Table 1.
Ten most abundant soil SEED hierarchical functional categories (A) and RefSeq bacterial and eukaryotic functional categories (B) in a 2 year soybean/corn crop rotation in L'Acadie, Quebec, Canada
|
(A) |
||
|
Functional databases |
Functional categories |
Relative abundance (%) |
|
Protein biosynthesis |
13.2 |
|
|
No hierarchy/na |
9.67 |
|
|
Transcription |
5.44 |
|
|
Protein folding |
5.29 |
|
|
SEED Hierarchical Profile (Level 1) |
Clustering-based subsystems |
4.46 |
|
Central carbohydrate metabolism |
3.56 |
|
|
Protein degradation |
2.5 |
|
|
Resistance to antibiotics and toxic compounds |
2.38 |
|
|
Lysine, threonine, methionine and cysteine |
2.04 |
|
|
Heat shock |
1.93 |
|
|
No hierarchy/na |
25.3 |
|
|
Protein metabolism |
21.6 |
|
|
Carbohydrates |
9.38 |
|
|
Amino acids and derivatives |
6.77 |
|
|
SEED Hierarchical Profile (Level 2) |
RNA metabolism |
6.74 |
|
Stress response |
5.33 |
|
|
Respiration |
3.83 |
|
|
Cofactors, vitamins, prosthetic groups, pigments |
3.25 |
|
|
Virulence, disease and defence |
2.54 |
|
|
Clustering-based subsystems |
2.15 |
|
|
No hierarchy/na |
9.57 |
|
|
Ribosome LSU bacterial |
4.6 |
|
|
GroEL GroES |
4.42 |
|
|
Ribosome SSU bacterial |
3.6 |
|
|
RNA polymerase bacterial |
3.02 |
|
|
SEED Hierarchical Profile (Level 3) |
Translation elongation factors bacterial |
1.98 |
|
Heat shock dnaK gene cluster extended |
1.93 |
|
|
Proteolysis in bacteria, ATP-dependent |
1.9 |
|
|
Transcription initiation, bacterial sigma factors |
1.63 |
|
|
Ton and Tol transport systems |
1.42 |
|
|
No hierarchy/na |
9.57 |
|
|
Heat shock protein 60 family chaperone GroEL |
3.8 |
|
|
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6) |
2.57 |
|
|
Chaperone protein DnaK |
1.21 |
|
| SEED Hierarchy (Level 4) |
Translation elongation factor Tu |
0.87 |
|
RNA polymerase sigma factor RpoD |
0.8 |
|
|
Translation elongation factor G |
0.76 |
|
|
ATP-dependent protease La (EC 3.4.21.53) Type I |
0.75 |
|
|
SSU ribosomal protein S1p |
0.71 |
|
|
Cell division protein FtsH (EC 3.4.24.-) |
0.65 |
|
|
(B) |
||
|
Molecular chaperone GroEL |
2.59 |
|
|
DNA-directed RNA polymerase subunit beta |
2 |
|
|
Molecular chaperone DnaK |
0.96 |
|
|
ABC transporter ATP-binding protein |
0.91 |
|
| RefSeq Bacteria |
MFS transporter |
0.65 |
|
Elongation factor G |
0.64 |
|
|
Endopeptidase La |
0.6 |
|
|
ABC transporter substrate-binding protein |
0.57 |
|
|
DNA-binding response regulator |
0.56 |
|
|
Elongation factor Tu |
0.54 |
|
| Heat shock protein 60, mitochondrial precursor |
4.33 |
|
|
Heat shock protein 78, mitochondrial precursor |
2.12 |
|
|
Putative chaperonin GroL |
1.73 |
|
|
Cold-shock DNA-binding domain-containing protein |
1.66 |
|
| RefSeq Eukaryotes |
Chaperonin homolog Hsp-60, mitochondrial |
1.53 |
|
Elongation factor Tu, mitochondrial precursor |
1.53 |
|
|
Chaperonin Hsp-60 |
1.45 |
|
|
Heat shock 60 kD protein 1 |
1.4 |
|
|
Chaperone protein DnaK |
1.3 |
|
|
Chaperonin homolog HSP60, mitochondrial precursor, partial |
1 |
na, Not applicable.