacterium leprae
nmz    Neisseria meningitidis
ns    Nostoc sp.
psa    Pseudomonas aeruginosa
pa    Pyrobaculum aerophilum
pab    Pyrococcus abyssi
pag    Pyrobaculum aerophilum
pf    Pyrococcus furiosus
ph    Pyrococcus horikoshii
rs    Ralstonia solanacearum
sty    Salmonella typhimurium
sm    Sinorhizobium meliloti
sam    Staphylococcus aureus
sp    Streptococcus pyogenes
sco    Streptomyces coelicolor
ss    Sulfolobus solfataricus
st    Sulfolobus tokodaii
sy    Synechocystis sp.
tt    Thermoanaerobacter tengcongensis
ta    Thermoplasma acidophilum
tv    Thermoplasma volcanium
tm    Thermotoga maritima
vc    Vibrio cholerae
xa    Xanthomonas axonopodis pv citri
xc    Xanthomonas campestris
xf    Xylella fastidiosa
yp    Yersinia pestis

Group Abbreviations:
alpha      Alpha-Proteobacteria (at,bm,cc,ml,sm)
beta        Beta-Proteobacteria (nmz,rs)
gamma   Gamma-Proteobacteria (ec,hi,psa,sty,vc,xa,xc,xf,yp)
epsilon    Epsilon-Proteobacteria (cj,hp)
bsa         Low GC Gram Positive (Firmicutes) Group 1 (bh,bs,sam)
ccs         Low GC Gram Positive Group 2 (ca,spe,sp)
lt            Low GC Gram Positive Group 3 (ll,tt)
lgc         Low GC Gram Positive Combined (bh,bs,sam,ca,spe,sp,ll,tt)
hgc        High GC Gram Positive (Actinobacteria; cg,mle,sco)
cyano    Cyanobacteria (ns,sy)
cren       Crenarchaeota (ap,pag,ss,st)
meth1    Methanogenic Archaea Group 1 (ma,mma)
meth2    Methanogenic Archaea Group 2 (mj,mk)
meth      Methanogenic Archeaea Combined (ma,mma,mj,mk)
pyro      Pyrococcus spp. (pab,pf,ph)
thermo   Thermoplasma spp. (ta,tv)