Data Files for AJS (2005) Genomic Publication
Zerkle, A.L., House, C.H., Brantley, S. 2005. Genomic Study of Biogeochemical Signatures for Microbial Metabolisms through Time. American Journal of Science, 305 (“Oct., Sept., Nov.” Issue): 467-502.
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)
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)
