Table 1.
Results obtained with FREDS. The top ten solutions are shown for each search. In italics are the structures with similar folds. The percent identity column was calculated by structure based sequence alignment with the program TM-align (Zhang and Skolnick, 2005).
| Densityℑ | Res. | Solutions | Residues | Z-score | IDℵ | Hours (CPU)ℜ |
|---|---|---|---|---|---|---|
| GroEL * | 6.0 Å | 1GRL_A1 | 254 | 21.4 | 100% | 65 (4) |
| (1457) | 1Q2V_A1 | 258 | 15.4 | 24% | ||
| 1R7R_A4 | 154 | 5.3 | ||||
| 1WGW_A1 | 87 | 4.6 | ||||
| 1DLY_A1 | 121 | 4.5 | ||||
| 2CZ2_A2 | 111 | 4.4 | ||||
| 1Z21_A1 | 69 | 4.3 | ||||
| 3F9V_A3 | 79 | 4.3 | ||||
| 1Q2V_A2 | 104 | 4.2 | ||||
| 2EWF_A3 | 73 | 4.1 | ||||
|
| ||||||
| GroEL † | 6.0 Å | 1GRL_A3 | 158 | 9.6 | 100% | 48 (4) |
| (1457) | 1GRL_A2 | 86 | 8.5 | 100% | ||
| 1Q2V_A3 | 156 | 5.6 | 15% | |||
| 2JPS_A1 | 95 | 5.2 | --- | |||
| 1Z96_A1 | 42 | 5.1 | ||||
| 1XB2_B1 | 43 | 5.0 | ||||
| 2O4T_A1 | 82 | 4.9 | ||||
| 2C5U_A4 | 59 | 4.9 | ||||
| 1L9Z_H4 | 58 | 4.8 | ||||
| 1C03_A1 | 163 | 4.5 | ||||
|
| ||||||
| Metarhodopsin | 6.0 Å | 1GZM_A1 | 328 | 16.4 | 100% | 144 (6) |
| (1079) | 3DDL_A1 | 252 | 6.5 | 6.5% | ||
| 2JMH_A1 | 105 | 4.8 | ||||
| 1K0N_A1 | 85 | 4.8 | ||||
| 1JNV_Z3 | 60 | 4.6 | ||||
| 2IAK_A1 | 120 | 4.5 | ||||
| 2B7M_A3 | 79 | 4.5 | ||||
| 1W63_A3 | 94 | 4.5 | ||||
| 3C72_A2 | 91 | 4.5 | ||||
| 2Z73_A1 | 350 | 4.4 | ||||
|
| ||||||
| RDV ‡ | 8.5 Å | 1UF2_A1 | 302 | 22.4 | 100% | 78 (8) |
| (1378) | 1UF2 A4 | 267 | 14.6 | 100% | ||
| 1UF2_A3 | 193 | 11.1 | 100% | |||
| 1UF2_A2 | 100 | 7.7 | 100% | |||
| 3GZU_A2 | 335 | 6.0 | 7.3% | |||
| 3GZU_A1 | 319 | 5.9 | 8.5% | |||
| 1UF2_A5 | 105 | 5.7 | 100% | |||
| 1WIJ_A1 | 66 | 4.4 | --- | |||
| 2FJI_13 | 115 | 3.9 | ||||
| 1NF1_A2 | 183 | 3.8 | ||||
|
| ||||||
| Stressosome | 8.0 Å | 1TID_B1 | 115 | 6.5 | --- | 45 (4) |
| (1552) | 2VY9_A1 | 112 | 5.8 | 16% | ||
| 3D02_A2 | 156 | 4.8 | ||||
| 1H4X_A1 | 110 | 4.7 | ||||
| 2V64_A1 | 210 | 4.6 | ||||
| 2PFF_H2 | 296 | 4.5 | ||||
| 1TQI_A2 | 101 | 4.4 | ||||
| 3BT7_A1 | 131 | 4.1 | ||||
| 2DFW_A2 | 83 | 4.1 | ||||
| 1U8S_A2 | 85 | 4.1 | ||||
|
| ||||||
| Lambda gpD | 7.0 Å | 1TD3_A1 | 103 | 8.1 | >30% | 70 (8) |
| 2Q5T_A1 | 394 | 4.3 | ||||
| (5012) | 2I8B_A1 | 116 | 3.7 | |||
| 1YA0_A2 | 364 | 3.6 | ||||
| 1K92_A1 | 395 | 3.6 | ||||
| 2Q6T_A1 | 112 | 3.3 | ||||
| 2Z8X_A1 | 348 | 3.2 | ||||
| 1JMJ_A1 | 386 | 3.2 | ||||
| 3C0Y_A1 | 386 | 3.1 | ||||
| 2BP1_A1 | 323 | 3.1 | ||||
|
| ||||||
| P22 gp1 | 8.0 Å | 1GNC_A1 | 164 | 5.8 | UNK | 96 (6) |
| (5051) | 1FXK_C1 | 68 | 5.3 | |||
| 1UCU_A1 | 80 | 5.1 | ||||
| 2K0N_A1 | 85 | 5.0 | ||||
| 1P49_A2 | 58 | 4.9 | ||||
| 2GHO_D3 | 40 | 4.9 | ||||
| 3GI7_A1 | 120 | 4.8 | ||||
| 2S35_A1 | 106 | 4.8 | ||||
| 1Z0K_B1 | 61 | 4.6 | ||||
| 2JES_A2 | 274 | 4.5 | ||||
|
| ||||||
| P22 gp4 | 8.0 Å | 1A6Q_A2 | 62 | 5.5 | UNK | 48 (4) |
| (5051) | 1LLQ_A6 | 95 | 5.0 | |||
| 2EFG_B1 | 55 | 4.5 | ||||
| 1E94_E3 | 109 | 4.4 | ||||
| 2Q5T_A1 | 394 | 4.2 | ||||
| 3CXB_A2 | 82 | 4.2 | ||||
| 2G62_A1 | 223 | 4.1 | ||||
| 1L9Z_H4 | 58 | 4.1 | ||||
| 2QGY_A1 | 385 | 4.0 | ||||
| 2NYY_A2 | 325 | 3.9 | ||||
|
| ||||||
| P22 gp10 | 8.0 Å | 1RI6_A1 | 333 | 6.9 | UNK | 120 (4) |
| (5051) | 1L0Q_A1 | 296 | 6.8 | |||
| 1GXR_A1 | 324 | 6.5 | ||||
| 2EYQ_A1 | 259 | 5.3 | ||||
| 3E11_A5 | 313 | 4.9 | ||||
| 3DAD_A2 | 224 | 4.4 | ||||
| 1PGU_A1 | 278 | 4.3 | ||||
| 3BWS_A2 | 232 | 4.1 | ||||
| 2VDU_B1 | 374 | 3.9 | ||||
| 2BED_A1 | 123 | 3.9 | ||||
Numbers in parenthesis are the electron microscopy data bank (EMDB) identification.
First segmented volume of GroEL
Second segmented volume of GroEL
Rice Dwarf Virus P3 subunit. The two italicized and two underlined structures are homologues of one another.
The percent identity between the crystal structure of the segmented electron density and the identified structure. This is calculated from structure based sequence alignment with the SSM server.
The time required for completing the search. In parenthesis is the number of Intel E5430 XEON-EMT processors used.
UNK Unknown sequence identity, as no crystal structure is available for the segmented electron density.