| lict |
| ID: | 1495115438 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 314 (276) | ||
| Sequences: | 1509 (1171.5) | ||
| Seq/Len: | 5.467 | ||
| Nf(neff/√len): | 70.5 |
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: 5.467).
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 |
| 141_K | 147_S | 4.507 | 1.00 |
| 186_V | 204_F | 3.550 | 1.00 |
| 14_V | 22_L | 3.252 | 1.00 |
| 76_E | 143_K | 3.230 | 1.00 |
| 7_I | 13_S | 3.117 | 1.00 |
| 77_I | 136_A | 2.898 | 1.00 |
| 101_I | 140_V | 2.843 | 1.00 |
| 80_Y | 135_E | 2.843 | 1.00 |
| 243_T | 263_L | 2.722 | 1.00 |
| 119_L | 154_G | 2.721 | 1.00 |
| 251_E | 257_K | 2.458 | 1.00 |
| 106_Q | 110_K | 2.430 | 1.00 |
| 84_Q | 135_E | 2.346 | 1.00 |
| 12_I | 39_V | 2.190 | 1.00 |
| 239_A | 271_E | 2.138 | 1.00 |
| 247_Q | 263_L | 2.100 | 1.00 |
| 70_C | 105_I | 2.051 | 1.00 |
| 182_I | 246_I | 2.050 | 1.00 |
| 33_K | 37_D | 1.925 | 1.00 |
| 189_H | 245_K | 1.864 | 1.00 |
| 122_T | 154_G | 1.857 | 1.00 |
| 214_R | 262_E | 1.851 | 1.00 |
| 185_I | 249_Y | 1.844 | 1.00 |
| 244_K | 263_L | 1.807 | 1.00 |
| 141_K | 145_G | 1.804 | 1.00 |
| 4_A | 15_V | 1.799 | 1.00 |
| 133_G | 157_A | 1.776 | 1.00 |
| 81_A | 160_I | 1.766 | 1.00 |
| 240_Y | 267_T | 1.750 | 1.00 |
| 187_K | 193_E | 1.749 | 1.00 |
| 73_V | 139_M | 1.731 | 1.00 |
| 175_I | 212_A | 1.651 | 0.99 |
| 70_C | 102_N | 1.631 | 0.99 |
| 81_A | 132_I | 1.612 | 0.99 |
| 12_I | 30_A | 1.600 | 0.99 |
| 134_K | 150_E | 1.599 | 0.99 |
| 181_E | 249_Y | 1.598 | 0.99 |
| 134_K | 153_A | 1.594 | 0.99 |
| 40_D | 43_R | 1.579 | 0.99 |
| 271_E | 274_V | 1.551 | 0.99 |
| 200_H | 276_Q | 1.536 | 0.99 |
| 137_L | 148_L | 1.534 | 0.99 |
| 190_F | 242_C | 1.531 | 0.99 |
| 233_K | 240_Y | 1.500 | 0.99 |
| 140_V | 148_L | 1.479 | 0.99 |
| 239_A | 270_I | 1.470 | 0.99 |
| 131_A | 134_K | 1.469 | 0.99 |
| 21_E | 46_K | 1.443 | 0.98 |
| 3_I | 6_V | 1.426 | 0.98 |
| 67_P | 102_N | 1.417 | 0.98 |
| 46_K | 50_L | 1.405 | 0.98 |
| 218_G | 256_H | 1.372 | 0.97 |
| 135_E | 138_V | 1.348 | 0.97 |
| 243_T | 267_T | 1.323 | 0.97 |
| 80_Y | 132_I | 1.319 | 0.97 |
| 80_Y | 84_Q | 1.317 | 0.97 |
| 6_V | 35_S | 1.302 | 0.96 |
| 14_V | 24_V | 1.301 | 0.96 |
| 264_L | 267_T | 1.289 | 0.96 |
| 215_L | 250_I | 1.283 | 0.96 |
| 151_D | 155_F | 1.283 | 0.96 |
| 116_N | 154_G | 1.267 | 0.95 |
| 24_V | 30_A | 1.266 | 0.95 |
| 128_D | 131_A | 1.252 | 0.95 |
| 202_Y | 210_F | 1.249 | 0.95 |
| 57_E | 60_K | 1.240 | 0.95 |
| 12_I | 24_V | 1.239 | 0.95 |
| 108_N | 149_P | 1.232 | 0.94 |
| 243_T | 270_I | 1.214 | 0.94 |
| 135_E | 139_M | 1.208 | 0.94 |
| 238_R | 241_E | 1.205 | 0.94 |
| 136_A | 139_M | 1.195 | 0.93 |
| 84_Q | 131_A | 1.191 | 0.93 |
| 137_L | 153_A | 1.185 | 0.93 |
| 74_S | 78_I | 1.182 | 0.93 |
| 120_W | 188_Y | 1.178 | 0.92 |
| 187_K | 194_F | 1.175 | 0.92 |
| 81_A | 136_A | 1.170 | 0.92 |
| 77_I | 139_M | 1.164 | 0.92 |
| 66_I | 98_T | 1.163 | 0.92 |
| 82_K | 88_K | 1.161 | 0.92 |
| 10_N | 117_A | 1.151 | 0.91 |
| 13_S | 30_A | 1.142 | 0.91 |
| 265_Y | 269_H | 1.142 | 0.91 |
| 11_V | 25_M | 1.140 | 0.91 |
| 133_G | 153_A | 1.139 | 0.91 |
| 7_I | 11_V | 1.127 | 0.90 |
| 232_V | 267_T | 1.121 | 0.90 |
| 119_L | 155_F | 1.120 | 0.90 |
| 75_E | 79_S | 1.115 | 0.89 |
| 84_Q | 128_D | 1.115 | 0.89 |
| 172_I | 176_T | 1.111 | 0.89 |
| 207_H | 269_H | 1.111 | 0.89 |
| 184_S | 188_Y | 1.110 | 0.89 |
| 108_N | 113_D | 1.102 | 0.89 |
| 141_K | 148_L | 1.099 | 0.89 |
| 123_K | 130_F | 1.086 | 0.88 |
| 229_L | 260_S | 1.084 | 0.88 |
| 183_L | 187_K | 1.083 | 0.88 |
| 103_F | 121_E | 1.078 | 0.87 |
| 14_V | 23_V | 1.078 | 0.87 |
| 169_M | 172_I | 1.076 | 0.87 |
| 262_E | 266_L | 1.075 | 0.87 |
| 5_K | 261_D | 1.075 | 0.87 |
| 227_F | 231_T | 1.070 | 0.87 |
| 181_E | 253_E | 1.070 | 0.87 |
| 68_I | 72_E | 1.069 | 0.87 |
| 242_C | 246_I | 1.063 | 0.86 |
| 231_T | 236_Y | 1.061 | 0.86 |
| 3_I | 92_S | 1.061 | 0.86 |
| 233_K | 237_H | 1.057 | 0.86 |
| 240_Y | 244_K | 1.057 | 0.86 |
| 3_I | 30_A | 1.057 | 0.86 |
| 6_V | 34_K | 1.055 | 0.86 |
| 78_I | 94_Y | 1.048 | 0.85 |
| 2_K | 38_D | 1.044 | 0.85 |
| 78_I | 93_I | 1.034 | 0.84 |
| 74_S | 77_I | 1.034 | 0.84 |
| 86_G | 128_D | 1.033 | 0.84 |
| 138_V | 147_S | 1.029 | 0.84 |
| 137_L | 141_K | 1.026 | 0.83 |
| 203_R | 269_H | 1.019 | 0.83 |
| 79_S | 83_L | 1.015 | 0.83 |
| 135_E | 198_S | 1.014 | 0.83 |
| 161_V | 211_F | 1.014 | 0.83 |
| 122_T | 155_F | 1.007 | 0.82 |
| 241_E | 244_K | 1.003 | 0.82 |
| 87_K | 128_D | 1.003 | 0.82 |
| 180_Q | 184_S | 1.000 | 0.81 |
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 | |
| 3rioA | 1 | 0.5287 | 100 | 0.563 | Contact Map |
| 1h99A | 1 | 0.7006 | 100 | 0.575 | Contact Map |
| 4r6iA | 2 | 0.9713 | 100 | 0.698 | Contact Map |
| 3sqnA | 2 | 0.9331 | 99.9 | 0.759 | Contact Map |
| 1l1cA | 2 | 0.1752 | 99.8 | 0.796 | Contact Map |
| 1auuA | 2 | 0.1752 | 99.7 | 0.8 | Contact Map |
| 3ufeA | 2 | 0.3471 | 99.7 | 0.804 | Contact Map |
| 3nufA | 2 | 0.3726 | 91.8 | 0.942 | Contact Map |
| 4d0lA | 3 | 0.4108 | 19.5 | 0.968 | Contact Map |
| 2xvyA | 1 | 0.2866 | 13 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)