Table 1.
MS data and homologues for the 201φ2-1 proteins identified by HPLC-ESI-MS/MS.
| Identification by MS1 |
||||||
|---|---|---|---|---|---|---|
| gp | M r(kDa) | Unique peptides | Total spectra | Spectra/Mw | % coverage | Function, homologues, paralogues2 |
| A. Proteins of established virion function according to Fokine et al. (2007) | ||||||
|
| ||||||
| 303 | 77.5 | 22 | 355 | 4.6 | 44 | major sheath protein, KZ429 (63% over 693); EL6 (21% over 707) |
| 2005 | 82.4 | 22 | 696 | 8.4 | 38 | major capsid protein, KZ120 (64% over 749); EL78 (20% over 325) |
| 2765 | 251.8 | 23 | 34 | 0.1 | 10 | cell-puncturing device, KZ181 (33% over 2387); KZ144 (45% over 187); EL183 (22% over 270) |
|
| ||||||
| B. RNA polymerase-related virion proteins | ||||||
|
| ||||||
| 139 | 49.6 | 8 | 34 | 0.7 | 24 | RNA polymerase, beta’ subunit, KZ80 (56% over 449); EL44 (23% over 447) |
| 273/274 | 173.4 | 24 | 87 | 0.5 | 19 | RNA polymerase, beta subunit, KZ178 (53% over 1548); EL186 (23% over 1142); EL187 (26% over 356) |
| 275 | 62.7 | 8 | 27 | 0.4 | 15 | RNA polymerase, beta subunit KZ180 (68% over 490); EL184 (32% over 491) |
|
| ||||||
| C. Other virion proteins | ||||||
|
| ||||||
| 273 | 62.3 | 8 | 47 | 0.8 | 21 | KZ26 (54% over 549), EL9 (29% over 540) |
| 286 | 101.8 | 11 | 28 | 0.3 | 15 | KZ27 (47% over 899); EL8 (26% over 898) |
| 29 | 35.7 | 4 | 24 | 0.7 | 15 | KZ28 (43% over 320); EL7 (21% over 181) |
| 32 | 32.1 | 10 | 149 | 4.6 | 51 | KZ30 (75% over 290); EL5 (20% over 217) |
| 36 | 47.9 | 4 | 9 | 0.2 | 11 | KZ32 (55% over 410); EL13 (27% over 373) |
| 48 | 29.9 | 4 | 17 | 0.6 | 16 | KZ34 (40% over 267) |
| 49 | 12.3 | 5 | 43 | 3.5 | 53 | |
| 73 | 31.2 | 3 | 10 | 0.3 | 11 | KZ42 (61% over 274); EL14 (23% over 213) |
| 81 | 14.7 | 4 | 4 | 0.3 | 25 | KZ49 (44% over 135); EL20 (34% over 49) |
| 98 | 41.9 | 5 | 19 | 0.5 | 17 | KZ52 (51% over 362) |
| 138 | 31.9 | 6 | 20 | 0.6 | 23 | KZ79 (38% over 286) |
| 145 | 49.0 | 9 | 34 | 0.7 | 26 | ligase, KZ84 (34% over 434); EL52 (19% over 348) |
| 146 | 15.9 | 7 | 63 | 4.0 | 74 | KZ85 (33% over 145) |
| 1487 | 47.5 | 9 | 38 | 0.8 (1.2) | 23 | KZ86 (24% over 378) |
| 149 | 109 | 8 | 19 | 0.17 | 10 | KZ87 (52% over 971); EL56 (25% over 981) |
| 150 | 41 | 2 | 6 | 0.15 | 5 | KZ88 (56% over 344); EL57 (28% over 334) |
| 1515,7 | 44.4 | 13 | 107 | 2.4 (4.0) | 29 | KZ89 (53% over 406); EL58 (28% over 225) |
| 152 | 34.4 | 12 | 121 | 3.5 | 43 | KZ90 (47% over 294) |
| 153 | 20.8 | 4 | 14 | 0.7 | 22 | KZ91 (51% over 170) |
| 154 | 49.1 | 8 | 28 | 0.6 | 22 | KZ92 (34% over 356) |
| 1557 | 65.6 | 17 | 121 | 1.8 (3.8) | 31 | KZ94 (26% over 305), paralogue family b |
| 1567 | 43.2 | 9 | 70 | 1.6 (2.6) | 25 | KZ94 (30% over 410), paralogue family b |
| 1577 | 53 | 9 | 62 | 1.2 (1.9) | 27 | KZ94 (22% over 380), paralogue family b |
| 158 | 41.6 | 2 | 4 | 0.1 | 5 | KZ96 (29% over 356) |
| 1597 | 97.4 | 10 | 133 | 1.4 (4.0) | 15 | KZ97 (27% over 540) |
| 162 | 54.8 | 3 | 13 | 0.2 | 6 | KZ99 (53% over 465); EL69 (21% over 259) |
| 164 | 51.9 | 2 | 3 | 0.06 | 5 | KZ101 (42% over 457); EL71 (28% over 395) |
| 1937 | 42.4 | 13 | 188 | 4.4 (7.0) | 33 | |
| 198 | 20.3 | 4 | 13 | 0.6 | 25 | KZ119 (52% over 178) |
| 211 | 15.9 | 2 | 6 | 0.4 | 17 | KZ126 (33% over 142) |
| 212 | 32.4 | 3 | 6 | 0.2 | 12 | KZ127 (37% over 291) |
| 213 | 84 | 5 | 11 | 0.1 | 8 | KZ128 (49% over 725); EL104 (26% over 599) |
| 214 | 102.3 | 8 | 21 | 0.2 | 15 | KZ129 (51% over 880); EL103 (20% over 323) |
| 215 | 48.9 | 4 | 18 | 0.4 | 18 | KZ130 (53% over 439); EL112 (23% over 299) |
| 216 | 79.7 | 9 | 43 | 0.5 | 17 | KZ131 (38% over 782); EL113 (27% over 199) (paralogue family a)7 |
| 217 | 11.8 | 6 | 45 | 3.8 | 76 | KZ132 (48% over 83); EL116 (27% over 77); (paralogue family a)7 |
| 218 | 50.7 | 6 | 14 | 0.3 | 14 | KZ133 (37% over 464); EL115 (18% over 264)(paralogue family a)7 |
| 219 | 50.4 | 5 | 9 | 0.2 | 16 | KZ134 (35% over 471); EL114 (23% over 247) (paralogue family a)7 |
| 220 | 48.5 | 3 | 10 | 0.2 | 9 | KZ 135 (38% over 347); EL115 (20% over 268)(paralogue family a)7 |
| 224 | 32.5 | 7 | 34 | 1.1 | 26 | KZ139 (66% over 292); EL106 (28% over 278) |
| 226 | 16.3 | 4 | 9 | 0.6 | 30 | KZ103 (26% over 97) |
| 2276 | 14.6 | 3 | 11 | 0.7 | 21 | KZ142 (31% over129) |
| 228 | 23.9 | 6 | 42 | 1.8 | 30 | KZ143 (46% over 181) |
| 229 | 29.1 | 1 | 1 | 0.03 | 5 | KZ144 (47% over 65) |
| 230 | 155.8 | 50 | 606 | 3.9 | 59 | KZ145 (51% over 222); KZ146 (27% over 760); EL156 (33% over 812) |
| 233 | 25.4 | 5 | 18 | 0.7 | 26 | KZ149 (62% over 221); EL175 (32% over 224) |
| 2388 | 35.7 | 14 | 76 | 2.1 | 41 | KZ153 (27% over 307) |
| 243 | 50.8 | 15 | 110 | 2.2 | 44 | KZ157 (53% over 442); EL169 (25% over 404) |
| 245 | 23.2 | 1 | 1 | 0.04 | 6 | KZ161 (42% over 203); EL168 (27% over 201) |
| 246N7 | 66.4 | 3 | 14 | (0.7) | 17 | KZ162 (24% over 330), paralogue family b |
| 246C7 | 19 | 197 | 3.0 (4.4) | 58 | ||
| 247 | 44.5 | 9 | 36 | 0.8 | 32 | KZ163 (45% over 375), paralogue family b |
| 261 | 40.8 | 12 | 25 | 0.6 | 42 | KZ174 (38% over 380) |
| 2686 | 31.9 | 5 | 36 | 1.1 | 18 | KZ175 (55% over 268); EL192 (35% over 207) |
| 269 | 27.1 | 1 | 5 | 0.2 | 5 | KZ176 (63% over 240); EL191 (25% over 242) |
| 2718 | 70.2 | 8 | 51 | 0.7 | 18 | KZ177 (41% over 489) |
| 277 | 59.0 | 3 | 5 | 0.07 | 4 | KZ182 (64% over 668); EL182 (23% over 352) |
| 280 | 21.1 | 2 | 18 | 0.9 | 14 | KZ184 (59% over 120) |
| 296 | 16.5 | 5 | 17 | 1.0 | 44 | exonuclease; KZ199 (61% over 139) |
| 298 | 70.1 | 4 | 10 | 0.1 | 7 | KZ201 (27% over 635) |
| 299 | 12.9 | 4 | 28 | 2.2 | 37 | KZ202 (25% over 99) |
| 300 | 81.1 | 7 | 17 | 0.2 | 12 | helicase of the SNF2/RAD54 family; KZ203 (51% over 710); EL166 (33% over 500) |
| 313 | 13.3 | 3 | 11 | 0.8 | 38 | KZ244 (24% over 119) |
| 382 | 12 | 2 | 24 | 2.0 | 37 | |
| 439 | 31.7 | 5 | 17 | 0.5 | 25 | |
| 440 | 32.1 | 6 | 36 | 1.1 | 32 | |
| 441 | 72.4 | 12 | 44 | 0.6 | 34 | |
| 442 | 35.5 | 6 | 19 | 0.5 | 20 | |
| 452 | 26.5 | 2 | 10 | 0.4 | 9 | KZ83 (25% over 243); EL155 (27% over 104), paralogue family c |
| 455 | 87.6 | 16 | 62 | 0.7 | 21 | KZ303 (28% over 406) |
| 456 | 45 | 6 | 27 | 0.6 | 18 | EL155 (26% over 191); KZ83 (26% over 183), paralogue family c |
All proteins had a protein identity probability of 100%, as determined by Scaffold (Proteome Software), with the exception of gp164 (99%) and gp229 (96%). Results displayed were obtained from a combined data set of the GeLCMS analysis, with the exception of gp276 which was only detected in analysis of an individual gel band (see text).
Homologues were determined using Psi-Blast and BlastP (% identities over the homologous region are provided). The best matching φKZ and EL homologue for each 201φ2-1 protein is listed. Paralogue families are as follows: paralogue family a refers to a domain found in 201φ2-1 gp216, 217, 218, 219, 220. A homologous domain exists in φKZ gp131, 132, 133, 134 and 135 and EL gp113, 114 and 115; paralogue family b refers to a domain found in 201φ2-1 gp155, 156, 157, 246, 247. Homologous domains exist in φKZ gp93, 94, 95, 162 and 163; paralogue family c refers to a domain found in 201φ2-1 gps 456 and 452. Homologous domains exists in φKZ gp83 and EL gp155.
An N-terminal peptide lacking only the initiator methionine was identified using semi-tryptic analysis.
KZ refers to φKZ.
N-terminus is expected to be processed as the φKZ homologue is processed. Although no semi-tryptic fragments were found to define the mature ends, there is also a lack of peptide coverage in the N-terminal region that would be consistent with processing.
A mature N-terminus containing the initiator methionine was confirmed by semi-tryptic analysis.
Gel analysis indicated that the protein is processed consistent with a lack of MS sequence coverage in the N-terminal region of these sequences, except for gp246N which lacks MS coverage of the C terminal region. The exact positions of the processed ends are unknown. The normalized spectrum count in parentheses was calculated using the apparent molecular weight of the processed form (Fig. 1).
Semi-tryptic analysis indicated removal of 63 and 60 N-terminal residues from gp238 and gp271, respectively.