TABLE 4.
Sequence and structure similaritiesa of the monomer of the capsid protein from rice yellow mottle virus (PDB code 1F2N) with structurally related proteins and with our model for PLRV
| Virusd | Sequence identity (%) | No. of Aligned/gap positions | Cα rmsdb | PDB code |
|---|---|---|---|---|
| CoMV | 33.5 | 185/6 | 1.1 | 1NG0 |
| SeMV | 23.8 | 185/12 | 1.6 | 1SMV |
| TNV | 18.5 | 178/6 | 1.8 | 1C8N |
| TBSV | 15.6 | 160/32 | 2.1 | 2TBV |
| PhMV | 10.1 | 148/44 | 2.8 | 1QJZ |
| BPMV | 8.8 | 136/69 | 3.7 | 1BMV |
| STNV | 5.7 | 140/68 | 3.5 | 2STV |
| PLRVc | 22.2 | 158/43 | 1.2 |
a
Computed by the CE method (28).
b
rmsd, root mean square deviations computed with the positions of the Cα atoms after optimal superposition.
c
Model of PLRV from this work.
d
CoMV, cocksfoot mottle virus; SeMV, sesbania mosiac virus; TNV, tobacco necrosis virus; TBSV, tomato bushy stunt virus; PhMV, physalis mottle virus; BPMV, bean pod mottle virus; STNV, satellite tobacco necrosis virus.