Safety in numbers: multiple occurrences of highly similar homologs among Azotobacter vinelandiicarbohydrate metabolism proteins probably confer adaptive benefits

Table 2 The genomes with the highest levels of very similar carbohydrate metabolism synologs ¹

Genome	Number of synolog groups
	Total	Central carbohydrate metabolism	Organic acids	Di- and oligo-saccharides	Fermentation	One-carbon metabolism	CO₂fixation	Amino-sugars	Poly-saccharides	Carbohydrates - no sub-category	Sugar alcohols	Mono-saccharides
*Soil* / *sediments*
Clostridium beijerinckii NCIMB 8052	16	3	-	2	5	-	-	-	-	-	-	6
Azotobacter vinelandii DJ	15	8	-	2	5	-	-	-	-	-	-	-
Burkholderia xenovorans LB400	12	3	1	-	4	-	-	-	-	-	1	3
Bacillus cereus E33L²	10	2	-	-	-	-	-	-	-	-	7	1
Nakamurella multipartita DSM 44233	9	4	4	-	-	-	-	-	-	-	1	-
Rhodoferax ferrireducens DSM 15236	9	3	-	-	3	-	-	-	-	-	-	3
Burkholderia cepacia R18194²	9	-	-	-	5	1	-	-	-	-	-	3
Nitrobacter hamburgensis X14	9	2	-	-	-	-	6	-	-	-	-	1
Frankia sp. EAN1pec	9	8	-	-	1	-	-	-	-	-	-	-
Paracoccus denitrificans PD1222	8	4	1	-	-	3	-	-	-	-	-	-
Ralstonia eutropha JMP134	8	3	1	-	2	2	-	-	-	-	-	-
Burkholderia vietnamiensis strain G4²	8	2	-	-	4	1	-	-	-	-	-	1
*Marine* / *aquatic*
Shewanella baltica OS155	12	10	-	2	-	-	-	-	-	-	-	-
Methylobacillus flagellatus KT	8	7	-	1	-	-	-	-	-	-	-	-
*Pathogens*
Vibrio cholerae MZO-3³	16	6	-	1	1	1	-	-	-	-	-	7
Shigella dysenteriae M131649	16	2	-	5	-	1	-	-	-	1	2	5
Escherichia coli B7A³	12	3	-	2	-	-	-	-	-	-	2	5
Streptococcus pneumoniae OXC141³	11	3	-	6	1	-	-	1	-	-	-	-
Escherichia coli E110019³	8	-	-	-	-	-	-	-	-	-	8	-
*Commensals*
Streptococcus mitis NCTC 12261³	9	1	-	6	-	-	-	-	-	1	1	-

¹The table lists the twenty genomes with the largest number of synolog groups among carbohydrate metabolism genes when a threshold of at least 90% amino acid sequence identity was used. The data set was extracted from the SEED database [19] and synologs were defined as intra-genome sequences assigned to the same FIGfam (see text). The total number of such synolog groups in these genomes as well as their distribution in the eleven subcategories defined in the SEED database is shown. The median number of synolog groups for the genomes in this data set was 2.0 ± 1.0.
²Opportunistic pathogen.
³All synologs in this table were evaluated manually with regards to genomic context. The manual evaluation revealed that several of the synologs in V. cholerae MZO-3, E. coli B7A, S. pneumoniae OXC141, S. mitis NCTC 12261 and E. coli E110019 might be mistakenly identified as highly similar synologs due to overlapping contigs or the presence of truncated sequences. These sequences were therefore disregarded in interpretation of the results.

ISSN: 1471-2164