Table S5. Distribution of genes in COG categories for Acidobacteria strains Ellin6076 and
Ellin345. Only categories with pronounced differences are shown. Shaded categories depict at
least a two-fold increase in gene content. The complete list of COG categories and comparisons
can be obtained through the Integrated Microbial Genomes system (http://img.jgi.doe.gov/cgibin/pub/main.cgi).
COG CATEGORY
Information storage and processing
(A) RNA processing and modification
(B) Chromatin structure and dynamics
(J) Translation
Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related
(K) Transcription
Serine/threonine protein kinase
DNA-directed RNA polymerase, sigma 24 homolog
Transcriptional regulators
Response regulators
(L) Replication, recombination, repair
Serine/threonine protein kinase
Site-specific recombinase XerD
Transposase and inactivated derivatives
Cellular processes
(D) Cell cycle control, mitosis, meiosis
(M) Cell wall/membrane biogenesis
Glycosyltransferase
4-amino-4-deoxy-L-arabinose transferase and related
Glycosyltransferases involved in cell wall biogenesis
L-alanine-DL-glutamate epimerase and related
Outer membrane protein
Nucleoside-diphosphate-sugar epimerases
ABC-type transport system, involved in lipoprotein release, permease
Membrane-fusion protein
Periplasmic protease
Endopolygalacturonase
Dihydropicolinate synthase/N-acetylneuraminate lyase
Cell division protein FtsI/penicillin-binding protein 2
Outer membrane protein/protective antigen OMA87
ABC-type polysaccharide/polyol phosphate export system, permease
ABC-type polysaccharide/polyol phosphate export system, ATPase
Periplasmic protein TonB
Soluble lytic murein transglycolase and related regulatory proteins
ADP-heptose:LPS heptosyltransferase
Membrane proteins related to metalloendopeptidases
Small-conductance mechanosensitive channel
Sortase
Lipid A core-O-antigen ligase and related
(N) Cell motility
Tfp pilus assembly protein PilF
Type II secretory pathway, pseudopilin PulG
Type II secretory pathway, component PulD
Methyl-accepting chemotaxis protein
Flp pilus assembly protein TadC
Predicted periplasmic or secreted lipoprotein
(O) Posttranslational modification, protein turnover, chaperones
Perirredoxin
Protein disulfide isomerase
ATPases with chaperone activity, ATP-binding subunit
Trypsin-like serine proteases, typically periplasmic, C-terminal PDZ
Peptidyl-prolyl cis-trans isomerase (rotamase) – cyclophilin family
Molecular chaperone
(T) Signal transduction mechanisms
Serine/threonine protein kinase
Response regulators
Signal transduction histidine kinase
Antirepressor regulating drug resistance, signal transduction comp.
Bacteriophytochrome
DnaK suppressor protein
(U) Intracellular trafficking, secretion
Strain Ellin6076
Strain Ellin345
Fold Increase+
0
3
183
13
471
79
70
114
141
328
79
32
64
1
2
164
6
295
30
28
53
119
158
30
6
10
0
1.5
1.1
2.2
1.6
2.6
2.5
2.2
1.2
2.1
2.6
5.3
6.4
26
444
36
26
36
25
40
29
17
14
13
11
9
7
6
6
6
6
6
5
5
5
6
4
101
26
5
4
4
3
3
183
21
8
8
8
7
10
421
79
141
88
12
9
7
174
25
257
15
7
15
4
17
20
11
8
2
0
2
4
3
0
0
11
4
2
1
2
1
2
84
10
9
2
3
0
0
134
9
4
3
4
2
5
316
30
119
58
3
2
2
110
1.0
1.7
2.4
3.7
2.4
6.3
2.4
1.5
1.6
1.8
6.5
> 11.0
4.5
1.8
2.0
> 6.0
> 6.0
NA
1.5
2.5
5.0
2.5
6.0
2.0
1.2
2.6
NA
2.0
1.3
> 3.0
> 3.0
1.4
2.3
2.0
2.7
2.0
3.5
2.0
1.3
2.6
1.2
1.5
4.0
4.5
3.5
1.6
Tfp pilus assembly protein PilF
Outer membrane protein
Periplasmic component of Tol biopolymer transport system
Flp pilus assembly protein TadD
Flp pilus assembly protein, ATPase CpaE
Flp pilus assembly protein, ATPase CpaF
Type II secretory pathway, component PulD
Signal peptidase I
Flp pilus assembly protein TadB
Flp pilus assembly protein CpaB
Flp pilus assembly protein TadC
Flp pilus assembly protein, secretin CpaC
Flp pilus assembly protein TadG
Flp pilus assembly protein, pilin Flp
Flp pilus assembly protein, protease CpaA
(V) Defense mechanisms
ABC-type antimicrobial peptide transport system
ABC-type multidrug transport system
Beta-lactamase class C and other penicillin binding proteins
Multidrug resistance efflux pump
Cation/multidrug efflux pump
Lantibiotic modifying enzyme
(W) Extracellular structures
(Z) Cytoskeleton
Metabolism
(C) Energy production, conversion
Predicted oxidoreductases
Aerobic-type carbon monoxide dehydrogenase, small subunit
Aerobic-type carbon monoxide dehydrogenase, large subunit
Glycosyltransferases, related to UDP-glucuronosyltransferase
FAD/FMN-containing dehydrogenases
Carbon dioxide conc. mechanism/carboxysome shell proteins
FOG:HEAT repeat
Rieske Fe-S protein
Predicted acetamidase/formamidase
Cytochrome b subunit
Cytochrome c2
(E) Amino acid transport, metabolism
Dipeptidyl aminopeptidases/acylaminoacylpeptidases
Acetylornithine deacetylase and related
Lysophospholipase L1 and related esterases
Threonine dehydrogenase and related Zn-dependent dehydrogenases
Aspartate/tyrosine/aromatic aminotransferase
Dihydropicolinate synthase/N-acetylneuraminate lyase
Choliine dehydrogenase and related
Xaa-Pro aminopeptidase
Histidinol phosphate/aromatic aminotransferase
Thiamine pyrophosphate-requiring enzymes
Threonine dehydratase
Spermidine synthase
Asparagine synthase (glutamate hydrolyzing)
ABC-type spremidine/putrescine transport systems, ATPase
Predicted ornithine cyclodeaminase
Methionine synthase II (cobalamin-independent)
(F) Nucleotide transport, metabolism
ADP-ribose pyrophosphatase
Inosine-uridine nucleoside N-ribohydrolase
5’-nucleotidase/2’,3’-cyclic phosphodiesterase and related esterases
(G) Carbohydrate transport, metabolism
Sugar phosphate isomerases/epimerases
Arabinose efflux permease
Glucose dehydrogenase
Nucleoside-diphosphate-sugar epimerases
Sugar phosphate permease
Gluconolactonase
Sugar kinases, ribokinase family
Beta-galactosidase/beta-glucuronidase
Alpha-L-arabinofuranosidase
Glycosyltransferases, related to UDP-glucuronosyltransferase
Alpha-L-fucosidase
26
25
18
17
4
4
4
4
3
3
3
2
2
2
1
236
124
44
23
18
19
2
0
0
10
10
7
9
0
0
2
3
0
0
0
0
0
0
0
116
54
21
13
9
8
0
0
0
2.6
2.5
2.6
1.9
> 4.0
> 4.0
2.0
1.3
> 3.0
> 3.0
> 3.0
> 2.0
> 2.0
> 2.0
> 1.0
2.0
2.6
2.1
1.8
2.0
2.4
> 2.0
0
0
344
20
9
8
8
8
9
6
5
4
4
3
392
25
17
16
12
9
9
8
7
6
6
5
5
4
3
3
3
93
6
3
2
427
41
27
26
29
16
13
10
9
8
8
7
223
8
3
3
3
2
0
0
0
0
0
0
268
10
5
1
5
6
2
2
3
3
3
2
0
0
1
0
0
68
2
0
0
213
6
12
0
20
6
2
3
4
2
3
1
1.5
2.5
3.0
2.7
2.7
4.0
> 9.0
> 6.0
> 5.0
> 4.0
> 4.0
> 3.0
1.5
2.5
3.4
16.0
2.4
1.5
4.5
4.0
3.5
2.0
2.0
2.5
> 5.0
> 4.0
3.0
> 3.0
> 3.0
1.4
3.0
> 3.0
> 2.0
2.0
6.8
2.3
> 26.0
1.5
2.7
6.5
3.3
2.3
4.0
2.7
7.0
Glucose/sorbosone dehydrogenases
ABC-type polysaccharide/polyol phosphate export system, permease
ABC-type polysaccharide/polyol phosphate export system, ATPase
Fucose permease
Predicted xylanase/chitin deacetylase
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Beta-glucosidase and related glycosidases
Mannose-6-phosphate isomerase
Ribulose-5-phosphate 4-epimerase and related
Beta-xylosidase
Beta-galactosidase
Beta-1,4-xylanase
Hydroxypyruvate isomerase
D-mannonate dehydratase
Ribose/xylose/arabinose/galactoside ABC-type transport, permease
(H) Coenzyme transport, metabolism
Methylase involved in ubiquinone/menaquinone biosynthesis
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
methylase
Mg-chelatase subunit ChlD
Demethylmenaquinone methyltransferase
(I) Lipid transport, metabolism
Dehydrogenases with different specificities
Esterase/lipase
Carboxylesterase type B
Acyl-CoA synthetases (AMP-forming)
(P) Inorganic ion transport, metabolism
Arylsulfatase A and related enzymes
Enterochelin esterase and related enzymes
Outer membrane receptor for ferrienterochelin and colicins
Mn2+ and Fe2+ transporters of the NRAMP family
Cytochrome c peroxidase
Putative silver efflux pump
(Q) Secondary metabolites
Dehydrogenases with different specificities
Imidazoloneproprionase and related amidohydrolases
Dienelactone hydrolase and related enzymes
Acyl-CoA synthetases (AMP-forming)
Carbon dioxide conc. mechanism/carboxysome shell proteins
N-acyl-D-aspartate/D-glutamate deacylase
Acyl carrier protein
Protein involved in biosynthesis of mitomycin antibiotics/fumonisin
Predicted enzyme involved in methoxymalonyl-ACP biodynthesis
3-oxoacyl-(acyl-carrier-protein) synthase
Polyketide synthase modules and related
Poorly characterized
(R) General function prediction
(S) Function unknown
(*) Not assigned
+ Not normalized for genome size
6
6
6
6
6
5
5
5
5
4
4
3
3
3
3
191
37
1
0
0
3
5
0
8
3
3
0
1
0
0
0
0
131
19
6.0
> 6.0
> 6.0
2.0
1.2
> 5.0
NA
1.7
1.7
> 4.0
4.0
> 3.0
> 3.0
> 3.0
> 3.0
1.5
2.0
18
8
7
182
39
11
9
8
179
18
16
7
6
6
3
148
39
21
8
8
9
5
5
4
4
4
3
4
4
0
110
15
5
0
4
118
0
2
3
3
0
1
70
15
11
1
4
0
2
3
0
1
2
1
4.5
2.0
> 7.0
1.7
2.6
2.2
> 9.0
2.0
1.5
> 18.0
8.0
2.3
3.0
> 6.0
3.0
2.1
2.6
1.9
8.0
2.0
> 9.0
2.5
1.7
> 4.0
4.0
2.0
3.0
833
477
2943
472
308
1612
1.8
1.5
1.8