| DegQ 30-390 |
| ID: | 1378872896 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 361 (360) | ||
| Sequences: | 2393 (1693.5) | ||
| Seq/Len: | 6.647 | ||
| Nf(neff/√len): | 89.3 |
HHblits Results: (2013_03)
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: 6.647).
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 |
| 131_N | 135_E | 6.288 | 1.00 |
| 227_S | 255_G | 4.774 | 1.00 |
| 256_L | 265_V | 4.515 | 1.00 |
| 28_I | 42_L | 3.477 | 1.00 |
| 285_A | 288_G | 3.406 | 1.00 |
| 19_N | 45_S | 3.172 | 1.00 |
| 69_D | 72_K | 3.135 | 1.00 |
| 120_I | 154_G | 3.056 | 1.00 |
| 53_L | 170_I | 2.964 | 1.00 |
| 66_A | 135_E | 2.943 | 1.00 |
| 255_G | 262_P | 2.919 | 1.00 |
| 97_V | 114_I | 2.830 | 1.00 |
| 71_D | 160_N | 2.749 | 1.00 |
| 69_D | 160_N | 2.748 | 1.00 |
| 229_N | 246_T | 2.736 | 1.00 |
| 253_K | 264_E | 2.684 | 1.00 |
| 7_I | 32_L | 2.615 | 1.00 |
| 251_K | 266_E | 2.584 | 1.00 |
| 40_A | 54_L | 2.555 | 1.00 |
| 73_L | 137_I | 2.545 | 1.00 |
| 305_I | 319_L | 2.543 | 1.00 |
| 38_F | 56_I | 2.465 | 1.00 |
| 211_G | 215_A | 2.453 | 1.00 |
| 335_S | 338_E | 2.441 | 1.00 |
| 41_K | 57_Q | 2.399 | 1.00 |
| 288_G | 294_G | 2.379 | 1.00 |
| 6_V | 128_A | 2.292 | 1.00 |
| 16_L | 162_A | 2.283 | 1.00 |
| 253_K | 266_E | 2.263 | 1.00 |
| 256_L | 263_L | 2.251 | 1.00 |
| 219_V | 256_L | 2.244 | 1.00 |
| 226_T | 257_L | 2.221 | 1.00 |
| 14_Y | 43_I | 2.221 | 1.00 |
| 323_D | 356_R | 2.201 | 1.00 |
| 6_V | 136_L | 2.164 | 1.00 |
| 8_I | 166_A | 2.111 | 1.00 |
| 128_A | 136_L | 2.093 | 1.00 |
| 227_S | 230_G | 2.092 | 1.00 |
| 219_V | 254_L | 2.090 | 1.00 |
| 251_K | 268_T | 2.085 | 1.00 |
| 16_L | 166_A | 2.082 | 1.00 |
| 205_V | 219_V | 2.068 | 1.00 |
| 29_S | 37_E | 2.035 | 1.00 |
| 328_V | 339_M | 2.010 | 1.00 |
| 65_I | 136_L | 1.960 | 1.00 |
| 255_G | 264_E | 1.956 | 1.00 |
| 228_L | 246_T | 1.924 | 1.00 |
| 227_S | 232_P | 1.920 | 1.00 |
| 205_V | 225_I | 1.917 | 1.00 |
| 73_L | 97_V | 1.892 | 1.00 |
| 219_V | 265_V | 1.885 | 1.00 |
| 78_F | 94_S | 1.870 | 1.00 |
| 15_V | 56_I | 1.844 | 1.00 |
| 180_L | 267_V | 1.823 | 1.00 |
| 65_I | 130_L | 1.821 | 1.00 |
| 284_P | 288_G | 1.819 | 1.00 |
| 27_K | 39_D | 1.814 | 1.00 |
| 167_Q | 171_D | 1.751 | 1.00 |
| 41_K | 55_Q | 1.712 | 1.00 |
| 186_E | 236_F | 1.682 | 1.00 |
| 334_N | 338_E | 1.665 | 1.00 |
| 288_G | 292_S | 1.607 | 1.00 |
| 355_V | 358_N | 1.601 | 1.00 |
| 5_G | 15_V | 1.573 | 1.00 |
| 67_I | 159_S | 1.537 | 0.99 |
| 51_I | 139_I | 1.536 | 0.99 |
| 14_Y | 53_L | 1.505 | 0.99 |
| 226_T | 255_G | 1.461 | 0.99 |
| 216_K | 270_D | 1.453 | 0.99 |
| 210_P | 215_A | 1.445 | 0.99 |
| 176_K | 271_T | 1.438 | 0.99 |
| 246_T | 269_L | 1.435 | 0.99 |
| 183_K | 207_E | 1.409 | 0.99 |
| 70_S | 160_N | 1.407 | 0.99 |
| 285_A | 294_G | 1.398 | 0.99 |
| 226_T | 262_P | 1.395 | 0.99 |
| 14_Y | 170_I | 1.387 | 0.98 |
| 67_I | 163_R | 1.387 | 0.98 |
| 174_E | 271_T | 1.386 | 0.98 |
| 172_F | 176_K | 1.375 | 0.98 |
| 201_R | 232_P | 1.375 | 0.98 |
| 146_P | 151_V | 1.366 | 0.98 |
| 247_E | 250_T | 1.366 | 0.98 |
| 7_I | 62_L | 1.352 | 0.98 |
| 139_I | 162_A | 1.351 | 0.98 |
| 6_V | 139_I | 1.350 | 0.98 |
| 6_V | 65_I | 1.348 | 0.98 |
| 178_G | 269_L | 1.329 | 0.98 |
| 6_V | 130_L | 1.325 | 0.98 |
| 289_A | 294_G | 1.324 | 0.98 |
| 23_N | 47_D | 1.313 | 0.98 |
| 285_A | 290_T | 1.308 | 0.98 |
| 16_L | 159_S | 1.301 | 0.97 |
| 163_R | 167_Q | 1.282 | 0.97 |
| 223_D | 258_R | 1.268 | 0.97 |
| 159_S | 162_A | 1.262 | 0.97 |
| 84_N | 89_G | 1.260 | 0.97 |
| 116_T | 129_L | 1.240 | 0.96 |
| 303_I | 333_V | 1.237 | 0.96 |
| 220_K | 259_N | 1.231 | 0.96 |
| 13_G | 55_Q | 1.231 | 0.96 |
| 168_Q | 172_F | 1.231 | 0.96 |
| 122_R | 146_P | 1.228 | 0.96 |
| 145_A | 148_G | 1.223 | 0.96 |
| 7_I | 56_I | 1.222 | 0.96 |
| 338_E | 341_K | 1.219 | 0.96 |
| 20_H | 50_D | 1.218 | 0.96 |
| 187_M | 197_L | 1.216 | 0.96 |
| 107_L | 142_A | 1.215 | 0.96 |
| 188_S | 191_I | 1.200 | 0.95 |
| 80_V | 132_L | 1.195 | 0.95 |
| 285_A | 289_A | 1.191 | 0.95 |
| 19_N | 23_N | 1.175 | 0.95 |
| 246_T | 252_V | 1.170 | 0.94 |
| 290_T | 307_E | 1.168 | 0.94 |
| 333_V | 338_E | 1.165 | 0.94 |
| 338_E | 342_V | 1.158 | 0.94 |
| 162_A | 166_A | 1.158 | 0.94 |
| 179_L | 273_T | 1.154 | 0.94 |
| 84_N | 142_A | 1.153 | 0.94 |
| 331_D | 342_V | 1.147 | 0.94 |
| 19_N | 47_D | 1.146 | 0.94 |
| 246_T | 250_T | 1.146 | 0.94 |
| 229_N | 250_T | 1.140 | 0.93 |
| 285_A | 292_S | 1.136 | 0.93 |
| 12_K | 55_Q | 1.136 | 0.93 |
| 68_A | 159_S | 1.135 | 0.93 |
| 187_M | 200_Q | 1.132 | 0.93 |
| 176_K | 269_L | 1.127 | 0.93 |
| 25_A | 28_I | 1.123 | 0.93 |
| 228_L | 243_I | 1.120 | 0.93 |
| 118_A | 154_G | 1.115 | 0.92 |
| 10_A | 61_K | 1.106 | 0.92 |
| 178_G | 248_P | 1.106 | 0.92 |
| 51_I | 157_I | 1.102 | 0.92 |
| 284_P | 289_A | 1.101 | 0.92 |
| 208_V | 221_A | 1.097 | 0.92 |
| 182_I | 203_A | 1.088 | 0.91 |
| 288_G | 291_L | 1.074 | 0.90 |
| 291_L | 294_G | 1.063 | 0.90 |
| 73_L | 114_I | 1.051 | 0.89 |
| 314_A | 318_G | 1.051 | 0.89 |
| 234_N | 238_E | 1.050 | 0.89 |
| 337_A | 341_K | 1.049 | 0.89 |
| 79_A | 137_I | 1.048 | 0.89 |
| 32_L | 56_I | 1.039 | 0.88 |
| 97_V | 137_I | 1.037 | 0.88 |
| 231_K | 242_R | 1.037 | 0.88 |
| 201_R | 234_N | 1.031 | 0.88 |
| 166_A | 170_I | 1.026 | 0.87 |
| 191_I | 195_F | 1.023 | 0.87 |
| 92_A | 96_I | 1.020 | 0.87 |
| 290_T | 294_G | 1.017 | 0.87 |
| 286_L | 289_A | 1.016 | 0.87 |
| 328_V | 333_V | 1.012 | 0.86 |
| 107_L | 111_E | 1.009 | 0.86 |
| 31_Q | 37_E | 1.009 | 0.86 |
| 108_E | 111_E | 1.005 | 0.86 |
| 100_L | 114_I | 1.001 | 0.86 |
| 326_I | 355_V | 1.000 | 0.86 |
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 | |
| 4a8cA | 12 | 1 | 100 | 0.278 | Contact Map |
| 1ky9A | 2 | 0.9612 | 100 | 0.293 | Contact Map |
| 3pv2A | 4 | 0.9584 | 100 | 0.297 | Contact Map |
| 4flnA | 3 | 0.9723 | 100 | 0.365 | Contact Map |
| 3stjA | 12 | 0.7535 | 100 | 0.428 | Contact Map |
| 1te0A | 2 | 0.759 | 100 | 0.473 | Contact Map |
| 4ic6A | 3 | 0.7645 | 100 | 0.479 | Contact Map |
| 3qo6A | 3 | 0.7452 | 100 | 0.503 | Contact Map |
| 3numA | 1 | 0.41 | 100 | 0.519 | Contact Map |
| 1y8tA | 3 | 0.7202 | 100 | 0.527 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)