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Table 1 Respiratory design of a facultative anaerobic P. putida KT2440. Number of unique protein domains obtained

From: A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration

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