Table 3.
Inventory of accessory attachment genes for polymer hydrolysis identified in the Fibrobacteres genomes, organized by Carbohydrate-binding modules (CBMs).
| CAZy family | pfam domain | Fibrobacteria | Chitinivibrionia | Cellulolytic bacteria (35 genomesa) | Bacterial average across 2038 sp. | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fibrobacteraceae | Fibromonadaceae | |||||||||||||
| F. succino-genes S85 | AD_80 | AD_111 | SR_36 | AD_312 | IN01_31 | IN01_221 | IN01_307 | C. alkali- philus ACht1 | MC_77 | Avg | Avg | Prevalence (%) | ||
| NON-CATALYTIC CBMS ASSOCIATED WITH: CELLULASES | ||||||||||||||
| CBM4 | pfam02018 | 8.3 | 10.9 | 9.6 | 8.6 | 12.2 | 5.9 | 6.7 | 13.3 | 12.5 | 15.4 | 5.6 | 0.5 | 5.5 |
| CBM30 | – | 0.0 | 0.0 | 0.0 | 1.7 | 0.0 | 5.9 | 6.7 | 0.0 | 0.0 | 0.0 | 0.6 | 0.1 | 1.3 |
| CBM51 | pfam14498 | 5.0 | 4.4 | 5.8 | 3.5 | 6.1 | 11.8 | 13.3 | 6.7 | 0.0 | 0.0 | 0.4 | 0.4 | 4.5 |
| Subtotals (%) | 13.3 | 15.2 | 15.4 | 13.8 | 18.4 | 23.5 | 26.7 | 20.0 | 12.5 | 15.4 | 6.6 | 1.0 | ||
| CHITINASES | ||||||||||||||
| CBM50 | – | 8.3 | 8.7 | 7.7 | 8.6 | 6.1 | 35.3 | 20.0 | 20.0 | 12.5 | 30.8 | 14.6 | 41.2 | 76.1 |
| Subtotals (%) | 8.3 | 8.7 | 7.7 | 8.6 | 6.1 | 35.3 | 20.0 | 20.0 | 12.5 | 30.8 | 14.6 | 41.2 | 76.1 | |
| HEMICELLULASES (DEBRANCHING AND OLIGOSACCHARIDE-DEGRADING ENZYMES) | ||||||||||||||
| CBM11 | pfam03425 | 6.7 | 8.7 | 7.7 | 6.9 | 8.2 | 23.5 | 26.7 | 26.7 | 25.0 | 0.0 | 0.1 | 0.0 | 0.6 |
| CBM13 | – | 0.0 | 0.0 | 0.0 | 0.0 | 4.1 | 0.0 | 0.0 | 6.7 | 0.0 | 0.0 | 3.7 | 1.6 | 10.7 |
| CBM22 | – | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 15.4 | 6.2 | 0.4 | 4.1 |
| CBM32 | – | 1.7 | 0.0 | 0.0 | 1.7 | 0.0 | 5.9 | 6.7 | 6.7 | 37.5 | 0.0 | 3.2 | 3.4 | 18.4 |
| CBM35 | – | 23.3 | 17.4 | 19.2 | 27.6 | 16.3 | 0.0 | 0.0 | 6.7 | 0.0 | 0.0 | 3.7 | 0.7 | 7.6 |
| CBM61 | – | 1.7 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.6 | 0.4 | 5.4 |
| CBM67 | – | 1.7 | 2.2 | 1.9 | 1.7 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.8 | 1.1 | 8.4 |
| Subtotals (%) | 35.0 | 28.3 | 28.8 | 37.9 | 28.6 | 29.4 | 33.3 | 46.7 | 62.5 | 15.4 | 19.3 | 7.6 | ||
| CELLULASES/HEMICELLULASES | ||||||||||||||
| CBM6 | pfam03422 | 41.7 | 45.7 | 46.2 | 37.9 | 44.9 | 5.9 | 6.7 | 6.7 | 0.0 | 15.4 | 4.9 | 0.7 | 8.2 |
| CBM9 | pfam02018 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 7.7 | 5.0 | 0.9 | 8.4 |
| Subtotals (%) | 41.7 | 45.7 | 46.2 | 37.9 | 44.9 | 5.9 | 6.7 | 6.7 | 0.0 | 23.1 | 9.9 | 1.6 | ||
| OTHERS | ||||||||||||||
| CBM48 | pfam02922 | 1.7 | 2.2 | 1.9 | 1.7 | 2.0 | 5.9 | 13.3 | 6.7 | 12.5 | 7.7 | 7.5 | 23.0 | 65.9 |
| CBM66 | – | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 7.7 | 1.1 | 1.1 | 7.6 |
| Subtotals (%) | 1.7 | 2.2 | 1.9 | 1.7 | 2.0 | 5.9 | 13.3 | 6.7 | 12.5 | 15.4 | 8.6 | 24.1 | ||
| Total estimated CBM | 60 | 46 | 52 | 58 | 49 | 17 | 15 | 15 | 8 | 13 | ||||
| Total estimated genes | 2871 | 2754 | 3008 | 2906 | 2344 | 3391 | 3347 | 2773 | 2304 | 2321 | ||||
| CBM to estimated genes (%) | 2.1 | 1.7 | 1.7 | 2.0 | 2.1 | 0.5 | 0.4 | 0.5 | 0.3 | 0.6 | 1.4b | 0.3c | ||
a
Based on Koeck et al. (2014).
b
Average of 52 CBMs to total genes across 35 cellulolytic bacteria genomes.
c
Average of 52 CBMs to total genes across 2038 bacterial species.