Table 1.
The motif-containing proteins (McPs) profile of poxviruses, table S1–S3
| Vaccinia virus WR | Variola virus DNA | Monkeypox virus strain Zaire-96-I-16 | Yaba monkey tumor virus | Fowlpox virus | Canarypox virus | Orf virus | Cowpox virus | Camelpox virus | Myxoma virus strain Lausanne | Nile crocodilepox virus | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GenBank ID | AY243312 | X69198 | AF380138 | AY386371 | AF198100 | AY318871 | AY386264 | AF482758 | AF438165 | AF170726 | DQ356948 |
| Number of proteins | 218 | 197 | 191 | 140 | 260 | 328 | 130 | 233 | 211 | 170 | 173 |
| Protein interaction, thiol-disulfide transfer [25] | |||||||||||
| CxxxC | 25 | 23 | 22 | 16 | 27 | 41 | 15 | 32 | 28 | 16 | 36 |
| CxxC | 35 | 33 | 32 | 27 | 48 | 64 | 30 | 44 | 35 | 31 | 28 |
| Binding to integrins, RGD-related motifs (3–8% of whole proteome) [26] | |||||||||||
| RGD | 9 | 6 | 10 | 5 | 8 | 10 | 11 | 7 | 10 | 6 | 14 |
| % | 4.1 | 3 | 5.2 | 3.6 | 3.1 | 3 | 8.5 | 3 | 4.7 | 3.5 | 8.1 |
| Binding to phospholipids, lipid raft-mediated endocytosis (3–27% of proteome) [27] | |||||||||||
| RxLR | 12 | 8 | 10 | 6 | 12 | 19 | 36 | 14 | 11 | 5 | 38 |
| % | 5.5 | 4.1 | 5.2 | 4.3 | 4.6 | 5.8 | 27.7 | 6 | 5.2 | 2.9 | 22 |
| Glycosylation sites (58–81% of proteome) - (http://prosite.expasy.org/PDOC00001)* | |||||||||||
| N{P}[ST]{P} | 165 | 153 | 154 | 112 | 209 | 264 | 78 | 181 | 167 | 128 | 101 |
| % | 75.7 | 77.7 | 80.6 | 80 | 80.4 | 80.5 | 60 | 77.7 | 79.1 | 75.3 | 58.4 |
| Nuclear localization sequence (NLS; KR-rich) motifs [28] | |||||||||||
| KRxR | 11 | 10 | 10 | 6 | 8 | 18 | 9 | 17 | 13 | 10 | 19 |
| KRx [10, 12] K[KR][KR] | 0 | 0 | 0 | 0 | 1 | 4 | 1 | 0 | 0 | 0 | 1 |
| KRx [10, 12] K[KR]X[KR] | 1 | 1 | 2 | 2 | 1 | 5 | 0 | 2 | 0 | 0 | 2 |
| K[KR]RK | 3 | 3 | 2 | 2 | 6 | 8 | 0 | 3 | 3 | 2 | 5 |
| KR[KR]R | 1 | 1 | 1 | 1 | 0 | 3 | 2 | 1 | 2 | 1 | 7 |
| [PR]xxKR{DE}[KR] | 0 | 0 | 0 | 3 | 5 | 5 | 1 | 0 | 0 | 3 | 1 |
| [RP]xxKR[KR]{DE} | 1 | 2 | 0 | 2 | 4 | 2 | 3 | 2 | 1 | 2 | 2 |
| RKRP | 1 | 1 | 1 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 0 |
| Protein folding, Rossmann folds motifs, bind FAD or NAD(P) [29] | |||||||||||
| Gx [1, 2] GxxG | 8 | 10 | 13 | 8 | 14 | 12 | 8 | 15 | 13 | 11 | 21 |
| Gxxx[GA] | 110 | 96 | 101 | 54 | 108 | 146 | 106 | 116 | 99 | 94 | 128 |
| SUMO binding (40–58 and 40–61% of proteome) [12] | |||||||||||
| [VI]x[VI][VI] | 105 | 102 | 98 | 78 | 141 | 191 | 53 | 122 | 107 | 78 | 72 |
| % | 48.2 | 51.8 | 51.3 | 55.7 | 54.2 | 58.2 | 40.8 | 52.4 | 50.7 | 45.9 | 41.6 |
| hKx[DE] | 119 | 110 | 112 | 82 | 147 | 194 | 52 | 128 | 116 | 104 | 74 |
| % | 54.6 | 55.8 | 58.6 | 58.6 | 56.5 | 59.1 | 40 | 54.9 | 55 | 61.2 | 42.8 |
| Recruit ESCRT pathway [30] | |||||||||||
| YxxL | 129 | 120 | 128 | 90 | 162 | 222 | 61 | 149 | 133 | 119 | 111 |
| % | 59.2 | 60.9 | 67 | 64.3 | 62.3 | 67.7 | 46.9 | 63.9 | 63 | 70 | 64.2 |
| hPxV | 42 | 41 | 42 | 30 | 53 | 79 | 44 | 47 | 41 | 51 | 72 |
| % | 19.3 | 20.8 | 22 | 21.4 | 20.4 | 24.1 | 33.8 | 20.2 | 19.4 | 30 | 41.6 |
| Walker A, A’ and B motifs [31] | |||||||||||
| [AG]xxxxGK[ST] | 5 | 5 | 4 | 7 | 12 | 13 | 5 | 6 | 5 | 6 | 5 |
| hhhhDxDxR | 3 | 3 | 3 | 1 | 2 | 2 | 1 | 3 | 3 | 2 | 5 |
| hhhDxxP | 15 | 13 | 19 | 8 | 19 | 13 | 23 | 18 | 17 | 15 | 31 |
Total number of McPs (proteins harboring at least one instance of query motif; if >1 instances, they considered as (1) are counted for each query motifs; “%” means percentage of proteins (McPs) to total number of proteins; “x” denotes any residue; “{P}” denotes any residues, but P; alternative residues are bracketed; and [1, 2] means the motif is flanked by one or two residue(s); “h” denotes non-polar or hydrophobic residues. In this study, we considered h is equivalent “A, C, F, G, V, L, I, P, W, M, or Y” residue, Table S1
* Glycosylation sites were searched in entire protein sequences, but not confined to N- or C-terminals