Supplemental File
The pyruvate - tricarboxylic acid cycle node: a focal point of virulence control in the enteric
pathogen Yersinia pseudotuberculosis*
René Bücker1, 2, Ann Kathrin Heroven3, Judith Becker1, Petra Dersch3, and Christoph
Wittmann1*
1
Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
2
Institute of Biochemical Engineering, Technische Universität Braunschweig, Germany
3
Department of Molecular Infection Biology, Helmholtz Centre for Infection Research,
Braunschweig, Germany
*Running title: Interplay between metabolism and virulence in Yersinia
To whom correspondence should be addressed: Christoph Wittmann, Institute of Systems
Biotechnology, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany, Tel: (49681)-30271971; Fax: (49-681)-30271972; E-mail: [email protected]
Table S1. Transcriptional profile of glucose-grown single-gene deletion mutants Y. pseudotuberculosis
YP3 (ΔrovA), YP53 (ΔcsrA) and YP89 (Δcrp). Data are given as the fold change in expression compared
to Y. pseudotuberculosis wild type (YPIII). The analysis comprised three biological replicates for each
strain and samples from three different time points during exponential growth phase to validate constant
expression during cultivation. The set of differentially expressed genes was filtered by the fold change
(|log2FC| >=0.8). All array data generated in this study were deposited in the Gene Expression Omnibus
(GEO) database and are available under accession number GSE54547.
Locus
Gene
name
Product, description
Fold change
Δcrp
VIRULENCE GENES
pYV0013
yadA
pYV0020
sycH
sycE,
pYV0024
yerA
pYV0025
yopE
pYV0055
yopK/yop
Q
yopB
pYV0057
lcrV
pYV0058
pYV0062
pYV0063
lcrG
yscX
sycN
pYV0064
tyeA
pYV0065
yopN,
lcrE
pYV0040
pYV0067
sctN
pYV0073
pYV0074
pYV0075
pYV0076
pYV0087
yscT
yscU
virG
lcrF, virF
yscK
yscM,
lcrQ
pYV0089
pYV0094
yopH
YPK_0051
YPK_0053
YPK_0054
YPK_0220
fimA-1
fimC-1
YPK_0251
yhhZ-1
YPK_0280
bfd
YPK_0281
bfr
YPK_0385
hcp1-1
hofM
YPK_0386
impB
YPK_0387
impC-1
YPK_0388
YPK_0389
YPK_0390
impG-1,
vasA-1
impH-1,
vasB-1
YPK_0391
impI,
vasC
YPK_0392
vasD, lip
YPK_0393
impJ,
vasE
YPK_0394
YPK_0395
clpB2
YPK_0398
vasJ
YPK_0399
impL,
vasK
YPK_0400
vasL
YPK_0694
YPK_0696
smfA-1
papD
YPK_0791
yspR
YPK_0792
yspI
YPK_0798
YPK_0871
yadF
YPK_1268
ailA
YPK_1304
YPK_1475
YPK_1479
fimA-2
ΔcsrA
ΔrovA
adhesin YadA
YopH targeting protein
1.60
-1.33
-2.06
-2.17
2.72
-1.56
YopE chaperone
-1.96
-2.00
-1.58
outer membrane virulence
protein
Yop targeting protein
YopK, YopQ
Yop targeting protein
V antigen, antihost
protein/regulator
Yop regulator
type III secretion protein
type III secretion protein
Yop secretion and
targeting protein
membrane-bound Yop
targeting protein
Yops secretion ATP
synthase
type III secretion protein
type III secretion protein
Yop targeting lipoprotein
thermoregulatory protein
type III secretion protein
type III secretion
regulatory
protein-tyrosine
phosphatase Yop effector
fimbrial protein
pili assembly chaperone
fimbrial protein
pilus assembly protein
type VI secretion system
effector, Hcp1 family
bacterioferritin-associated
ferredoxin
bacterioferritin
type VI secretion system
effector, Hcp1 family
type VI secretion protein,
VC_A0107 family
type VI secretion protein,
EvpB/VC_A0108 family
type VI secretion system
lysozyme-related protein
type VI secretion protein,
VC_A0110 family
type VI secretion protein,
VC_A0111 family
type VI secretion cluster,
FHA domain containing
protein
type VI secretion cluster,
putative lipoprotein
type VI secretion protein,
VC_A0114 family
type VI secretion cluster,
conserved protein
type VI secretion ATPase,
ClpV1 family
type VI secretionassociated protein,
VC_A0119 family
type VI secretion protein
IcmF
type VI secretion cluster,
ImpA domain protein
fimbrial protein
pili assembly chaperone
transcriptional regulator,
LuxR family
autoinducer synthesis
protein
type VI secretion protein,
VC_A0107 family
YadA domain protein
virulence-related outer
membrane protein
type VI secretion system
effector, Hcp1 family
fimbrial protein
type VI secretion protein,
VC_A0107 family
type VI secretion system
effector, Hcp1 family
YPK_1522
smfA-2
fimbrial protein
transcriptional regulator,
YPK_1559
rovM
LysR family
ompX/ail
virulence-related outer
YPK_1606
D
membrane protein
transcriptional regulator,
YPK_1655
ypsR
LuxR family
autoinducer synthesis
YPK_1656
ypsI
protein
YPK_1705
ycfJ
17 kDa surface antigen
YPK_1761
yadE
YadA domain protein
YPK_1775
fimC-2
chaperone protein
YPK_1786
fimA-3
fimbrial protein
transcriptional regulator,
YPK_1876
rovA
MarR family
putative virulence factor
YPK_1953
srfB
SrfB
filamentous
YPK_2156
hlyA
haemagglutinin domain
protein
YPK_2429
invA
invasin region 3
YPK_2758
psaB
pili assembly chaperone
pH 6 antigen precursor
YPK_2759
psaA
(antigen 4) (adhesin)
conserved hypothetical
YPK_2760
psaF
protein
transcriptional regulator,
YPK_2761
psaE
CadC
secretion protein HlyD
YPK_2900
ybhG, yhiI
family protein
type VI secretion system
YPK_3060
yhhZ-2
effector, Hcp1 family
haemolysin expression
YPK_3214
ymoA
modulating family protein
YPK_3289
crl
transcriptional regulator Crl
type VI secretion protein
YPK_3550
icmF
IcmF
type IV / VI secretion
YPK_3551
system protein, DotU
family
type VI secretion protein,
YPK_3552
VC_A0114 family
type VI secretion cluster,
YPK_3553
putative lipoprotein
pentapeptide repeat
YPK_3556
protein
pentapeptide repeat
YPK_3557
protein
type VI secretion system
YPK_3558
vgrG
Vgr family protein
type VI secretion ATPase,
YPK_3559
clpB
ClpV1 family
impH-2,
type VI secretion protein,
YPK_3560
vasB-2
VC_A0111 family
impG-2,
type VI secretion protein,
YPK_3561
vasA-2
VC_A0110 family
type VI secretion system
YPK_3562
impH-3
lysozyme-related protein
type VI secretion cluster,
YPK_3563
impC-2
unknown protein DUF796
type VI secretion protein,
YPK_3564
impC-3
EvpB/VC_A0108 family
type VI secretion protein,
YPK_3565
VC_A0107 family
YPK_3566
ImpA domain protein
YPK_4042
fimA-5
fimbrial protein
heme-binding A family
YPK_4085
HasA
protein
secretion protein HlyD
YPK_4109
raxA
family protein
CELL MOTILITY AND CHEMOTAXIS
flagellar transcriptional
YPK_1745
flhD
activator
flagellar transcriptional
YPK_1746
flhC
activator FlhC
YPK_1747
motA
chemotaxis protein MotA
OmpA/MotB domain
YPK_1748
motB
protein
CheA signal transduction
YPK_1749
cheA
histidine kinase
YPK_1750
cheW
CheW protein
methyl-accepting
YPK_1753
cheD
chemotaxis sensory
transducer
chemotaxis phosphatase,
YPK_1759
cheZ
CheZ
YPK_1481
-1.29
-1.89
-1.13
-2.67
-3.43
-1.69
2.01
1.15
1.79
-1.24
-2.66
-1.15
-1.29
1.75
2.20
-2.77
1.55
1.78
-1.31
1.64
1.61
2.36
1.75
1.64
2.16
1.85
1.69
1.01
-1.97
-1.32
-1.30
-1.33
-1.73
-1.35
-1.38
-2.28
-2.58
-2.01
-1.96
-1.96
-1.46
-1.48
-1.80
-1.58
-1.13
-1.47
-2.05
-1.72
3.39
1.60
1.61
9.57
2.72
2.00
1.11
-1.43
1.13
-1.17
2.08
-1.06
-1.17
-1.22
1.16
-2.16
1.84
-1.47
-1.98
-5.76
-1.64
3.07
-1.18
-1.58
1.92
-1.41
-1.31
2.55
-1.11
-1.01
3.51
1.60
1.65
3.14
1.46
1.33
2.40
1.20
1.22
2.39
1.16
1.46
1.77
1.27
-1.17
2.12
1.18
1.25
2.53
1.52
1.41
2.00
1.39
1.28
1.95
1.32
1.39
1.78
1.23
1.18
1.82
1.27
1.20
1.77
1.28
1.37
-2.35
1.75
-1.86
1.02
-1.47
1.31
-1.87
1.01
-1.41
-3.15
-1.35
-1.94
1.25
1.75
1.26
2.25
-1.02
1.05
3.27
1.56
1.96
-2.53
-2.91
-1.72
-1.89
1.71
-1.62
1.46
1.76
1.49
-1.67
2.40
-1.54
-2.35
-1.84
-1.48
1.40
-7.63
-1.66
-1.20
3.16
-2.09
-1.58
-2.20
-1.64
-5.06
-3.82
-2.00
3.74
5.76
1.82
-1.75
9.70
-1.54
1.09
-3.06
1.15
1.16
1.12
-1.40
-1.67
1.84
-2.66
-5.02
-5.58
1.16
-1.25
-1.58
-1.84
-1.06
-1.68
2.54
1.94
-1.15
-1.70
-1.18
12.53
-1.43
-2.87
-1.44
-3.05
-3.48
-1.28
-3.18
1.68
1.93
1.37
-1.43
2.67
-1.43
-1.34
-1.21
-1.76
-2.41
-1.20
-1.78
5.40
2.01
1.23
7.82
2.48
1.48
9.03
3.31
2.14
11.73
3.65
2.17
9.28
3.54
1.74
6.26
2.86
1.74
8.29
2.52
1.52
4.25
1.77
1.20
7.04
2.63
1.20
5.48
2.81
1.56
11.86
3.88
1.70
15.52
8.71
1.73
11.93
2.94
2.14
9.65
2.79
2.16
5.90
-2.24
1.92
-1.95
1.06
-1.29
-3.46
-3.00
-1.99
-1.01
-1.77
-1.09
-17.65
-14.68
-1.56
-9.69
-10.49
-1.14
-4.78
-5.14
-1.21
-2.42
-2.65
-1.11
-2.59
-3.10
1.29
-3.85
-4.97
-1.11
-2.14
-2.41
-1.01
-1.66
-2.05
-1.16
YPK_2378
fliZ
YPK_2380
fliA
YPK_2381
fliC
YPK_2382
fliD
YPK_2383
YPK_2384
fliS
fliT
YPK_2390
fliE
YPK_2391
fliF
YPK_2392
fliG
YPK_2393
fliH
YPK_2394
YPK_2395
fliI
fliJ
YPK_2396
fliK-1
YPK_2398
fliL
YPK_2399
fliM
YPK_2400
fliN
YPK_2401
fliO
YPK_2402
fliP
YPK_2403
fliQ
YPK_2415
flgL
YPK_2416
flgK
YPK_2417
flgJ
YPK_2418
YPK_2419
flgI
flgH
YPK_2420
flgG
YPK_2421
flgF
YPK_2422
flgE
YPK_2423
flgD
YPK_2424
flgC
YPK_2425
flgB
YPK_2426
flgA
YPK_2427
YPK_2428
flgM
flgN
YPK_2430
flhE
YPK_2431
flhA
YPK_2432
flhB
STRESS ADAPTATION
YPK_0011
ibpA
YPK_0012
ibpB
YPK_0035
sodA
YPK_0120
uspA
YPK_0121
uspB
YPK_0442
cspA-1
YPK_0443
cspA-2
YPK_0444
cspA-3
YPK_1124
cspB-1
YPK_1740
cspC-1
YPK_1894
pspA
YPK_1896
pspC
YPK_1943
uspE
YPK_2017
cstA-1
YPK_2355
uvrC
YPK_2474
cspC-2
YPK_2662
cspB-2
YPK_2694
YPK_2855
cspD-2
katA
YPK_3031
cspE
YPK_3032
cspC-3
YPK_3161
ybbN
YPK_3269
ggt
YPK_3388
YPK_3445
katY
sodC
flagella biosynthesis
protein FliZ
RNA polymerase, sigma
28 subunit, FliA/WhiG
flagellin domain protein
flagellar hook-associated 2
domain protein
flagellar protein FliS
flagellar export chaperone
flagellar hook-basal body
complex subunit FliE
flagellar M-ring protein FliF
flagellar motor switch
protein FliG
flagellar assembly protein
FliH
ATPase, FliI/YscN family
flagellar export protein FliJ
flagellar hook-length
control protein
flagellar basal bodyassociated protein FliL
flagellar motor switch
protein FliM
flagellar motor switch
protein FliN
flagellar biosynthesis
protein FliO
flagellar biosynthetic
protein FliP
flagellar biosynthetic
protein FliQ
flagellar hook-associated
protein 3
flagellar hook-associated
protein FlgK
flagellar rod assembly
protein/muramidase FlgJ
flagellar P-ring protein
flagellar L-ring protein
flagellar basal-body rod
protein FlgG
flagellar basal-body rod
protein FlgF
flagellar basal body FlaE
domain protein
flagellar hook capping
protein
flagellar basal-body rod
protein FlgC
flagellar basal-body rod
protein FlgB
flagella basal body P-ring
formation protein FlgA
anti-sigma-28 factor, FlgM
FlgN family protein
flagellar FlhE family
protein
flagellar biosynthesis
protein FlhA
flagellar biosynthetic
protein FlhB
heat shock protein Hsp20
heat shock protein Hsp20
superoxide dismutase
UspA domain protein
universal stress protein B
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
phage shock protein A,
PspA
phage shock protein C,
PspC
UspA domain protein
carbon starvation protein
CstA
exonuclease ABC, C
subunit
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
catalase
cold-shock DNA-binding
domain protein
cold-shock DNA-binding
domain protein
thioredoxin domain
gammaglutamyltransferase
catalase/peroxidase HPI
superoxide dismutase
-15.14
-19.04
-20.62
-22.06
1.07
-27.81
-39.53
-1.69
-6.01
-6.23
1.03
-3.32
-4.58
-3.69
-5.57
-1.22
-1.50
-6.28
-8.33
1.24
-4.72
-4.84
1.18
-6.57
-7.65
1.29
-4.29
-3.95
1.21
-4.81
-4.71
-5.49
-5.16
-1.24
1.08
-2.98
-3.61
1.22
-8.36
-8.56
-1.28
-3.12
-2.83
-1.05
-3.83
-3.97
1.19
-3.30
-3.77
1.15
-3.45
-4.22
-1.11
-2.40
-2.48
1.12
-2.08
-2.04
1.23
-2.39
-2.63
1.54
-3.64
-3.63
-1.06
-2.70
-2.67
-3.06
-3.07
1.28
1.43
-5.49
-5.15
1.22
-3.28
-4.07
1.66
-4.10
-4.42
1.58
-7.69
-7.87
1.54
-11.36
-10.73
1.43
-16.49
-18.73
1.04
-3.25
-4.74
-1.10
-2.11
-3.31
-2.47
-4.17
1.07
-1.33
-1.73
-1.78
1.18
-5.32
-6.59
-1.33
-2.69
-3.48
1.14
-2.58
-2.15
-2.23
-2.38
2.65
-1.26
1.23
-3.45
-1.40
1.03
-2.04
-1.72
-1.93
-2.02
-1.24
-4.30
-1.56
-1.60
-4.06
-1.53
-1.76
-2.57
-1.05
-1.77
-6.04
-4.23
-2.10
-8.23
-4.13
-2.03
1.81
1.46
1.25
1.78
1.22
1.05
2.93
2.52
1.12
-1.43
1.75
1.03
2.25
1.66
1.27
-1.41
-2.81
-3.53
-2.02
-4.26
1.56
-1.56
-1.09
2.66
2.40
2.20
YPK_3876
YPK_3877
1.82
stress protein
1.18
1.83
stress protein
-1.05
carbon starvation protein
YPK_3948
-3.83
cstA-2
-1.74
CstA
YPK_4035
-1.97
-3.84
trxA
thioredoxin
protein of unknown
YPK_4131
-1.98
6.21
cpxP
function Spy-related
INFORMATION STORAGE AND PROCESSING
REPLICATION, CELL DEVISION
YPK_0004
gyrB
DNA gyrase, B subunit
1.67
1.70
YPK_0228
-2.11
-2.37
dam
DNA adenine methylase
DNA protecting protein
YPK_0317
2.07
smf, dprA
1.25
DprA
YPK_0888
2.41
dam
DNA adenine methylase
-1.31
DNA mismatch repair
YPK_1032
2.04
mutH
-1.10
endonuclease mutH
exodeoxyribonuclease V,
YPK_1043
1.87
RecB
1.68
beta subunit
camphor resistance CrcB
YPK_1142
1.85
2.47
ccrB-1
protein
YPK_1143
2.12
2.75
ccrB-2
CrcB protein
exodeoxyribonuclease VII,
YPK_1301
-2.03
xseA
-1.12
large subunit
YPK_1431
-1.82
-2.27
zipA
cell division protein ZipA
YPK_1680
-2.28
-2.30
maf
Maf protein
LPP repeat-containing
YPK_1854
-2.64
-4.93
lpp
protein
septum site-determining
YPK_2121
1.84
minC
1.32
protein MinC
septum site-determining
YPK_2122
2.14
minD
1.51
protein MinD
YPK_2625
1.92
helD
UvrD/REP helicase
1.44
YPK_2641
2.30
rlmL
RNA methylase
1.29
chromosome segregation
YPK_2655
3.18
mukB
and condensation protein
1.11
MukB
chromosome segregation
YPK_2656
2.69
mukE
and condensation protein
-1.07
MukE
chromosome segregation
YPK_2657
2.58
mukF
and condensation protein
1.02
MukF
YPK_2685
3.32
ftsK
cell division FtsK/SpoIIIE
1.52
apurinic endonuclease
YPK_2756
2.94
nfo
1.60
Apn1
YPK_2765
2.01
NUDIX hydrolase
1.42
DNA circulation family
YPK_2815
2.88
1.04
protein
YPK_2846
1.92
gyrA
DNA gyrase, A subunit
1.05
SMC (structural
maintenance of
YPK_3144
1.98
ybjD
1.55
chromosomes) family
protein
competence protein
YPK_3229
4.03
comEA
ComEA helix-hairpin-helix
1.03
repeat protein
YPK_3508
-1.77
mutT
mutator MutT protein
-1.69
YPK_3513
2.69
2.31
ftsZ
cell division protein FtsZ
TatD-related
YPK_3629
1.75
yjjV
1.46
deoxyribonuclease
primosomal replication
YPK_3783
priB
-1.16
1.61
protein N
single-strand binding
YPK_3850
-1.90
ssb
-1.44
protein
septal ring assembly
YPK_4111
zapB
-1.12
-1.47
protein ZapB
GENERAL TRANSCRIPTION, TRANSCRIPTION FACTORS, SIGNAL
TRANSDUCTION
repB, repA2, copB;
repB,
pYV0007
-2.77
-2.44
putative replication
copB
transcriptional regulator
ATP-dependent
YPK_0160
-2.44
malT
transcriptional regulator,
-1.15
MalT-like, LuxR family
two component
YPK_0172
1.83
ompR
transcriptional regulator,
1.38
winged helix family
integral membrane sensor
YPK_0173
1.80
envZ
signal transduction
1.30
histidine kinase
transcriptional regulator,
YPK_0248
-24.13
crp
-1.43
Crp/Fnr family
DNA-directed RNA
YPK_0308
1.85
2.41
rpoA
polymerase, alpha subunit
DNA-directed RNA
YPK_0341
1.81
1.93
rpoC
polymerase, beta' subunit
terA
terZ
YPK_0348
rsd
YPK_0452
fis
YPK_0493
rnk
YPK_0516
mlaB
-2.10
1.58
1.23
-1.46
-1.84
YPK_0565
YPK_0642
-2.02
-1.90
-1.89
YPK_0725
1.13
1.83
1.14
2.45
1.49
1.25
2.69
-1.35
-1.68
4.74
1.20
-1.37
ygiM
YPK_0995
agaR
YPK_1156
kdpD
regulator of RpoD,
Rsd/AlgQ
transcriptional regulator,
Fis family
GreA/GreB family
elongation factor
putative anti-sigma B
factor antagonist
putative kinase protein
SH3 domain protein
putative transcriptional
regulator, CadC
transcriptional regulator,
DeoR family
osmosensitive K+ channel
signal transduction
histidine kinase
1.73
1.60
-1.02
-1.83
-1.58
1.80
-1.53
1.02
1.04
-1.04
1.35
-1.13
-1.13
-1.38
-1.96
-1.79
-2.93
1.51
1.61
1.25
1.54
1.37
1.31
1.09
1.36
1.58
1.06
1.16
1.19
1.54
-1.04
-1.33
1.74
1.08
1.76
-1.15
-1.86
-1.64
1.03
1.20
1.37
-1.29
2.19
1.59
-1.11
-1.83
-1.48
-2.75
-3.07
-1.40
-6.24
-3.16
-1.67
2.13
1.11
-1.09
1.79
1.62
1.24
3.17
1.40
1.05
1.76
-1.06
-1.01
-1.78
-1.84
-1.47
1.98
1.53
1.23
YPK_1183
rseA
YPK_1184
rseB
YPK_1185
rseC
YPK_1262
glnB
YPK_1349
speG
YPK_1671
csgD
YPK_1724
cscR
YPK_1793
kdgR
YPK_1927
YPK_1982
ynfL
YPK_2009
YPK_2078
rssB
YPK_2083
rssB
YPK_2100
prkA
YPK_2109
fadR
YPK_2235
phoH
YPK_2269
fimZ
YPK_2356
uvrY
YPK_2385
YPK_2470
atoS1
YPK_2484
YPK_2491
thuR
YPK_2499
uhpA
YPK_2628
tfoX
YPK_2667
ihfB
YPK_2686
lrp
YPK_2780
uxuR
YPK_2843
rcsB
YPK_3206
acrR
YPK_3231
hupB
YPK_3337
emrR
YPK_3368
luxS
YPK_3372
csrA
YPK_3425
rpoS
YPK_3468
dksA
YPK_3492
pdhR
YPK_3606
arcA
YPK_3612
YPK_3638
trpR
hmsT
YPK_3649
ydeW
YPK_3682
yjgM
YPK_3731
nusA
YPK_3739
greA
YPK_3762
argR
YPK_3792
nsrR
YPK_3832
YPK_3841
rhaR
YPK_3975
YPK_3976
rpoH
YPK_4064
hdfR
YPK_4101
cytR
TRANSLATION
YPK_0023
glyS
anti sigma-E protein, RseA
sigma E regulatory protein,
MucB/RseB
positive regulator of sigma
E, RseC/MucC
nitrogen regulatory protein
P-II
GCN5-related Nacetyltransferase
transcriptional regulator,
LuxR family
transcriptional regulator,
LacI family
transcriptional regulator,
IclR family
transcriptional regulator,
XRE family
transcriptional regulator,
LysR family
transcriptional regulator,
AraC family
response regulator
receiver protein
transcriptional regulator,
LysR family
putative serine protein
kinase, PrkA
fatty acid metabolism
transcriptional regulator
FadR
PhoH family protein
two component
transcriptional regulator,
LuxR family
two component
transcriptional regulator,
LuxR family
transcriptional regulator,
AraC family
diguanylate cyclase with
PAS/PAC sensor
transcriptional regulator,
AraC family
transcriptional regulator,
LacI family
two component
transcriptional regulator,
LuxR family
regulator of competencespecific genes
integration host factor,
beta subunit
transcriptional regulator,
AsnC family
GntR domain protein
two component
transcriptional regulator,
LuxR family
transcriptional regulator,
TetR family
histone family protein
DNA-binding protein
transcriptional regulator,
MarR family
quorum-sensing
autoinducer 2 (AI-2), LuxS
carbon storage regulator,
CsrA
RNA polymerase, sigma
70 subunit, RpoD family
transcriptional regulator,
TraR/DksA family
GntR domain protein
two component
transcriptional regulator,
winged helix family
Trp operon repressor
diguanylate cyclase
transcriptional regulator,
DeoR family
GCN5-related Nacetyltransferase
NusA antitermination
factor
transcription elongation
factor GreA
arginine repressor, ArgR
transcriptional regulator,
BadM/Rrf2 family
transcriptional regulator,
TetR family
transcriptional regulator,
AraC family
GCN5-related Nacetyltransferase
RNA polymerase, sigma
32 subunit, RpoH
transcriptional regulator,
LysR family
transcriptional regulator,
LacI family
glycyl-tRNA, B subunit
1.81
1.07
-1.30
1.91
1.32
1.18
2.35
1.62
1.22
2.00
1.50
1.55
-2.04
-1.87
-1.41
-1.89
2.72
-1.53
1.78
1.11
1.21
-1.85
-1.78
-1.69
1.40
2.50
1.11
1.73
2.08
-1.25
-1.25
-1.85
-1.39
2.65
1.26
1.17
-1.04
-1.01
1.02
3.37
2.48
1.53
-1.32
-2.56
-1.71
3.57
1.82
1.16
1.08
-4.23
-1.49
1.78
1.50
1.05
-2.29
-2.43
-1.74
3.43
1.30
1.13
-1.54
-2.59
-1.72
1.38
1.88
1.28
-2.45
-2.50
-1.76
-1.24
6.15
-1.68
1.90
1.82
-1.05
1.37
2.44
1.54
-1.23
5.89
1.01
-1.55
-1.24
-1.95
-1.83
-1.48
-1.68
-1.78
-2.48
-1.71
2.05
4.59
1.41
2.23
-1.50
-1.45
-1.41
132.92
-1.68
3.64
1.34
-1.01
-4.31
-1.55
-1.55
-2.45
-1.38
-1.03
-1.30
-2.36
-1.45
-1.51
1.24
-2.12
-2.69
-1.65
-1.61
5.62
1.82
1.28
-1.21
-1.95
-1.46
1.07
1.78
1.57
-2.66
-1.70
-1.62
-2.69
-2.63
-1.28
-1.51
-1.79
-1.38
1.75
1.06
1.00
-2.12
-1.07
-1.07
-1.80
-1.58
-1.52
2.43
1.16
1.24
-1.37
-1.88
-1.53
-1.75
-1.14
1.72
1.12
1.20
1.82
translation elongation
1.82
1.41
factor G
1.81
ribosomal protein S10
1.13
3.01
ribosomal protein L3
1.63
3.14
ribosomal protein L4/L1e
1.59
3.05
ribosomal protein L25/L23
1.59
2.72
ribosomal protein L2
1.56
2.34
ribosomal protein S19
1.44
2.13
ribosomal protein L22
1.26
1.78
ribosomal protein S3
1.11
2.05
ribosomal protein S14
1.49
1.96
2.56
ribosomal protein S8
2.20
ribosomal protein L6
1.49
1.86
2.44
ribosomal protein L18
2.25
ribosomal protein S5
1.60
2.21
2.63
ribosomal protein L30
2.20
2.27
ribosomal protein L15
1.84
2.28
ribosomal protein S13
2.38
ribosomal protein S11
1.73
2.25
2.75
ribosomal protein S4
-2.76
peptide deformylase
-1.72
-2.40
ribosomal protein L11
-1.57
-2.54
ribosomal protein L1
-1.68
-2.22
-1.80
ribosomal protein L10
-2.29
-1.80
ribosomal protein L7/L12
TIM-barrel protein, nifR3
YPK_0453
-2.42
-2.19
dusB
family
sigma 54 modulation
YPK_0504
2.30
yhbH
protein/ribosomal protein
-1.04
S30EA
YPK_0524
-2.37
-1.78
rplM
ribosomal protein L13
YPK_0525
-2.54
rpsI
ribosomal protein S9
-1.69
YPK_0636
-3.69
-3.30
rpsU
ribosomal protein S21
multifunctional tRNA
nucleotidyl
YPK_0641
1.78
3.41
cca
transferase/2'3'-cyclic
phosphodiesterase/2'nucle
otidase/phosphatase
YPK_0924
lysS
lysyl-tRNA synthetase
1.52
1.73
translation elongation
YPK_1067
1.79
tsf
1.03
factor Ts
UDP-3-O-(3hydroxymyristoyl)
YPK_1076
2.08
1.91
lpxD
glucosamine Nacyltransferase
RNA methyltransferase,
YPK_1274
-2.10
-1.96
trmJ
TrmH family, group 1
pseudouridine synthase,
YPK_1678
-2.09
-2.30
rluC
RluA family
YPK_1682
-2.32
-3.23
rpmF
ribosomal protein L32
phenylalanyl-tRNA
YPK_1824
pheS
1.14
1.71
synthetase, alpha subunit
YPK_2129
-1.98
-2.38
endoribonuclease L-PSP
GCN5-related NYPK_2161
2.25
rimJ
-1.40
acetyltransferase
peptide chain release
YPK_2179
-1.84
prfA
-1.56
factor 1
methionyl-tRNA
YPK_2554
2.01
2.66
metG
synthetase
asparaginyl-tRNA
YPK_2648
1.79
asnC
1.02
synthetase
YPK_2668
2.14
rpsA
ribosomal protein S1
1.66
YPK_2681
2.62
serS
seryl-tRNA synthetase
1.29
translation initiation factor
YPK_2691
-1.84
infA
1.31
IF-1
YPK_2795
-1.80
rplY
ribosomal protein L25
-1.34
dihydrouridine synthase
YPK_2887
1.88
dusC
-1.22
DuS
YPK_3015
1.77
2.14
leuS
leucyl-tRNA synthetase
YPK_3069
-2.28
rluF
pseudouridine synthase
-1.44
YPK_3590
-3.70
-5.04
rpsT
ribosomal protein S20
DEAD/DEAH box helicase
YPK_3724
3.71
deaD
1.48
domain protein
YPK_3727
-2.45
rpsO
ribosomal protein S15
-1.65
translation initiation factor
YPK_3730
1.90
infB
1.48
IF-2
protein of unknown
YPK_3738
-2.87
-3.97
yhbY
function UPF0044
YPK_3756
-2.38
-2.27
rpmA
ribosomal protein L27
YPK_3757
-2.52
-2.33
rplU
ribosomal protein L21
translation elongation
YPK_3818
-2.40
-2.65
efp-2
factor P
tRNA (uracil-5-)YPK_4074
-2.41
-2.73
trmA
methyltransferase
YPK_4098
-4.90
-5.37
rpmE
ribosomal protein L31
trmL,
RNA methyltransferase,
YPK_4135
-2.13
-1.87
cspR
TrmH family, group 2
YPK_4153
-2.83
-2.97
rpmG
ribosomal protein L33
YPK_4154
-2.74
-2.47
rpmB
ribosomal protein L28
YPK_4160
-1.90
rph
ribonuclease PH
-1.67
YPK_4249
-2.09
rpmH
ribosomal protein L34
-1.35
POSTTRANSLATIONAL MODIFICATION, PROTEIN TURNOVER
peptidyl-prolyl cis-trans
YPK_0242
-2.64
ppiA
1.46
isomerase cyclophilin type
peptidylprolyl isomerase
YPK_0268
-2.12
-2.50
slyD
FKBP-type
glutathione S-transferase
YPK_0437
1.83
yghU
1.20
domain
YPK_0520
2.15
degQ
protease Do
1.25
YPK_0849
-1.88
ycaL, loiP peptidase M48 Ste24p
-1.68
putative protein-disulfide
YPK_1019
2.49
1.68
isomerase
YPK_0277
fusA
1.64
YPK_0282
YPK_0283
YPK_0284
YPK_0285
YPK_0286
YPK_0287
YPK_0288
YPK_0289
YPK_0296
YPK_0297
YPK_0298
YPK_0299
YPK_0300
YPK_0301
YPK_0302
YPK_0305
YPK_0306
YPK_0307
YPK_0316
YPK_0335
YPK_0336
YPK_0337
YPK_0338
rpsJ
rplC
rplD
rplW
rplB
rpsS
rplV
rpsC
rpsN
rpsH
rplF
rplR
rpsE
rpmD
rplO
rpsM
rpsK
rpsD
def
rplK
rplA
rplJ
rplL
1.57
2.68
2.76
2.50
2.29
2.04
1.92
1.73
1.72
2.44
2.01
2.27
1.99
2.28
2.08
1.92
1.92
2.48
-1.77
-1.11
-1.24
-1.02
-1.00
-1.21
-1.52
-1.31
-1.13
-1.74
1.09
2.05
1.71
1.49
-1.42
-1.40
-1.79
1.76
-1.81
1.09
-1.22
1.96
1.49
1.43
1.32
-1.07
-1.50
1.36
1.79
-1.38
-2.10
2.09
-1.96
1.74
-2.00
-1.48
-1.52
-1.61
-1.54
-1.95
-1.08
-1.84
-1.67
-1.01
-1.70
-1.45
-1.25
1.15
1.36
-1.34
1.36
YPK_1042
ptrA
YPK_1119
nrdH
YPK_1134
ureE
YPK_1135
ureF
YPK_1137
ureD
YPK_1340
YPK_1360
ydcP-1,
yegQ-1,
yhbU-1
yegD
bcp
YPK_1848
sufB
YPK_1866
grxD
YPK_1878
anmK
YPK_1883
gst
YPK_1903
YPK_1917
tpx
hslJ
YPK_2683
ycaJ
YPK_2690
aat
YPK_2692
clpA
YPK_2733
grxA
YPK_2747
yliJ, gst
YPK_2974
GrpE
YPK_3153
ppiB
YPK_3232
lon
YPK_3234
clpP
YPK_3235
tig
YPK_3267
ahpC
YPK_3366
ypjD
YPK_1325
YPK_3444
ygcF
YPK_3452
YPK_3593
htrA
dnaJ
YPK_3778
fklB
YPK_3796
YPK_3822
YPK_3823
YPK_3986
hflK
groEL
groES
tusA, sirA
YPK_4040
ppiC
peptidase M16 domain
protein
glutaredoxin-like protein
NrdH
urease accessory protein
UreE
urease accessory protein
UreF
urease accessory protein
UreD
2.08
2.07
1.06
2.03
1.57
1.21
1.92
5.21
1.64
1.10
2.50
1.23
1.25
2.02
1.23
peptidase U32
1.81
1.34
1.65
putative chaperone protein
peroxiredoxin
FeS assembly protein
SufB
glutaredoxin-like protein
anhydro-N-acetylmuramic
acid kinase
glutathione S-transferase
domain
redoxin domain protein
heat-inducible protein
AAA ATPase central
domain protein
leucyltransferase
ATP-dependent Clp
protease, ATP-binding
subunit clpA
glutaredoxin, GrxA family
glutathione S-transferase
domain
GrpE protein
peptidyl-prolyl cis-trans
isomerase cyclophilin type
ATP-dependent protease
La
ATP-dependent Clp
protease, proteolytic
subunit ClpP
trigger factor
alkyl hydroperoxide
reductase/thiol specific
antioxidant/ Mal allergen
cytochrome c assembly
protein
radical SAM domain
protein
protease Do
chaperone protein DnaJ
peptidylprolyl isomerase
FKBP-type
HflK protein
chaperonin GroEL
chaperonin Cpn10
SirA family protein
PpiC-type peptidyl-prolyl
cis-trans isomerase
DSBA oxidoreductase
-2.05
1.09
-1.38
-1.81
-1.00
-1.06
1.77
1.20
1.68
-1.22
-2.63
-1.74
1.69
3.88
1.12
2.96
1.51
1.29
2.37
2.75
1.34
1.02
1.04
-1.04
1.07
1.88
-1.00
1.11
1.79
1.19
1.97
4.10
1.66
-1.86
-1.54
-1.94
YPK_4196
dsbA
METABOLISM
ENERGY PRODUCTION AND CONVERSION
FAD dependent
YPK_0152
glpD
oxidoreductase
phosphoenolpyruvate
YPK_0174
pckA
carboxykinase (ATP)
nitrite reductase
YPK_0235
nirB
(NAD(P)H), large subunit
YPK_0364
aceB
malate synthase A
YPK_0365
aceA
isocitrate lyase
succinic semialdehyde
YPK_0486
gabD-1
dehydrogenase
YPK_0492
cybC-1
cytochrome b562
probable Fe(2+)-trafficking
YPK_0819
yggX
protein
YPK_1031
tas
aldo/keto reductase
formate CYPK_1174
grcA
acetyltransferase glycine
radical
iron-sulfur cluster-binding
YPK_1194
fdx
protein
ferredoxin-type protein
YPK_1385
napF
NapF
periplasmic nitrate (or
nitrite) reductase c-type
YPK_1389
napC
cytochrome, NapC/NirT
family
malate dehydrogenase
(oxaloacetateYPK_1391
maeB
decarboxylating)
(NADP(+)), Phosphate
acetyltransferase
phosphate
YPK_1550
pta
acetyltransferase
NADH dehydrogenase I, D
YPK_1562
nuoD
subunit
NADH-quinone
YPK_1563
nuoE
oxidoreductase, E subunit
NADH-quinone
YPK_1564
nuoF
oxidoreductase, F subunit
isocitrate dehydrogenase,
YPK_1723
icdA
NADP-dependent
YPK_1974
aldA
aldehyde dehydrogenase
2.71
2.17
1.19
-2.21
-1.43
-1.51
-2.10
-1.96
-1.68
1.62
2.22
2.28
1.64
1.83
1.68
-1.97
-1.22
1.07
-1.10
-1.79
-1.47
-1.46
-2.52
-1.91
1.11
2.16
1.05
2.65
1.06
6.41
1.75
1.75
1.78
-4.06
-2.50
-1.42
2.01
2.14
1.59
-1.94
2.14
2.74
1.85
-1.80
1.77
2.32
1.65
-1.49
-2.48
-2.58
-1.42
1.79
1.91
1.23
-4.09
1.35
1.01
3.47
2.36
1.35
-1.36
-2.63
-1.17
1.82
1.73
2.96
1.83
1.47
1.36
2.97
1.54
1.09
-1.08
-1.84
-1.52
1.62
2.10
1.16
1.75
1.66
1.43
-2.91
-3.61
-2.12
-1.84
-1.94
-1.78
1.08
-2.90
-1.21
1.11
-1.95
-1.16
1.20
1.82
1.68
1.03
1.88
1.64
1.57
1.73
1.80
2.09
1.68
1.75
1.85
1.62
1.76
2.67
2.57
1.90
1.10
2.23
1.21
YPK_2030
acnA
3.05
3.75
1.82
YPK_2072
adhE
-11.06
-3.31
-1.18
-2.32
-1.85
-1.17
1.90
1.93
1.10
2.73
-1.35
1.07
2.39
1.81
1.33
1.05
2.53
1.42
1.69
1.84
-1.30
1.29
1.71
1.64
1.86
2.75
1.97
1.10
1.12
1.40
1.45
1.94
1.11
-1.25
1.75
1.42
-2.48
1.12
1.01
-1.11
2.90
1.86
1.09
3.67
2.13
-1.04
3.43
1.91
-1.46
2.63
1.49
-1.21
3.50
1.74
-1.56
3.33
1.62
-1.70
2.58
1.35
-2.69
2.11
1.19
1.43
-3.59
3.01
-3.28
1.91
-1.88
2.87
2.41
1.31
1.88
1.32
1.49
-1.23
3.36
-1.15
1.03
1.98
1.04
1.47
1.57
-2.53
-1.94
-1.37
-1.03
1.20
1.77
1.67
2.68
1.80
2.01
1.43
1.57
2.19
1.11
1.53
1.82
aconitate hydratase 1
iron-containing alcohol
dehydrogenase
YPK_2090
ydjA
putative nitroreductase
succinylglutamic
YPK_2227
astD
semialdehyde
dehydrogenase
YPK_2363
wrbA
flavoprotein WrbA
FMN-dependent alphaYPK_2506
lldD
hydroxy acid
dehydrogenase
malate dehydrogenase
YPK_2562
sfcA
(oxaloacetatedecarboxylating)
FAD linked oxidase
YPK_2614
domain protein
YPK_2677
pflB
formate acetyltransferase
YPK_2771
gabD-2
aldehyde dehydrogenase
YPK_2884
dld
D-lactate dehydrogenase
NADH:flavin
YPK_2906
morB
oxidoreductase/NADH
oxidase
cytochrome d ubiquinol
YPK_2963
cydB
oxidase, subunit II
cytochrome bd ubiquinol
YPK_2964
cydA
oxidase subunit I
succinyl-CoA synthetase,
YPK_2965
sucD
alpha subunit
succinyl-CoA synthetase,
YPK_2966
sucC
beta subunit
2-oxoglutarate
dehydrogenase, E2
YPK_2967
sucB
subunit, dihydrolipoamide
succinyltransferase
2-oxoglutarate
YPK_2968
sucA
dehydrogenase, E1
subunit
succinate dehydrogenase
YPK_2969
sdhB
and fumarate reductase
iron-sulfur protein
succinate dehydrogenase,
YPK_2970
sdhA
flavoprotein subunit
succinate dehydrogenase,
YPK_2971
sdhD
hydrophobic membrane
anchor protein
succinate dehydrogenase,
YPK_2972
sdhC
cytochrome b556 subunit
YPK_2973
gltA
citrate synthase I
YPK_2990
fldA
flavodoxin
tRNA-i(6)A37
YPK_3005
miaB
thiotransferase enzyme
MiaB
deoxyxylulose-5YPK_3253
dxs
phosphate synthase
glycerophosphoryl diester
YPK_3297
phosphodiesterase
NADH:ubiquinone
YPK_3302
nqrD
oxidoreductase, subunit D
YPK_3389
cybC-2
cytochrome B562
YPK_3390
cybB
cytochrome B561
hydrolyase, Fe-S type,
YPK_3404
fumA
tartrate/fumarate
subfamily, beta subunit
YPK_3487
acnB
aconitate hydratase 2
pyruvate dehydrogenase
YPK_3490
aceF
complex dihydrolipoamide
acetyltransferase
3-isopropylmalate
YPK_3536
leuB
dehydrogenase
carbohydrate kinase
YPK_3648
ydeV
FGGY
YPK_3767
ppa
inorganic diphosphatase
glycerophosphoryl diester
YPK_3992
glpQ
phosphodiesterase
YPK_4113
glpK
glycerol kinase
oxidoreductase
YPK_4115
fpr
FAD/NAD(P)-binding
domain protein
flavodoxin/nitric oxide
YPK_4216
mioC
synthase
YPK_4219
atpI
ATP synthase I chain
ATP synthase F0, A
YPK_4220
atpB
subunit
ATP synthase F0, C
YPK_4221
atpE
subunit
ATP synthase F0, B
YPK_4222
atpF
subunit
ATP synthase F1, delta
YPK_4223
atpH
subunit
ATP synthase F1, alpha
YPK_4224
atpA
subunit
ATP synthase F1, gamma
YPK_4225
atpG
subunit
ATP synthase F1, beta
YPK_4226
atpD
subunit
ATP synthase F1, epsilon
YPK_4227
atpC
subunit
CARBOHYDRATE METABOLISM
alpha amylase catalytic
YPK_0016
malS
region
1,4-alpha-glucan
YPK_0147
glgB
branching enzyme
3.86
1.55
1.06
-2.83
-4.26
-1.90
1.10
1.82
1.11
-2.47
4.10
1.78
1.88
1.35
1.46
-1.30
-2.33
-1.62
-7.82
-1.49
-1.30
-6.33
-1.23
-1.11
-4.22
1.17
1.03
-3.89
1.28
1.23
-3.90
1.37
1.33
-3.13
1.57
1.55
-2.43
1.88
1.90
-2.45
1.68
1.55
-3.47
1.12
1.23
1.96
1.78
1.20
1.13
1.85
1.11
glycogen debranching
enzyme GlgX
glycogen/starch synthase,
YPK_0150
glgA
ADP-glucose type
glycogen/starch/alphaYPK_0151
glgP-1
glucan phosphorylase
glycogen/starch/alphaYPK_0161
glgP-2
glucan phosphorylase
4-alphaYPK_0162
malQ
glucanotransferase
YPK_0379
glycosidase
FGGY-family pentulose
YPK_0435
kinase
alpha,alphaYPK_0494
treC
phosphotrehalase
YPK_0850
tktA
transketolase
YPK_0973
bgaB
beta-galactosidase
YPK_1111
hpxB
urate catabolism protein
inositol-phosphate
YPK_1273
suhB
phosphatase
phosphoenolpyruvateYPK_1427
ptsI
protein
phosphotransferase
YPK_1444
glk
glucokinase
YPK_1727
NmrA family protein
YPK_1811
yniA
fructosamine kinase
polysaccharide
YPK_1834
pmrJ
deacetylase
phosphoenolpyruvate
YPK_1843
ppsA
synthase
NAD-dependent
YPK_2014
epimerase/dehydratase
YPK_2019
mipB
transaldolase
ribose/galactose
YPK_2204
rpiB-2
isomerase
polysaccharide
YPK_2502
deacetylase
UTP-glucose-1-phosphate
YPK_2536
galF
uridylyltransferase
UTP-glucose-1-phosphate
YPK_2537
galU
uridylyltransferase
YPK_2624
mgsA
methylglyoxal synthase
NAD-dependent
YPK_2706
epimerase/dehydratase
YPK_2763
fruK
1-phosphofructokinase
ribose 5-phosphate
YPK_2769
rpiA
isomerase
glycoside hydrolase family
YPK_2805
bglA
1
transglycosylaseYPK_2879
associated protein
glycoside hydrolase family
YPK_3072
bglB
3 domain protein
YPK_3176
gsk
Inosine kinase
glucose-1-phosphate
YPK_3191
ddhA
cytidylyltransferase
phosphoheptose
YPK_3308
gmhA
isomerase
L-ribulose-5-phosphate 4YPK_3395
araD-2
epimerase
2-oxo-acid dehydrogenase
YPK_3491
aceE
E1 subunit, homodimeric
type
YPK_3625
deoB
phosphopentomutase
3'(2'),5'-bisphosphate
YPK_3775
cysQ
nucleotidase
carbohydrate kinase, YjeF
YPK_3804
related protein
putative ATP/GTP-binding
YPK_3882
protein
UDP-N-acetylglucosamine
YPK_4228
glmU
pyrophosphorylase
AMINO ACID METABOLISM
YPK_0008
ilvA, tdcB threonine dehydratase
YPK_0077
hutH
histidine ammonia-lyase
YPK_0088
dppA
4-phytase
aspartate-semialdehyde
YPK_0141
asd
dehydrogenase
YPK_0225
aroK
shikimate kinase
succinylornithine
YPK_0245
argD
transaminase family
homoserine OYPK_0363
metA
succinyltransferase
YPK_0372
lysC
aspartate kinase
UDP-N-acetylglucosamine
YPK_0518
murA
1-carboxyvinyltransferase
glutamate synthase, small
YPK_0529
gltD
subunit
glutamate synthase
YPK_0530
gltB
(ferredoxin)
YPK_0671
metC
cystathionine beta-lyase
YPK_0749
pepT-1
peptidase T
YPK_0845
speA
arginine decarboxylase
D-isomer specific 2hydroxyacid
YPK_0859
serA-1
dehydrogenase NADbinding
glycine cleavage system H
YPK_0868
gcsH
protein
phosphoadenosine
YPK_0891
phosphosulfate reductase
YPK_0148
glgX
1.46
2.13
1.37
1.48
2.59
1.11
6.79
5.10
1.78
1.45
2.28
1.88
1.59
2.54
1.49
-2.12
1.39
-1.07
3.65
YPK_1063
dapD
YPK_1096
metN-1
YPK_1097
gmhB
-1.06
YPK_1131
YPK_1132
YPK_1133
ureA
ureB
ureC
1.23
1.83
YPK_1136
ureG
1.64
1.44
YPK_1167
1.84
-1.83
2.65
1.55
-1.39
4.13
1.98
1.13
1.34
-1.78
-1.37
1.10
-1.82
1.33
1.83
-2.98
1.89
2.18
-1.25
2.02
-1.68
-1.11
1.13
-1.31
1.76
1.30
-1.06
2.10
2.19
1.30
2.06
1.35
1.41
1.24
-1.83
-1.07
-3.31
-2.68
-1.81
1.29
2.14
1.14
2.56
6.72
1.31
YPK_1252
YPK_1265
glyA
YPK_1302
guaB
YPK_1429
cysK
YPK_1558
alaA
YPK_1737
YPK_1849
sufC
YPK_1869
gloA
YPK_1950
ilvB
YPK_2069
oppB
YPK_2184
prsA
YPK_2225
astE
YPK_2226
astB
2.35
7.26
1.35
-2.00
-1.13
-1.38
YPK_2228
astA
1.29
1.93
1.38
YPK_2229
astC
-2.13
1.40
1.41
1.51
2.14
1.03
1.49
2.71
1.24
YPK_2254
YPK_2257
YPK_2442
YPK_2451
glsA
aspAT
ptrB
sdaA
YPK_2525
hisG
3.35
4.64
-1.32
YPK_2526
hisD
1.68
2.86
1.40
YPK_2527
hisC
-1.24
-1.92
-1.51
YPK_2528
hisB
1.27
1.84
1.27
YPK_2529
hisH
-1.42
-2.03
-1.20
1.12
2.37
-1.06
YPK_2530
hisA
1.37
1.48
2.35
YPK_2531
hisF
YPK_2532
hisI
YPK_2571
frmA,
adhC
1.95
1.22
2.20
-1.25
-2.32
-1.51
-1.15
-1.77
-1.36
1.75
1.31
1.51
1.89
-1.24
1.28
YPK_2670
aroA
1.20
1.88
1.34
1.96
1.57
1.77
1.50
1.16
1.48
YPK_2703
poxB
-1.16
-2.33
1.03
YPK_2705
YPK_2709
ltaA
pheA-1
-2.08
-1.81
-1.31
-1.98
-1.95
-1.28
-1.80
1.17
1.06
-3.63
-4.54
-1.04
1.37
1.80
1.16
1.78
-1.75
1.15
1.85
-1.18
1.57
-1.29
-1.55
1.67
-2.38
-4.54
2.08
-1.23
1.15
1.57
1.47
-2.08
1.22
-2.17
-1.02
-2.70
2.18
-1.44
YPK_2746
YPK_2773
serA-2
YPK_2867
ddc
YPK_2932
bioA
YPK_2949
aroG
YPK_3001
asnB
YPK_3273
brnQ
YPK_3282
aroL
YPK_3357
aroF
YPK_3436
cysD
-1.02
2,3,4,5-tetrahydropyridine2,6-dicarboxylate Nsuccinyltransferase
D-methionine ABC
transporter, ATPase
subunit
D,D-heptose 1,7bisphosphate phosphatase
urease, gamma subunit
urease, beta subunit
urease, alpha subunit
urease accessory protein
UreG
allophanate hydrolase
subunit 1
lytic transglycosylase
catalytic
glycine
hydroxymethyltransferase
inosine-5'-monophosphate
dehydrogenase
cysteine synthase A
aminotransferase class I
and II
NAD(P)H quinone
oxidoreductase, PIG3
family
FeS assembly ATPase
SufC
lactoylglutathione lyase
acetolactate synthase,
large subunit, biosynthetic
type
alkaline phosphatase
ribose-phosphate
pyrophosphokinase
succinylglutamate
desuccinylase
succinylarginine
dihydrolase
arginine Nsuccinyltransferase
succinylornithine
transaminase family
glutaminase
putative aminostransferase
oligopeptidase B
L-serine dehydratase 1
ATP
phosphoribosyltransferase
histidinol dehydrogenase
histidinol-phosphate
aminotransferase
histidinol-phosphatase
imidazole glycerol
phosphate synthase,
glutamine
amidotransferase subunit
phosphoribosylformimino5-aminoimidazole
carboxamide ribotide
isomerase
imidazoleglycerol
phosphate synthase,
cyclase subunit
phosphoribosyl-ATP
diphosphatase
S(hydroxymethyl)glutathione
dehydrogenase/class III
alcohol dehydrogenase
3-phosphoshikimate 1carboxyvinyltransferase
thiamine pyrophosphate
protein TPP binding
domain protein
threonine aldolase
chorismate mutase
HAD-superfamily
subfamily IB hydrolase,
TIGR01490
D-isomer specific 2hydroxyacid
dehydrogenase NADbinding
aromatic-L-amino-acid
decarboxylase
adenosylmethionine-8amino-7-oxononanoate
aminotransferase
phospho-2-dehydro-3deoxyheptonate aldolase
asparagine synthase
(glutamine-hydrolyzing)
branched-chain amino acid
transport system II carrier
protein
shikimate kinase
phospho-2-dehydro-3deoxyheptonate aldolase
sulfate
adenylyltransferase, small
subunit
-2.98
-2.49
-1.70
-2.16
1.08
-1.00
-1.02
-1.77
-1.39
1.07
1.10
1.55
3.66
3.76
5.22
1.13
1.18
1.66
1.30
2.30
1.21
-1.84
-1.21
1.49
-1.75
-1.45
-1.44
2.27
1.50
2.20
3.45
1.34
1.75
1.84
1.32
1.40
1.80
1.08
1.84
2.47
1.96
1.72
1.76
1.35
1.98
-2.91
-2.41
-1.76
-1.41
2.89
1.21
1.49
1.87
1.63
1.84
1.27
1.59
1.87
1.79
1.34
1.80
1.70
-1.23
1.83
1.83
-1.01
1.86
2.20
1.06
1.86
1.06
1.74
1.15
-2.56
-2.09
1.83
1.84
1.29
-1.15
1.59
1.26
1.10
3.57
1.36
1.43
4.77
1.55
1.77
4.89
1.85
1.59
4.11
1.79
1.46
3.83
1.69
1.36
3.84
1.25
1.55
4.45
1.65
1.13
2.95
1.26
1.25
1.72
1.90
1.60
2.16
1.68
2.18
7.42
1.55
1.16
2.06
2.07
4.36
-1.09
1.02
2.13
2.16
1.22
1.35
1.76
-1.07
3.43
1.31
1.23
-1.95
-1.88
-1.34
1.52
2.40
1.33
1.97
2.08
1.54
-2.71
-1.15
-1.08
-2.13
-2.13
-1.36
-1.60
-1.96
1.18
-1.08
1.35
1.85
YPK_3537
YPK_3584
leuC
dapB
YPK_3595
yaaH
YPK_3604
thrA
YPK_3819
YPK_3825
aspA
YPK_3853
tyrB
YPK_3884
metF-1
YPK_3952
YPK_3994
metE
ybhA,
ybjI, yidA,
yigL
3-isopropylmalate
dehydratase, large subunit
dihydrodipicolinate
reductase
GPR1/FUN34/yaaH family
protein
aspartate kinase
lysine 2,3-aminomutase
YodO family protein
aspartate ammonia-lyase
aromatic-amino-acid
transaminase
methylenetetrahydrofolate
reductase
5methyltetrahydropteroyltrig
lutamate--homocysteine Smethyltransferase
putative sugar
phosphatase
dihydroxy-acid
YPK_4057
ilvD
dehydratase
N-acetyl-gamma-glutamylYPK_4089
argC
phosphate reductase
YPK_4094
metL
aspartate kinase
O-succinylhomoserine
YPK_4095
metB
(thiol)-lyase
methionine repressor,
YPK_4096
metJ
MetJ
L-threonine 3YPK_4144
tdh
dehydrogenase
YPK_4214
asnA
aspartate-ammonia ligase
NUCLEOTIDE METABOLISM
phosphoribosylamineYPK_0356
purD
glycine ligase
YPK_1118
nrdI
NrdI protein
nucleoside-diphosphate
YPK_1289
ndk
kinase
GMP synthase, large
YPK_1303
guaA
subunit
phosphoribosylglycinamide
YPK_1350
purN
formyltransferase
phosphoribosylformylglycin
YPK_1351
purI
amidine cyclo-ligase
phosphoribosylaminoimida
YPK_1364
purC
zole-succinocarboxamide
synthase
dihydroorotase,
YPK_1675
pyrC
homodimeric type
YPK_1718
purB
adenylosuccinate lyase
glutamine
YPK_2043
trpG
amidotransferase of
anthranilate synthase
formyltetrahydrofolate
YPK_2080
purU
deformylase
phosphoribosylglycinamide
YPK_2447
purT
formyltransferase 2
YPK_2561
cdd
cytidine deaminase
YPK_2644
pyrD
dihydroorotate oxidase
YPK_2669
cmk
cytidylate kinase
phosphoribosylaminoimida
YPK_3155
purE
zole carboxylase, catalytic
subunit
phosphoribosylaminoimida
YPK_3156
purK
zole carboxylase, ATPase
subunit
nucleoside-triphosphateYPK_3194
adk
adenylate kinase
xanthine
YPK_3291
gpt
phosphoribosyltransferase
deoxyguanosinetriphospha
YPK_3453
dgt
te triphosphohydrolase
guanosine
YPK_3501
guaC
monophosphate reductase
purine nucleoside
YPK_3624
deoD
phosphorylase
YPK_3626
deoA
thymidine phosphorylase
deoxyribose-phosphate
YPK_3627
deoC-2
aldolase
YPK_3950
udp
uridine phosphorylase
YPK_4015
cyaA
putative adenylate cyclase
deoxyuridine 5'YPK_4157
dut
triphosphate
nucleotidohydrolase Dut
orotate
YPK_4159
pyrE
phosphoribosyltransferase
YPK_4182
xanP
uracil-xanthine permease
COENZYME METABOLISM
YPK_0328
coaA
pantothenate kinase
thiazole biosynthesis
YPK_0342
thiH
protein ThiH
thiazole biosynthesis
YPK_0343
thiG
family protein
thiamine biosynthesis
YPK_0344
thiS
protein ThiS
UBA/THIF-type NAD/FAD
YPK_0345
thiF
binding protein
thiamine-phosphate
YPK_0346
thiE
pyrophosphorylase
thiamine biosynthesis
YPK_0347
thiC
protein ThiC
1.19
-1.58
1.59
-1.80
1.85
1.03
-5.37
-4.08
-1.81
-2.03
-2.32
1.23
2.14
1.44
1.44
1.61
2.67
1.43
1.45
1.06
1.82
2.50
-1.41
-1.56
1.41
-1.94
2.26
-3.11
3.13
-1.74
YPK_0649
ribB
YPK_1261
nadE
YPK_1393
hemF
YPK_1532
folC
YPK_1880
pdxH
YPK_2029
ribA
YPK_2038
btuR
YPK_2089
YPK_2180
selD
hemA
YPK_2930
bioF
YPK_2931
bioB
YPK_2952
pnuC
YPK_2953
nadA
ispA
gshA
1.05
1.33
1.91
YPK_3252
YPK_3369
-1.52
-1.80
-1.11
YPK_3437
cysG
-2.04
1.27
1.27
YPK_3443
ygcM
-1.90
-1.09
-1.18
YPK_3474
panD
-2.27
-1.89
-1.58
YPK_3497
nadC
YPK_3578
YPK_3758
folA
ispB
YPK_4145
kbl
1.20
2.67
1.16
-2.81
-2.79
-1.13
-1.02
-1.14
1.83
2.16
1.91
1.36
-8.02
-2.40
-1.53
2.35
-1.06
1.56
-1.37
-1.95
-1.18
-1.20
-1.83
1.10
-1.10
-2.92
-1.22
1.77
1.31
1.64
1.14
1.19
1.75
-2.30
-1.48
-1.23
-1.43
-1.95
-1.28
-1.85
-2.46
1.03
-1.26
1.83
2.54
-1.04
2.79
2.12
5.56
1.36
1.42
-2.19
-2.06
-1.10
-1.98
-1.94
1.03
-2.14
-1.57
-1.07
-4.27
-4.28
-1.92
1.66
2.30
1.20
-2.11
-3.41
-1.58
1.18
-1.94
1.52
2.22
1.20
2.52
2.81
1.16
3.83
1.10
1.96
-1.12
-1.37
8.07
-1.08
-1.64
-1.84
-1.08
-1.75
-2.35
-1.22
-2.07
-4.39
-1.07
-3.31
-2.81
-1.93
1.25
1.37
2.02
1.26
1.51
2.03
1.07
1.44
1.94
1.13
1.49
1.95
1.13
1.63
1.94
1.06
1.76
2.04
3,4-dihydroxy-2-butanone
4-phosphate synthase
NAD+ synthetase
coproporphyrinogen
oxidase
FolC bifunctional protein
pyridoxamine 5'-phosphate
oxidase
GTP cyclohydrolase II
cob(I)alamin
adenosyltransferase
selenide, water dikinase
glutamyl-tRNA reductase
8-amino-7-oxononanoate
synthase
biotin synthase
nicotinamide
mononucleotide
transporter PnuC
quinolinate synthetase
complex, A subunit
polyprenyl synthetase
glutamate--cysteine ligase
uroporphyrin-III Cmethyltransferase
queuosine biosynthesis
protein QueD
aspartate 1-decarboxylase
nicotinate-nucleotide
pyrophosphorylase
dihydrofolate reductase
polyprenyl synthetase
2-amino-3-ketobutyrate
coenzyme A ligase
1.75
1.49
2.08
1.44
1.78
-1.71
-1.92
-1.47
2.04
3.27
1.52
1.43
2.36
1.05
-2.04
-2.55
-1.24
1.32
1.82
1.58
1.51
-1.44
-1.35
-1.90
-2.03
-1.20
-1.41
-1.92
-1.67
-1.06
-1.98
-1.66
-1.03
-1.05
1.85
-1.09
1.11
2.19
1.44
1.78
1.85
1.34
1.41
1.63
1.54
-2.39
-2.09
-1.02
-4.33
-4.91
-1.81
1.88
-3.71
1.02
-1.51
-2.08
-1.17
-2.95
-1.28
-1.35
-1.81
-1.85
-1.15
1.01
2.70
1.22
LIPID METABOLISM
3-hydroxyisobutyrate
1.79
1.52
dehydrogenase
1-deoxy-D-xylulose 5YPK_1070
1.94
2.82
dxr
phosphate
reductoisomerase
acetyl-CoA carboxylase,
YPK_1082
-3.04
accA
carboxyl transferase, alpha -2.54
subunit
holo-acyl-carrier-protein
YPK_1193
2.00
acpS
1.08
synthase
diacylglycerol kinase
YPK_1324
2.36
yegS
1.38
catalytic region
membrane protein
YPK_1506
-2.44
2.48
fadL
involved in aromatic
hydrocarbon degradation
acetyl-CoA CYPK_1508
2.02
fadI
-1.35
acyltransferase FadI
fatty acid oxidation
YPK_1509
3.03
fadJ
complex, alpha subunit
1.27
FadJ
NAD(P)H dehydrogenase
YPK_1924
-1.94
acpD
1.14
(quinone)
short-chain
YPK_2510
2.55
2.36
dehydrogenase/reductase
SDR
3-oxoacyl-(acyl-carrierYPK_2636
1.88
1.88
fabF2
protein) synthase 2
YPK_2735
1.90
membrane protein
1.46
undecaprenylYPK_2736
2.11
5.44
diphosphatase
YPK_3283
2.49
putative methyltransferase
-1.16
carbamoyl-phosphate
YPK_3582
carB
-1.03
1.42
synthase, large subunit
fatty oxidation complex,
YPK_3933
-2.91
2.69
fadB
alpha subunit FadB
acetyl-CoA CYPK_3934
3.23
fadA
-1.13
acyltransferase FadA
SECONDARY METABOLITES BIOSYNTHESIS AND CATABOLISM
YPK_0118
3.11
serralysin
-1.09
YPK_0261
-2.92
tauD
taurine dioxygenase
-1.40
mammalian cell entry
YPK_0514
1.96
yrbD
1.27
related domain protein
toluene tolerance family
YPK_0515
3.62
2.14
yrbC
protein
YPK_0447
intradiol ring-cleavage
dioxygenase
YPK_1687
acpP
acyl carrier protein
cyclopropane-fatty-acylYPK_1858
cfa
phospholipid synthase
rRNA (guanine-N(1)-)YPK_2472
rrmA
methyltransferase
5-oxopent-3-ene-1,2,5YPK_2509
tricarboxylate
decarboxylase
YPK_2658
smtA
methyltransferase type 11
NAD-dependent
YPK_2707
epimerase/dehydratase
biotin biosynthesis protein
YPK_2929
bioC
BioC
YPK_3921
rcs
acetate-CoA ligase
carboxymethylenebutenoli
YPK_3951
ysgA
dase
YPK_4218
gidB
methyltransferase GidB
INORGANIC ION METABOLISM
carbohydrate kinase,
gntK,
YPK_0136
thermoresistant
idnK
glucokinase family
YPK_0159
glpE
rhodanese domain protein
YPK_0789
-1.18
1.26
-1.48
1.40
1.05
1.64
-1.07
1.12
-1.33
1.17
1.53
1.21
1.01
-1.75
1.86
-1.06
1.27
1.22
-1.09
-1.02
1.46
5.30
1.29
-1.02
-2.00
-4.07
-1.49
3.61
1.50
1.18
-2.46
-2.69
-1.65
1.62
1.97
-1.06
-1.81
1.21
-1.58
1.23
1.89
1.30
-1.77
-1.47
1.03
1.15
3.33
1.47
1.59
3.37
1.79
-2.84
-3.76
-1.63
1.10
-1.86
-1.47
-2.29
-2.50
-1.45
YPK_1001
YPK_1355
YPK_1386
cynT, can
yfgD
napD
YPK_1492
phnA
YPK_1602
dps
YPK_1661
mdoG
YPK_1914
qacE
YPK_2364
efeB
YPK_2438
YPK_2743
YPK_3205
YPK_3875
YPK_3888
ftnA
metQ-2
ynjE,
sseA
ychN
terB
hemP
YPK_3890
hmuS
YPK_4013
YPK_4140
cyaY
YPK_4245
trmE
YPK_2866
carbonic anhydrase
arsenate reductase
NapD family protein
alkylphosphonate
utilization operon protein
PhnA
ferritin Dps family protein
periplasmic glucan
biosynthesis protein MdoG
small multidrug resistance
protein
Dyp-type peroxidase
family
Ferroxidase
NLPA lipoprotein
-1.62
2.26
1.38
2.33
1.81
-2.01
-1.36
1.74
1.15
-2.37
-1.60
-1.77
1.73
1.30
-1.84
2.31
2.91
1.45
-1.77
-2.72
-1.62
-1.09
-1.80
1.62
1.81
-1.17
1.59
2.08
-2.23
1.13
rhodanese domain protein
1.09
1.90
-1.06
DsrE family protein
tellurite resistance TerB
hemin uptake protein
haemin-degrading family
protein
iron donor protein CyaY
rhodanese domain protein
tRNA modification GTPase
TrmE
-1.73
1.42
-2.97
-1.58
2.81
-3.71
-1.87
1.76
-1.15
1.12
7.75
1.86
-1.54
-1.83
-2.58
-2.05
-1.46
-1.36
-1.13
-1.88
-1.27
major facilitator
superfamily MFS_1
-1.75
-1.34
-1.15
ABC transporter related
-1.44
-1.75
1.06
TRANSPORT
YPK_0048
YPK_0068
YPK_0070
YPK_0083
mdfA
fhuC-1,
fepC-1,
fecE-1
fhuB-2,
fepG-2,
fecD-2
uhpC
YPK_0098
dctA
YPK_0122
pitA
YPK_0238
tsgA
YPK_0247
YPK_0258
tauA-1
YPK_0259
tauB
YPK_0260
tauC
YPK_0378
malE
YPK_0380
YPK_0381
malK
lamB-1
YPK_0431
yphF-1,
ytfQ-1
YPK_0495
treB
YPK_0507
lptA
YPK_0512
mlaF
YPK_0513
mlaE
YPK_0698
YPK_0748
YPK_0975
YPK_1094
fepB
abgT
cycB,
ganO
lamB-2
metQ-1
YPK_1114
proW
YPK_0968
YPK_1125
ddpA-1
YPK_1128
YPK_1129
ddpD-1
ddpF-1
YPK_1157
kdpC
YPK_1158
kdpB
YPK_1159
kdpA
YPK_1333
ydcT
YPK_1375
afuA,
fbpA
YPK_1376
afuB,
fbpB
YPK_1377
afuC
YPK_1408
cysP
YPK_1409
cysT
YPK_1410
cysW
transport system
permease protein
phosphoglycerate
transporter
sodium:dicarboxylate
symporter
phosphate transporter
major facilitator
superfamily MFS_1
integral membrane protein,
YccS/YhfK family
taurine ABC transporter,
periplasmic binding protein
ABC transporter related
binding-protein-dependent
transport systems inner
membrane component
extracellular solute-binding
protein family 1
ABC transporter related
porin LamB type
carbohydrate uptake
(CUT2 family) ABC
transporter, periplasmic
carbohydrate-binding
protein
PTS system, trehalosespecific IIBC subunit
lipopolysaccharide
transport periplasmic
protein LptA
ABC transporter related
putative ABC transporter
system permease protein
periplasmic binding protein
AbgT putative transporter
extracellular solute-binding
protein family 1
porin LamB type
lipoprotein, YaeC family
binding-protein-dependent
transport systems inner
membrane component
extracellular solute-binding
protein family 5
ABC transporter related
ABC transporter related
potassium-transporting
ATPase, C subunit
K+-transporting ATPase, B
subunit
potassium-transporting
ATPase, A subunit
spermidine/putrescine
ABC transporter ATPase
subunit
extracellular solute-binding
protein family 1
binding-protein-dependent
transport systems inner
membrane component
ABC transporter related
sulfate ABC transporter,
periplasmic sulfate-binding
protein
sulfate ABC transporter,
inner membrane subunit
sulfate ABC transporter,
inner membrane subunit
CysW
-1.41
-1.78
-1.11
-1.63
13.74
-1.51
-1.01
2.33
-1.18
-2.03
-2.26
-1.28
1.45
-1.28
3.98
1.82
-1.14
1.02
-1.81
-1.08
1.20
-2.20
-1.35
-1.01
-3.04
-2.00
-1.30
-1.02
2.57
1.31
-1.89
-1.72
1.87
1.82
1.38
1.30
-2.47
1.07
1.42
2.72
1.51
YPK_1428
ptsH
YPK_1430
cysZ
YPK_1438
nupC1
YPK_1538
hisJ
YPK_1546
ulaA
YPK_1547
ulaB
YPK_1548
ulaC
YPK_1555
YPK_1598
glnQ
YPK_1599
glnP
YPK_1600
glnH
YPK_1694
ptsG
YPK_1744
mgtB
YPK_1791
yebQ
YPK_1795
gltP
YPK_1886
tppB
YPK_1906
mppA
YPK_1939
arcD,
lys1, lysP
YPK_1949
ilvN
YPK_1958
tauA-2
YPK_1979
clcB
YPK_1983
ynfM
YPK_2070
oppA
YPK_2174
YPK_2233
YPK_2246
YPK_2252
ychM
chaA
ybbA-2
efeU-1
YPK_2253
YPK_2256
ansP
YPK_2367
putP
YPK_2376
fliY
YPK_2463
yoaE
YPK_2464
manX
YPK_2466
manZ
YPK_2477
aroP
YPK_2487
mdlA-2
1.18
1.53
1.80
1.20
2.16
1.34
1.03
1.81
1.20
1.04
4.07
1.27
-1.13
-4.70
1.14
1.56
-1.94
-1.42
1.22
-2.04
-1.83
-1.47
-1.10
1.01
-1.17
1.20
1.82
1.13
2.26
1.86
1.23
2.50
1.84
1.52
1.25
1.13
1.08
1.96
1.31
-1.05
1.96
1.52
1.06
2.05
1.60
1.12
2.66
2.18
1.34
-1.28
6.37
2.68
-1.23
3.85
1.70
-1.41
2.80
1.51
-1.79
-1.75
1.03
-1.77
-1.92
-1.18
-1.89
-1.94
-1.19
YPK_2512
YPK_2517
yeeF
YPK_2556
yphF-3,
ytfQ-3
YPK_2564
mglC
YPK_2565
mglA
YPK_2566
mglB
YPK_2618
tusE
YPK_2676
focA
YPK_2688
cydD
YPK_2689
cydC
YPK_2695
YPK_2710
macB-2
artP
YPK_2711
artI
YPK_2712
artQ
phosphotransferase
system, phosphocarrier
protein HPr
putative sulfate transport
protein CysZ
nucleoside transporter
cationic amino acid ABC
transporter, periplasmic
binding protein
putative sugar-specific
permease SgaT/UlaA
phosphotransferase
system lactose/cellobiosespecific IIB subunit
putative PTS IIA-like
nitrogen-regulatory protein
PtsN
citrate transporter
ABC transporter related
polar amino acid ABC
transporter, inner
membrane subunit
cationic amino acid ABC
transporter, periplasmic
binding protein
PTS system, glucosespecific IIBC subunit
magnesium-translocating
P-type ATPase
major facilitator
superfamily MFS_1
sodium:dicarboxylate
symporter
amino acid/peptide
transporter
extracellular solute-binding
protein family 5
arginine/ornithine
antiporter
amino acid-binding ACT
domain protein
ABC transporter,
periplasmic substratebinding protein
chloride channel core
major facilitator
superfamily MFS_1
extracellular solute-binding
protein family 5
sulfate transporter
calcium/proton exchanger
ABC transporter related
iron permease FTR1
major facilitator
superfamily MFS_1
amino acid permeaseassociated region
sodium/proline symporter
extracellular solute-binding
protein family 3
Integral membrane protein
TerC
PTS system,
mannose/fructose/sorbose
family, IIB subunit
PTS system,
mannose/fructose/sorbose
family, IID subunit
amino acid permeaseassociated region
ABC transporter related
major facilitator
superfamily MFS_1
amino acid permeaseassociated region
putative sugar ABC
transporter
monosaccharidetransporting ATPase
ABC transporter related
periplasmic binding
protein/LacI transcriptional
regulator
sulfur relay protein,
TusE/DsrC/DsvC family
formate/nitrite transporter
ABC transporter, CydDC
cysteine exporter (CydDCE) family, permease/ATPbinding protein CydD
ABC transporter, CydDC
cysteine exporter (CydDCE) family, permease/ATPbinding protein CydC
ABC transporter related
ABC transporter related
cationic amino acid ABC
transporter, periplasmic
binding protein
polar amino acid ABC
transporter, inner
membrane subunit
-2.53
1.04
1.47
-1.33
-1.81
-1.82
3.91
-2.61
3.43
-1.22
2.01
1.44
-5.09
-2.41
1.45
-6.35
-2.91
1.26
-7.05
-3.83
-1.06
-1.19
2.17
-1.85
2.71
-1.64
1.54
2.19
2.92
1.18
1.22
1.78
-1.19
-23.68
-1.86
1.03
-1.25
-1.51
-2.02
1.02
-3.08
-1.10
-2.99
-2.58
1.10
-2.85
1.13
-1.24
2.03
1.94
1.14
-1.78
-1.11
-1.39
-1.24
3.50
1.19
1.78
1.09
1.27
1.25
2.56
-1.03
-1.07
1.76
-1.03
1.23
2.34
2.05
-1.02
-2.71
1.92
-1.62
5.43
-1.81
1.31
-2.35
-1.16
-1.61
1.44
-1.30
2.18
-1.76
1.49
-1.47
3.33
1.10
-3.32
1.65
1.32
-1.89
-1.49
1.03
-1.86
-1.20
1.15
-1.92
1.17
1.72
-1.87
1.09
1.49
-1.81
-1.35
1.12
-1.54
-1.77
1.10
1.56
1.88
1.20
-1.87
-1.93
1.33
-1.39
1.97
1.77
-2.36
1.09
1.09
-2.86
1.30
1.17
-5.00
1.68
1.10
-1.84
-1.38
-1.45
-2.00
-1.69
-1.99
1.11
1.97
1.24
1.22
2.68
-1.02
1.17
-3.72
2.32
1.57
1.00
-1.32
-3.94
1.74
-1.18
-2.92
1.93
-1.00
YPK_2713
artM
YPK_2724
artJ
YPK_2739
YPK_2742
sdaC
metN-2
fhuC-2,
fepC-2,
fecE-2
fhuB-3,
fepG-3,
fecD-3
fhuD-3,
fepB-3,
fecB-3
YPK_2749
YPK_2750
YPK_2751
YPK_2752
lysP
YPK_2764
fruB
YPK_2767
yphE-4,
ytfR-4
YPK_2768
yphF-4,
ytfQ-4
YPK_2789
yejF
YPK_2853
tyrP
YPK_2862
opuBD-1
YPK_2863
opuA
YPK_2864
opuBD-2
YPK_2865
opuC
YPK_2940
modF
YPK_3010
ybeJ/gltI
YPK_3158
ybbA-1
YPK_3189
ddhC
YPK_3190
ddhB
YPK_3272
proY
YPK_3309
fadE
YPK_3339
emrB
YPK_3442
cysJ
YPK_3460
fhuB
YPK_3461
YPK_3462
fhuD
fhuC
YPK_3597
YPK_3618
yjjK
YPK_3686
ddpA-2
YPK_3688
ddpC-2
YPK_3874
terC
YPK_3891
hmuT
YPK_3892
hmuU
YPK_3893
hmuV
YPK_3920
gltP
YPK_3923
actP
YPK_3954
madN
YPK_3970
YPK_3971
livF
livG
YPK_3972
livM
YPK_3973
livH
YPK_3974
livK
YPK_4001
rarD
YPK_4018
hemX
YPK_4112
glpF
YPK_4125
sbp1
YPK_4127
fieF
YPK_4181
gltS
YPK_4231
pstS
polar amino acid ABC
transporter, inner
membrane subunit
cationic amino acid ABC
transporter, periplasmic
binding protein
serine transporter
ABC transporter related
-2.53
1.76
1.01
-2.54
2.01
1.10
-3.64
1.09
-1.12
2.24
-1.51
1.41
ABC transporter related
-2.18
-1.70
-1.06
transport system
permease protein
-1.85
-1.01
1.20
periplasmic binding protein
-2.30
-1.40
1.07
-3.19
-2.66
-1.07
-2.61
1.19
1.22
1.35
1.76
-1.01
amino acid permeaseassociated region
phosphocarrier, HPr
family
ABC transporter related
ABC transporter,
periplasmic sugar-binding
protein
ABC transporter related
aromatic amino acid
transporter
binding-protein-dependent
transport systems inner
membrane component
ABC transporter related
binding-protein-dependent
transport systems inner
membrane component
substrate-binding region of
ABC-type glycine betaine
transport system
ABC transporter related
extracellular solute-binding
protein family 3
ABC transporter related
DegT/DnrJ/EryC1/StrS
aminotransferase
CDP-glucose 4,6dehydratase
amino acid permeaseassociated region
acyl-CoA dehydrogenase
drug resistance
transporter, EmrB/QacA
subfamily
sulfite reductase (NADPH)
flavoprotein, alpha chain
transport system
permease protein
periplasmic binding protein
ABC transporter related
major facilitator
superfamily MFS_1
ABC transporter related
extracellular solute-binding
protein family 5
binding-protein-dependent
transport systems inner
membrane component
integral membrane protein
TerC
periplasmic binding protein
transport system
permease protein
ABC transporter related
sodium:dicarboxylate
symporter
cation/acetate symporter
ActP
carboxylate/amino
acid/amine transporter
ABC transporter related
ABC transporter related
inner-membrane
translocator
inner-membrane
translocator
extracellular ligand-binding
receptor
RarD protein, DMT
superfamily transporter
putative uroporphyrinogen
III C-methyltransferase
MIP family channel protein
sulfate ABC transporter,
periplasmic sulfate-binding
protein
cation diffusion facilitator
family transporter
sodium/glutamate
symporter
phosphate ABC
transporter, periplasmic
phosphate-binding protein
1.44
1.80
1.15
1.34
2.64
1.26
-1.41
1.93
-1.24
1.13
2.30
1.10
1.32
2.74
1.05
1.23
2.30
-1.05
1.66
3.98
1.27
-1.96
1.21
-1.39
-1.76
1.33
-1.29
-1.14
1.84
1.18
1.19
1.75
1.28
1.70
2.64
1.90
-2.21
1.01
-1.06
1.32
2.07
1.09
1.07
2.17
1.26
extracellular solute-binding
-2.15
-1.04
protein family 3
polar amino acid ABC
YPK_4238
-1.76
transporter, inner
1.24
membrane subunit
polar amino acid ABC
YPK_4239
-2.77
transporter, inner
-1.38
membrane subunit
GENERAL MEMBRANE TRANSPORT, SECRETION AND STRUCTURAL
PROTEINS
glycosyl transferase family
YPK_0262
-2.20
rafQ
-1.50
9
large conductance
YPK_0312
-3.26
mscL
mechanosensitive channel
-1.44
protein
YPK_0410
2.13
YD repeat protein
-1.04
type I secretion outer
YPK_0654
1.75
1.93
tolC
membrane protein, TolC
family
TonB system transport
YPK_0673
-2.62
exbD
-1.12
protein ExbD
putative flagellar hookYPK_0729
1.88
fliK-2
1.68
length control protein
putative integral
YPK_0740
-1.87
-1.23
membrane efflux protein
membrane-associated zinc
YPK_1073
1.85
rscP
1.24
metalloprotease
outer membrane protein
YPK_1074
2.12
2.43
yaeT
assembly complex, YaeT
protein
outer membrane
YPK_1075
1.79
ompH
1.14
chaperone Skp (OmpH)
copper resistance
YPK_1090
1.96
cutF
1.01
lipoprotein NlpE
phosphogluconate
YPK_1533
2.61
dedD
1.70
dehydratase
mechanosensitive ion
YPK_1641
1.88
mscM
1.60
channel MscS
glycosyl transferase family
YPK_1662
1.87
2.73
mdoH
2
lipid A biosynthesis lauroyl
YPK_1665
2.32
htrB
(or palmitoleoyl)
1.04
acyltransferase
YPK_1783
1.92
prc
carboxyl-terminal protease
1.66
osmotically inducible
YPK_2022
2.50
osmB
1.11
lipoprotein B precursor
YPK_4237
YPK_2055
tonB
YPK_2508
YPK_2630
ompA
YPK_2649
ompF
-2.40
-2.08
-1.12
-1.76
-2.46
-1.07
-1.44
-1.79
-2.26
-2.74
-1.05
-1.31
YPK_2684
lolA
-1.35
-2.18
-1.13
YPK_2696
macA-2
1.81
1.48
1.77
YPK_2740
dacC
1.82
1.11
1.26
YPK_2784
YPK_2839
spr
ompC-2
-1.74
-1.89
-1.30
YPK_2885
pbpG
1.26
1.78
1.65
1.22
5.54
1.55
-1.11
4.65
1.22
YPK_2678
-1.32
2.41
1.00
-2.62
-1.82
-1.12
1.15
2.85
1.10
-2.08
-2.97
-1.37
2.46
2.61
-1.06
-1.23
1.25
1.33
2.09
-1.23
1.23
3.08
1.00
1.57
3.15
-1.57
1.30
-1.36
-1.92
1.38
YPK_2954
YPK_2955
pal
YPK_2956
tolB
YPK_3009
lnt
YPK_3028
tatE
YPK_3182
fcl
YPK_3185
wzy
YPK_3187
YPK_3238
yajG
-1.20
YPK_3263
yajC
1.80
1.39
YPK_3338
emrA
-7.60
1.62
-1.47
YPK_3463
mrcB
-2.91
-1.48
1.16
YPK_3512
lpxC
-1.44
-2.19
-1.85
-3.37
1.55
1.00
YPK_3521
mraY
2.61
1.44
1.07
YPK_3613
slt
YPK_3632
osmY
TonB family protein
mandelate
racemase/muconate
lactonizing protein
OmpA domain protein
transmembrane regioncontaining protein
porin Gram-negative type
glycosyl transferase family
25
outer membrane
lipoprotein carrier protein
LolA
efflux transporter, RND
family, MFP subunit
serine-type D-Ala-D-Ala
carboxypeptidase
NLP/P60 protein
porin Gram-negative type
peptidase S11 D-alanyl-Dalanine carboxypeptidase
1
tol-pal system protein
YbgF
peptidoglycan-associated
lipoprotein
Tol-Pal system beta
propeller repeat protein
TolB
apolipoprotein Nacyltransferase
twin-arginine translocation
protein, TatA/E family
subunit
NAD-dependent
epimerase/dehydratase
O-antigen biosynthesis
protein
glycosyl transferase family
2
uncharacterized lipoprotein
preprotein translocase,
YajC subunit
efflux pump membrane
protein
penicillin-binding protein
1B
UDP-3-0-acyl Nacetylglucosamine
deacetylase
phospho-Nacetylmuramoylpentapeptide-transferase
lytic transglycosylase
catalytic
hyperosmotically inducible
periplasmic protein
1.27
1.07
-1.62
-1.42
-1.65
1.15
1.62
1.14
1.45
-1.43
1.00
1.64
-1.17
-1.49
1.30
1.42
1.09
1.12
1.71
-1.20
-2.02
-2.66
-1.17
2.42
1.74
1.15
1.85
2.76
1.68
-2.34
-2.00
-1.29
-1.28
1.93
-1.27
1.06
2.07
-1.03
1.31
3.56
1.37
2.16
4.21
1.63
-3.53
-1.12
3.40
3.72
-1.09
-1.28
-1.01
1.76
1.17
2.46
3.84
1.39
1.99
3.05
-1.06
2.51
5.13
1.15
1.16
2.00
1.32
1.84
2.48
-1.09
1.72
1.77
1.64
-2.24
-3.07
-1.91
-1.51
-2.22
-1.78
-2.21
-2.31
-1.95
-1.82
-1.68
-1.36
1.09
2.73
1.32
1.46
2.62
1.57
1.93
1.66
1.14
-1.23
-1.76
-1.24
1.04
2.06
1.36
3.55
28.04
1.17
YPK_3733
secG
YPK_3779
ytfB
YPK_4028
rffH
YPK_4030
wecC
YPK_4031
rffE
YPK_4032
wzzE
YPK_4149
kdtA
YPK_4229
glmS
preprotein translocase,
SecG subunit
opacity-associated protein
A
glucose-1-phosphate
thymidylyltransferase
nucleotide sugar
dehydrogenase
UDP-N-acetylglucosamine
2-epimerase
lipopolysaccharide
biosynthesis protein
three-deoxy-D-mannooctulosonic-acid
transferase domain protein
glucosamine-fructose-6phosphate
aminotransferase,
isomerizing
-2.42
-2.20
-1.26
YPK_0613
1.36
-1.21
-1.13
YPK_0638
1.70
2.13
1.29
YPK_0647
1.53
2.26
1.31
YPK_0661
mdaB
1.41
1.92
1.22
YPK_0822
yggL
1.90
3.07
1.29
YPK_0856
yggE
YPK_0861
zapA
-1.47
-1.81
-1.40
2.34
-1.19
1.33
1.00
2.98
-1.07
YPK_0895
1.06
1.92
-1.01
YPK_0951
1.34
2.50
1.51
YPK_1020
1.26
1.96
1.09
1.43
2.59
1.09
1.89
3.22
1.30
2.97
3.21
-1.09
YPK_0885
cas-1
YPK_1645
cas-3
YPK_1646
csy-1
YPK_1647
csy-2
YPK_1648
csy-3
YPK_1649
csy-4
YPK_1760
cwlA,
xlyA, xlyB
YPK_2050
yciC
YPK_2836
ampH
YPK_3642
mexB
YPK_3665
YPK_3671
mcrC
YPK_3672
hsdM-2
YPK_3674
hsdR
OTHERS
pYV0019
pYV0039
pYV0046
pYV0095
YPK_0025
yiaF
YPK_0066
YPK_0067
YPK_0080
eptB
YPK_0100
YPK_0106
yhjD
YPK_0154
YPK_0158
glpG
YPK_0166
YPK_0189
YPK_0311
arfA
YPK_0353
yjaG
YPK_0355
yjaH
YPK_0375
yjbA
YPK_0406
YPK_0427
YPK_0445
pcp
YPK_0456
yhdT
YPK_0462
yedY
YPK_0487
YPK_0502
yhbJ
YPK_0508
yrbK
YPK_0509
kdsC
YPK_0521
yhcB
YPK_0534
YPK_0551
YPK_0602
elbB
CRISPR-associated
protein Cas1
CRISPR-associated
helicase Cas3 family
CRISPR-associated
protein, Csy1 family
CRISPR-associated
protein, Csy2 family
CRISPR-associated
protein, Csy3 family
CRISPR-associated
protein, Csy4 family
N-acetylmuramyl-L-alanine
amidase, negative
regulator of AmpC, AmpD
protein of unknown
function UPF0259
beta-lactamase
acriflavin resistance
protein
type I restrictionmodification system, M
subunit
5-methylcytosine
restriction system
component
type I restrictionmodification system, M
subunit
type I site-specific
deoxyribonuclease, HsdR
family
putative transposase
putative transposase
putative transposase
remnant
putative transposase
putative lipoprotein
transposase IS3/IS911
family protein
integrase catalytic region
sulfatase
peptidase M16 domain
protein
ribonuclease
protein of unknown
function DUF943
rhomboid family protein
protein of unknown
function DUF1471
DNA circulation family
protein
protein of unknown
function DUF331
protein of unknown
function DUF416
protein of unknown
function DUF1481
phosphate-starvationinducible E
putative cytoplasmic
protein
transposase mutator type
17 kDa surface antigen
protein of unknown
function DUF997
oxidoreductase
molybdopterin binding
guanine-specific
ribonuclease N1 and T1
conserved hypothetical
protein
protein of unknown
function DUF1239
3-deoxy-D-mannooctulosonate 8-phosphate
phosphatase, YrbI family
protein of unknown
function DUF1043
ThiJ/PfpI domain protein
putative lipoprotein
YheO domain protein
YPK_0887
YPK_0890
DEFENSE MECHANISMS
YPK_1644
xtmA
-2.10
-1.38
1.91
1.76
1.44
1.34
-2.44
1.08
-2.01
-2.42
-1.34
-1.47
-1.67
-2.00
-1.35
YPK_1049
sufE
YPK_1058
syd
YPK_1086
YPK_1087
YPK_1088
YPK_1177
yplB
YPK_1200
YPK_1296
yfgL
YPK_1323
YPK_1326
yegP
YPK_1398
yfeY
YPK_1451
-2.35
-2.83
1.21
-1.80
-1.82
1.09
1.92
-1.96
1.46
-1.85
1.43
-1.43
YPK_1577
-1.76
-1.21
-1.21
YPK_1585
2.08
3.89
1.09
-1.20
1.08
1.19
YPK_1601
1.75
1.17
1.16
YPK_1624
1.94
-1.72
1.02
-1.84
-1.07
-1.32
YPK_1676
1.67
2.19
1.36
YPK_1681
yceD
1.18
1.81
1.04
YPK_1697
ycfL
-2.34
-1.75
-1.84
-1.69
-2.11
-1.41
2.45
-1.15
-1.76
YPK_1512
YPK_1530
dedA
YPK_1557
yfbR
elaB
trp14A
YPK_1741
YPK_1772
YPK_1776
-1.27
-1.81
-1.51
-1.08
-1.75
-1.41
-1.99
-1.17
-1.62
1.38
1.86
1.37
YPK_1778
YPK_1806
YPK_1807
YPK_1870
sepC
YPK_1885
1.12
-1.94
-1.27
2.23
1.24
1.25
YPK_1926
YPK_1951
1.47
-1.17
2.91
-9.78
1.44
-1.57
-1.97
-1.29
-1.33
YPK_1977
2.10
-1.09
1.13
YPK_1978
2.17
1.23
1.06
YPK_1987
1.57
1.77
1.26
YPK_1995
1.61
2.04
1.19
1.67
2.36
1.29
-2.31
-1.93
-2.05
1.95
-1.44
-1.84
1.90
-1.85
-1.83
1.48
-1.34
-1.45
YPK_1952
YPK_2048
YPK_2079
YPK_2102
yeaH
YPK_2103
YPK_2105
YPK_2108
spoVR
putative phage terminase,
small subunit
protein of unknown
function DUF205
protein of unknown
function DUF526
NAD(P)H dehydrogenase
(quinone)
protein of unknown
function DUF469
protein of unknown
function DUF541
protein of unknown
function DUF710
regulatory CII family
protein
gpB bacteriophage P2-like
protein
putative replication
initiation protein
transcriptional activator
Ogr/delta
filamentation induced by
cAMP protein Fic
beta-lactamase domain
protein
cysteine desulfurase,
sulfur acceptor subunit
CsdE
Syd family protein
transcriptional
antiterminator, Rof
protein of unknown
function UPF0253
YaeQ family protein
ankyrin
Arc domain protein DNA
binding domain protein
outer membrane assembly
lipoprotein YfgL
inhibitor of vertebrate
lysozyme
protein of unknown
function DUF1508
protein of unknown
function DUF1131
protein of unknown
function DUF799
Smr protein/MutS2
SNARE associated Golgi
protein
metal dependent
phosphohydrolase
protein of unknown
function DUF187
protein of unknown
function DUF883 ElaB
protein of unknown
function DUF218
transposase IS3/IS911
family protein
antibiotic biosynthesis
monooxygenase
protein of unknown
function DUF177
protein of unknown
function DUF1425
DsrB protein
protein of unknown
function DUF1480
spore coat U domain
protein
spore coat U domain
protein
transposase mutator type
transposase
Rhs family protein-like
protein
protein of unknown
function DUF1282
protein of unknown
function DUF891
protein of unknown
function DUF1460
putative virulence factor
protein of unknown
function DUF1283
protein of unknown
function DUF1161
protein of unknown
function DUF945
oxidoreductase domain
protein
transport-associated
SEC-C motif domain
protein
protein of unknown
function DUF444
protein of unknown
function DUF6
transmembrane
pirin domain protein
SpoVR family protein
1.86
1.45
1.46
-2.03
-2.59
-2.02
-1.50
-2.42
-1.58
-2.13
-4.10
-1.09
-1.39
-1.82
-1.30
3.29
18.46
1.58
-1.60
-3.34
-1.74
-1.13
2.35
1.07
-1.80
2.38
-1.56
-1.63
3.48
-1.08
-1.10
-1.73
-1.79
1.14
1.87
-1.23
2.36
1.84
1.42
-1.16
-1.81
-1.56
-1.31
-2.01
-1.49
-1.63
-2.46
-1.84
-1.75
-2.92
-1.95
1.07
1.87
-1.16
1.19
1.01
-1.14
-1.95
-1.67
-1.33
1.76
1.55
1.41
2.03
1.95
1.09
2.39
-1.03
-1.15
1.51
2.24
1.19
-1.35
-1.94
-1.01
-1.58
-1.77
-1.59
1.40
1.98
1.34
-1.09
-1.89
-1.24
1.15
1.96
1.06
-1.74
2.99
-1.58
-1.22
1.79
1.06
2.07
-1.21
-1.04
-1.70
-2.52
-1.72
-2.59
-2.75
-1.74
1.82
2.15
1.65
-2.13
-3.34
-1.70
1.92
1.12
-2.05
2.01
-1.07
1.01
3.70
1.05
1.17
1.43
1.35
2.99
2.14
1.56
1.04
2.76
1.55
1.28
4.04
1.94
-1.14
1.71
2.54
1.14
2.06
2.31
-1.40
-1.62
-2.15
1.06
1.42
3.17
1.26
2.39
16.59
-1.64
1.90
4.12
1.46
1.87
1.04
1.10
4.42
2.66
-1.47
-1.11
-1.74
-1.26
2.57
2.20
-1.01
2.19
1.13
-1.35
-1.64
2.60
-2.14
1.83
-1.54
1.40
protein of unknown
function DUF709
protein of unknown
function DUF28
Sel1 domain protein
repeat-containing protein
amidohydrolase 2
putative lipoprotein
transposase
transposase mutator type
YPK_2120
YPK_2146
YPK_2205
YPK_2260
YPK_2264
YPK_2291
YPK_2292
YPK_2358
ydgC,
glpM
YPK_2388
doc
YPK_2444
yqfB
YPK_2448
yoaH
YPK_2473
YPK_2488
YPK_2489
YPK_2514
YPK_2548
YPK_2559
YPK_2629
fhuF
yohJ
frmB,
fghA
sulA
YPK_2638
pqiB
YPK_2639
pqiA
YPK_2572
YPK_2643
YPK_2652
YPK_2653
YPK_2661
YPK_2666
YPK_2693
comEC
clpS
YPK_2708
YPK_2744
YPK_2797
yejL
YPK_2802
YPK_2808
YPK_2809
YPK_2810
YPK_2811
YPK_2812
YPK_2813
YPK_2814
YPK_2817
YPK_2819
YPK_2820
YPK_2827
YPK_2830
YPK_2854
msgA
YPK_2874
YPK_2918
YPK_2947
YPK_2961
YPK_2962
ybhL,
ybhM,
yccA
psiF
YPK_2978
YPK_2989
YPK_3014
YPK_3025
ybeD
YPK_3036
YPK_3075
YPK_3076
YPK_3118
YPK_3122
YPK_3147
dkgA-2
GlpM family protein
death-on-curing family
protein
protein of unknown
function DUF437
protein of unknown
function UPF0181
protein of unknown
function DUF152
protein of unknown
function RIO1
YCII-related
protein of unknown
function DUF496
ferric iron reductase
LrgA family protein
S-formylglutathione
hydrolase
cell division inhibitor SulA
mammalian cell entry
related domain protein
integral membrane protein,
PqiA family
protein of unknown
function DUF1379
beta-lactamase domain
protein
protein of unknown
function DUF882
protein of unknown
function DUF343
DNA internalization-related
competence protein
ComEC/Rec2
ATP-dependent Clp
protease adaptor protein
ClpS
putative lipoprotein
2OG-Fe(II) oxygenase
protein of unknown
function DUF1414
Colicin D
tail assembly chaperone
gp38
putative bacteriophage tail
fiber protein
putative bacteriophage
protein GP48
baseplate J family protein
GP46 family protein
phage baseplate assembly
protein V
Mu P family protein
putative bacteriophage
protein
Mu tail sheath family
protein
putative bacteriophage
protein
antitermination Q family
protein
DinI family protein
YfaZ family protein
protein of unknown
function DUF1456
protein of unknown
function UPF0005
PsiF repeat protein
cyd operon protein YbgE
cyd operon protein YbgT
protein of unknown
function UPF0125
CopG domain protein
DNA-binding domain
protein
protein of unknown
function DUF1451
protein of unknown
function DUF493
antibiotic biosynthesis
monooxygenase
2,5-didehydrogluconate
reductase
aldo/keto reductase
phage-related membrane
protein
Mu tail sheath family
protein
tetratricopeptide TPR_2
repeat protein
1.55
1.76
1.86
-1.08
1.23
1.45
1.13
1.82
1.16
9.21
1.79
1.22
1.29
-1.29
-1.28
1.89
2.00
1.07
-1.28
1.18
1.12
-1.48
-1.77
-1.81
-1.04
-1.84
-1.74
3.75
1.53
-1.51
-2.53
2.19
1.32
YPK_3157
ybbP-3
YPK_3166
YPK_3186
YPK_3216
ybaY
YPK_3228
ybaW
YPK_3247
yajQ
YPK_3281
yaiE
YPK_3317
mtnK
-1.15
YPK_3505
yacG
-1.83
YPK_3528
ygaW
YPK_3607
creA
1.15
YPK_3619
1.80
1.23
1.36
YPK_3623
smp
YPK_3630
yjjU
1.33
-1.98
-1.77
-3.11
-3.67
-1.96
-1.98
-1.93
-2.63
-1.31
-1.55
-1.71
-1.34
1.87
1.17
-1.85
1.21
-1.49
YPK_3668
1.33
1.94
1.18
YPK_3677
yjgQ
yjgP
YPK_3631
YPK_3663
1.41
2.13
1.17
YPK_3678
-1.40
-1.11
-1.94
YPK_3683
1.52
2.36
1.15
YPK_3746
xtmA2
1.53
2.64
1.25
YPK_3763
yhcN
-1.79
-1.06
-1.75
1.09
1.85
-1.16
YPK_3768
YPK_3773
YPK_3838
insB
YPK_3922
1.28
1.81
1.03
1.75
-1.96
2.43
1.59
1.35
1.08
-1.61
-1.53
-1.92
1.18
2.44
-1.14
-2.24
2.06
-1.41
-1.80
2.28
1.04
YPK_3925
YPK_3983
YPK_3984
yhhN
YPK_4063
yifE
YPK_4097
YPK_4116
YPK_4128
-1.17
2.90
-1.00
-1.25
-1.10
2.10
2.43
-1.00
1.03
-1.02
3.47
1.15
-1.05
2.85
1.39
-1.25
3.80
1.08
-1.24
3.97
1.39
-1.32
3.62
1.11
-1.06
2.21
1.07
-2.22
1.81
1.17
1.19
-1.42
1.14
-2.76
-1.96
-1.99
YPK_4164
YPK_4187
yrfG-4,
yigB-4,
yihX-4
YPK_4247
yidD
HYPOTHETICAL
pYV0010
pYV0012
pYV0026
pYV0027
pYV0044
pYV0077
yscA
pYV0078
YPK_0006
YPK_0030
-2.08
-1.64
-2.06
2.58
-1.90
-1.96
3.58
-1.39
-1.39
-1.14
-1.67
-1.58
1.29
1.83
1.06
-2.67
-2.15
-1.94
YPK_0031
YPK_0044
YPK_0046
YPK_0047
YPK_0049
2.71
2.48
1.25
YPK_0062
-1.89
-1.69
-1.71
YPK_0063
-2.40
-1.84
-1.76
YPK_0132
1.92
2.29
1.37
YPK_0153
2.25
2.20
1.38
-1.35
-1.83
-1.69
YPK_0156
YPK_0250
1.80
1.29
1.13
YPK_0397
-1.78
-2.09
-1.53
YPK_0405
yibL
protein of unknown
function DUF214
GumN family protein
LPS side chain defect:
putative O-antigen
transferase
putative lipoprotein
thioesterase superfamily
protein
protein of unknown
function DUF520
protein of unknown
function DUF1255
5-methylthioribose kinase
protein of unknown
function DUF329
protein of unknown
function DUF1144
CreA family protein
filamentation induced by
cAMP protein Fic
putative membrane protein
Smp
patatin
protein of unknown
function DUF1328
protein of unknown
function DUF898
transmembrane
integrase family protein
permease YjgP/YjgQ
family protein
permease YjgP/YjgQ
family protein
protein of unknown
function DUF1260
putative phage terminase,
small subunit
protein of unknown
function DUF1471
AIG2 family protein
protein of unknown
function DUF1107
IS1 transposase
protein of unknown
function DUF485
integrase catalytic region
domain of unknown
function DUF1820
YhhN family protein
protein of unknown
function DUF413
YiaAB two helix domain
protein
protein of unknown
function DUF805
transposase, IS4 family
protein
phage transcriptional
regulator, AlpA
HAD-superfamily
hydrolase, subfamily IA,
variant 3
protein of unknown
function DUF37
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
YPK_0006
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0049
conserved hypothetical
protein
hypothetical protein
YPK_0063
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0156
hypothetical protein
YPK_0250
conserved hypothetical
protein
hypothetical protein
YPK_0405
1.09
2.05
1.18
1.15
2.04
1.05
-1.70
-2.42
-1.81
-1.74
2.86
-1.70
-1.24
1.94
-1.10
-2.07
-1.54
-1.22
-1.76
-2.07
-1.52
-2.29
1.26
1.11
-1.31
-2.49
-1.62
1.84
1.38
-1.29
1.22
-2.01
-1.65
-1.89
-1.20
-1.24
-1.13
-1.76
-1.58
1.22
2.70
-1.13
3.79
22.04
1.19
-1.83
-1.24
-1.04
-1.54
-1.78
-1.18
1.17
2.31
1.03
1.01
1.96
-1.10
2.67
1.45
1.67
1.93
1.36
1.51
1.19
-1.79
2.71
-1.43
-2.16
-1.75
1.30
2.43
-1.50
-1.40
-2.10
-1.64
1.09
2.34
1.24
2.05
-1.13
-1.19
-1.93
-2.27
-1.92
-1.05
-2.23
-1.73
-1.51
-2.04
-1.66
-1.44
-2.57
-1.57
-2.40
-2.93
-1.09
-1.41
-2.68
-1.94
-1.79
-1.40
-1.39
3.48
1.24
-1.32
-1.84
-1.63
-1.05
-2.04
-1.40
1.04
1.07
-2.21
-1.35
-1.11
-3.78
-3.27
-2.49
-2.51
-2.04
-2.96
-2.06
-1.17
1.09
-1.46
-1.45
-1.42
-1.76
-1.40
-1.99
-2.25
-1.37
-2.75
-4.29
-2.10
1.78
1.08
1.34
-3.93
-1.98
-2.24
-2.12
1.60
-1.74
-1.55
-1.83
-1.64
-1.97
-2.19
-1.39
-1.65
-1.96
-1.39
-2.59
-3.74
-1.99
-1.68
-2.95
-1.19
-1.74
-2.12
-1.32
-1.95
-2.01
-1.36
-1.89
2.08
-1.72
2.00
1.25
1.15
1.77
1.25
1.23
YPK_0411
YPK_0441
YPK_0457
YPK_0497
YPK_0522
YPK_0528
YPK_0566
YPK_0574
YPK_0579
YPK_0580
YPK_0609
YPK_0615
YPK_0631
YPK_0633
YPK_0653
YPK_0732
YPK_0742
YPK_0759
YPK_0769
YPK_0777
YPK_0840
YPK_0870
YPK_0884
YPK_0886
YPK_0889
YPK_0894
YPK_0946
YPK_0947
YPK_0954
YPK_0963
YPK_0969
YPK_1030
YPK_1051
YPK_1056
ygdH
YPK_1062
YPK_1121
YPK_1150
YPK_1160
YPK_1178
YPK_1186
YPK_1216
YPK_1244
YPK_1256
YPK_1295
yfgM
YPK_1369
YPK_1397
YPK_1405
YPK_1413
YPK_1434
YPK_1440
YPK_1457
ygiW
conserved hypothetical
protein
hypothetical protein
YPK_0441
hypothetical protein
YPK_0457
conserved hypothetical
protein
hypothetical protein
YPK_0522
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0574
conserved hypothetical
protein
hypothetical protein
YPK_0580
conserved hypothetical
protein
hypothetical protein
YPK_0615
hypothetical protein
YPK_0631
hypothetical protein
YPK_0633
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0769
conserved hypothetical
protein
hypothetical protein
YPK_0840
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0886
conserved hypothetical
protein
hypothetical protein
YPK_0894
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_0969
conserved hypothetical
protein
hypothetical protein
YPK_1051
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_1216
hypothetical protein
YPK_1244
hypothetical protein
YPK_1256
conserved hypothetical
protein
hypothetical protein
YPK_1369
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
-1.21
-2.49
-1.41
YPK_1458
-1.51
-1.99
-1.55
YPK_1507
-4.11
-4.43
-2.05
YPK_1537
8.64
1.84
1.47
YPK_1556
-1.46
-2.00
-1.49
YPK_1587
-1.05
1.88
-1.12
YPK_1617
1.79
1.27
1.09
YPK_1623
-1.11
-1.79
-1.45
YPK_1626
1.86
1.70
1.24
YPK_1659
1.22
1.83
-1.28
YPK_1670
-1.39
-2.10
-1.79
YPK_1725
-1.70
-2.10
-1.54
YPK_1729
-1.66
-3.26
-1.59
YPK_1731
-2.36
-5.11
-1.68
YPK_1734
-1.42
-2.19
-1.58
YPK_1735
-1.99
-1.13
-1.90
YPK_1738
-2.69
-3.57
-1.60
YPK_1762
-1.20
-1.81
-1.22
YPK_1763
-2.25
-1.31
-2.04
YPK_1765
-1.53
2.07
-1.40
YPK_1767
-2.10
-2.06
-1.41
YPK_1769
2.00
1.61
-1.15
YPK_1818
-1.27
2.37
-1.04
YPK_1819
1.19
2.97
1.38
YPK_1827
-1.36
3.38
-1.19
YPK_1865
-2.03
-1.23
-1.85
YPK_1867
-1.40
2.14
-1.63
YPK_1879
-1.02
1.79
1.03
YPK_1887
1.98
3.40
1.36
YPK_1899
ycjF
-2.31
-1.48
-1.93
YPK_1921
ydbL
-1.86
-1.44
1.26
YPK_1938
-1.47
-1.94
-1.53
YPK_1954
-1.46
-1.98
-1.37
YPK_1989
1.08
2.65
1.14
YPK_1990
-1.04
-2.31
-1.47
YPK_2005
1.05
3.36
-1.42
YPK_2020
-2.04
-1.45
-1.45
YPK_2025
-1.19
-1.45
-2.30
YPK_2034
1.78
1.13
-1.30
YPK_2035
1.33
4.39
-1.32
YPK_2058
-1.75
-1.77
-1.76
YPK_2059
-1.46
-1.68
-2.17
YPK_2062
1.17
-2.22
-2.87
YPK_2065
1.90
1.64
1.48
YPK_2082
-1.36
-1.81
-1.19
YPK_2084
2.00
3.24
1.07
YPK_2101
-1.97
-1.96
-1.48
YPK_2183
-3.16
-3.00
-1.69
YPK_2185
-1.94
-2.62
-1.65
YPK_2197
1.66
5.73
-1.23
YPK_2198
1.05
5.19
-1.55
YPK_2199
ylaC
hypothetical protein
YPK_1458
conserved hypothetical
protein
hypothetical protein
YPK_1537
conserved hypothetical
protein
hypothetical protein
YPK_1587
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_1734
conserved hypothetical
protein
hypothetical protein
YPK_1738
conserved hypothetical
protein
hypothetical protein
YPK_1763
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_1867
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_1989
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2082
conserved hypothetical
protein
hypothetical protein
YPK_2101
hypothetical protein
YPK_2183
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
-1.26
1.76
-1.07
-1.49
-2.32
-1.68
1.41
-1.22
-1.77
1.62
2.01
-1.72
-1.18
1.39
-2.17
-1.34
-1.90
-1.65
-2.30
-2.39
-1.66
-1.39
-1.09
-2.20
-2.08
-2.70
-1.97
-1.82
-1.06
-1.60
-3.81
-3.72
-1.95
-1.38
-2.33
-1.76
-1.30
-3.69
-1.65
-1.42
-2.06
-1.60
-1.49
-2.05
-1.76
1.39
1.85
-1.49
2.83
1.06
1.13
1.38
-2.16
-1.66
1.89
-1.17
-1.26
-1.21
-2.11
-1.29
-2.29
-1.44
-2.05
-13.93
-1.85
-1.55
-1.46
-2.79
-2.06
1.11
-2.26
-1.21
-1.18
-2.29
-1.63
-1.54
-1.88
-1.75
1.30
3.27
-1.36
1.06
2.01
1.42
1.79
1.44
1.33
2.01
1.43
1.45
-1.24
-1.94
-1.81
-6.28
-6.23
-1.10
-7.00
1.21
-1.10
-3.63
1.68
1.08
-1.51
-2.22
-1.93
-1.59
-3.77
-1.69
-1.50
-2.84
-2.04
-1.72
-2.65
-1.51
-2.09
-3.80
-2.01
1.08
12.84
-1.64
-2.99
-1.05
-1.19
-1.57
-1.95
-1.58
-2.95
-1.78
-1.71
1.11
1.08
1.02
-1.97
-1.49
-1.05
2.55
1.92
1.07
1.92
1.18
1.37
-1.13
2.08
-1.18
2.20
3.71
-1.05
2.19
3.26
1.04
2.91
3.91
-1.13
YPK_2200
YPK_2236
YPK_2251
YPK_2263
YPK_2298
YPK_2299
YPK_2308
YPK_2309
YPK_2339
YPK_2357
YPK_2359
YPK_2368
YPK_2379
YPK_2389
YPK_2397
YPK_2405
YPK_2433
YPK_2441
YPK_2443
YPK_2471
YPK_2475
YPK_2480
YPK_2481
YPK_2482
YPK_2483
YPK_2485
YPK_2486
YPK_2500
YPK_2501
YPK_2507
YPK_2522
YPK_2523
YPK_2623
YPK_2726
YPK_2731
YPK_2745
YPK_2772
YPK_2781
YPK_2790
YPK_2801
YPK_2804
YPK_2806
YPK_2816
YPK_2818
YPK_2821
YPK_2822
YPK_2868
YPK_2880
YPK_2892
YPK_2984
YPK_2988
yaiL
hypothetical protein
YPK_2200
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2308
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2405
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2483
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2522
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2806
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_2988
21.47
7.16
-1.93
YPK_3035
3.17
1.79
-1.04
YPK_3038
1.26
-2.13
-1.16
YPK_3061
1.77
-1.45
-1.12
YPK_3062
-1.73
2.76
-1.53
YPK_3070
-1.45
3.10
-1.56
YPK_3089
1.23
1.97
1.09
YPK_3101
1.96
1.85
1.22
YPK_3121
1.06
2.97
-1.32
YPK_3123
-2.38
-2.66
-2.05
YPK_3138
-1.53
-1.82
-1.95
YPK_3203
-3.47
1.31
1.19
YPK_3212
-4.41
-6.14
1.08
YPK_3218
-1.01
-2.22
-1.73
YPK_3236
-2.63
-2.80
1.13
YPK_3240
-1.59
-1.48
-2.16
YPK_3285
-1.03
2.28
1.09
YPK_3396
2.12
-2.08
-1.88
YPK_3481
yacC
yacL
3.64
1.70
-1.09
YPK_3486
-5.82
-5.33
-1.93
YPK_3549
-3.03
-3.43
-2.08
YPK_3554
-1.72
-2.65
-1.87
YPK_3555
1.22
1.51
-1.89
YPK_3567
-2.07
-4.04
-1.84
YPK_3576
1.12
-1.92
-2.05
YPK_3608
-1.13
-3.51
-1.80
YPK_3615
-1.14
-4.74
-1.89
YPK_3644
-1.46
-2.07
-1.63
YPK_3645
-1.37
-2.15
-1.40
YPK_3656
2.21
1.84
1.09
YPK_3721
-1.46
-2.57
-1.40
YPK_3749
-1.29
-1.86
-1.28
YPK_3753
1.22
2.02
1.12
YPK_3764
-2.61
-1.58
-1.61
YPK_3774
-3.04
-1.91
-1.69
YPK_3821
-3.44
1.08
-1.21
YPK_3836
1.58
2.05
-1.12
YPK_3837
-8.43
5.22
-2.11
YPK_3867
-1.23
-1.19
-1.80
YPK_3956
1.46
2.61
1.29
YPK_3963
-2.04
6.61
-1.55
YPK_4014
1.33
1.96
1.12
YPK_4039
1.08
2.17
1.03
YPK_4053
-1.24
4.87
1.32
YPK_4092
1.03
4.13
1.36
YPK_4107
-1.11
3.00
1.29
YPK_4108
2.45
1.08
-1.00
YPK_4124
1.17
6.05
-1.02
YPK_4130
1.51
1.87
1.35
YPK_4172
-1.94
-2.09
-1.73
YPK_4242
-2.26
-2.01
-1.84
ytfJ
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3101
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3138
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3218
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3608
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3645
conserved hypothetical
protein
hypothetical protein
YPK_3721
hypothetical protein
YPK_3749
hypothetical protein
YPK_3753
hypothetical protein
YPK_3764
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_3836
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_4014
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_4092
conserved hypothetical
protein
conserved hypothetical
protein
hypothetical protein
YPK_4124
hypothetical protein
YPK_4130
hypothetical protein
YPK_4172
conserved hypothetical
protein
-11.46
-5.14
-2.17
-1.57
-2.38
-1.86
-1.23
2.04
-1.26
-1.80
2.06
-1.53
-1.26
2.00
-1.40
1.76
1.82
1.04
-1.19
1.83
-1.16
1.86
1.56
1.25
1.80
-1.00
-1.20
1.12
1.99
1.17
-2.02
-1.21
-1.74
-1.33
-2.15
-1.78
-1.99
-1.94
-1.56
-1.83
-1.27
-1.14
-3.16
-1.86
-1.41
-1.95
-2.70
-2.05
-1.83
-1.38
-1.45
-2.00
-2.25
-1.56
2.28
1.47
1.59
6.01
1.42
-1.11
7.92
3.05
1.79
6.25
2.62
1.80
4.33
-2.03
-1.20
-2.01
-1.65
-1.57
1.49
-2.06
-1.71
-1.29
-1.88
-1.66
1.15
-2.64
-1.09
-1.59
-2.16
-1.76
4.10
17.85
1.70
-1.32
-1.92
-1.62
-1.66
-1.31
-1.78
-1.58
-2.27
-1.30
-1.31
-1.88
-1.60
1.79
1.84
1.13
-1.36
-1.83
-1.52
-1.58
-4.87
-1.40
-2.30
-2.99
-2.04
1.28
6.38
1.23
-2.05
-2.05
-1.47
-1.47
3.60
-1.66
-1.29
-1.79
-1.76
-1.94
-1.65
-1.58
-4.88
-3.66
-2.21
-1.95
-2.16
-1.30
6.05
-1.05
-1.05
2.16
2.30
-1.36
-2.06
-1.45
1.12
-1.35
-1.80
-2.05
-1.26
-1.91
-1.47
-1.80
-1.75
-1.44
Table S2. Metabolic network and calculated fluxes with 95% confidence intervals (CI) of glucosegrown Yersinia pseudotuberculosis wild type (YPIII) and the single-gene deletion mutants YP3
(ΔrovA), YP53 (ΔcsrA), and YP89 (Δcrp). The network comprises reaction equations (rxnEQ) and
carbon transitions (cTrans) for metabolite and isotopomer balancing, respectively. All fluxes are
expressed as a molar percentage of the corresponding specific glucose uptake rate, which was set as
100%. Abbreviations: GLC, glucose; PEP, phosphoenolpyruvate; GLC6P, glucose 6-phosphate; PYR,
pyruvate; F6P, fructose 6-phosphate; F16BP, fructose 1,6-bisphosphate; DHAP, dihydroxyacetone
phosphate; G3P, glyceraldehyde 3-phosphate; 6PG, 6-phosphogluconate; P5P, ribulose 5-phosphate /
ribose 5-phosphate; CO2, carbon dioxide; S7P, sedoheptulose 7-phosphate; E4P, erythrose 4-phosphate;
3PG, 3-Phosphoglycerate; SER, serine; GLY, glycine; MTHF, 5,10-Methylenetetrahydrofolate; OAA,
oxaloacetate; ACCOA, acetyl coenzyme A; CIT, citrate; ICIT, isocitrate; AKG, α-ketoglutarate; SUC,
succinate; GLYO, glyoxylate; MAL, malate; FUM, fumarate; ACE, acetate; FORM, formate; EtOH,
ethanol; LAC, lactate; VAL, valine; SHKM, shikimate; CHRM, chorismate; PHEX, phenylalanine,
TYRX, tyrosine; ASPX, aspartate; GLUX, glutamate; THR, threonine, _B/_BT, metabolite is a biomass
precursor; _EX, secreted metabolite. Possible reaction types: F, irreversible; F(X), irreversible and
assigned as a free flux; FR, reversible; B, reaction that is only used for metabolite balancing; S, reaction
that is used to map the measured label distribution of metabolites to their precursors.
rxnEQ
GLC_EX + PEP = GLC6P + PYR
GLC6P = F6P
F6P = F16BP
F16BP = DHAP + G3P
DHAP = G3P
GLC6P = 6PG
6PG = P5P + CO2
6PG = PYR + G3P
P5P + P5P = S7P + G3P
S7P + G3P = E4P + F6P
E4P + P5P = F6P + G3P
G3P = 3PG
3PG = PEP
3PG_B = SER
SER = GLY + MTHF
PEP = PYR
PEP + CO2 = OAA
PYR = ACCOA + CO2
ACCOA + OAA = CIT
CIT = ICIT
ICIT = AKG + CO2
ICIT = 0.5 SUC + 0.5 SUC + GLYO
GLYO + ACCOA = MAL
AKG = 0.5 SUC + 0.5 SUC + CO2
SUC = FUM
FUM = MAL
MAL = OAA
MAL = PYR + CO2
ACCOA = ACE
PYR = FORM + ACCOA
ACE = ETOH
PYR = LAC
CO2 = CO2_EX
AKG = AKG_EX
PYR = PYR_EX
SUC = SUC_EX
LAC = LAC_EX
FORM = FORM_EX
FUM = FUM_EX
ACE = ACE_EX
ETOH = ETOH_EX
GLC6P = GLC6P_B
F6P = F6P_B
P5P = P5P_B
E4P = E4P_B
G3P = G3P_B
3PG = 3PG_B
PEP = PEP_B
PYR = PYR_B
ACCOA = ACCOA_B
AKG = AKG_B
OAA = OAA_B
PYR_B + PYR_B = VAL + CO2
E4P_B + PEP_B = SHKM
SHKM + PEP_B = CHRM
CHRM = PHEX + CO2
CHRM = TYRX + CO2
cTrans
abcdef + ghi = abcdef + ghi
abcdef = abcdef
abcdef = abcdef
abcdef = cba + def
abc = abc
abcdef = abcdef
abcdef = bcdef + a
abcdef = abc + def
abcde + fghij = fgabcde + hij
abcdefg + hij = defg + abchij
abcd + efghi = efabcd + ghi
abc = abc
abc = abc
abc = abc
abc = ab + c
abc = abc
abc + d = abcd
abc = bc + a
ab + cdef = fedbac
abcdef = abcdef
abcdef = abcde + f
abcdef = 0.5 edcf + 0.5 fcde + ab
ab + cd = abdc
abcde = 0.5 bcde + 0.5 edcb + a
abcd = abcd
abcd = abcd
abcd = abcd
abcd = abc + d
ab = ab
abc = a + bc
ab = ab
abc = abc
a=a
abcde = abcde
abcd = abcd
abc = abc
abc = abc
abc = abc
ab = ab
abcd = abcd
abc + def = abefc + d
abcd + efg = efgabcd
abcdefg + hij = abcdefghij
abcdefghij = hijbcdefg + a
abcdefghij = hijbcdefg + a
Type
F
F
F
F
F
F(X)
F
F(X)
FR
FR
FR
F
F
F
F
F
FR
F
F
F
F
F(X)
F
F
F
F
F(X)
F
F
F
F
F
FR
B
B
B
B
B
B
B
B
B
B
F
F
B
F
F
F
F
B
F
F
F
F
F
F
Wild
type
Flux
100.0
66.6
84.9
84.9
84.9
32.5
32.5
0.0
10.1
10.1
8.6
177.8
171.4
1.3
1.3
51.5
16.9
83.5
62.8
62.8
62.8
0.0
0.0
56.2
56.0
55.9
54.3
1.5
10.1
2.9
3.3
7.2
221.2
1.1
46.5
0.2
7.2
2.9
0.1
6.8
3.3
0.9
0.3
3.8
1.5
0.6
6.4
2.9
13.0
13.5
5.5
8.5
0.9
0.7
0.7
0.5
0.3
CI
0.1
0.1
0.1
0.1
0.1
0.1
0.0
0.0
0.0
0.0
0.1
0.1
0.3
0.3
0.9
1.0
0.4
0.5
0.5
0.5
0.0
0.0
0.5
0.5
0.5
1.2
0.9
0.2
0.1
0.2
0.2
1.5
0.0
0.4
0.0
0.2
0.1
0.0
0.1
0.2
0.0
0.0
0.0
0.0
0.0
0.1
0.0
0.2
0.1
0.1
0.1
0.2
0.2
0.2
0.1
0.1
YP3
(∆rovA)
Flux
100.0
70.0
86.1
86.1
86.1
29.1
29.1
0.0
8.9
8.9
7.5
179.0
172.8
1.4
1.4
53.7
16.2
73.3
52.0
52.0
52.0
0.0
0.0
44.9
44.7
44.6
44.4
0.2
10.7
2.6
3.8
8.3
185.1
1.5
56.7
0.2
8.3
2.6
0.1
6.8
3.8
0.9
0.3
3.8
1.5
0.6
6.3
2.9
12.9
13.3
5.5
8.6
1.0
0.8
0.8
0.5
0.3
CI
0.1
0.1
0.1
0.1
0.1
0.1
0.0
0.0
0.0
0.0
0.1
0.2
0.3
0.3
0.3
0.3
1.0
1.1
1.1
1.1
0.0
0.0
1.1
1.1
1.1
1.0
0.3
0.3
0.0
0.2
0.2
3.2
0.0
1.0
0.0
0.2
0.0
0.0
0.2
0.2
0.0
0.0
0.1
0.0
0.0
0.1
0.1
0.2
0.2
0.1
0.1
0.2
0.2
0.2
0.1
0.1
YP53
(∆csrA)
Flux
100.0
69.0
85.7
85.7
85.7
30.1
30.1
0.0
9.3
9.3
7.8
178.6
172.3
1.6
1.6
153.8
15.5
85.2
69.3
69.3
69.3
0.0
0.0
62.9
63.0
63.0
62.3
0.7
3.0
0.4
0.3
3.5
234.8
0.9
52.5
0.0
3.5
0.4
0.0
2.7
0.3
0.9
0.3
3.8
1.5
0.6
6.4
2.9
12.9
13.3
5.5
8.5
1.1
0.9
0.9
0.6
0.3
CI
0.1
0.0
0.0
0.0
0.1
0.1
0.0
0.0
0.0
0.0
0.1
0.1
0.3
0.3
0.6
0.6
0.8
0.8
0.8
0.8
0.1
0.1
0.8
0.8
0.8
1.1
0.6
0.3
0.1
0.1
0.1
2.4
0.0
0.7
0.0
0.1
0.1
0.0
0.3
0.1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.1
0.1
0.0
0.0
0.2
0.1
0.1
0.1
0.0
YP89
(∆crp)
Flux
100.0
58.5
80.2
80.2
80.2
40.1
40.1
0.0
12.2
12.2
9.9
169.4
159.6
1.3
1.3
32.1
23.0
111.0
91.1
91.1
91.1
0.0
0.0
81.9
81.9
81.9
81.2
0.8
0.1
0.8
0.0
0.9
303.5
0.8
0.1
0.0
0.9
0.8
0.0
0.1
0.0
1.4
0.5
5.7
2.3
0.9
9.8
4.4
20.1
20.5
8.4
13.1
0.9
0.7
0.7
0.5
0.3
CI
0.1
0.1
0.1
0.1
0.1
0.1
0.0
0.1
0.1
0.1
0.1
0.2
0.4
0.4
0.7
0.7
0.4
0.4
0.4
0.4
0.0
0.0
0.5
0.5
0.5
0.8
0.6
0.0
0.0
0.0
0.0
1.5
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.1
0.0
0.0
0.1
0.1
0.2
0.2
0.1
0.2
0.3
0.2
0.2
0.1
0.1
OAA_B = OAA_BT
E4P_B = E4P_BT
P5P_B = P5P_BT
PYR_B = PYR_BT
PEP_B = PEP_BT
ACCOA_B = ACCOA_BT
3PG_B = 3PG_BT
0.333 VAL + 0.483 GLY + 0.180 PHEX + 0.091 TYRX = BIOMASS
PYR = ALA
OAA = ASPX
AKG = GLUX
OAA = THR
B
B
B
B
B
B
B
B
S
S
S
S
8.5
0.7
3.8
11.2
1.5
13.5
5.1
2.7
0.1
0.2
0.0
0.5
0.3
0.1
0.3
0.6
8.6
0.7
3.8
11.0
1.4
13.3
4.9
2.9
0.1
0.2
0.1
0.4
0.3
0.2
0.3
0.6
8.5
0.5
3.8
10.6
1.1
13.3
4.7
3.4
0.0
0.1
0.0
0.3
0.3
0.1
0.3
0.5
13.1
1.5
5.7
18.3
3.0
20.5
8.5
2.7
0.2
0.2
0.1
0.6
0.4
0.2
0.4
0.8