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Table 2 Comparison of different members of the Rhizobiales

From: Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales

  Re NGR Bj R7A Ml Sm At Bm
Genome         
   Upper strand matches*      82 43 31 12
   RpoN controlled gene products      184 62 69 24
   Size (Mb)      7.59 6.69 5.67 3.29
   Matches/Mb      10.80 6.43 5.47 3.65
   GC content (%)      62.4 62.1 58.1 57
Symbiotic region         
   Upper strand matches* 24 23 31 25 24 15   
   RpoN controlled gene products 52 60 87 55 58 30   
   Size (Mb) 0.37 0.54 0.41 0.50 0.61 1.35   
   Matches/Mb 64.86 42.59 75.61 50.00 39.34 11.11   
   GC content (%) 57.3 58.5 59.1 59.3 59.7 60.4   
Intergenic GC content (%) 55.0 55.9 57.3 58.0 57.0 56.4 52.0 49.9
Lower strand matches* 7 11 21 16 67¥ 32¥ 23¥ 12¥
-12 (C) distance to start codon (bp)§ 91 (231) 88 (149) 156 (214) 156 (288) 102 (209) 97 (210) 74 142) 123 (345)
Possible EBPs 1 2 2 3 8 7 6 3
  1. *Matches (possible RpoN-binding sites or -24/-12-type promoters) were predicted using PATSER (see Materials and methods). p42d (Re); pNGR234a (NGR); 410 kb region on chromosome (Bj); 502 kb symbiotic island on chromosome (R7A); 610 kb symbiotic island on chromosome (Ml); pSymA (Sm). The GC-content of the intergenic (non-coding) sequences was calculated with FramePlot 2.3.2 [68]. §The distribution of the -12 (C) position on the intergenic sequences is biased towards the corresponding downstream CDS (this distribution is visualized by means of a boxplot in the Additional data files, page 29). Therefore the median and third quartile (between brackets) were used as indicative parameters for these distances. Possible EBPs were predicted using HMMER 2.2 g (see Materials and methods) (see also Table 3). ¥The upstream intergenic region of the rpoN gene is included. At, Agrobacterium tumefaciens C58; Bm, Brucella melitensis 16 M; Bj, Bradyrhizobium japonicum USDA110; Ml, Mesorhizobium loti MAFF303099; NGR, Rhizobium sp. NGR234; R7A, M. loti R7A; Re, Rhizobium etli CFN42; Sm, Sinorhizobium meliloti 1021.