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Table 4 Comparison of identified COG and specific Pfams

From: Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads

  Spirulina-S1 dataset Maize-Rye dataset
Initial # reads 1019333 1019333
Initial # ORF 6115998 6115998
  Hits % Hits %
COG
Total # hits 206325   323947  
Information storage and processing 47949 23.2a 85124 26.3a
Cellular processes and signaling 37543 18.2a 59222 18.3a
Metabolism 89072 43.2a 124053 38.3a
Poorly characterized 31761 15.4a 55548 17.1a
Ratio AaM/CMb 1.27   0.91  
PFAMs
Total identified PFAMs 1132766   2205177  
Cellulose degradation PFAMs 1881 0.17c 6554 0.30c
Amino acid degradation PFAMs 10628 0.94c 16052 0.73c
Protein degradation PFAMs 7148 0.63c 11498 0.52c
Ratio proteases/cellulases (P/C) 3.80   1.75  
Ratio amino acid/cellulases (A/C) 5.65   2.45  
  1. a% of total identified COGs
  2. b“Amino acid transport and metabolism”/“Carbohydrate transport and Metabolism”
  3. c% of total identified PFAMs
  4. Comparison of the COG categories obtained with the MG-Rast platform (E-value 1e−5; min 60 % identity; 15 bp min length) and the selected Pfams obtained with the Hmmscan (E-value cutoff 1.0)