TABLE 2.
In-depth analysis, using contextual information, of a random subset of proteins classified as genus restricted by all automated methods
| Accession no. | Protein name | Taxonomic position (family, genus, species) | Taxonomic distribution found by automated methods | Taxonomic distribution found by in-depth manual analysis | Type of protein (reference) | Evidence |
|---|---|---|---|---|---|---|
| YP_227375 | Large coat protein | Secoviridae, unclassified, Strawberry latent ringspot virus | 2 species | >40 families | Contains two domains of capsids with a jellyroll fold (PFAM clan Viral_ssRNA_CP) (49) | Marginal HHpred hits (E = 0.28 for region 241–308 and E = 7.5 for 43–159 region) to PFAM family RhV, HHalign comparison with RhV alignment (E = 5 × 10−2), functional confirmation (50) |
| NP_042511 | Coat protein | Barnaviridae, Barnavirus, Mushroom bacilliform virus | 1 species | >40 families | Capsid with a jellyroll fold (PFAM clan Viral_ssRNA_CP) (49) | Marginal HHpred hit (E = 0.2) to PFAM family Viral_Coat for 67–181 region, HHalign comparison with Viral_coat (E = 1.4 × 10−3), functional confirmation (51) |
| YP_308882 | 6K2 | Potyviridae, Ipomovirus, Cucumber vein yellowing virus | 4 species | 4 genera in Potyviridae family (Ipomovirus, Poacevirus, Tritimovirus, Macluravirus) | 6K2 (87) | Subsignificant CSI-BLAST hits to other 6K2 proteins (also located between CI protein and VPg protein), significant HHalign comparison between full-length 6K2 of Ipomovirus and 6K2 of Tritimovirus, Poacevirus, and Macluravirus (E = 2.9 × 10−7) |
| NP_776026 | Putative matrix protein M | Flaviviridae, Flavivirus, Tamana bat virus | 1 species | At least 1 whole genus (Flavivirus), may also be homologous to matrix protein of related genus Pegivirus | Membrane protein (52) | Subsignificant CSI-BLAST hits of M proteins of flaviviruses to Tamana bat virus M protein, which has identical domain position within polyprotein (between C and E proteins), significant HHalign comparison between 53–159 region of M of Tamana bat virus and M of other flaviviruses (E = 6 × 10−6) |
| NP_778215 | VPg | Unclassified, Sobemovirus, Turnip rosette virus | 1 species | 1 whole genus (Sobemovirus) | Genome-linked protein Vpg (88) | CSI-BLAST finds full-length significant matches to VPg of many sobemoviruses, further iterative sequence searches identify as homologs VPg of all other sobemoviruses, all have same position within 2a/2b polyprotein (downstream of serine protease domain) |
| YP_293702 | P9 | Closteroviridae, Crinivirus, Tomato chlorosis virus | 1 genus | 1 genus | P9 (53) | |
| NP_619694 | Hypothetical protein p34 | Closteroviridae, Crinivirus, Lettuce infectious yellows virus | 1 species | 2 speciesa | Endonuclease | HHpred hit to RNase Dicera (PDBb accession no. 3c4b, E = 2.10−4) |
| NP_851570 | p22 | Closteroviridae, Crinivirus, Cucurbit yellow stunting disorder virus | 1 species | 1 species | ||
| YP_293697 | p5 | Closteroviridae, Crinivirus, Tomato chlorosis virus | 1 species | 1 species | ||
| YP_053926 | Hypothetical peptide | Comoviridae, Nepovirus (subgroup A), Tobacco ringspot virus | 1 species | 1 species |
a
p34 has homologs in only two viral species but is homologous to a vast family of RNases from cellular organisms and thus most probably originated by horizontal transfer, which is beyond the scope of this study (see Materials and Methods and Discussion).
b
PDB, Protein Data Bank.