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Table 1 Clusters from the graph visualization of species

From: Gene duplications in prokaryotes can be associated with environmental adaptation

Clus

N

Main species

Main terms

1

65

Shigella sp. (10.8%)

Yersinia pestis (7.7%)

GO BP 0006259 DNA metabolic process (98.5%)

GO BP 0006313 transposition, DNA-mediated (75.8%)

2

44

Burkholderia sp. (15.9%)

GO BP 0006810 transport (37.8%)

3

39

Pseudomonas sp. (25.6%)

Methanococcus sp. (15.4%)

GO BP 0006082 organic acid metabolic process (37.5%)

GO BP 0008652 cellular amino acid biosynthetic process (35.0%)

4

34

Streptococcus sp. (47.1%)

Clostridium sp. (20.6%)

GO BP 0005975 carbohydrate metabolic process (40.0%)

GO MF 0050044 galactose-6-phosphate isomerase activity (31.4%)

5

23

Synechococcus sp. (30.4%)

Prochlorococcus marinus (26.1%)

GO BP 0015979 photosynthesis (91.7%)

6

23

Burkholderia sp. (13.0%)

GO BP 0045449 regulation of transcription (91.7%)

7

19

Escherichia coli (89.5%)

GO MF 0051539 4 iron, 4 sulfur cluster binding (90.0%)

8

16

Salmonella enterica (87.5%)

GO BP 0017004 cytochrome complex assembly (94.1%)

GO MF 0016829 lyase activity (88.2%)

9

16

Bacillus sp. (87.5%)

GO MF 0022857 transmembrane transporter activity (64.7%)

GO BP 0009254 peptidoglycan turnover (64.7%)

10

16

Staphylococcus sp. (100%)

GO CC 0005576 extracellular region (82.4%)

GO BP 0009405 pathogenesis (76.5%)

11

16

Campylobacter jejuni (18.8%)

GO CC 0044460 flagellum part (88.2%)

12

15

Rhodopseudomonas palustris (33.3%)

GO BP 0040011 locomotion (93.8%)

GO BP 0006935 chemotaxis (93.8%)

13

12

Mycobacterium sp. (83.3%)

INTERPRO IPR009416 Protein of unknown function (76.9%)

COG ONTOLOGY Cell motility and secretion (46.2%)

  1. For each cluster (Clus) in Figure 4 the number of species (N), the dominating species (in percentage of N) and selected dominating annotation term(s) from the overrepresentation analysis (in percentage of N in which this term was found) is shown. Several annotation terms will be highly similar, representing the same type of property, therefore only a selection of terms is shown.