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Table 3 Candidates for gene expansion in the D. aromatica genome.

From: Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

Protein/protein family function

Number of duplicates

Number of triplicates

Transport (membrane)

12

 

Signal transduction or regulatory – includes:

9

 

   FlhD homolog

(1)

 

   FlhC homolog

(1)

 

   Nitrogen regulatory protein PII homolog

(1)

 

Hydrolase/transhydrogenase or hydratase

4

1

Cytochromes

3

2

Mhp family

2

2

Phospholipase/phosphohydrolase

2

1

Phasin

1

 

Dioxygenase

1

 

NapH homolog

1

 

NosZ homolog

1

 

Unknown function

7

 
  1. Proteins within the genome that show evidence of possible recent gene duplication are tabulated by general functional group, or, in some cases, specific proteins (NapH, NosZ, FlhCD, Nitrogen regulatory protein PII). Duplicates and triplicates were determined by adjacent clustering of the D. aromatica proteins in a phylogenomic tree profile. The percent identity between the D. aromatica duplicate and triplicate candidates is higher than identity to other species' protein candidates, indicating a possible gene family expansion event. Areas of duplicated clusters of proteins (for instance, the regions surrounding VIMSS582581, 582612, 582641, 582657, 582863, 583914 and 583592), including phage elements and Tra-type conjugation proteins, are not included in this table. Parentheses indicate these duplication events have been tabulated in the general category of signal transduction or regulatory proteins – individual protein types of particular interest are noted separately by protein name.