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

Table 4 Comparison of identified COG and specific Pfams

	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	23.2^a	85124	26.3^a
Cellular processes and signaling	37543	18.2^a	59222	18.3^a
Metabolism	89072	43.2^a	124053	38.3^a
Poorly characterized	31761	15.4^a	55548	17.1^a
Ratio AaM/CM^b	1.27		0.91
PFAMs
Total identified PFAMs	1132766		2205177
Cellulose degradation PFAMs	1881	0.17^c	6554	0.30^c
Amino acid degradation PFAMs	10628	0.94^c	16052	0.73^c
Protein degradation PFAMs	7148	0.63^c	11498	0.52^c
Ratio proteases/cellulases (P/C)	3.80		1.75
Ratio amino acid/cellulases (A/C)	5.65		2.45

^a% of total identified COGs
^b“Amino acid transport and metabolism”/“Carbohydrate transport and Metabolism”
^c% of total identified PFAMs
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)

ISSN: 1471-2180