Table 1.

Respiratory design of a facultative anaerobic P. putida KT2440. Number of unique protein domains obtained

Method	# Unique protein domains
Genome domain comparisons
Input aerobic domain core	1029
Input anaerobic domain core	1182
Long list, 1628 strains [95% threshold]
Shared domain core	755
Aerobic specific domain core	274
Anaerobic specific domain core	427
Long list, 1628 strains [1% threshold]
Shared domain core	1015
Aerobic specific domain core	14
Anaerobic specific domain core	167
Restricted list, 225 strains [90% threshold]
Shared domain core	1012
Aerobic specific domain core	17
Anaerobic specific domain core	170
Restricted list, 225 strains [1% threshold]
Shared domain core	934
Aerobic specific domain core	95
Anaerobic specific domain core	248
Transcriptome analysis	175
GSM simulations	18
RandomForest [input]	5831
Domains with a cumulative Gini coefficient ≥ 20	360
Domains with a cumulative Gini coefficient ≥ 100	5