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Supplementary Material S2: Differences in enzyme gene sets between halophilic archaea. Alternative, mostly non-orthologous, enzymes that catalyze the same pathway
steps are marked by arrows ().
H. marismortui
H. walsbyi
N. pharaonis
H. salinarum
glucose 1-dehydrogenase (EC 1.1.1.47)
conserved Entner-Douderoff pathway gene
conserved Entner-Douderoff pathway gene
D-gluconate dehydratase (gnaD), homolog to SSO3198
2-keto-3-deoxygluconate kinase (EC 2.7.1.45), homol. to SSO3195
2-keto-3-deoxyphosphogluconate (KDPG) aldolase (EC 4.1.2.14)
 KD(P)G aldolase, homolog to SSO3197
rrnAC0917
rrnAC0927
rrnAC2547
rrnAC0575
rrnAC0545, rrnAC2551
rrnAC3121
rrnAC0960
HQ1663A
HQ1664A
HQ2411A
HQ2412A
HQ1455A
HQ1495A
HQ2365A
-
OE1669F
OE1672F
OE1668R
OE1664R
OE1266R
OE1665R
glycerol dehydrogenase (EC 1.1.1.6)
glycerol kinase (EC 2.7.1.30)
glycerol-3P dehydrogenase (EC 1.1.99.5)
sn-glycerol-3-phosphate ABC transport system
rrnAC0550
rrnAC0554-rrnAC0556
rrnB0311-rrnB0315
HQ1733A
HQ1734A-HQ1736A
HQ1989A-HQ1992A
-
OE5160F (PL)
OE3762R
OE3763F-OE3765F
OE5166F-OE5170F
GAP dehydrogenase (EC 1.2.1.59)
 GAP dehydrogenase, archaeal-type
phosphoenolpyruvate carboxylase (EC 4.1.1.31)
dihydroxyacetone kinase (EC 2.7.1.29)
sugar phosphotransferase system, ptsI subunit (EC 2.7.3.9)
ptsIIB/C subunits
rrnAC2262
rrnAC2363
rrnAC0562
pNG7391 (PL)
pNG7392/pNG7387 (PL)
HQ1360A, HQ2025A
HQ1394A
HQ3197A
HQ2672A, HQ2673A
HQ2709A
-
NP0012A
-
OE1154F
-
isocitrate lyase (EC 4.1.3.1), glyoxylate cycle
malate synthase (EC 4.1.3.2), glyoxylate cycle
rrnAC1965
HQ3094A
HQ1720A
NP4432A
NP4430A
-
1-phosphofructokinase (EC 2.7.1.56)
sucrose-6P hydrolase (EC 3.2.1.26)
4-alpha-glucanotransferase (EC 2.4.1.25), malQ
maltose ABC transporter
α-glucosidases
rrnAC0342
rrnAC1479
rrnAC1957
rrnAC2346-rrnAC2349
rrnAC0224, rrnAC1962,
rrnAC2350
rrnAC1961, rrnAC2353
rrnAC0237
pNG7029 (PL)
-
-
-
-
-
-
rrnAC0090/rrnAC0091,
rrnAC3147/rrnAC3148
rrn0731-rrn0733,
rrnAC1196 (fusion protein)
-
-
NP3168A/NP3170A
OE4005F/OE4007F
HQ3198A &
HQ1550A/HQ1551A
-
-
OE1872R-OE1876R
-
OE6185F/OE6186F (PL)
Central/sugar metabolism and transport
glycosyl hydrolases
trehalose-6P synthase (EC 2.4.1.15), otsA
rhamnulokinase (EC 2.7.1.5)
electron transfer flavoprotein
pet genes (complex III)
cytochrome d oxidase
Amino acid and nitrogen metabolism
arginine biosynthesis enzymes, e.g. argB
branched-chain amino acid biosynthesis enzymes, e.g. leuB
lysine biosynthesis enzymes, e.g. dapB
succinyl-dap desuccinylase (EC 3.5.1.18, dapE)
diaminopimelate epimerase (EC 5.1.1.7, dapF)
rrnAC0078, rrnAC2676
rrnAC0340
rrnAC0206
rrnAC0196
-
HQ3716A
HQ2707A
HQ1508A
HQ1512A
HQ1511A
NP5262A
NP2190A
NP1492A
-
-
hydroxypyruvate reductase (EC 1.1.1.81), Ser biosynthesis
threonine aldolase (EC 4.1.2.5), Gly metabolism
pNG7015 (PL)
-
HQ1667A
-
NP1162A
-
OE4436R
proline synthesis enzymes (proCBA)
 proline dehydrogenase (EC 1.5.99.8)
rrnAC2471
HQ1844-HQ1846A
-
NP3974A-NP3978A
-
OE3955F
arginine deiminase pathway enzymes
argininase (EC 3.5.3.1)
rrnAC0383, rrnAC0453
-
-
OE5205R-OE5209R (PL)
-
methylaspartate mutase (EC 5.4.99.1), Glu fermentation
methylaspartate ammonia-lyase (EC 4.3.1.2)
urocanate metabolism (hut genes), His degradation
tryptophanase (EC 4.1.99.1)
kynureninase (EC 3.7.1.3)
tyrosine decarboxylase (EC 4.1.1.25)
glycine cleavage system (EC 1.4.4.2)
rrnAC0684/rrnAC0685
rrnAC0687
rrnAC1787-rrnAC1791
rrnAC2439
rrnAC1798
rrnAC1497/rrnAC1499 &
pNG7366/pNG7370 (PL)
-
NP1194A
NP4772A/NP4774 &
NP4594A/NP4596A
OE4204F/OE4206F
OE4207F
OE2734F-OE2739F
OE4331R
OE2332F
OE1498R
OE3274R-OE3278R
urease & ABC urea transporter
nitrate assimilation pathway enzymes & transporter
glutamate synthase
nitrate reductase (respiratory)
nitrous-oxide reductase
nitrilase
nitric-oxide synthase (EC 1.14.13.39), oxygenase subunit
N-methylhydantoinase (ATP-hydrolyzing) (EC 3.5.2.14)
pNG7123-pNG7129 (PL)
rrnAC2625-rrnAC2627
rrnAC0169
rrnAC1199/rrnAC1200
rrnAC0390
rrnAC0810(pNG7354,PL)
pNG7165/pNG7165 (PL)
HQ3625A-HQ3631A
HQ2210A-HQ2213A
HQ1714A
HQ2241A/HQ2242A
-
formamidase (EC 3.5.1.49)
pNG7060 (PL)
-
NP2008A-NP2020A
NP4224-NP4228A
NP1794A
NP0374A, NP0178A
NP1908A
NP2952A/NP2952A
(NP6216A/NP6218A, PL)
NP6204A (PL)
probable sulfite dehydrogenase (EC 1.8.2.1)
-
NP2718A, NP2044A
OE2569R
probable sulfite reductase
rrnAC1375, rrnAC1624,
rrnAC3141
rrnAC2992, rrnAC2625
HQ1116A, HQ2212A
-
thiosulfate sulfurtransferase (EC 2.8.1.1)
rrnAC2128/rrnAC2129
HQ3729A/HQ3730A,
HQ2038A
NP4004A (Cterm),NP1146A
NP3186A, NP4004A
(N-terminus)
Nitrogen and sulfur metabolism
-
OE4355R/OE4356F
Cofactor, nucleotide, and lipid metabolism
α-ribazole-phosphate phosphatase (EC 3.1.3.71, cobC)
thiamine-P pyrophosphorylase (EC 2.5.1.3, thiE)
 thiN (Morett et al. 2003)
HQ3517A
HQ2655A
HQ1277A
thiamine biosynthesis protein (thiC)
  tenA (Morett et al. 2003)
hydroxyethylthiazole kinase (EC 2.7.1.50, thiM)
rrnAC2859
rrnAC2143
rrnAC1764, rrnAC1777,
rrnAC2449 (thiDN)
rrnAC1182
rrnAC1765/rrnAC1767
-
HQ2369A
HQ2656A
NP1332A
NP4054A
NP5168A,
NP0546A (thiDN)
NP2210A
NP4080A/NP4082A
NP4052A
OE1385F,
OE4654F (thiDN)
OE2057F
-
biotin biosynthesis enzymes (bioB, bioF)
dethiobiotin synthase (EC 6.3.3.3, bioD)
rrnAC0883/rrnAC0885
-
-
NP4232A/NP4236A
NP4230A
-
GTP cyclohydrolase I (EC 3.5.4.16), archaeal-type
 GTP cyclohydrolase I, bacterial-type
dihydrofolate reductase (EC 1.5.1.3, folA),
 prd domain protein, with reduced activity
folate biosynthesis enzymes (metF)
folate biosynthesis enzymes (fhs)
rrnAC3309
pNG7382 (PL)
rrnAC0859(pNG7359,PL)
rrnAC0184
pNG7363(PL)
pNG7380 (PL)
HQ3317A
HQ1842A, HQ2455A
HQ1767A
HQ1756A
HQ1768A
NP2514A
NP2922A
NP1478A
-
OE3673F
OE1615R
-
thymidylate synthase (EC 2.1.1.45, thyA)
 thymidylate synthase (thyX)
uridine kinase (EC 2.7.1.48)
thymidine kinase (EC 2.7.1.21)
rrnAC1121
-
HQ2456A
HQ1795A
NP2924A
-
OE2898R
OE2749F
OE3159R
AMP phosphorylase
ribose-1,5-bisphosphate isomerase
RuBisCO (EC 4.1.1.39), type III
-
-
NP3958A
NP3202A
NP2770A
OE3610R
-
IPP isomerase (EC 5.3.3.2), type I, bacterial-type
 IPP isomerase, type II, archaeal type
β-carotene monooxygenase, homolog to cyanobacterial enzyme
rrnAC3484
pNG7272 (PL)
HQ2772A
(HQ2847A)
HQ2381A, HQ2020A &
HQ3007A (plant-like)
NP4826A
NP0360A (NP5124A)
-
OE3560F
OE6213R (PL)
-
alkaline phosphatase
  alkaline phosphatase D
rrnAC0273
-
-
OE5192R (PL)
-
chitinase
-
-
-
halolysin/subtilisin-like serine proteases
-
-
carboxypeptidase
  LD-type carboxypeptidase
  probable carboxypeptidase
rrnAC1893
rrnAC2092
HQ2062A
HQ1367A
NP1682A/NP4612F/
NP4628A
NP5372A
NP0944A
OE2201F/OE2205F/
OE2206F
OE4612F (halolysin R4)/
OE3740R
OE4673F
Secretion enzymes
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