| ncor -force run |
| ID: | 1509730835 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 271 (267) | ||
| Sequences: | 61 (39.3) | ||
| Seq/Len: | 0.228 | ||
| Nf(neff/√len): | 2.4 |
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: 0.228).
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 |
| 24_T | 29_R | 1.968 | 0.63 |
| 23_I | 26_D | 1.928 | 0.61 |
| 237_D | 254_P | 1.757 | 0.51 |
| 119_H | 128_L | 1.617 | 0.42 |
| 22_I | 27_F | 1.606 | 0.41 |
| 78_R | 81_P | 1.588 | 0.40 |
| 113_P | 176_L | 1.560 | 0.38 |
| 40_T | 43_T | 1.536 | 0.37 |
| 24_T | 28_A | 1.511 | 0.36 |
| 12_L | 20_C | 1.496 | 0.35 |
| 208_S | 217_P | 1.480 | 0.34 |
| 50_S | 54_R | 1.475 | 0.34 |
| 26_D | 29_R | 1.460 | 0.33 |
| 251_G | 259_T | 1.447 | 0.32 |
| 182_G | 185_D | 1.438 | 0.31 |
| 184_S | 217_P | 1.412 | 0.30 |
| 251_G | 260_S | 1.403 | 0.30 |
| 147_S | 185_D | 1.380 | 0.28 |
| 45_P | 48_L | 1.375 | 0.28 |
| 35_Q | 120_E | 1.368 | 0.28 |
| 117_A | 133_V | 1.368 | 0.28 |
| 138_Q | 181_G | 1.357 | 0.27 |
| 139_R | 164_M | 1.349 | 0.27 |
| 136_A | 147_S | 1.349 | 0.27 |
| 185_D | 244_V | 1.337 | 0.26 |
| 205_G | 208_S | 1.336 | 0.26 |
| 23_I | 29_R | 1.327 | 0.26 |
| 88_S | 96_S | 1.324 | 0.26 |
| 21_Q | 27_F | 1.317 | 0.25 |
| 56_K | 96_S | 1.314 | 0.25 |
| 246_M | 264_S | 1.303 | 0.25 |
| 37_S | 41_F | 1.293 | 0.24 |
| 234_S | 242_H | 1.278 | 0.24 |
| 22_I | 28_A | 1.275 | 0.23 |
| 208_S | 236_D | 1.261 | 0.23 |
| 125_M | 128_L | 1.253 | 0.22 |
| 164_M | 176_L | 1.243 | 0.22 |
| 143_R | 160_S | 1.227 | 0.21 |
| 146_G | 220_N | 1.223 | 0.21 |
| 28_A | 31_Q | 1.222 | 0.21 |
| 146_G | 164_M | 1.219 | 0.21 |
| 173_F | 217_P | 1.212 | 0.21 |
| 113_P | 178_S | 1.209 | 0.21 |
| 217_P | 271_E | 1.208 | 0.21 |
| 252_I | 262_V | 1.204 | 0.20 |
| 110_I | 241_D | 1.193 | 0.20 |
| 14_T | 18_H | 1.189 | 0.20 |
| 190_Q | 193_T | 1.185 | 0.20 |
| 190_Q | 195_I | 1.185 | 0.20 |
| 190_Q | 196_F | 1.185 | 0.20 |
| 190_Q | 197_N | 1.185 | 0.20 |
| 191_P | 195_I | 1.185 | 0.20 |
| 191_P | 196_F | 1.185 | 0.20 |
| 191_P | 197_N | 1.185 | 0.20 |
| 192_G | 195_I | 1.185 | 0.20 |
| 192_G | 196_F | 1.185 | 0.20 |
| 192_G | 197_N | 1.185 | 0.20 |
| 193_T | 196_F | 1.185 | 0.20 |
| 193_T | 197_N | 1.185 | 0.20 |
| 132_G | 256_S | 1.185 | 0.20 |
| 257_A | 260_S | 1.181 | 0.19 |
| 185_D | 254_P | 1.180 | 0.19 |
| 76_G | 207_V | 1.180 | 0.19 |
| 88_S | 97_P | 1.170 | 0.19 |
| 61_Y | 78_R | 1.165 | 0.19 |
| 20_C | 135_P | 1.160 | 0.19 |
| 83_N | 270_D | 1.155 | 0.18 |
| 250_V | 259_T | 1.152 | 0.18 |
| 181_G | 270_D | 1.147 | 0.18 |
| 47_A | 50_S | 1.146 | 0.18 |
| 63_P | 217_P | 1.145 | 0.18 |
| 114_Q | 138_Q | 1.144 | 0.18 |
| 235_F | 242_H | 1.142 | 0.18 |
| 106_P | 182_G | 1.140 | 0.18 |
| 139_R | 146_G | 1.139 | 0.18 |
| 253_M | 257_A | 1.138 | 0.18 |
| 54_R | 87_K | 1.130 | 0.18 |
| 81_P | 87_K | 1.127 | 0.17 |
| 62_S | 96_S | 1.125 | 0.17 |
| 38_T | 41_F | 1.124 | 0.17 |
| 190_Q | 202_T | 1.119 | 0.17 |
| 191_P | 202_T | 1.119 | 0.17 |
| 192_G | 202_T | 1.119 | 0.17 |
| 193_T | 202_T | 1.119 | 0.17 |
| 195_I | 202_T | 1.119 | 0.17 |
| 196_F | 202_T | 1.119 | 0.17 |
| 197_N | 202_T | 1.119 | 0.17 |
| 86_D | 218_A | 1.119 | 0.17 |
| 209_S | 219_S | 1.118 | 0.17 |
| 207_V | 217_P | 1.115 | 0.17 |
| 107_Y | 110_I | 1.113 | 0.17 |
| 142_S | 145_P | 1.111 | 0.17 |
| 114_Q | 178_S | 1.102 | 0.17 |
| 251_G | 261_V | 1.100 | 0.16 |
| 78_R | 87_K | 1.097 | 0.16 |
| 147_S | 247_S | 1.097 | 0.16 |
| 57_T | 97_P | 1.094 | 0.16 |
| 25_Q | 29_R | 1.091 | 0.16 |
| 79_V | 211_S | 1.089 | 0.16 |
| 201_V | 219_S | 1.082 | 0.16 |
| 253_M | 263_T | 1.079 | 0.16 |
| 82_E | 135_P | 1.076 | 0.16 |
| 190_Q | 200_A | 1.076 | 0.16 |
| 191_P | 200_A | 1.076 | 0.16 |
| 192_G | 200_A | 1.076 | 0.16 |
| 193_T | 200_A | 1.076 | 0.16 |
| 195_I | 200_A | 1.076 | 0.16 |
| 196_F | 200_A | 1.076 | 0.16 |
| 197_N | 200_A | 1.076 | 0.16 |
| 205_G | 236_D | 1.075 | 0.16 |
| 13_I | 236_D | 1.075 | 0.16 |
| 128_L | 132_G | 1.068 | 0.15 |
| 181_G | 212_H | 1.064 | 0.15 |
| 56_K | 95_K | 1.063 | 0.15 |
| 250_V | 253_M | 1.061 | 0.15 |
| 37_S | 42_Q | 1.060 | 0.15 |
| 21_Q | 26_D | 1.054 | 0.15 |
| 103_P | 208_S | 1.053 | 0.15 |
| 72_H | 89_R | 1.049 | 0.15 |
| 155_F | 158_L | 1.045 | 0.15 |
| 155_F | 162_S | 1.045 | 0.15 |
| 155_F | 175_K | 1.045 | 0.15 |
| 158_L | 162_S | 1.045 | 0.15 |
| 158_L | 175_K | 1.045 | 0.15 |
| 162_S | 175_K | 1.045 | 0.15 |
| 77_P | 83_N | 1.044 | 0.15 |
| 89_R | 93_P | 1.042 | 0.15 |
| 62_S | 95_K | 1.042 | 0.15 |
| 82_E | 101_H | 1.040 | 0.15 |
| 114_Q | 219_S | 1.034 | 0.14 |
| 143_R | 212_H | 1.033 | 0.14 |
| 23_I | 27_F | 1.033 | 0.14 |
| 254_P | 263_T | 1.031 | 0.14 |
| 173_F | 208_S | 1.026 | 0.14 |
| 139_R | 176_L | 1.025 | 0.14 |
| 156_T | 174_R | 1.025 | 0.14 |
| 164_M | 172_I | 1.024 | 0.14 |
| 97_P | 100_S | 1.023 | 0.14 |
| 40_T | 240_E | 1.022 | 0.14 |
| 46_S | 50_S | 1.021 | 0.14 |
| 187_A | 241_D | 1.021 | 0.14 |
| 173_F | 177_N | 1.018 | 0.14 |
| 250_V | 255_G | 1.018 | 0.14 |
| 124_S | 130_Q | 1.013 | 0.14 |
| 254_P | 262_V | 1.012 | 0.14 |
| 140_S | 237_D | 1.010 | 0.14 |
| 250_V | 260_S | 1.010 | 0.14 |
| 110_I | 187_A | 1.009 | 0.14 |
| 46_S | 119_H | 1.006 | 0.13 |
| 59_S | 62_S | 1.003 | 0.13 |
| 148_I | 213_S | 1.001 | 0.13 |
| 253_M | 260_S | 1.000 | 0.13 |
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 | |
| 2ovmB | 1 | 0.0406 | 99.3 | 0.894 | Contact Map |
| 2gpvG | 3 | 0.0443 | 99 | 0.903 | Contact Map |
| 3n00B | 1 | 0.0775 | 98.2 | 0.925 | Contact Map |
| 2wh0Q | 2 | 0.0406 | 9.5 | 0.98 | Contact Map |
| 2d10E | 4 | 0.0738 | 2.9 | 0.984 | Contact Map |
| 2d11E | 4 | 0.0664 | 2.8 | 0.984 | Contact Map |
| 4lqkC | 4 | 0.1624 | 2.7 | 0.984 | Contact Map |
| 3tm8A | 2 | 0.2177 | 2.7 | 0.984 | Contact Map |
| 3btpA | 1 | 0.0185 | 2.2 | 0.985 | Contact Map |
| 2a40C | 2 | 0.0812 | 2 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)