| 1j1i |
| ID: | 1496313082 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 296 (265) | ||
| Sequences: | 41437 (27671.7) | ||
| Seq/Len: | 156.366 | ||
| Nf(neff/√len): | 1699.9 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 156.366).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 74_L | 94_H | 4.540 | 1.00 |
| 109_S | 133_A | 4.474 | 1.00 |
| 32_E | 67_R | 3.921 | 1.00 |
| 226_L | 278_F | 3.205 | 1.00 |
| 231_K | 257_P | 3.195 | 1.00 |
| 256_I | 274_A | 3.002 | 1.00 |
| 58_V | 272_A | 2.990 | 1.00 |
| 96_H | 123_V | 2.674 | 1.00 |
| 254_Y | 274_A | 2.660 | 1.00 |
| 138_G | 233_D | 2.640 | 1.00 |
| 124_S | 134_L | 2.390 | 1.00 |
| 100_K | 130_L | 2.343 | 1.00 |
| 245_L | 251_S | 2.335 | 1.00 |
| 107_K | 132_N | 2.329 | 1.00 |
| 110_I | 120_G | 2.304 | 1.00 |
| 117_G | 139_S | 2.271 | 1.00 |
| 267_H | 270_D | 2.223 | 1.00 |
| 96_H | 127_H | 2.189 | 1.00 |
| 99_I | 108_V | 2.165 | 1.00 |
| 137_M | 271_F | 2.160 | 1.00 |
| 109_S | 132_N | 2.115 | 1.00 |
| 231_K | 255_I | 2.115 | 1.00 |
| 123_V | 127_H | 2.059 | 1.00 |
| 252_W | 281_L | 2.042 | 1.00 |
| 93_R | 126_L | 1.986 | 1.00 |
| 109_S | 135_V | 1.955 | 1.00 |
| 27_E | 80_A | 1.948 | 1.00 |
| 109_S | 279_L | 1.944 | 1.00 |
| 96_H | 100_K | 1.909 | 1.00 |
| 133_A | 282_R | 1.907 | 1.00 |
| 38_P | 69_I | 1.862 | 1.00 |
| 31_L | 52_E | 1.844 | 1.00 |
| 96_H | 130_L | 1.814 | 1.00 |
| 120_G | 134_L | 1.804 | 1.00 |
| 65_H | 276_L | 1.771 | 1.00 |
| 135_V | 275_T | 1.754 | 1.00 |
| 43_H | 73_M | 1.741 | 1.00 |
| 29_R | 78_K | 1.733 | 1.00 |
| 122_G | 126_L | 1.730 | 1.00 |
| 38_P | 67_R | 1.702 | 1.00 |
| 30_Y | 98_F | 1.689 | 1.00 |
| 136_L | 139_S | 1.672 | 1.00 |
| 238_V | 255_I | 1.640 | 1.00 |
| 43_H | 76_F | 1.638 | 1.00 |
| 273_N | 277_S | 1.606 | 1.00 |
| 42_I | 95_L | 1.589 | 1.00 |
| 61_I | 272_A | 1.588 | 1.00 |
| 64_R | 276_L | 1.566 | 1.00 |
| 225_T | 248_I | 1.566 | 1.00 |
| 50_E | 53_G | 1.558 | 1.00 |
| 42_I | 120_G | 1.545 | 1.00 |
| 32_E | 69_I | 1.516 | 1.00 |
| 259_C | 267_H | 1.510 | 1.00 |
| 44_G | 114_S | 1.509 | 1.00 |
| 274_A | 277_S | 1.499 | 1.00 |
| 71_M | 95_L | 1.495 | 1.00 |
| 135_V | 226_L | 1.493 | 1.00 |
| 66_Y | 280_S | 1.488 | 1.00 |
| 217_F | 220_K | 1.476 | 1.00 |
| 242_Y | 246_D | 1.473 | 1.00 |
| 95_L | 123_V | 1.466 | 1.00 |
| 114_S | 261_H | 1.452 | 1.00 |
| 41_L | 111_V | 1.451 | 1.00 |
| 89_D | 126_L | 1.449 | 1.00 |
| 42_I | 73_M | 1.439 | 1.00 |
| 226_L | 254_Y | 1.437 | 1.00 |
| 270_D | 274_A | 1.425 | 1.00 |
| 256_I | 259_C | 1.418 | 1.00 |
| 59_I | 70_A | 1.406 | 0.99 |
| 243_K | 247_L | 1.394 | 0.99 |
| 66_Y | 109_S | 1.383 | 0.99 |
| 127_H | 130_L | 1.379 | 0.99 |
| 72_D | 77_G | 1.335 | 0.99 |
| 123_V | 131_V | 1.328 | 0.99 |
| 92_I | 122_G | 1.328 | 0.99 |
| 121_L | 136_L | 1.310 | 0.99 |
| 40_I | 99_I | 1.306 | 0.99 |
| 252_W | 274_A | 1.305 | 0.99 |
| 36_G | 67_R | 1.297 | 0.99 |
| 37_Q | 109_S | 1.286 | 0.99 |
| 61_I | 276_L | 1.285 | 0.99 |
| 28_T | 79_T | 1.279 | 0.99 |
| 242_Y | 255_I | 1.278 | 0.99 |
| 87_T | 90_R | 1.276 | 0.99 |
| 71_M | 98_F | 1.270 | 0.99 |
| 39_V | 66_Y | 1.259 | 0.99 |
| 61_I | 64_R | 1.254 | 0.99 |
| 100_K | 127_H | 1.239 | 0.98 |
| 33_A | 70_A | 1.227 | 0.98 |
| 111_V | 137_M | 1.226 | 0.98 |
| 232_D | 258_H | 1.225 | 0.98 |
| 41_L | 68_V | 1.222 | 0.98 |
| 20_F | 27_E | 1.221 | 0.98 |
| 49_A | 54_N | 1.216 | 0.98 |
| 29_R | 52_E | 1.201 | 0.98 |
| 122_G | 125_V | 1.201 | 0.98 |
| 26_V | 74_L | 1.198 | 0.98 |
| 38_P | 104_F | 1.196 | 0.98 |
| 271_F | 275_T | 1.193 | 0.98 |
| 37_Q | 66_Y | 1.192 | 0.98 |
| 73_M | 119_T | 1.190 | 0.98 |
| 134_L | 225_T | 1.188 | 0.98 |
| 69_I | 98_F | 1.186 | 0.98 |
| 135_V | 279_L | 1.178 | 0.98 |
| 96_H | 126_L | 1.177 | 0.98 |
| 228_V | 256_I | 1.171 | 0.98 |
| 29_R | 72_D | 1.170 | 0.97 |
| 276_L | 280_S | 1.163 | 0.97 |
| 238_V | 242_Y | 1.158 | 0.97 |
| 104_F | 108_V | 1.158 | 0.97 |
| 52_E | 70_A | 1.156 | 0.97 |
| 125_V | 217_F | 1.155 | 0.97 |
| 66_Y | 279_L | 1.147 | 0.97 |
| 133_A | 278_F | 1.145 | 0.97 |
| 229_Q | 241_A | 1.139 | 0.97 |
| 242_Y | 253_G | 1.134 | 0.97 |
| 110_I | 131_V | 1.134 | 0.97 |
| 245_L | 253_G | 1.124 | 0.97 |
| 219_R | 247_L | 1.120 | 0.96 |
| 123_V | 130_L | 1.119 | 0.96 |
| 98_F | 102_M | 1.101 | 0.96 |
| 99_I | 123_V | 1.100 | 0.96 |
| 37_Q | 132_N | 1.091 | 0.96 |
| 28_T | 94_H | 1.085 | 0.96 |
| 259_C | 263_A | 1.083 | 0.96 |
| 108_V | 131_V | 1.080 | 0.95 |
| 228_V | 271_F | 1.075 | 0.95 |
| 248_I | 251_S | 1.067 | 0.95 |
| 52_E | 72_D | 1.062 | 0.95 |
| 39_V | 68_V | 1.061 | 0.95 |
| 231_K | 258_H | 1.061 | 0.95 |
| 42_I | 71_M | 1.061 | 0.95 |
| 61_I | 269_E | 1.060 | 0.95 |
| 92_I | 119_T | 1.057 | 0.95 |
| 52_E | 78_K | 1.051 | 0.94 |
| 243_K | 246_D | 1.047 | 0.94 |
| 23_A | 97_D | 1.045 | 0.94 |
| 254_Y | 270_D | 1.044 | 0.94 |
| 22_N | 27_E | 1.038 | 0.94 |
| 39_V | 62_L | 1.037 | 0.94 |
| 229_Q | 238_V | 1.037 | 0.94 |
| 228_V | 274_A | 1.036 | 0.94 |
| 269_E | 273_N | 1.016 | 0.93 |
| 59_I | 68_V | 1.014 | 0.93 |
| 112_G | 117_G | 1.009 | 0.93 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1j1iA | 1 | 0.8547 | 100 | 0.1 | Contact Map |
| 1ehyA | 4 | 0.8818 | 100 | 0.116 | Contact Map |
| 1iupA | 1 | 0.902 | 100 | 0.129 | Contact Map |
| 2pujA | 1 | 0.8953 | 100 | 0.133 | Contact Map |
| 3om8A | 2 | 0.875 | 100 | 0.147 | Contact Map |
| 3oosA | 1 | 0.8716 | 100 | 0.149 | Contact Map |
| 4inzA | 2 | 0.8716 | 100 | 0.152 | Contact Map |
| 4lxhA | 1 | 0.8986 | 100 | 0.157 | Contact Map |
| 2wueA | 2 | 0.8919 | 100 | 0.164 | Contact Map |
| 2xuaA | 2 | 0.8547 | 100 | 0.165 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)