Table 2.
Genomic features of the Novosphingobium strains
| Feature |
Strain within the Novosphingobium group |
|||||
|---|---|---|---|---|---|---|
| Y88 | US6-1 | Rr 2-17 | AP12 | DSM 12444 | PP1Y | |
| Chromosome size (bps) |
4,148,048 |
5,344,974 |
4,539,029 |
5,611,617 |
4,233,314 |
5,313,905 |
| Plasmid size(s) (bps) |
n.d |
n.d |
n.d |
n.d |
184,462 and 487,268 |
1,161,602, 192,103 and 48,714 |
| GC% |
63.95 |
63.07 |
62.71 |
65.91 |
65.11 |
63.26 |
| N50 |
192,509 |
117,882 |
130,074 |
54,713 |
n.r |
n.r |
| CDS |
|
|
|
|
|
|
| Total |
3,801 |
5,234 |
4,302 |
5,214 |
3,937 |
4,664 |
| # GO assigned (%) |
2,733 (72) |
3,330 (64) |
2,874 (67) |
3,489 (67) |
2,805 (71) |
3,376 (72) |
| # EC assigned (%) |
989 (26) |
1,193 (23) |
827 (19) |
913 (18) |
1,089 (28) |
1,339 (29) |
| # IPR assigned (%) |
3,273 (86) |
4,155 (79) |
3,543 (82) |
4,400 (84) |
3,435 (87) |
4,162 (89) |
| Calculated median pI of total proteome |
6.18 |
5.86 |
6.17 |
5.89 |
5.98 |
5.79 |
| tRNAs |
49 |
46 |
47 |
45 |
57 |
58 |
| # Scaffolds |
19 |
n.r |
n.r |
n.r |
n.r |
n.r |
| # Contigs | 77 | 123 | 166 | 187 | n.r | n.r |
Abbreviations: GO Gene ontology, EC Enzyme code, IPR Interproscan, CDS coding domain sequence, n.r not relevant, n.d not yet determined.