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

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

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 -
  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.
  2. 2Opportunistic pathogen.
  3. 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.