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Table S3. Full list of overrepresented COG groups in the MC metagenomes relative to the CT
metagenomesa.
COG
COG description
Metabolism
0243
Anaerobic
dehydrogenases, typically
selenocysteine-containing
0348
Polyferredoxin
Class
Class description
C
Energy production and
conversion
97
361
2.0
C
18
220
6.6
1018
Flavodoxin reductases
(ferredoxin-NADPH
reductases) family 1
Aconitase B
C
Energy production and
conversion
Energy production and
conversion
40
203
2.8
22
236
5.8
C
6
80
7.2
30
214
3.9
2
72
19.5
6
110
10.0
1362
Formylmethanofuran
dehydrogenase subunit A
NAD(P)H-nitrite
reductase
Predicted
NADH:ubiquinone
oxidoreductase, subunit
RnfD
Nitrate reductase alpha
subunit
Aspartyl aminopeptidase
Energy production and
conversion
Energy production and
conversion
Energy production and
conversion
Energy production and
conversion
1
94
51.0
0418
Dihydroorotase
F
13
118
4.9
0120
G
13
125
5.2
18
121
3.7
3957
Ribose 5-phosphate
isomerase
Predicted Nacetylglucosaminyl
transferase
Phosphoketolase
16
151
5.1
5309
Exo-beta-1,3-glucanase
G
3
87
15.7
0635
Coproporphyrinogen III
oxidase and related Fe-S
oxidoreductases
2-polyprenyl-6methoxyphenol
hydroxylase and related
FAD-dependent
oxidoreductases
H
71
295
2.3
111
414
2.0
1049
1229
1251
4658
5013
2956
0654
C
C
C
C
E
G
G
HC
Energy production and
conversion
Amino acid transport
and metabolism
Nucleotide transport and
metabolism
Carbohydrate transport
and metabolism
Carbohydrate transport
and metabolism
Carbohydrate transport
and metabolism
Carbohydrate transport
and metabolism
Coenzyme transport and
metabolism
Multiple classes
CT
MC
ORMC/CT
1502
Phosphatidylserine/phosp
hatidylglycerophosphate/c
ardiolipin synthases and
related enzymes
Catalase
I
Lipid transport and
metabolism
P
P
2223
ABC-type sulfate
transport system,
periplasmic component
Nitrate/nitrite transporter
Inorganic ion transport
and metabolism
Inorganic ion transport
and metabolism
3158
K+ transporter
P
0753
1613
3256
P
Nitric oxide reductase
P
large subunit
3696
Putative silver efflux
P
pump
4208
ABC-type sulfate
P
transport system,
permease component
4651
Kef-type K+ transport
P
system, predicted NADbinding component
4774
Outer membrane receptor P
for monomeric catechols
1020
Non-ribosomal peptide
Q
synthetase modules and
related proteins
3321
Polyketide synthase
Q
modules and related
proteins
Information storage and processing
0751
Glycyl-tRNA synthetase,
J
beta subunit
1187
16S rRNA uridine-516
J
pseudouridylate synthase
and related
pseudouridylate synthases
0557
Exoribonuclease R
K
0583
Transcriptional regulator
K
3437
Response regulator
KT
containing a CheY-like
receiver domain and an
HD-GYP domain
0708
Exonuclease III
L
38
286
4.1
6
80
7.2
10
148
8.0
10
168
9.1
115
394
1.9
13
118
4.9
254
938
2.0
11
113
5.6
Inorganic ion transport
and metabolism
29
171
3.2
Inorganic ion transport
and metabolism
Secondary metabolites
biosynthesis, transport
and catabolism
Secondary metabolites
biosynthesis, transport
and catabolism
40
365
5.0
92
895
5.3
94
621
3.6
Translation, ribosomal
structure and biogenesis
Translation, ribosomal
structure and biogenesis
38
214
3.1
74
348
2.6
71
182
30
336
888
213
2.6
2.7
3.9
45
219
2.6
Inorganic ion transport
and metabolism
Inorganic ion transport
and metabolism
Inorganic ion transport
and metabolism
Inorganic ion transport
and metabolism
Inorganic ion transport
and metabolism
Transcription
Transcription
Multiple classes
Replication,
1643
HrpA-like helicases
L
4389
Site-specific recombinase
L
86
315
2.0
7
112
8.7
Cell
wall/membrane/envelop
e biogenesis
Cell
wall/membrane/envelop
e biogenesis
16
124
4.2
9
126
7.6
29
178
3.3
81
337
2.3
MU
N
Cell
wall/membrane/envelop
e biogenesis
Cell
wall/membrane/envelop
e biogenesis
Multiple classes
Cell motility
106
10
624
128
3.2
7.0
NT
Multiple classes
64
348
3.0
NT
Multiple classes
43
442
5.6
NU
Multiple classes
96
370
2.1
NU
Multiple classes
166
551
1.8
NU
Multiple classes
11
113
5.6
NU
Multiple classes
21
256
6.6
O
Posttranslational
modification, protein
turnover, chaperones
Posttranslational
modification, protein
5
78
8.5
92
352
2.1
Cellular processes and signaling
0729
Outer membrane protein
M
1368
Phosphoglycerol
transferase and related
proteins, alkaline
phosphatase superfamily
Organic solvent tolerance
protein OstA
M
Outer membrane
protein/protective antigen
OMA87
Outer membrane protein
Flagellar motor
component
Chemotaxis protein
histidine kinase and
related kinases
Methyl-accepting
chemotaxis protein
Type II secretory
pathway, component PulF
Type II secretory
pathway, ATPase
PulE/Tfp pilus assembly
pathway, ATPase PilB
Tfp pilus assembly
protein, tip-associated
adhesin PilY1
Tfp pilus assembly
protein, ATPase PilU
ABC-type sulfate
transport system,
permease component
Glutathione S-transferase
M
1452
4775
1538
1291
0643
0840
1459
2804
3419
5008
0555
0625
recombination and
repair
Replication,
recombination and
repair
Replication,
recombination and
repair
M
O
3278
Cbb3-type cytochrome
oxidase, subunit 1
3484
Predicted proteasome-type O
protease
3634
Alkyl hydroperoxide
reductase, large subunit
O
1391
OT
2199
Glutamine synthetase
adenylyltransferase
Signal transduction
histidine kinase
cAMP-binding proteins catabolite gene activator
and regulatory subunit of
cAMP-dependent protein
kinases
FOG: GGDEF domain
2200
FOG: EAL domain
T
2202
FOG: PAS/PAC domain
T
2204
Response regulator
containing CheY-like
receiver, AAA-type
ATPase, and DNAbinding domains
HD-GYP domain
T
Predicted signal
transduction protein
containing EAL and
modified HD-GYP
domains
Response regulator
containing a CheY-like
receiver domain and a
GGDEF domain
Signal transduction
histidine kinase involved
in nitrogen fixation and
metabolism regulation
Predicted signal
T
0642
0664
2206
3434
3706
5000
5001
O
turnover, chaperones
Posttranslational
modification, protein
turnover, chaperones
Posttranslational
modification, protein
turnover, chaperones
Posttranslational
modification, protein
turnover, chaperones
Multiple classes
55
260
2.6
8
90
6.1
15
172
6.2
46
238
2.8
Signal transduction
mechanisms
Signal transduction
mechanisms
343
962
1.5
95
367
2.1
Signal transduction
mechanisms
Signal transduction
mechanisms
Signal transduction
mechanisms
Signal transduction
mechanisms
121
1331
6.0
88
1387
8.6
49
381
4.2
317
909
1.6
Signal transduction
mechanisms
Signal transduction
mechanisms
15
167
6.0
2
70
19.0
T
Signal transduction
mechanisms
49
395
4.4
T
Signal transduction
mechanisms
42
234
3.0
T
Signal transduction
17
168
5.4
T
T
T
T
transduction protein
mechanisms
containing a membrane
domain, an EAL and a
GGDEF domain
3267
Type II secretory
U
Intracellular trafficking,
10
103
5.6
pathway, component
secretion, and vesicular
ExeA (predicted ATPase)
transport
3451
Type IV secretory
U
Intracellular trafficking,
7
99
7.7
pathway, VirB4
secretion, and vesicular
components
transport
4796
Type II secretory
U
Intracellular trafficking,
17
145
4.6
pathway, component
secretion, and vesicular
HofQ
transport
0841
Cation/multidrug efflux
V
Defense mechanisms
512 1693
1.8
pump
1566
Multidrug resistance
V
Defense mechanisms
104
376
2.0
efflux pump
Poorly characterized
2194
Predicted membraneR
General function
22
274
6.8
associated, metalprediction only
dependent hydrolase
2509
Uncharacterized FADR
General function
27
152
3.1
dependent
prediction only
dehydrogenases
3178
Predicted
R
General function
15
128
4.6
phosphotransferase related
prediction only
to Ser/Thr protein kinases
4783
Putative Zn-dependent
R
General function
97
350
2.0
protease, contains TPR
prediction only
repeats
1795
Uncharacterized
S
Function unknown
12
101
4.6
conserved protein
2354
Uncharacterized protein
S
Function unknown
2
72
19.5
conserved in bacteria
3164
Predicted membrane
S
Function unknown
24
177
4.0
protein
3220
Uncharacterized protein
S
Function unknown
10
103
5.6
conserved in bacteria
5316
Uncharacterized
S
Function unknown
5
82
8.9
conserved protein
5501
Predicted secreted protein S
Function unknown
2
70
19.0
a
The copy number of putative gene sequences in the CT and MC metagenomes and odds ratios
(OR) between them are provided. The list of underrepresented COG groups is provided in Table
S5.